Daily Papers

Extracting meaningful insights from large and complex datasets poses significant challenges, particularly in ensuring the accuracy and relevance of retrieved information. Traditional data retrieval methods such as sequential search and index-based retrieval often fail when handling intricate and interconnected data structures, resulting in incomplete or misleading outputs. To overcome these limitations, we introduce Structured-GraphRAG, a versatile framework designed to enhance information retrieval across structured datasets in natural language queries. Structured-GraphRAG utilizes multiple knowledge graphs, which represent data in a structured format and capture complex relationships between entities, enabling a more nuanced and comprehensive retrieval of information. This graph-based approach reduces the risk of errors in language model outputs by grounding responses in a structured format, thereby enhancing the reliability of results. We demonstrate the effectiveness of Structured-GraphRAG by comparing its performance with that of a recently published method using traditional retrieval-augmented generation. Our findings show that Structured-GraphRAG significantly improves query processing efficiency and reduces response times. While our case study focuses on soccer data, the framework's design is broadly applicable, offering a powerful tool for data analysis and enhancing language model applications across various structured domains.

This paper presents OmniDataComposer, an innovative approach for multimodal data fusion and unlimited data generation with an intent to refine and uncomplicate interplay among diverse data modalities. Coming to the core breakthrough, it introduces a cohesive data structure proficient in processing and merging multimodal data inputs, which include video, audio, and text. Our crafted algorithm leverages advancements across multiple operations such as video/image caption extraction, dense caption extraction, Automatic Speech Recognition (ASR), Optical Character Recognition (OCR), Recognize Anything Model(RAM), and object tracking. OmniDataComposer is capable of identifying over 6400 categories of objects, substantially broadening the spectrum of visual information. It amalgamates these diverse modalities, promoting reciprocal enhancement among modalities and facilitating cross-modal data correction. The final output metamorphoses each video input into an elaborate sequential document, virtually transmuting videos into thorough narratives, making them easier to be processed by large language models. Future prospects include optimizing datasets for each modality to encourage unlimited data generation. This robust base will offer priceless insights to models like ChatGPT, enabling them to create higher quality datasets for video captioning and easing question-answering tasks based on video content. OmniDataComposer inaugurates a new stage in multimodal learning, imparting enormous potential for augmenting AI's understanding and generation of complex, real-world data.

Tabular data -- structured, heterogeneous, spreadsheet-style data with rows and columns -- is widely used in practice across many domains. However, while recent foundation models have reduced the need for developing task-specific datasets and predictors in domains such as language modeling and computer vision, this transfer learning paradigm has not had similar impact in the tabular domain. In this work, we seek to narrow this gap and present TabuLa-8B, a language model for tabular prediction. We define a process for extracting a large, high-quality training dataset from the TabLib corpus, proposing methods for tabular data filtering and quality control. Using the resulting dataset, which comprises over 1.6B rows from 3.1M unique tables, we fine-tune a Llama 3-8B large language model (LLM) for tabular data prediction (classification and binned regression) using a novel packing and attention scheme for tabular prediction. Through evaluation across a test suite of 329 datasets, we find that TabuLa-8B has zero-shot accuracy on unseen tables that is over 15 percentage points (pp) higher than random guessing, a feat that is not possible with existing state-of-the-art tabular prediction models (e.g. XGBoost, TabPFN). In the few-shot setting (1-32 shots), without any fine-tuning on the target datasets, TabuLa-8B is 5-15 pp more accurate than XGBoost and TabPFN models that are explicitly trained on equal, or even up to 16x more data. We release our model, code, and data along with the publication of this paper.

Underlying data structures, such as symmetries or invariances to transformations, are often exploited to improve the solution of learning tasks. However, embedding these properties in models or learning algorithms can be challenging and computationally intensive. Data augmentation, on the other hand, induces these symmetries during training by applying multiple transformations to the input data. Despite its ubiquity, its effectiveness depends on the choices of which transformations to apply, when to do so, and how often. In fact, there is both empirical and theoretical evidence that the indiscriminate use of data augmentation can introduce biases that outweigh its benefits. This work tackles these issues by automatically adapting the data augmentation while solving the learning task. To do so, it formulates data augmentation as an invariance-constrained learning problem and leverages Monte Carlo Markov Chain (MCMC) sampling to solve it. The result is a practical algorithm that not only does away with a priori searches for augmentation distributions, but also dynamically controls if and when data augmentation is applied. Our experiments illustrate the performance of this method, which achieves state-of-the-art results in automatic data augmentation benchmarks for CIFAR datasets. Furthermore, this approach can be used to gather insights on the actual symmetries underlying a learning task.

We present a distributed data structure, which we call the rainbow skip graph. To our knowledge, this is the first peer-to-peer data structure that simultaneously achieves high fault tolerance, constant-sized nodes, and fast update and query times for ordered data. It is a non-trivial adaptation of the SkipNet/skip-graph structures of Harvey et al. and Aspnes and Shah, so as to provide fault-tolerance as these structures do, but to do so using constant-sized nodes, as in the family tree structure of Zatloukal and Harvey. It supports successor queries on a set of n items using O(log n) messages with high probability, an improvement over the expected O(log n) messages of the family tree.

The generalization performance of a machine learning algorithm such as a neural network depends in a non-trivial way on the structure of the data distribution. To analyze the influence of data structure on test loss dynamics, we study an exactly solveable model of stochastic gradient descent (SGD) on mean square loss which predicts test loss when training on features with arbitrary covariance structure. We solve the theory exactly for both Gaussian features and arbitrary features and we show that the simpler Gaussian model accurately predicts test loss of nonlinear random-feature models and deep neural networks trained with SGD on real datasets such as MNIST and CIFAR-10. We show that the optimal batch size at a fixed compute budget is typically small and depends on the feature correlation structure, demonstrating the computational benefits of SGD with small batch sizes. Lastly, we extend our theory to the more usual setting of stochastic gradient descent on a fixed subsampled training set, showing that both training and test error can be accurately predicted in our framework on real data.

Tabular data is arguably one of the most commonly used data structures in various practical domains, including finance, healthcare and e-commerce. The inherent heterogeneity allows tabular data to store rich information. However, based on a recently published tabular benchmark, we can see deep neural networks still fall behind tree-based models on tabular datasets. In this paper, we propose Trompt--which stands for Tabular Prompt--a novel architecture inspired by prompt learning of language models. The essence of prompt learning is to adjust a large pre-trained model through a set of prompts outside the model without directly modifying the model. Based on this idea, Trompt separates the learning strategy of tabular data into two parts. The first part, analogous to pre-trained models, focus on learning the intrinsic information of a table. The second part, analogous to prompts, focus on learning the variations among samples. Trompt is evaluated with the benchmark mentioned above. The experimental results demonstrate that Trompt outperforms state-of-the-art deep neural networks and is comparable to tree-based models.

This paper introduces Graph Convolutional Recurrent Network (GCRN), a deep learning model able to predict structured sequences of data. Precisely, GCRN is a generalization of classical recurrent neural networks (RNN) to data structured by an arbitrary graph. Such structured sequences can represent series of frames in videos, spatio-temporal measurements on a network of sensors, or random walks on a vocabulary graph for natural language modeling. The proposed model combines convolutional neural networks (CNN) on graphs to identify spatial structures and RNN to find dynamic patterns. We study two possible architectures of GCRN, and apply the models to two practical problems: predicting moving MNIST data, and modeling natural language with the Penn Treebank dataset. Experiments show that exploiting simultaneously graph spatial and dynamic information about data can improve both precision and learning speed.

Open3D is an open-source library that supports rapid development of software that deals with 3D data. The Open3D frontend exposes a set of carefully selected data structures and algorithms in both C++ and Python. The backend is highly optimized and is set up for parallelization. Open3D was developed from a clean slate with a small and carefully considered set of dependencies. It can be set up on different platforms and compiled from source with minimal effort. The code is clean, consistently styled, and maintained via a clear code review mechanism. Open3D has been used in a number of published research projects and is actively deployed in the cloud. We welcome contributions from the open-source community.

Shampoo is an online and stochastic optimization algorithm belonging to the AdaGrad family of methods for training neural networks. It constructs a block-diagonal preconditioner where each block consists of a coarse Kronecker product approximation to full-matrix AdaGrad for each parameter of the neural network. In this work, we provide a complete description of the algorithm as well as the performance optimizations that our implementation leverages to train deep networks at-scale in PyTorch. Our implementation enables fast multi-GPU distributed data-parallel training by distributing the memory and computation associated with blocks of each parameter via PyTorch's DTensor data structure and performing an AllGather primitive on the computed search directions at each iteration. This major performance enhancement enables us to achieve at most a 10% performance reduction in per-step wall-clock time compared against standard diagonal-scaling-based adaptive gradient methods. We validate our implementation by performing an ablation study on training ImageNet ResNet50, demonstrating Shampoo's superiority over standard training recipes with minimal hyperparameter tuning.

Tabular data, a prevalent data type across various domains, presents unique challenges due to its heterogeneous nature and complex structural relationships. Achieving high predictive performance and robustness in tabular data analysis holds significant promise for numerous applications. Influenced by recent advancements in natural language processing, particularly transformer architectures, new methods for tabular data modeling have emerged. Early techniques concentrated on pre-training transformers from scratch, often encountering scalability issues. Subsequently, methods leveraging pre-trained language models like BERT have been developed, which require less data and yield enhanced performance. The recent advent of large language models, such as GPT and LLaMA, has further revolutionized the field, facilitating more advanced and diverse applications with minimal fine-tuning. Despite the growing interest, a comprehensive survey of language modeling techniques for tabular data remains absent. This paper fills this gap by providing a systematic review of the development of language modeling for tabular data, encompassing: (1) a categorization of different tabular data structures and data types; (2) a review of key datasets used in model training and tasks used for evaluation; (3) a summary of modeling techniques including widely-adopted data processing methods, popular architectures, and training objectives; (4) the evolution from adapting traditional Pre-training/Pre-trained language models to the utilization of large language models; (5) an identification of persistent challenges and potential future research directions in language modeling for tabular data analysis. GitHub page associated with this survey is available at: https://github.com/lanxiang1017/Language-Modeling-on-Tabular-Data-Survey.git.

With the increasing adoption of graph neural networks (GNNs) in the machine learning community, GPUs have become an essential tool to accelerate GNN training. However, training GNNs on very large graphs that do not fit in GPU memory is still a challenging task. Unlike conventional neural networks, mini-batching input samples in GNNs requires complicated tasks such as traversing neighboring nodes and gathering their feature values. While this process accounts for a significant portion of the training time, we find existing GNN implementations using popular deep neural network (DNN) libraries such as PyTorch are limited to a CPU-centric approach for the entire data preparation step. This "all-in-CPU" approach has negative impact on the overall GNN training performance as it over-utilizes CPU resources and hinders GPU acceleration of GNN training. To overcome such limitations, we introduce PyTorch-Direct, which enables a GPU-centric data accessing paradigm for GNN training. In PyTorch-Direct, GPUs are capable of efficiently accessing complicated data structures in host memory directly without CPU intervention. Our microbenchmark and end-to-end GNN training results show that PyTorch-Direct reduces data transfer time by 47.1% on average and speeds up GNN training by up to 1.6x. Furthermore, by reducing CPU utilization, PyTorch-Direct also saves system power by 12.4% to 17.5% during training. To minimize programmer effort, we introduce a new "unified tensor" type along with necessary changes to the PyTorch memory allocator, dispatch logic, and placement rules. As a result, users need to change at most two lines of their PyTorch GNN training code for each tensor object to take advantage of PyTorch-Direct.

Graph Neural Networks (GNNs) have shown success in learning from graph-structured data, with applications to fraud detection, recommendation, and knowledge graph reasoning. However, training GNN efficiently is challenging because: 1) GPU memory capacity is limited and can be insufficient for large datasets, and 2) the graph-based data structure causes irregular data access patterns. In this work, we provide a method to statistical analyze and identify more frequently accessed data ahead of GNN training. Our data tiering method not only utilizes the structure of input graph, but also an insight gained from actual GNN training process to achieve a higher prediction result. With our data tiering method, we additionally provide a new data placement and access strategy to further minimize the CPU-GPU communication overhead. We also take into account of multi-GPU GNN training as well and we demonstrate the effectiveness of our strategy in a multi-GPU system. The evaluation results show that our work reduces CPU-GPU traffic by 87-95% and improves the training speed of GNN over the existing solutions by 1.6-2.1x on graphs with hundreds of millions of nodes and billions of edges.

We present a benchmark for large language models designed to tackle one of the most knowledge-intensive tasks in data science: writing feature engineering code, which requires domain knowledge in addition to a deep understanding of the underlying problem and data structure. The model is provided with a dataset description in a prompt and asked to generate code transforming it. The evaluation score is derived from the improvement achieved by an XGBoost model fit on the modified dataset compared to the original data. By an extensive evaluation of state-of-the-art models and comparison to well-established benchmarks, we demonstrate that the FeatEng of our proposal can cheaply and efficiently assess the broad capabilities of LLMs, in contrast to the existing methods.

Vector Symbolic Architectures (VSAs) have emerged as a novel framework for enabling interpretable machine learning algorithms equipped with the ability to reason and explain their decision processes. The basic idea is to represent discrete information through high dimensional random vectors. Complex data structures can be built up with operations over vectors such as the "binding" operation involving element-wise vector multiplication, which associates data together. The reverse task of decomposing the associated elements is a combinatorially hard task, with an exponentially large search space. The main algorithm for performing this search is the resonator network, inspired by Hopfield network-based memory search operations. In this work, we introduce a new variant of the resonator network, based on self-attention based update rules in the iterative search problem. This update rule, based on the Hopfield network with log-sum-exp energy function and norm-bounded states, is shown to substantially improve the performance and rate of convergence. As a result, our algorithm enables a larger capacity for associative memory, enabling applications in many tasks like perception based pattern recognition, scene decomposition, and object reasoning. We substantiate our algorithm with a thorough evaluation and comparisons to baselines.

Projection maintenance is one of the core data structure tasks. Efficient data structures for projection maintenance have led to recent breakthroughs in many convex programming algorithms. In this work, we further extend this framework to the Kronecker product structure. Given a constraint matrix {sf A} and a positive semi-definite matrix Win R^{ntimes n} with a sparse eigenbasis, we consider the task of maintaining the projection in the form of {sf B}^top({sf B}{sf B}^top)^{-1}{sf B}, where {sf B}={sf A}(Wotimes I) or {sf B}={sf A}(W^{1/2}otimes W^{1/2}). At each iteration, the weight matrix W receives a low rank change and we receive a new vector h. The goal is to maintain the projection matrix and answer the query {sf B}^top({sf B}{sf B}^top)^{-1}{sf B}h with good approximation guarantees. We design a fast dynamic data structure for this task and it is robust against an adaptive adversary. Following the beautiful and pioneering work of [Beimel, Kaplan, Mansour, Nissim, Saranurak and Stemmer, STOC'22], we use tools from differential privacy to reduce the randomness required by the data structure and further improve the running time.

Significant progress has been made in open-vocabulary mobile manipulation, where the goal is for a robot to perform tasks in any environment given a natural language description. However, most current systems assume a static environment, which limits the system's applicability in real-world scenarios where environments frequently change due to human intervention or the robot's own actions. In this work, we present DynaMem, a new approach to open-world mobile manipulation that uses a dynamic spatio-semantic memory to represent a robot's environment. DynaMem constructs a 3D data structure to maintain a dynamic memory of point clouds, and answers open-vocabulary object localization queries using multimodal LLMs or open-vocabulary features generated by state-of-the-art vision-language models. Powered by DynaMem, our robots can explore novel environments, search for objects not found in memory, and continuously update the memory as objects move, appear, or disappear in the scene. We run extensive experiments on the Stretch SE3 robots in three real and nine offline scenes, and achieve an average pick-and-drop success rate of 70% on non-stationary objects, which is more than a 2x improvement over state-of-the-art static systems. Our code as well as our experiment and deployment videos are open sourced and can be found on our project website: https://dynamem.github.io/

Evaluating and enhancing the general capabilities of large language models (LLMs) has been an important research topic. Graph is a common data structure in the real world, and understanding graph data is a crucial part for advancing general intelligence. To evaluate and enhance the graph understanding abilities of LLMs, in this paper, we propose a benchmark named GraphInstruct, which comprehensively includes 21 classical graph reasoning tasks, providing diverse graph generation pipelines and detailed reasoning steps. Based on GraphInstruct, we further construct GraphLM through efficient instruction-tuning, which shows prominent graph understanding capability. In order to enhance the LLM with graph reasoning capability as well, we propose a step mask training strategy, and construct a model named GraphLM+. As one of the pioneering efforts to enhance the graph understanding and reasoning abilities of LLMs, extensive experiments have demonstrated the superiority of GraphLM and GraphLM+ over other LLMs. We look forward to more researchers exploring the potential of LLMs in the graph data mining domain through GraphInstruct. Our code for generating GraphInstruct is released publicly at: https://github.com/CGCL-codes/GraphInstruct.

Convolution is a broadly useful operation with applications including signal processing, machine learning, probability, optics, polynomial multiplication, and efficient parsing. Usually, however, this operation is understood and implemented in more specialized forms, hiding commonalities and limiting usefulness. This paper formulates convolution in the common algebraic framework of semirings and semimodules and populates that framework with various representation types. One of those types is the grand abstract template and itself generalizes to the free semimodule monad. Other representations serve varied uses and performance trade-offs, with implementations calculated from simple and regular specifications. Of particular interest is Brzozowski's method for regular expression matching. Uncovering the method's essence frees it from syntactic manipulations, while generalizing from boolean to weighted membership (such as multisets and probability distributions) and from sets to n-ary relations. The classic trie data structure then provides an elegant and efficient alternative to syntax. Pleasantly, polynomial arithmetic requires no additional implementation effort, works correctly with a variety of representations, and handles multivariate polynomials and power series with ease. Image convolution also falls out as a special case.

This paper discusses about a sorting algorithm which uses the concept of buckets where each bucket represents a certain number of digits. A two dimensional data structure is used where one dimension represents buckets i. e; number of digits and each bucket's corresponding dimensions represents the input numbers that belong to that bucket. Each bucket is then individually sorted. Since every preceding bucket elements will always be smaller than the succeeding buckets no comparison between them is required. By doing this we can significantly reduced the time complexity of any sorting algorithm used to sort the given set of inputs.

Graphs are essential data structures for modeling complex interactions in domains such as social networks, molecular structures, and biological systems. Graph-level tasks, which predict properties or classes for the entire graph, are critical for applications, such as molecular property prediction and subgraph counting. Graph Neural Networks (GNNs) have shown promise in these tasks, but their evaluations are often limited to narrow datasets, tasks, and inconsistent experimental setups, restricting their generalizability. To address these limitations, we propose a unified evaluation framework for graph-level GNNs. This framework provides a standardized setting to evaluate GNNs across diverse datasets, various graph tasks (e.g., graph classification and regression), and challenging scenarios, including noisy, imbalanced, and few-shot graphs. Additionally, we propose a novel GNN model with enhanced expressivity and generalization capabilities. Specifically, we enhance the expressivity of GNNs through a k-path rooted subgraph approach, enabling the model to effectively count subgraphs (e.g., paths and cycles). Moreover, we introduce a unified graph contrastive learning algorithm for graphs across diverse domains, which adaptively removes unimportant edges to augment graphs, thereby significantly improving generalization performance. Extensive experiments demonstrate that our model achieves superior performance against fourteen effective baselines across twenty-seven graph datasets, establishing it as a robust and generalizable model for graph-level tasks.

Recent advances in Neural radiance fields (NeRF) have enabled high-fidelity scene reconstruction for novel view synthesis. However, NeRF requires hundreds of network evaluations per pixel to approximate a volume rendering integral, making it slow to train. Caching NeRFs into explicit data structures can effectively enhance rendering speed but at the cost of higher memory usage. To address these issues, we present Hyb-NeRF, a novel neural radiance field with a multi-resolution hybrid encoding that achieves efficient neural modeling and fast rendering, which also allows for high-quality novel view synthesis. The key idea of Hyb-NeRF is to represent the scene using different encoding strategies from coarse-to-fine resolution levels. Hyb-NeRF exploits memory-efficiency learnable positional features at coarse resolutions and the fast optimization speed and local details of hash-based feature grids at fine resolutions. In addition, to further boost performance, we embed cone tracing-based features in our learnable positional encoding that eliminates encoding ambiguity and reduces aliasing artifacts. Extensive experiments on both synthetic and real-world datasets show that Hyb-NeRF achieves faster rendering speed with better rending quality and even a lower memory footprint in comparison to previous state-of-the-art methods.

Vector data is one of the two core data structures in geographic information science (GIS), essential for accurately storing and representing geospatial information. Shapefile, the most widely used vector data format, has become the industry standard supported by all major geographic information systems. However, processing this data typically requires specialized GIS knowledge and skills, creating a barrier for researchers from other fields and impeding interdisciplinary research in spatial data analysis. Moreover, while large language models (LLMs) have made significant advancements in natural language processing and task automation, they still face challenges in handling the complex spatial and topological relationships inherent in GIS vector data. To address these challenges, we propose ShapefileGPT, an innovative framework powered by LLMs, specifically designed to automate Shapefile tasks. ShapefileGPT utilizes a multi-agent architecture, in which the planner agent is responsible for task decomposition and supervision, while the worker agent executes the tasks. We developed a specialized function library for handling Shapefiles and provided comprehensive API documentation, enabling the worker agent to operate Shapefiles efficiently through function calling. For evaluation, we developed a benchmark dataset based on authoritative textbooks, encompassing tasks in categories such as geometric operations and spatial queries. ShapefileGPT achieved a task success rate of 95.24%, outperforming the GPT series models. In comparison to traditional LLMs, ShapefileGPT effectively handles complex vector data analysis tasks, overcoming the limitations of traditional LLMs in spatial analysis. This breakthrough opens new pathways for advancing automation and intelligence in the GIS field, with significant potential in interdisciplinary data analysis and application contexts.

This thesis introduces quantum natural language processing (QNLP) models based on a simple yet powerful analogy between computational linguistics and quantum mechanics: grammar as entanglement. The grammatical structure of text and sentences connects the meaning of words in the same way that entanglement structure connects the states of quantum systems. Category theory allows to make this language-to-qubit analogy formal: it is a monoidal functor from grammar to vector spaces. We turn this abstract analogy into a concrete algorithm that translates the grammatical structure onto the architecture of parameterised quantum circuits. We then use a hybrid classical-quantum algorithm to train the model so that evaluating the circuits computes the meaning of sentences in data-driven tasks. The implementation of QNLP models motivated the development of DisCoPy (Distributional Compositional Python), the toolkit for applied category theory of which the first chapter gives a comprehensive overview. String diagrams are the core data structure of DisCoPy, they allow to reason about computation at a high level of abstraction. We show how they can encode both grammatical structures and quantum circuits, but also logical formulae, neural networks or arbitrary Python code. Monoidal functors allow to translate these abstract diagrams into concrete computation, interfacing with optimised task-specific libraries. The second chapter uses DisCopy to implement QNLP models as parameterised functors from grammar to quantum circuits. It gives a first proof-of-concept for the more general concept of functorial learning: generalising machine learning from functions to functors by learning from diagram-like data. In order to learn optimal functor parameters via gradient descent, we introduce the notion of diagrammatic differentiation: a graphical calculus for computing the gradients of parameterised diagrams.

Temporal networks have been widely used to model real-world complex systems such as financial systems and e-commerce systems. In a temporal network, the joint neighborhood of a set of nodes often provides crucial structural information useful for predicting whether they may interact at a certain time. However, recent representation learning methods for temporal networks often fail to extract such information or depend on online construction of structural features, which is time-consuming. To address the issue, this work proposes Neighborhood-Aware Temporal network model (NAT). For each node in the network, NAT abandons the commonly-used one-single-vector-based representation while adopting a novel dictionary-type neighborhood representation. Such a dictionary representation records a downsampled set of the neighboring nodes as keys, and allows fast construction of structural features for a joint neighborhood of multiple nodes. We also design a dedicated data structure termed N-cache to support parallel access and update of those dictionary representations on GPUs. NAT gets evaluated over seven real-world large-scale temporal networks. NAT not only outperforms all cutting-edge baselines by averaged 1.2% and 4.2% in transductive and inductive link prediction accuracy, respectively, but also keeps scalable by achieving a speed-up of 4.1-76.7x against the baselines that adopt joint structural features and achieves a speed-up of 1.6-4.0x against the baselines that cannot adopt those features. The link to the code: https: //github.com/Graph-COM/Neighborhood-Aware-Temporal-Network.

Language Language Models (LLMs) have shown impressive abilities in natural language understanding and generation, leading to their use in applications such as chatbots and virtual assistants. However, existing LLM frameworks face limitations in handling domain-specific data analytics tasks with rich data structures. Moreover, they struggle with flexibility to meet diverse user requirements. To address these issues, TaskWeaver is proposed as a code-first framework for building LLM-powered autonomous agents. It converts user requests into executable code and treats user-defined plugins as callable functions. TaskWeaver provides support for rich data structures, flexible plugin usage, and dynamic plugin selection, and leverages LLM coding capabilities for complex logic. It also incorporates domain-specific knowledge through examples and ensures the secure execution of generated code. TaskWeaver offers a powerful and flexible framework for creating intelligent conversational agents that can handle complex tasks and adapt to domain-specific scenarios. The code is open-sourced at https://github.com/microsoft/TaskWeaver/.

While transformers have shown remarkable success in natural language processing, their attention mechanism's large memory requirements have limited their ability to handle longer contexts. Prior approaches, such as recurrent memory or retrieval-based augmentation, have either compromised the random-access flexibility of attention (i.e., the capability to select any token in the entire context) or relied on separate mechanisms for relevant context retrieval, which may not be compatible with the model's attention. In this paper, we present a novel approach that allows access to the complete context while retaining random-access flexibility, closely resembling running attention on the entire context. Our method uses a landmark token to represent each block of the input and trains the attention to use it for selecting relevant blocks, enabling retrieval of blocks directly through the attention mechanism instead of by relying on a separate mechanism. Our approach seamlessly integrates with specialized data structures and the system's memory hierarchy, enabling processing of arbitrarily long context lengths. We demonstrate that our method can obtain comparable performance with Transformer-XL while significantly reducing the number of retrieved tokens in each step. Finally, we show that fine-tuning LLaMA 7B with our method successfully extends its context length capacity up to 32k tokens, allowing for inference at the context lengths of GPT-4.

We introduce PyTorch Geometric, a library for deep learning on irregularly structured input data such as graphs, point clouds and manifolds, built upon PyTorch. In addition to general graph data structures and processing methods, it contains a variety of recently published methods from the domains of relational learning and 3D data processing. PyTorch Geometric achieves high data throughput by leveraging sparse GPU acceleration, by providing dedicated CUDA kernels and by introducing efficient mini-batch handling for input examples of different size. In this work, we present the library in detail and perform a comprehensive comparative study of the implemented methods in homogeneous evaluation scenarios.

Language models have been effective in a wide range of applications, yet the most sophisticated models are often proprietary. For example, GPT-4 by OpenAI and various models by Anthropic are expensive and consume substantial energy. In contrast, the open-source community has produced competitive models, like Llama3. Furthermore, niche-specific smaller language models, such as those tailored for legal, medical or financial tasks, have outperformed their proprietary counterparts. This paper introduces a novel approach that employs functional tokens to integrate multiple open-source models, each optimized for particular tasks. Our newly developed Octopus v4 model leverages functional tokens to intelligently direct user queries to the most appropriate vertical model and reformat the query to achieve the best performance. Octopus v4, an evolution of the Octopus v1, v2, and v3 models, excels in selection and parameter understanding and reformatting. Additionally, we explore the use of graph as a versatile data structure that effectively coordinates multiple open-source models by harnessing the capabilities of the Octopus model and functional tokens. Use our open-sourced GitHub (https://www.nexa4ai.com/) to try Octopus v4 models (https://huggingface.co/NexaAIDev/Octopus-v4), and contrite to a larger graph of language models. By activating models less than 10B parameters, we achieved SOTA MMLU score of 74.8 among the same level models.

Given a database of bit strings A_1,ldots,A_min {0,1}^n, a fundamental data structure task is to estimate the distances between a given query Bin {0,1}^n with all the strings in the database. In addition, one might further want to ensure the integrity of the database by releasing these distance statistics in a secure manner. In this work, we propose differentially private (DP) data structures for this type of tasks, with a focus on Hamming and edit distance. On top of the strong privacy guarantees, our data structures are also time- and space-efficient. In particular, our data structure is epsilon-DP against any sequence of queries of arbitrary length, and for any query B such that the maximum distance to any string in the database is at most k, we output m distance estimates. Moreover, - For Hamming distance, our data structure answers any query in widetilde O(mk+n) time and each estimate deviates from the true distance by at most widetilde O(k/e^{epsilon/log k}); - For edit distance, our data structure answers any query in widetilde O(mk^2+n) time and each estimate deviates from the true distance by at most widetilde O(k/e^{epsilon/(log k log n)}). For moderate k, both data structures support sublinear query operations. We obtain these results via a novel adaptation of the randomized response technique as a bit flipping procedure, applied to the sketched strings.

The increasing use of Large Language Models (LLMs) in software development has garnered significant attention from researchers assessing the quality of the code they generate. However, much of the research focuses on controlled datasets such as HumanEval, which fail to adequately represent how developers actually utilize LLMs' code generation capabilities or clarify the characteristics of LLM-generated code in real-world development scenarios. To bridge this gap, our study investigates the characteristics of LLM-generated code and its corresponding projects hosted on GitHub. Our findings reveal several key insights: (1) ChatGPT and Copilot are the most frequently utilized for generating code on GitHub. In contrast, there is very little code generated by other LLMs on GitHub. (2) Projects containing ChatGPT/Copilot-generated code are often small and less known, led by individuals or small teams. Despite this, most projects are continuously evolving and improving. (3) ChatGPT/Copilot is mainly utilized for generating Python, Java, and TypeScript scripts for data processing and transformation. C/C++ and JavaScript code generation focuses on algorithm and data structure implementation and user interface code. Most ChatGPT/Copilot-generated code snippets are relatively short and exhibit low complexity. (4) Compared to human-written code, ChatGPT/Copilot-generated code exists in a small proportion of projects and generally undergoes fewer modifications. Additionally, modifications due to bugs are even fewer, ranging from just 3% to 8% across different languages. (5) Most comments on ChatGPT/Copilot-generated code lack detailed information, often only stating the code's origin without mentioning prompts, human modifications, or testing status. Based on these findings, we discuss the implications for researchers and practitioners.

Maximizing monotone submodular functions under a matroid constraint is a classic algorithmic problem with multiple applications in data mining and machine learning. We study this classic problem in the fully dynamic setting, where elements can be both inserted and deleted in real-time. Our main result is a randomized algorithm that maintains an efficient data structure with an O(k^2) amortized update time (in the number of additions and deletions) and yields a 4-approximate solution, where k is the rank of the matroid.

This paper presents a spell checker and correction tool specifically designed for Wolof, an under-represented spoken language in Africa. The proposed spell checker leverages a combination of a trie data structure, dynamic programming, and the weighted Levenshtein distance to generate suggestions for misspelled words. We created novel linguistic resources for Wolof, such as a lexicon and a corpus of misspelled words, using a semi-automatic approach that combines manual and automatic annotation methods. Despite the limited data available for the Wolof language, the spell checker's performance showed a predictive accuracy of 98.31% and a suggestion accuracy of 93.33%. Our primary focus remains the revitalization and preservation of Wolof as an Indigenous and spoken language in Africa, providing our efforts to develop novel linguistic resources. This work represents a valuable contribution to the growth of computational tools and resources for the Wolof language and provides a strong foundation for future studies in the automatic spell checking and correction field.

The ability of deep neural networks to generalise well even when they interpolate their training data has been explained using various "simplicity biases". These theories postulate that neural networks avoid overfitting by first learning simple functions, say a linear classifier, before learning more complex, non-linear functions. Meanwhile, data structure is also recognised as a key ingredient for good generalisation, yet its role in simplicity biases is not yet understood. Here, we show that neural networks trained using stochastic gradient descent initially classify their inputs using lower-order input statistics, like mean and covariance, and exploit higher-order statistics only later during training. We first demonstrate this distributional simplicity bias (DSB) in a solvable model of a neural network trained on synthetic data. We empirically demonstrate DSB in a range of deep convolutional networks and visual transformers trained on CIFAR10, and show that it even holds in networks pre-trained on ImageNet. We discuss the relation of DSB to other simplicity biases and consider its implications for the principle of Gaussian universality in learning.

Mahjong is a popular multi-player imperfect-information game developed in China in the late 19th-century, with some very challenging features for AI research. Sanma, being a 3-player variant of the Japanese Riichi Mahjong, possesses unique characteristics including fewer tiles and, consequently, a more aggressive playing style. It is thus challenging and of great research interest in its own right, but has not yet been explored. In this paper, we present Meowjong, an AI for Sanma using deep reinforcement learning. We define an informative and compact 2-dimensional data structure for encoding the observable information in a Sanma game. We pre-train 5 convolutional neural networks (CNNs) for Sanma's 5 actions -- discard, Pon, Kan, Kita and Riichi, and enhance the major action's model, namely the discard model, via self-play reinforcement learning using the Monte Carlo policy gradient method. Meowjong's models achieve test accuracies comparable with AIs for 4-player Mahjong through supervised learning, and gain a significant further enhancement from reinforcement learning. Being the first ever AI in Sanma, we claim that Meowjong stands as a state-of-the-art in this game.

Polygonal meshes are ubiquitous, but have only played a relatively minor role in the deep learning revolution. State-of-the-art neural generative models for 3D shapes learn implicit functions and generate meshes via expensive iso-surfacing. We overcome these challenges by employing a classical spatial data structure from computer graphics, Binary Space Partitioning (BSP), to facilitate 3D learning. The core operation of BSP involves recursive subdivision of 3D space to obtain convex sets. By exploiting this property, we devise BSP-Net, a network that learns to represent a 3D shape via convex decomposition without supervision. The network is trained to reconstruct a shape using a set of convexes obtained from a BSP-tree built over a set of planes, where the planes and convexes are both defined by learned network weights. BSP-Net directly outputs polygonal meshes from the inferred convexes. The generated meshes are watertight, compact (i.e., low-poly), and well suited to represent sharp geometry. We show that the reconstruction quality by BSP-Net is competitive with those from state-of-the-art methods while using much fewer primitives. We also explore variations to BSP-Net including using a more generic decoder for reconstruction, more general primitives than planes, as well as training a generative model with variational auto-encoders. Code is available at https://github.com/czq142857/BSP-NET-original.

Large language models have become the cornerstone of natural language processing, but their use comes with substantial costs in terms of compute and memory resources. Sparsification provides a solution to alleviate these resource constraints, and recent works have shown that trained models can be sparsified post-hoc. Existing sparsification techniques face challenges as they need additional data structures and offer constrained speedup with current hardware. In this paper we present SliceGPT, a new post-training sparsification scheme which replaces each weight matrix with a smaller (dense) matrix, reducing the embedding dimension of the network. Through extensive experimentation, we show that SliceGPT can remove up to 25% of the model parameters (including embeddings) for LLAMA2-70B, OPT 66B and Phi-2 models while maintaining 99%, 99% and 90% zero-shot task performance of the dense model respectively. Our sliced models run on fewer GPUs and run faster without any additional code optimization: on 24GB consumer GPUs we reduce the total compute for inference on LLAMA2-70B to 64% of that of the dense model; on 40GB A100 GPUs we reduce it to 66%. We offer a new insight, computational invariance in transformer networks, which enables SliceGPT and we hope it will inspire and enable future avenues to reduce memory and computation demands for pre-trained models. Code is available at: https://github.com/microsoft/TransformerCompression

Hyperbolic embeddings offer excellent quality with few dimensions when embedding hierarchical data structures like synonym or type hierarchies. Given a tree, we give a combinatorial construction that embeds the tree in hyperbolic space with arbitrarily low distortion without using optimization. On WordNet, our combinatorial embedding obtains a mean-average-precision of 0.989 with only two dimensions, while Nickel et al.'s recent construction obtains 0.87 using 200 dimensions. We provide upper and lower bounds that allow us to characterize the precision-dimensionality tradeoff inherent in any hyperbolic embedding. To embed general metric spaces, we propose a hyperbolic generalization of multidimensional scaling (h-MDS). We show how to perform exact recovery of hyperbolic points from distances, provide a perturbation analysis, and give a recovery result that allows us to reduce dimensionality. The h-MDS approach offers consistently low distortion even with few dimensions across several datasets. Finally, we extract lessons from the algorithms and theory above to design a PyTorch-based implementation that can handle incomplete information and is scalable.

Large language models (LLMs) have demonstrated remarkable success across a wide range of tasks; however, they still encounter challenges in reasoning tasks that require understanding and inferring relationships between distinct pieces of information within text sequences. This challenge is particularly pronounced in tasks involving multi-step processes, such as logical reasoning and multi-hop question answering, where understanding implicit relationships between entities and leveraging multi-hop connections in the given context are crucial. Graphs, as fundamental data structures, explicitly represent pairwise relationships between entities, thereby offering the potential to enhance LLMs' reasoning capabilities. External graphs have proven effective in supporting LLMs across multiple tasks. However, in many reasoning tasks, no pre-existing graph structure is provided. Can we structure implicit knowledge derived from context into graphs to assist LLMs in reasoning? In this paper, we propose Reasoning with Graphs (RwG) by first constructing explicit graphs from the context and then leveraging these graphs to enhance LLM reasoning performance on reasoning tasks. Extensive experiments demonstrate the effectiveness of the proposed method in improving both logical reasoning and multi-hop question answering tasks.

We give a quantum algorithm for computing an epsilon-approximate Nash equilibrium of a zero-sum game in a m times n payoff matrix with bounded entries. Given a standard quantum oracle for accessing the payoff matrix our algorithm runs in time O(m + ncdot epsilon^{-2.5} + epsilon^{-3}) and outputs a classical representation of the epsilon-approximate Nash equilibrium. This improves upon the best prior quantum runtime of O(m + n cdot epsilon^{-3}) obtained by [vAG19] and the classic O((m + n) cdot epsilon^{-2}) runtime due to [GK95] whenever epsilon = Omega((m +n)^{-1}). We obtain this result by designing new quantum data structures for efficiently sampling from a slowly-changing Gibbs distribution.

Point cloud is an important type of geometric data structure. Due to its irregular format, most researchers transform such data to regular 3D voxel grids or collections of images. This, however, renders data unnecessarily voluminous and causes issues. In this paper, we design a novel type of neural network that directly consumes point clouds and well respects the permutation invariance of points in the input. Our network, named PointNet, provides a unified architecture for applications ranging from object classification, part segmentation, to scene semantic parsing. Though simple, PointNet is highly efficient and effective. Empirically, it shows strong performance on par or even better than state of the art. Theoretically, we provide analysis towards understanding of what the network has learnt and why the network is robust with respect to input perturbation and corruption.

The emergence of programmable switches allows operators to collect a vast amount of fine-grained telemetry data in real time. However, consolidating the telemetry reports at centralized collectors to gain a network-wide view poses an immense challenge. The received data has to be transported from the switches, parsed, manipulated, and inserted in queryable data structures. As the network scales, this requires excessive CPU processing. RDMA is a transport protocol that bypasses the CPU and allows extremely high data transfer rates. Yet, RDMA is not designed for telemetry collection: it requires a stateful connection, supports only a small number of concurrent writers, and has limited writing primitives, which restricts its data aggregation applicability. We introduce Direct Telemetry Access (DTA), a solution that allows fast and efficient telemetry collection, aggregation, and indexing. Our system establishes RDMA connections only from collectors' ToR switches, called translators, that process DTA reports from all other switches. DTA features novel and expressive reporting primitives such as Key-Write, Append, Sketch-Merge, and Key-Increment that allow integration of telemetry systems such as INT and others. The translators then aggregate, batch, and write the reports to collectors' memory in queryable form.

Integrating information from different reference data sources is a major challenge for Retrieval-Augmented Generation (RAG) systems because each knowledge source adopts a unique data structure and follows different conventions. Retrieving from multiple knowledge sources with one fixed strategy usually leads to under-exploitation of information. To mitigate this drawback, inspired by Mix-of-Expert, we introduce Mix-of-Granularity (MoG), a method that dynamically determines the optimal granularity of a knowledge database based on input queries using a router. The router is efficiently trained with a newly proposed loss function employing soft labels. We further extend MoG to Mix-of-Granularity-Graph (MoGG), where reference documents are pre-processed into graphs, enabling the retrieval of relevant information from distantly situated chunks. Extensive experiments demonstrate that both MoG and MoGG effectively predict optimal granularity levels, significantly enhancing the performance of the RAG system in downstream tasks. The code of both MoG and MoGG will be made public.

We present PyTorch Frame, a PyTorch-based framework for deep learning over multi-modal tabular data. PyTorch Frame makes tabular deep learning easy by providing a PyTorch-based data structure to handle complex tabular data, introducing a model abstraction to enable modular implementation of tabular models, and allowing external foundation models to be incorporated to handle complex columns (e.g., LLMs for text columns). We demonstrate the usefulness of PyTorch Frame by implementing diverse tabular models in a modular way, successfully applying these models to complex multi-modal tabular data, and integrating our framework with PyTorch Geometric, a PyTorch library for Graph Neural Networks (GNNs), to perform end-to-end learning over relational databases.

Code generation by Llama 3.1 models, such as Meta's Llama 3.1 405B, represents a significant advancement in the field of artificial intelligence, particularly in natural language processing and programming automation. This paper explores the capabilities and applications of Llama-driven code generation, highlighting its ability to translate natural language prompts into executable code across multiple programming languages. Key features include contextual awareness, multi-language support, and enhanced debugging and optimization functionalities. By examining these aspects, we illustrate how Llama can serve as a versatile tool for developers of all skill levels, improving productivity and efficiency in software development. The potential implications for education, industry, and the future of coding practices are also discussed, underscoring the transformative impact of AI in programming. Experimentation shows that while Llama 3.1 405B performs well with simple algorithmic and data structure based problems, it still struggles with problems on Quantum Computing, Bioinformatics, and Artificial Intelligence.

Environment, Social, and Governance (ESG) KPIs assess an organization's performance on issues such as climate change, greenhouse gas emissions, water consumption, waste management, human rights, diversity, and policies. ESG reports convey this valuable quantitative information through tables. Unfortunately, extracting this information is difficult due to high variability in the table structure as well as content. We propose Statements, a novel domain agnostic data structure for extracting quantitative facts and related information. We propose translating tables to statements as a new supervised deep-learning universal information extraction task. We introduce SemTabNet - a dataset of over 100K annotated tables. Investigating a family of T5-based Statement Extraction Models, our best model generates statements which are 82% similar to the ground-truth (compared to baseline of 21%). We demonstrate the advantages of statements by applying our model to over 2700 tables from ESG reports. The homogeneous nature of statements permits exploratory data analysis on expansive information found in large collections of ESG reports.

Large language models (LLMs) have reshaped the landscape of program synthesis. However, contemporary LLM-based code completion systems often hallucinate broken code because they lack appropriate context, particularly when working with definitions not in the training data nor near the cursor. This paper demonstrates that tight integration with the type and binding structure of a language, as exposed by its language server, can address this contextualization problem in a token-efficient manner. In short, we contend that AIs need IDEs, too! In particular, we integrate LLM code generation into the Hazel live program sketching environment. The Hazel Language Server identifies the type and typing context of the hole being filled, even in the presence of errors, ensuring that a meaningful program sketch is always available. This allows prompting with codebase-wide contextual information not lexically local to the cursor, nor necessarily in the same file, but that is likely to be semantically local to the developer's goal. Completions synthesized by the LLM are then iteratively refined via further dialog with the language server. To evaluate these techniques, we introduce MVUBench, a dataset of model-view-update (MVU) web applications. These applications serve as challenge problems due to their reliance on application-specific data structures. We find that contextualization with type definitions is particularly impactful. After introducing our ideas in the context of Hazel we duplicate our techniques and port MVUBench to TypeScript in order to validate the applicability of these methods to higher-resource languages. Finally, we outline ChatLSP, a conservative extension to the Language Server Protocol (LSP) that language servers can implement to expose capabilities that AI code completion systems of various designs can use to incorporate static context when generating prompts for an LLM.

Large language models (LLMs) are expected to follow instructions from users and engage in conversations. Techniques to enhance LLMs' instruction-following capabilities typically fine-tune them using data structured according to a predefined chat template. Although chat templates are shown to be effective in optimizing LLM performance, their impact on safety alignment of LLMs has been less understood, which is crucial for deploying LLMs safely at scale. In this paper, we investigate how chat templates affect safety alignment of LLMs. We identify a common vulnerability, named ChatBug, that is introduced by chat templates. Our key insight to identify ChatBug is that the chat templates provide a rigid format that need to be followed by LLMs, but not by users. Hence, a malicious user may not necessarily follow the chat template when prompting LLMs. Instead, malicious users could leverage their knowledge of the chat template and accordingly craft their prompts to bypass safety alignments of LLMs. We develop two attacks to exploit the ChatBug vulnerability. We demonstrate that a malicious user can exploit the ChatBug vulnerability of eight state-of-the-art (SOTA) LLMs and effectively elicit unintended responses from these models. Moreover, we show that ChatBug can be exploited by existing jailbreak attacks to enhance their attack success rates. We investigate potential countermeasures to ChatBug. Our results show that while adversarial training effectively mitigates the ChatBug vulnerability, the victim model incurs significant performance degradation. These results highlight the trade-off between safety alignment and helpfulness. Developing new methods for instruction tuning to balance this trade-off is an open and critical direction for future research

Audio-visual zero-shot learning aims to classify samples consisting of a pair of corresponding audio and video sequences from classes that are not present during training. An analysis of the audio-visual data reveals a large degree of hyperbolicity, indicating the potential benefit of using a hyperbolic transformation to achieve curvature-aware geometric learning, with the aim of exploring more complex hierarchical data structures for this task. The proposed approach employs a novel loss function that incorporates cross-modality alignment between video and audio features in the hyperbolic space. Additionally, we explore the use of multiple adaptive curvatures for hyperbolic projections. The experimental results on this very challenging task demonstrate that our proposed hyperbolic approach for zero-shot learning outperforms the SOTA method on three datasets: VGGSound-GZSL, UCF-GZSL, and ActivityNet-GZSL achieving a harmonic mean (HM) improvement of around 3.0%, 7.0%, and 5.3%, respectively.

Point cloud analysis is challenging due to the irregularity of the point cloud data structure. Existing works typically employ the ad-hoc sampling-grouping operation of PointNet++, followed by sophisticated local and/or global feature extractors for leveraging the 3D geometry of the point cloud. Unfortunately, the sampling-grouping operations do not address the point cloud's irregularity, whereas the intricate local and/or global feature extractors led to poor computational efficiency. In this paper, we introduce a novel DualNorm module after the sampling-grouping operation to effectively and efficiently address the irregularity issue. The DualNorm module consists of Point Normalization, which normalizes the grouped points to the sampled points, and Reverse Point Normalization, which normalizes the sampled points to the grouped points. The proposed framework, PointNorm, utilizes local mean and global standard deviation to benefit from both local and global features while maintaining a faithful inference speed. Experiments show that we achieved excellent accuracy and efficiency on ModelNet40 classification, ScanObjectNN classification, ShapeNetPart Part Segmentation, and S3DIS Semantic Segmentation. Code is available at https://github.com/ShenZheng2000/PointNorm-for-Point-Cloud-Analysis.

Traffic signal control is an emerging application scenario for reinforcement learning. Besides being as an important problem that affects people's daily life in commuting, traffic signal control poses its unique challenges for reinforcement learning in terms of adapting to dynamic traffic environment and coordinating thousands of agents including vehicles and pedestrians. A key factor in the success of modern reinforcement learning relies on a good simulator to generate a large number of data samples for learning. The most commonly used open-source traffic simulator SUMO is, however, not scalable to large road network and large traffic flow, which hinders the study of reinforcement learning on traffic scenarios. This motivates us to create a new traffic simulator CityFlow with fundamentally optimized data structures and efficient algorithms. CityFlow can support flexible definitions for road network and traffic flow based on synthetic and real-world data. It also provides user-friendly interface for reinforcement learning. Most importantly, CityFlow is more than twenty times faster than SUMO and is capable of supporting city-wide traffic simulation with an interactive render for monitoring. Besides traffic signal control, CityFlow could serve as the base for other transportation studies and can create new possibilities to test machine learning methods in the intelligent transportation domain.

We present 3DGS-LM, a new method that accelerates the reconstruction of 3D Gaussian Splatting (3DGS) by replacing its ADAM optimizer with a tailored Levenberg-Marquardt (LM). Existing methods reduce the optimization time by decreasing the number of Gaussians or by improving the implementation of the differentiable rasterizer. However, they still rely on the ADAM optimizer to fit Gaussian parameters of a scene in thousands of iterations, which can take up to an hour. To this end, we change the optimizer to LM that runs in conjunction with the 3DGS differentiable rasterizer. For efficient GPU parallization, we propose a caching data structure for intermediate gradients that allows us to efficiently calculate Jacobian-vector products in custom CUDA kernels. In every LM iteration, we calculate update directions from multiple image subsets using these kernels and combine them in a weighted mean. Overall, our method is 30% faster than the original 3DGS while obtaining the same reconstruction quality. Our optimization is also agnostic to other methods that acclerate 3DGS, thus enabling even faster speedups compared to vanilla 3DGS.

Although retrieval-augmented generation(RAG) significantly improves generation quality by retrieving external knowledge bases and integrating generated content, it faces computational efficiency bottlenecks, particularly in knowledge retrieval tasks involving hierarchical structures for Tree-RAG. This paper proposes a Tree-RAG acceleration method based on the improved Cuckoo Filter, which optimizes entity localization during the retrieval process to achieve significant performance improvements. Tree-RAG effectively organizes entities through the introduction of a hierarchical tree structure, while the Cuckoo Filter serves as an efficient data structure that supports rapid membership queries and dynamic updates. The experiment results demonstrate that our method is much faster than naive Tree-RAG while maintaining high levels of generative quality. When the number of trees is large, our method is hundreds of times faster than naive Tree-RAG. Our work is available at https://github.com/TUPYP7180/CFT-RAG-2025.

Many hybrid quantum-classical algorithms for the application of ground state energy estimation in quantum chemistry involve estimating the expectation value of a molecular Hamiltonian with respect to a quantum state through measurements on a quantum device. To guide the selection of measurement methods designed for this observable estimation problem, we propose a benchmark called CSHOREBench (Common States and Hamiltonians for ObseRvable Estimation Benchmark) that assesses the performance of these methods against a set of common molecular Hamiltonians and common states encountered during the runtime of hybrid quantum-classical algorithms. In CSHOREBench, we account for resource utilization of a quantum computer through measurements of a prepared state, and a classical computer through computational runtime spent in proposing measurements and classical post-processing of acquired measurement outcomes. We apply CSHOREBench considering a variety of measurement methods on Hamiltonians of size up to 16 qubits. Our discussion is aided by using the framework of decision diagrams which provides an efficient data structure for various randomized methods and illustrate how to derandomize distributions on decision diagrams. In numerical simulations, we find that the methods of decision diagrams and derandomization are the most preferable. In experiments on IBM quantum devices against small molecules, we observe that decision diagrams reduces the number of measurements made by classical shadows by more than 80%, that made by locally biased classical shadows by around 57%, and consistently require fewer quantum measurements along with lower classical computational runtime than derandomization. Furthermore, CSHOREBench is empirically efficient to run when considering states of random quantum ansatz with fixed depth.

Neural graphics primitives are faster and achieve higher quality when their neural networks are augmented by spatial data structures that hold trainable features arranged in a grid. However, existing feature grids either come with a large memory footprint (dense or factorized grids, trees, and hash tables) or slow performance (index learning and vector quantization). In this paper, we show that a hash table with learned probes has neither disadvantage, resulting in a favorable combination of size and speed. Inference is faster than unprobed hash tables at equal quality while training is only 1.2-2.6x slower, significantly outperforming prior index learning approaches. We arrive at this formulation by casting all feature grids into a common framework: they each correspond to a lookup function that indexes into a table of feature vectors. In this framework, the lookup functions of existing data structures can be combined by simple arithmetic combinations of their indices, resulting in Pareto optimal compression and speed.

How can we perform computations over natural language representations to solve tasks that require symbolic and numeric reasoning? We propose natural language embedded programs (NLEP) as a unifying framework for addressing math/symbolic reasoning, natural language understanding, and instruction following tasks. Our approach prompts a language model to generate full Python programs that define functions over data structures which contain natural language representations of structured knowledge. A Python interpreter then executes the generated code and prints the output. Despite using a task-general prompt, we find that this approach can improve upon strong baselines across a range of different tasks including math and symbolic reasoning, text classification, question answering, and instruction following. We further find the generated programs are often interpretable and enable post-hoc verification of the intermediate reasoning steps.

Vectors are universal mathematical objects that can represent text, images, speech, or a mix of these data modalities. That happens regardless of whether data is represented by hand-crafted features or learnt embeddings. Collect a large enough quantity of such vectors and the question of retrieval becomes urgently relevant: Finding vectors that are more similar to a query vector. This monograph is concerned with the question above and covers fundamental concepts along with advanced data structures and algorithms for vector retrieval. In doing so, it recaps this fascinating topic and lowers barriers of entry into this rich area of research.

The limited context window of contemporary large language models (LLMs) remains a huge barrier to their broader application across various domains. While continual pre-training on long-context data is a straightforward and effective solution, it incurs substantial costs in terms of data acquisition and computational resources. To alleviate this issue, we propose SharedLLM, a novel approach grounded in the design philosophy of multi-grained context compression and query-aware information retrieval. SharedLLM is composed of two short-context LLMs such as LLaMA-2, termed upper model and lower model. The lower model functions as a compressor while the upper model acts as a decoder. The upper model receives compressed, multi-grained context information from the lower model and performs context-aware modeling on the running text. Information transfer between the compressor and decoder occurs only at the lowest layers to refrain from long forward paths in the lower model and redundant cross-attention modules in the upper model. Based on this architecture, we introduce a specialized tree-style data structure to efficiently encode, store and retrieve multi-grained contextual information for text chunks. This structure, combined with a search algorithm, enables rapid encoding and retrieval of relevant information from various levels of the tree based on the input query. This entire process, wherein the sender and receiver are derived from the same LLM layer, is referred to as self-injection.

Driven by the appealing properties of neural fields for storing and communicating 3D data, the problem of directly processing them to address tasks such as classification and part segmentation has emerged and has been investigated in recent works. Early approaches employ neural fields parameterized by shared networks trained on the whole dataset, achieving good task performance but sacrificing reconstruction quality. To improve the latter, later methods focus on individual neural fields parameterized as large Multi-Layer Perceptrons (MLPs), which are, however, challenging to process due to the high dimensionality of the weight space, intrinsic weight space symmetries, and sensitivity to random initialization. Hence, results turn out significantly inferior to those achieved by processing explicit representations, e.g., point clouds or meshes. In the meantime, hybrid representations, in particular based on tri-planes, have emerged as a more effective and efficient alternative to realize neural fields, but their direct processing has not been investigated yet. In this paper, we show that the tri-plane discrete data structure encodes rich information, which can be effectively processed by standard deep-learning machinery. We define an extensive benchmark covering a diverse set of fields such as occupancy, signed/unsigned distance, and, for the first time, radiance fields. While processing a field with the same reconstruction quality, we achieve task performance far superior to frameworks that process large MLPs and, for the first time, almost on par with architectures handling explicit representations.

For a broad range of research, governmental and commercial applications it is important to understand the allegiances, communities and structure of key players in society. One promising direction towards extracting this information is to exploit the rich relational data in digital social networks (the social graph). As social media data sets are very large, most approaches make use of distributed computing systems for this purpose. Distributing graph processing requires solving many difficult engineering problems, which has lead some researchers to look at single-machine solutions that are faster and easier to maintain. In this article, we present a single-machine real-time system for large-scale graph processing that allows analysts to interactively explore graph structures. The key idea is that the aggregate actions of large numbers of users can be compressed into a data structure that encapsulates user similarities while being robust to noise and queryable in real-time. We achieve single machine real-time performance by compressing the neighbourhood of each vertex using minhash signatures and facilitate rapid queries through Locality Sensitive Hashing. These techniques reduce query times from hours using industrial desktop machines operating on the full graph to milliseconds on standard laptops. Our method allows exploration of strongly associated regions (i.e. communities) of large graphs in real-time on a laptop. It has been deployed in software that is actively used by social network analysts and offers another channel for media owners to monetise their data, helping them to continue to provide free services that are valued by billions of people globally.

In this paper, we revisit one of the simplest problems in data structures: the task of inserting elements into an open-addressed hash table so that elements can later be retrieved with as few probes as possible. We show that, even without reordering elements over time, it is possible to construct a hash table that achieves far better expected search complexities (both amortized and worst-case) than were previously thought possible. Along the way, we disprove the central conjecture left by Yao in his seminal paper ``Uniform Hashing is Optimal''. All of our results come with matching lower bounds.

The difficulty of the information extraction task lies in dealing with the task-specific label schemas and heterogeneous data structures. Recent work has proposed methods based on large language models to uniformly model different information extraction tasks. However, these existing methods are deficient in their information extraction capabilities for Chinese languages other than English. In this paper, we propose an end-to-end chat-enhanced instruction tuning framework for universal information extraction (YAYI-UIE), which supports both Chinese and English. Specifically, we utilize dialogue data and information extraction data to enhance the information extraction performance jointly. Experimental results show that our proposed framework achieves state-of-the-art performance on Chinese datasets while also achieving comparable performance on English datasets under both supervised settings and zero-shot settings.

Web-scale search systems learn an encoder to embed a given query which is then hooked into an approximate nearest neighbor search (ANNS) pipeline to retrieve similar data points. To accurately capture tail queries and data points, learned representations typically are rigid, high-dimensional vectors that are generally used as-is in the entire ANNS pipeline and can lead to computationally expensive retrieval. In this paper, we argue that instead of rigid representations, different stages of ANNS can leverage adaptive representations of varying capacities to achieve significantly better accuracy-compute trade-offs, i.e., stages of ANNS that can get away with more approximate computation should use a lower-capacity representation of the same data point. To this end, we introduce AdANNS, a novel ANNS design framework that explicitly leverages the flexibility of Matryoshka Representations. We demonstrate state-of-the-art accuracy-compute trade-offs using novel AdANNS-based key ANNS building blocks like search data structures (AdANNS-IVF) and quantization (AdANNS-OPQ). For example on ImageNet retrieval, AdANNS-IVF is up to 1.5% more accurate than the rigid representations-based IVF at the same compute budget; and matches accuracy while being up to 90x faster in wall-clock time. For Natural Questions, 32-byte AdANNS-OPQ matches the accuracy of the 64-byte OPQ baseline constructed using rigid representations -- same accuracy at half the cost! We further show that the gains from AdANNS translate to modern-day composite ANNS indices that combine search structures and quantization. Finally, we demonstrate that AdANNS can enable inference-time adaptivity for compute-aware search on ANNS indices built non-adaptively on matryoshka representations. Code is open-sourced at https://github.com/RAIVNLab/AdANNS.

In this paper, we introduce a new class of score-based generative models (SGMs) designed to handle high-cardinality data distributions by leveraging concepts from mean-field theory. We present mean-field chaos diffusion models (MF-CDMs), which address the curse of dimensionality inherent in high-cardinality data by utilizing the propagation of chaos property of interacting particles. By treating high-cardinality data as a large stochastic system of interacting particles, we develop a novel score-matching method for infinite-dimensional chaotic particle systems and propose an approximation scheme that employs a subdivision strategy for efficient training. Our theoretical and empirical results demonstrate the scalability and effectiveness of MF-CDMs for managing large high-cardinality data structures, such as 3D point clouds.

Learned sparse retrieval systems aim to combine the effectiveness of contextualized language models with the scalability of conventional data structures such as inverted indexes. Nevertheless, the indexes generated by these systems exhibit significant deviations from the ones that use traditional retrieval models, leading to a discrepancy in the performance of existing query optimizations that were specifically developed for traditional structures. These disparities arise from structural variations in query and document statistics, including sub-word tokenization, leading to longer queries, smaller vocabularies, and different score distributions within posting lists. This paper introduces Block-Max Pruning (BMP), an innovative dynamic pruning strategy tailored for indexes arising in learned sparse retrieval environments. BMP employs a block filtering mechanism to divide the document space into small, consecutive document ranges, which are then aggregated and sorted on the fly, and fully processed only as necessary, guided by a defined safe early termination criterion or based on approximate retrieval requirements. Through rigorous experimentation, we show that BMP substantially outperforms existing dynamic pruning strategies, offering unparalleled efficiency in safe retrieval contexts and improved tradeoffs between precision and efficiency in approximate retrieval tasks.

Image ranking is to rank images based on some known ranked images. In this paper, we propose an improved linear ordinal distance metric learning approach based on the linear distance metric learning model. By decomposing the distance metric A as L^TL, the problem can be cast as looking for a linear map between two sets of points in different spaces, meanwhile maintaining some data structures. The ordinal relation of the labels can be maintained via classical multidimensional scaling, a popular tool for dimension reduction in statistics. A least squares fitting term is then introduced to the cost function, which can also maintain the local data structure. The resulting model is an unconstrained problem, and can better fit the data structure. Extensive numerical results demonstrate the improvement of the new approach over the linear distance metric learning model both in speed and ranking performance.

This technical report presents SSL4EO-S12 v1.1, a multimodal, multitemporal Earth Observation dataset designed for pretraining large-scale foundation models. Building on the success of SSL4EO-S12 v1.0, the new version addresses the previous challenges of data misalignment and a limited data structure for low-barrier, analysis-ready EO processing. SSL4EO-S12 v1.1 covers the world's 10,000 largest cities and its surroundings within a 50 km radius across four seasons, resulting in a diverse collection of nearly one million patches. SSL4EO-S12 v1.1 packages the data in Zarr file format for cloud-efficient loading and representation of meta-information such as including cloud masks and geolocation. Released under the CC-BY-4.0 license, SSL4EO-S12 v1.1 facilitates open research and provides a robust foundation for future advancements in self-supervised learning and geospatial analysis. The dataset is available online through https://datapub.fz-juelich.de/ssl4eo-s12, and we provided additional resources at https://github.com/DLR-MF-DAS/SSL4EO-S12-v1.1.

While accurately detecting and correcting factual contradictions in language model outputs has become increasingly important as their capabilities improve, doing so is highly challenging. We propose a novel method, FACTTRACK, for tracking atomic facts and addressing factual contradictions. Crucially, FACTTRACK also maintains time-aware validity intervals for each fact, allowing for change over time. At a high level, FACTTRACK consists of a four-step pipeline to update a world state data structure for each new event: (1) decompose the event into directional atomic facts; (2) determine the validity interval of each atomic fact using the world state; (3) detect contradictions with existing facts in the world state; and finally (4) add new facts to the world state and update existing atomic facts. When we apply FACTTRACK to contradiction detection on structured story outlines, we find that FACTTRACK using LLaMA2-7B-Chat substantially outperforms a fair baseline using LLaMA2-7B-Chat, and achieves performance comparable to a GPT4 baseline. Moreover, when using GPT4, FACTTRACK significantly outperforms the GPT4 baseline.

Large Vision-Language Models (LVLMs) are capable of handling diverse data types such as imaging, text, and physiological signals, and can be applied in various fields. In the medical field, LVLMs have a high potential to offer substantial assistance for diagnosis and treatment. Before that, it is crucial to develop benchmarks to evaluate LVLMs' effectiveness in various medical applications. Current benchmarks are often built upon specific academic literature, mainly focusing on a single domain, and lacking varying perceptual granularities. Thus, they face specific challenges, including limited clinical relevance, incomplete evaluations, and insufficient guidance for interactive LVLMs. To address these limitations, we developed the GMAI-MMBench, the most comprehensive general medical AI benchmark with well-categorized data structure and multi-perceptual granularity to date. It is constructed from 285 datasets across 39 medical image modalities, 18 clinical-related tasks, 18 departments, and 4 perceptual granularities in a Visual Question Answering (VQA) format. Additionally, we implemented a lexical tree structure that allows users to customize evaluation tasks, accommodating various assessment needs and substantially supporting medical AI research and applications. We evaluated 50 LVLMs, and the results show that even the advanced GPT-4o only achieves an accuracy of 52%, indicating significant room for improvement. Moreover, we identified five key insufficiencies in current cutting-edge LVLMs that need to be addressed to advance the development of better medical applications. We believe that GMAI-MMBench will stimulate the community to build the next generation of LVLMs toward GMAI. Project Page: https://uni-medical.github.io/GMAI-MMBench.github.io/

Many methods in differentially private model training rely on computing the similarity between a query point (such as public or synthetic data) and private data. We abstract out this common subroutine and study the following fundamental algorithmic problem: Given a similarity function f and a large high-dimensional private dataset X subset R^d, output a differentially private (DP) data structure which approximates sum_{x in X} f(x,y) for any query y. We consider the cases where f is a kernel function, such as f(x,y) = e^{-|x-y|_2^2/sigma^2} (also known as DP kernel density estimation), or a distance function such as f(x,y) = |x-y|_2, among others. Our theoretical results improve upon prior work and give better privacy-utility trade-offs as well as faster query times for a wide range of kernels and distance functions. The unifying approach behind our results is leveraging `low-dimensional structures' present in the specific functions f that we study, using tools such as provable dimensionality reduction, approximation theory, and one-dimensional decomposition of the functions. Our algorithms empirically exhibit improved query times and accuracy over prior state of the art. We also present an application to DP classification. Our experiments demonstrate that the simple methodology of classifying based on average similarity is orders of magnitude faster than prior DP-SGD based approaches for comparable accuracy.

Randomized controlled trials are susceptible to imbalance on covariates predictive of the outcome. Rerandomization and deterministic treatment assignment are two proposed solutions. This paper explores the relationship between rerandomization and deterministic assignment, showing how deterministic assignment is an extreme case of rerandomization. The paper argues that in small experiments, both fully randomized and fully deterministic assignment have limitations. Instead, the researcher should consider setting the rerandomization acceptance probability based on an analysis of covariates and assumptions about the data structure to achieve an optimal alignment between randomness and balance. This allows for the calculation of minimum p-values along with valid permutation tests and fiducial intervals. The paper also introduces tools, including a new, open-source R package named fastrerandomize, to implement rerandomization and explore options for optimal rerandomization acceptance thresholds.

Large Language Models (LLMs) have shown remarkable progress in automated code generation. Yet, LLM-generated code may contain errors in API usage, class, data structure, or missing project-specific information. As much of this project-specific context cannot fit into the prompts of LLMs, we must find ways to allow the model to explore the project-level code context. We present CoCoGen, a new code generation approach that uses compiler feedback to improve the LLM-generated code. CoCoGen first leverages static analysis to identify mismatches between the generated code and the project's context. It then iteratively aligns and fixes the identified errors using information extracted from the code repository. We integrate CoCoGen with two representative LLMs, i.e., GPT-3.5-Turbo and Code Llama (13B), and apply it to Python code generation. Experimental results show that CoCoGen significantly improves the vanilla LLMs by over 80% in generating code dependent on the project context and consistently outperforms the existing retrieval-based code generation baselines.

We define and investigate the problem of c-approximate window search: approximate nearest neighbor search where each point in the dataset has a numeric label, and the goal is to find nearest neighbors to queries within arbitrary label ranges. Many semantic search problems, such as image and document search with timestamp filters, or product search with cost filters, are natural examples of this problem. We propose and theoretically analyze a modular tree-based framework for transforming an index that solves the traditional c-approximate nearest neighbor problem into a data structure that solves window search. On standard nearest neighbor benchmark datasets equipped with random label values, adversarially constructed embeddings, and image search embeddings with real timestamps, we obtain up to a 75times speedup over existing solutions at the same level of recall.

Source-free unsupervised domain adaptation (SFUDA) aims to obtain high performance in the unlabeled target domain using the pre-trained source model, not the source data. Existing SFUDA methods assign the same importance to all target samples, which is vulnerable to incorrect pseudo-labels. To differentiate between sample importance, in this study, we propose a novel sample-wise confidence score, the Joint Model-Data Structure (JMDS) score for SFUDA. Unlike existing confidence scores that use only one of the source or target domain knowledge, the JMDS score uses both knowledge. We then propose a Confidence score Weighting Adaptation using the JMDS (CoWA-JMDS) framework for SFUDA. CoWA-JMDS consists of the JMDS scores as sample weights and weight Mixup that is our proposed variant of Mixup. Weight Mixup promotes the model make more use of the target domain knowledge. The experimental results show that the JMDS score outperforms the existing confidence scores. Moreover, CoWA-JMDS achieves state-of-the-art performance on various SFUDA scenarios: closed, open, and partial-set scenarios.

Time-series representation learning is a fundamental task for time-series analysis. While significant progress has been made to achieve accurate representations for downstream applications, the learned representations often lack interpretability and do not expose semantic meanings. Different from previous efforts on the entangled feature space, we aim to extract the semantic-rich temporal correlations in the latent interpretable factorized representation of the data. Motivated by the success of disentangled representation learning in computer vision, we study the possibility of learning semantic-rich time-series representations, which remains unexplored due to three main challenges: 1) sequential data structure introduces complex temporal correlations and makes the latent representations hard to interpret, 2) sequential models suffer from KL vanishing problem, and 3) interpretable semantic concepts for time-series often rely on multiple factors instead of individuals. To bridge the gap, we propose Disentangle Time Series (DTS), a novel disentanglement enhancement framework for sequential data. Specifically, to generate hierarchical semantic concepts as the interpretable and disentangled representation of time-series, DTS introduces multi-level disentanglement strategies by covering both individual latent factors and group semantic segments. We further theoretically show how to alleviate the KL vanishing problem: DTS introduces a mutual information maximization term, while preserving a heavier penalty on the total correlation and the dimension-wise KL to keep the disentanglement property. Experimental results on various real-world benchmark datasets demonstrate that the representations learned by DTS achieve superior performance in downstream applications, with high interpretability of semantic concepts.

Even though machine learning has become the major scene in dialogue research community, the real breakthrough has been blocked by the scale of data available. To address this fundamental obstacle, we introduce the Multi-Domain Wizard-of-Oz dataset (MultiWOZ), a fully-labeled collection of human-human written conversations spanning over multiple domains and topics. At a size of 10k dialogues, it is at least one order of magnitude larger than all previous annotated task-oriented corpora. The contribution of this work apart from the open-sourced dataset labelled with dialogue belief states and dialogue actions is two-fold: firstly, a detailed description of the data collection procedure along with a summary of data structure and analysis is provided. The proposed data-collection pipeline is entirely based on crowd-sourcing without the need of hiring professional annotators; secondly, a set of benchmark results of belief tracking, dialogue act and response generation is reported, which shows the usability of the data and sets a baseline for future studies.

Multimodal Large Language Models (MLLMs) have demonstrated an excellent understanding of images and 3D data. However, both modalities have shortcomings in holistically capturing the appearance and geometry of objects. Meanwhile, Neural Radiance Fields (NeRFs), which encode information within the weights of a simple Multi-Layer Perceptron (MLP), have emerged as an increasingly widespread modality that simultaneously encodes the geometry and photorealistic appearance of objects. This paper investigates the feasibility and effectiveness of ingesting NeRF into MLLM. We create LLaNA, the first general-purpose NeRF-language assistant capable of performing new tasks such as NeRF captioning and Q\&A. Notably, our method directly processes the weights of the NeRF's MLP to extract information about the represented objects without the need to render images or materialize 3D data structures. Moreover, we build a dataset of NeRFs with text annotations for various NeRF-language tasks with no human intervention. Based on this dataset, we develop a benchmark to evaluate the NeRF understanding capability of our method. Results show that processing NeRF weights performs favourably against extracting 2D or 3D representations from NeRFs.

Fueled by the Large Language Models (LLMs) wave, Large Visual-Language Models (LVLMs) have emerged as a pivotal advancement, bridging the gap between image and text. However, video making it challenging for LVLMs to perform adequately due to the complexity of the relationship between language and spatial-temporal data structure. Recent Large Video-Language Models (LVidLMs) align feature of static visual data like image into latent space of language feature, by general multi-modal tasks to leverage abilities of LLMs sufficiently. In this paper, we explore fine-grained alignment approach via object trajectory for different modalities across both spatial and temporal dimensions simultaneously. Thus, we propose a novel LVidLM by trajectory-guided Pixel-Temporal Alignment, dubbed PiTe, that exhibits promising applicable model property. To achieve fine-grained video-language alignment, we curate a multi-modal pre-training dataset PiTe-143k, the dataset provision of moving trajectories in pixel level for all individual objects, that appear and mention in the video and caption both, by our automatic annotation pipeline. Meanwhile, PiTe demonstrates astounding capabilities on myriad video-related multi-modal tasks through beat the state-of-the-art methods by a large margin.

Deep learning models are increasingly data-hungry, requiring significant resources to collect and compile the datasets needed to train them, with Earth Observation (EO) models being no exception. However, the landscape of datasets in EO is relatively atomised, with interoperability made difficult by diverse formats and data structures. If ever larger datasets are to be built, and duplication of effort minimised, then a shared framework that allows users to combine and access multiple datasets is needed. Here, Major TOM (Terrestrial Observation Metaset) is proposed as this extensible framework. Primarily, it consists of a geographical indexing system based on a set of grid points and a metadata structure that allows multiple datasets with different sources to be merged. Besides the specification of Major TOM as a framework, this work also presents a large, open-access dataset, MajorTOM-Core, which covers the vast majority of the Earth's land surface. This dataset provides the community with both an immediately useful resource, as well as acting as a template for future additions to the Major TOM ecosystem. Access: https://huggingface.co/Major-TOM

Diffusion models have shown promising ability in generating high-quality time series (TS) data. Despite the initial success, existing works mostly focus on the authenticity of data at the individual level, but pay less attention to preserving the population-level properties on the entire dataset. Such population-level properties include value distributions for each dimension and distributions of certain functional dependencies (e.g., cross-correlation, CC) between different dimensions. For instance, when generating house energy consumption TS data, the value distributions of the outside temperature and the kitchen temperature should be preserved, as well as the distribution of CC between them. Preserving such TS population-level properties is critical in maintaining the statistical insights of the datasets, mitigating model bias, and augmenting downstream tasks like TS prediction. Yet, it is often overlooked by existing models. Hence, data generated by existing models often bear distribution shifts from the original data. We propose Population-aware Diffusion for Time Series (PaD-TS), a new TS generation model that better preserves the population-level properties. The key novelties of PaD-TS include 1) a new training method explicitly incorporating TS population-level property preservation, and 2) a new dual-channel encoder model architecture that better captures the TS data structure. Empirical results in major benchmark datasets show that PaD-TS can improve the average CC distribution shift score between real and synthetic data by 5.9x while maintaining a performance comparable to state-of-the-art models on individual-level authenticity.

Event sequences, characterized by irregular sampling intervals and a mix of categorical and numerical features, are common data structures in various real-world domains such as healthcare, finance, and user interaction logs. Despite advances in temporal data modeling techniques, there is no standardized benchmarks for evaluating their performance on event sequences. This complicates result comparison across different papers due to varying evaluation protocols, potentially misleading progress in this field. We introduce EBES, a comprehensive benchmarking tool with standardized evaluation scenarios and protocols, focusing on regression and classification problems with sequence-level targets. Our library simplifies benchmarking, dataset addition, and method integration through a unified interface. It includes a novel synthetic dataset and provides preprocessed real-world datasets, including the largest publicly available banking dataset. Our results provide an in-depth analysis of datasets, identifying some as unsuitable for model comparison. We investigate the importance of modeling temporal and sequential components, as well as the robustness and scaling properties of the models. These findings highlight potential directions for future research. Our benchmark aim is to facilitate reproducible research, expediting progress and increasing real-world impacts.

Code synthesis, which requires a deep understanding of complex natural language problem descriptions, generation of code instructions for complex algorithms and data structures, and the successful execution of comprehensive unit tests, presents a significant challenge. While large language models (LLMs) demonstrate impressive proficiency in natural language processing, their performance in code generation tasks remains limited. In this paper, we introduce a new approach to code generation tasks leveraging multi-agent prompting that uniquely replicates the full cycle of program synthesis as observed in human developers. Our framework, MapCoder, consists of four LLM agents specifically designed to emulate the stages of this cycle: recalling relevant examples, planning, code generation, and debugging. After conducting thorough experiments, with multiple LLM ablations and analyses across eight challenging competitive problem-solving and program synthesis benchmarks, MapCoder showcases remarkable code generation capabilities, achieving new state-of-the-art results (pass@1) on HumanEval (93.9%), MBPP (83.1%), APPS (22.0%), CodeContests (28.5%), and xCodeEval (45.3%). Moreover, our method consistently delivers superior performance across various programming languages and varying problem difficulties. We open-source our framework at https://github.com/Md-Ashraful-Pramanik/MapCoder.

The challenge of mapping AI architectures to GPU hardware is creating a critical bottleneck in AI progress. Despite substantial efforts, hand-written custom kernels fail to meet their theoretical performance thresholds, even on well-established operations like linear attention. The diverse hardware capabilities of GPUs might suggest that we need a wide variety of techniques to achieve high performance. However, our work explores whether a small number of key abstractions can drastically simplify the process. We present ThunderKittens (TK), a framework for writing performant AI kernels while remaining easy to use and maintain. Our abstractions map to the three levels of the GPU hierarchy: (1) at the warp-level, we provide 16x16 matrix tiles as basic data structures and PyTorch-like parallel compute operations over tiles, (2) at the thread-block level, we provide a template for overlapping asynchronous operations across parallel warps, and (3) at the grid-level, we provide support to help hide the block launch and tear-down, and memory costs. We show the value of TK by providing kernels that match or outperform prior kernels for a range of AI operations. We match CuBLAS and FlashAttention-3 on GEMM and attention inference performance and outperform the strongest baselines by 10-40% on attention backwards, 8times on state space models, and 14times on linear attention.

The rapid advancement of Large Language Models (LLMs) has brought about remarkable generative capabilities but also raised concerns about their potential misuse. While strategies like supervised fine-tuning and reinforcement learning from human feedback have enhanced their safety, these methods primarily focus on natural languages, which may not generalize to other domains. This paper introduces CodeAttack, a framework that transforms natural language inputs into code inputs, presenting a novel environment for testing the safety generalization of LLMs. Our comprehensive studies on state-of-the-art LLMs including GPT-4, Claude-2, and Llama-2 series reveal a new and universal safety vulnerability of these models against code input: CodeAttack bypasses the safety guardrails of all models more than 80\% of the time. We find that a larger distribution gap between CodeAttack and natural language leads to weaker safety generalization, such as encoding natural language input with data structures. Furthermore, we give our hypotheses about the success of CodeAttack: the misaligned bias acquired by LLMs during code training, prioritizing code completion over avoiding the potential safety risk. Finally, we analyze potential mitigation measures. These findings highlight new safety risks in the code domain and the need for more robust safety alignment algorithms to match the code capabilities of LLMs.

Large language models (LLMs) have made significant progress in code generation tasks, but their performance in tackling programming problems with complex data structures and algorithms remains suboptimal. To address this issue, we propose an in-context learning approach that guides LLMs to debug by using a "print debugging" method, which involves inserting print statements to trace and analysing logs for fixing the bug. We collect a Leetcode problem dataset and evaluate our method using the Leetcode online judging system. Experiments with GPT-4 demonstrate the effectiveness of our approach, outperforming rubber duck debugging in easy and medium-level Leetcode problems by 1.5% and 17.9%.

We present X^3 (pronounced XCube), a novel generative model for high-resolution sparse 3D voxel grids with arbitrary attributes. Our model can generate millions of voxels with a finest effective resolution of up to 1024^3 in a feed-forward fashion without time-consuming test-time optimization. To achieve this, we employ a hierarchical voxel latent diffusion model which generates progressively higher resolution grids in a coarse-to-fine manner using a custom framework built on the highly efficient VDB data structure. Apart from generating high-resolution objects, we demonstrate the effectiveness of XCube on large outdoor scenes at scales of 100mtimes100m with a voxel size as small as 10cm. We observe clear qualitative and quantitative improvements over past approaches. In addition to unconditional generation, we show that our model can be used to solve a variety of tasks such as user-guided editing, scene completion from a single scan, and text-to-3D. More results and details can be found at https://research.nvidia.com/labs/toronto-ai/xcube/.

Columnar storage is a core component of a modern data analytics system. Although many database management systems (DBMSs) have proprietary storage formats, most provide extensive support to open-source storage formats such as Parquet and ORC to facilitate cross-platform data sharing. But these formats were developed over a decade ago, in the early 2010s, for the Hadoop ecosystem. Since then, both the hardware and workload landscapes have changed. In this paper, we revisit the most widely adopted open-source columnar storage formats (Parquet and ORC) with a deep dive into their internals. We designed a benchmark to stress-test the formats' performance and space efficiency under different workload configurations. From our comprehensive evaluation of Parquet and ORC, we identify design decisions advantageous with modern hardware and real-world data distributions. These include using dictionary encoding by default, favoring decoding speed over compression ratio for integer encoding algorithms, making block compression optional, and embedding finer-grained auxiliary data structures. We also point out the inefficiencies in the format designs when handling common machine learning workloads and using GPUs for decoding. Our analysis identified important considerations that may guide future formats to better fit modern technology trends.

High-performance sparse matrix-matrix (SpMM) multiplication is paramount for science and industry, as the ever-increasing sizes of data prohibit using dense data structures. Yet, existing hardware, such as Tensor Cores (TC), is ill-suited for SpMM, as it imposes strict constraints on data structures that cannot be met by unstructured sparsity found in many applications. To address this, we introduce (S)parse (Ma)trix Matrix (T)ensor Core-accelerated (SMaT): a novel SpMM library that utilizes TCs for unstructured sparse matrices. Our block-sparse library leverages the low-level CUDA MMA (matrix-matrix-accumulate) API, maximizing the performance offered by modern GPUs. Algorithmic optimizations such as sparse matrix permutation further improve performance by minimizing the number of non-zero blocks. The evaluation on NVIDIA A100 shows that SMaT outperforms SotA libraries (DASP, cuSPARSE, and Magicube) by up to 125x (on average 2.6x). SMaT can be used to accelerate many workloads in scientific computing, large-model training, inference, and others.

We extend neural radiance fields (NeRFs) to dynamic large-scale urban scenes. Prior work tends to reconstruct single video clips of short durations (up to 10 seconds). Two reasons are that such methods (a) tend to scale linearly with the number of moving objects and input videos because a separate model is built for each and (b) tend to require supervision via 3D bounding boxes and panoptic labels, obtained manually or via category-specific models. As a step towards truly open-world reconstructions of dynamic cities, we introduce two key innovations: (a) we factorize the scene into three separate hash table data structures to efficiently encode static, dynamic, and far-field radiance fields, and (b) we make use of unlabeled target signals consisting of RGB images, sparse LiDAR, off-the-shelf self-supervised 2D descriptors, and most importantly, 2D optical flow. Operationalizing such inputs via photometric, geometric, and feature-metric reconstruction losses enables SUDS to decompose dynamic scenes into the static background, individual objects, and their motions. When combined with our multi-branch table representation, such reconstructions can be scaled to tens of thousands of objects across 1.2 million frames from 1700 videos spanning geospatial footprints of hundreds of kilometers, (to our knowledge) the largest dynamic NeRF built to date. We present qualitative initial results on a variety of tasks enabled by our representations, including novel-view synthesis of dynamic urban scenes, unsupervised 3D instance segmentation, and unsupervised 3D cuboid detection. To compare to prior work, we also evaluate on KITTI and Virtual KITTI 2, surpassing state-of-the-art methods that rely on ground truth 3D bounding box annotations while being 10x quicker to train.

Recent advancements in vision-language pre-training (e.g. CLIP) have shown that vision models can benefit from language supervision. While many models using language modality have achieved great success on 2D vision tasks, the joint representation learning of 3D point cloud with text remains under-explored due to the difficulty of 3D-Text data pair acquisition and the irregularity of 3D data structure. In this paper, we propose a novel Text4Point framework to construct language-guided 3D point cloud models. The key idea is utilizing 2D images as a bridge to connect the point cloud and the language modalities. The proposed Text4Point follows the pre-training and fine-tuning paradigm. During the pre-training stage, we establish the correspondence of images and point clouds based on the readily available RGB-D data and use contrastive learning to align the image and point cloud representations. Together with the well-aligned image and text features achieved by CLIP, the point cloud features are implicitly aligned with the text embeddings. Further, we propose a Text Querying Module to integrate language information into 3D representation learning by querying text embeddings with point cloud features. For fine-tuning, the model learns task-specific 3D representations under informative language guidance from the label set without 2D images. Extensive experiments demonstrate that our model shows consistent improvement on various downstream tasks, such as point cloud semantic segmentation, instance segmentation, and object detection. The code will be available here: https://github.com/LeapLabTHU/Text4Point

Adversarial training is a widely used strategy for making neural networks resistant to adversarial perturbations. For a neural network of width m, n input training data in d dimension, it takes Omega(mnd) time cost per training iteration for the forward and backward computation. In this paper we analyze the convergence guarantee of adversarial training procedure on a two-layer neural network with shifted ReLU activation, and shows that only o(m) neurons will be activated for each input data per iteration. Furthermore, we develop an algorithm for adversarial training with time cost o(m n d) per iteration by applying half-space reporting data structure.

Knowledge-intensive language tasks require NLP systems to both provide the correct answer and retrieve supporting evidence for it in a given corpus. Autoregressive language models are emerging as the de-facto standard for generating answers, with newer and more powerful systems emerging at an astonishing pace. In this paper we argue that all this (and future) progress can be directly applied to the retrieval problem with minimal intervention to the models' architecture. Previous work has explored ways to partition the search space into hierarchical structures and retrieve documents by autoregressively generating their unique identifier. In this work we propose an alternative that doesn't force any structure in the search space: using all ngrams in a passage as its possible identifiers. This setup allows us to use an autoregressive model to generate and score distinctive ngrams, that are then mapped to full passages through an efficient data structure. Empirically, we show this not only outperforms prior autoregressive approaches but also leads to an average improvement of at least 10 points over more established retrieval solutions for passage-level retrieval on the KILT benchmark, establishing new state-of-the-art downstream performance on some datasets, while using a considerably lighter memory footprint than competing systems. Code and pre-trained models at https://github.com/facebookresearch/SEAL.

As mathematical computing becomes more democratized in high-level languages, high-performance symbolic-numeric systems are necessary for domain scientists and engineers to get the best performance out of their machine without deep knowledge of code optimization. Naturally, users need different term types either to have different algebraic properties for them, or to use efficient data structures. To this end, we developed Symbolics.jl, an extendable symbolic system which uses dynamic multiple dispatch to change behavior depending on the domain needs. In this work we detail an underlying abstract term interface which allows for speed without sacrificing generality. We show that by formalizing a generic API on actions independent of implementation, we can retroactively add optimized data structures to our system without changing the pre-existing term rewriters. We showcase how this can be used to optimize term construction and give a 113x acceleration on general symbolic transformations. Further, we show that such a generic API allows for complementary term-rewriting implementations. We demonstrate the ability to swap between classical term-rewriting simplifiers and e-graph-based term-rewriting simplifiers. We showcase an e-graph ruleset which minimizes the number of CPU cycles during expression evaluation, and demonstrate how it simplifies a real-world reaction-network simulation to halve the runtime. Additionally, we show a reaction-diffusion partial differential equation solver which is able to be automatically converted into symbolic expressions via multiple dispatch tracing, which is subsequently accelerated and parallelized to give a 157x simulation speedup. Together, this presents Symbolics.jl as a next-generation symbolic-numeric computing environment geared towards modeling and simulation.

Transformers and large language models~(LLMs) have seen rapid adoption in all domains. Their sizes have exploded to hundreds of billions of parameters and keep increasing. Under these circumstances, the training of transformers is very expensive and often hits a ``memory wall'', i.e., even when using 3D parallelism (pipeline, tensor, data) and aggregating the memory of many GPUs, it is still not enough to hold the necessary data structures (model parameters, optimizer state, gradients, activations) in GPU memory. To compensate, state-of-the-art approaches offload the optimizer state, at least partially, to the host memory and perform hybrid CPU-GPU computations. However, the management of the combined host-GPU memory is often suboptimal and results in poor overlapping between data movements and computations. This leads to missed opportunities to simultaneously leverage the interconnect bandwidth and computational capabilities of CPUs and GPUs. In this paper, we leverage a key observation that the interleaving of the forward, backward and update phases generate fluctuations in the GPU memory utilization, which can be exploited to dynamically move a part of the optimizer state between the host and the GPU memory at each iteration. To this end, we design and implement \proj, a novel technique to split the LLM into subgroups, whose update phase is scheduled on either the CPU or the GPU based on our proposed performance model that addresses the trade-off between data movement cost, acceleration on the GPUs vs the CPUs, and competition for shared resources. We integrate our approach with DeepSpeed and demonstrate 2.5times faster iterations over state-of-the-art approaches using extensive experiments.

We present DART, an open domain structured DAta Record to Text generation dataset with over 82k instances (DARTs). Data-to-Text annotations can be a costly process, especially when dealing with tables which are the major source of structured data and contain nontrivial structures. To this end, we propose a procedure of extracting semantic triples from tables that encodes their structures by exploiting the semantic dependencies among table headers and the table title. Our dataset construction framework effectively merged heterogeneous sources from open domain semantic parsing and dialogue-act-based meaning representation tasks by utilizing techniques such as: tree ontology annotation, question-answer pair to declarative sentence conversion, and predicate unification, all with minimum post-editing. We present systematic evaluation on DART as well as new state-of-the-art results on WebNLG 2017 to show that DART (1) poses new challenges to existing data-to-text datasets and (2) facilitates out-of-domain generalization. Our data and code can be found at https://github.com/Yale-LILY/dart.

HAL (Hyper Articles en Ligne) is the French national publication repository, used by most higher education and research organizations for their open science policy. As a digital library, it is a rich repository of scholarly documents, but its potential for advanced research has been underutilized. We present HALvest, a unique dataset that bridges the gap between citation networks and the full text of papers submitted on HAL. We craft our dataset by filtering HAL for scholarly publications, resulting in approximately 700,000 documents, spanning 34 languages across 13 identified domains, suitable for language model training, and yielding approximately 16.5 billion tokens (with 8 billion in French and 7 billion in English, the most represented languages). We transform the metadata of each paper into a citation network, producing a directed heterogeneous graph. This graph includes uniquely identified authors on HAL, as well as all open submitted papers, and their citations. We provide a baseline for authorship attribution using the dataset, implement a range of state-of-the-art models in graph representation learning for link prediction, and discuss the usefulness of our generated knowledge graph structure.

We introduce a hierarchical filtering procedure for generative models of sequences on trees, enabling control over the range of positional correlations in the data. Leveraging this controlled setting, we provide evidence that vanilla encoder-only transformer architectures can implement the optimal Belief Propagation algorithm on both root classification and masked language modeling tasks. Correlations at larger distances corresponding to increasing layers of the hierarchy are sequentially included as the network is trained. We analyze how the transformer layers succeed by focusing on attention maps from models trained with varying degrees of filtering. These attention maps show clear evidence for iterative hierarchical reconstruction of correlations, and we can relate these observations to a plausible implementation of the exact inference algorithm for the network sizes considered.

This paper introduces a neural model for concept-to-text generation that scales to large, rich domains. We experiment with a new dataset of biographies from Wikipedia that is an order of magnitude larger than existing resources with over 700k samples. The dataset is also vastly more diverse with a 400k vocabulary, compared to a few hundred words for Weathergov or Robocup. Our model builds upon recent work on conditional neural language model for text generation. To deal with the large vocabulary, we extend these models to mix a fixed vocabulary with copy actions that transfer sample-specific words from the input database to the generated output sentence. Our neural model significantly out-performs a classical Kneser-Ney language model adapted to this task by nearly 15 BLEU.

While most conversational agents are grounded on either free-text or structured knowledge, many knowledge corpora consist of hybrid sources. This paper presents the first conversational agent that supports the full generality of hybrid data access for large knowledge corpora, through a language we developed called SUQL (Structured and Unstructured Query Language). Specifically, SUQL extends SQL with free-text primitives (summary and answer), so information retrieval can be composed with structured data accesses arbitrarily in a formal, succinct, precise, and interpretable notation. With SUQL, we propose the first semantic parser, an LLM with in-context learning, that can handle hybrid data sources. Our in-context learning-based approach, when applied to the HybridQA dataset, comes within 8.9% exact match and 7.1% F1 of the SOTA, which was trained on 62K data samples. More significantly, unlike previous approaches, our technique is applicable to large databases and free-text corpora. We introduce a dataset consisting of crowdsourced questions and conversations on Yelp, a large, real restaurant knowledge base with structured and unstructured data. We show that our few-shot conversational agent based on SUQL finds an entity satisfying all user requirements 90.3% of the time, compared to 63.4% for a baseline based on linearization.

We propose a semi-automatic staging area for efficiently building an accurate database of experimental physical properties of superconductors from literature, called SuperCon2, to enrich the existing manually-built superconductor database SuperCon. Here we report our curation interface (SuperCon2 Interface) and a workflow managing the state transitions of each examined record, to validate the dataset of superconductors from PDF documents collected using Grobid-superconductors in a previous work. This curation workflow allows both automatic and manual operations, the former contains ``anomaly detection'' that scans new data identifying outliers, and a ``training data collector'' mechanism that collects training data examples based on manual corrections. Such training data collection policy is effective in improving the machine-learning models with a reduced number of examples. For manual operations, the interface (SuperCon2 interface) is developed to increase efficiency during manual correction by providing a smart interface and an enhanced PDF document viewer. We show that our interface significantly improves the curation quality by boosting precision and recall as compared with the traditional ``manual correction''. Our semi-automatic approach would provide a solution for achieving a reliable database with text-data mining of scientific documents.

Efficiently processing and interpreting network data is critical for the operation of increasingly complex networks. Recent advances in Large Language Models (LLM) and Retrieval-Augmented Generation (RAG) techniques have improved data processing in network management. However, existing RAG methods like VectorRAG and GraphRAG struggle with the complexity and implicit nature of semi-structured technical data, leading to inefficiencies in time, cost, and retrieval. This paper introduces FastRAG, a novel RAG approach designed for semi-structured data. FastRAG employs schema learning and script learning to extract and structure data without needing to submit entire data sources to an LLM. It integrates text search with knowledge graph (KG) querying to improve accuracy in retrieving context-rich information. Evaluation results demonstrate that FastRAG provides accurate question answering, while improving up to 90% in time and 85% in cost compared to GraphRAG.

Semantic parsing, which converts natural language questions into logic forms, plays a crucial role in reasoning within structured environments. However, existing methods encounter two significant challenges: reliance on extensive manually annotated datasets and limited generalization capability to unseen examples. To tackle these issues, we propose Targeted Synthetic Data Generation (TARGA), a practical framework that dynamically generates high-relevance synthetic data without manual annotation. Starting from the pertinent entities and relations of a given question, we probe for the potential relevant queries through layer-wise expansion and cross-layer combination. Then we generate corresponding natural language questions for these constructed queries to jointly serve as the synthetic demonstrations for in-context learning. Experiments on multiple knowledge base question answering (KBQA) datasets demonstrate that TARGA, using only a 7B-parameter model, substantially outperforms existing non-fine-tuned methods that utilize close-sourced model, achieving notable improvements in F1 scores on GrailQA(+7.7) and KBQA-Agent(+12.2). Furthermore, TARGA also exhibits superior sample efficiency, robustness, and generalization capabilities under non-I.I.D. settings.

In this paper, we study how to improve the zero-shot reasoning ability of large language models~(LLMs) over structured data in a unified way. Inspired by the study on tool augmentation for LLMs, we develop an Iterative Reading-then-Reasoning~(IRR) approach for solving question answering tasks based on structured data, called StructGPT. In our approach, we construct the specialized function to collect relevant evidence from structured data (\ie reading), and let LLMs concentrate the reasoning task based on the collected information (\ie reasoning). Specially, we propose an invoking-linearization-generation procedure to support LLMs in reasoning on the structured data with the help of the external interfaces. By iterating this procedures with provided interfaces, our approach can gradually approach the target answer to a given query. Extensive experiments conducted on three types of structured data demonstrate the effectiveness of our approach, which can significantly boost the performance of ChatGPT and achieve comparable performance against the full-data supervised-tuning baselines. Our codes and data are publicly available at~https://github.com/RUCAIBox/StructGPT.

Despite the power of Large Language Models (LLMs) like GPT-4, they still struggle with tasks that require generating complex, structured outputs. In this study, we assess the capability of Current LLMs in generating complex structured data and propose a structure-aware fine-tuning approach as a solution to improve this ability. To perform a comprehensive evaluation, we propose Struc-Bench, include five representative LLMs (i.e., GPT-NeoX 20B, GPT-3.5, GPT-4, and Vicuna) and evaluate them on our carefully constructed datasets spanning raw text, HTML, and LaTeX tables. Based on our analysis of current model performance, we identify specific common formatting errors and areas of potential improvement. To address complex formatting requirements, we utilize FormatCoT (Chain-of-Thought) to generate format instructions from target outputs. Our experiments show that our structure-aware fine-tuning method, when applied to LLaMA-7B, significantly improves adherence to natural language constraints, outperforming other evaluated LLMs. Based on these results, we present an ability map of model capabilities from six dimensions (i.e., coverage, formatting, reasoning, comprehension, pragmatics, and hallucination). This map highlights the weaknesses of LLMs in handling complex structured outputs and suggests promising directions for future work. Our code and models can be found at https://github.com/gersteinlab/Struc-Bench.

In the field of business data analysis, the ability to extract actionable insights from vast and varied datasets is essential for informed decision-making and maintaining a competitive edge. Traditional rule-based systems, while reliable, often fall short when faced with the complexity and dynamism of modern business data. Conversely, Artificial Intelligence (AI) models, particularly Large Language Models (LLMs), offer significant potential in pattern recognition and predictive analytics but can lack the precision necessary for specific business applications. This paper explores the efficacy of hybrid approaches that integrate the robustness of rule-based systems with the adaptive power of LLMs in generating actionable business insights.

Large language models (LLMs) are becoming attractive as few-shot reasoners to solve Natural Language (NL)-related tasks. However, the understanding of their capability to process structured data like tables remains an under-explored area. While tables can be serialized as input for LLMs, there is a lack of comprehensive studies on whether LLMs genuinely comprehend this data. In this paper, we try to understand this by designing a benchmark to evaluate the structural understanding capabilities of LLMs through seven distinct tasks, e.g., cell lookup, row retrieval and size detection. Specially, we perform a series of evaluations on the recent most advanced LLM models, GPT-3.5 and GPT-4 and observe that performance varied with different input choices, including table input format, content order, role prompting, and partition marks. Drawing from the insights gained through the benchmark evaluations, we propose self-augmentation for effective structural prompting, such as critical value / range identification using internal knowledge of LLMs. When combined with carefully chosen input choices, these structural prompting methods lead to promising improvements in LLM performance on a variety of tabular tasks, e.g., TabFact(uparrow2.31%), HybridQA(uparrow2.13%), SQA(uparrow2.72%), Feverous(uparrow0.84%), and ToTTo(uparrow5.68%). We believe that our open source benchmark and proposed prompting methods can serve as a simple yet generic selection for future research. The code and data of this paper will be temporality released at https://anonymous.4open.science/r/StructuredLLM-76F3/README.md and will be replaced with an official one at https://github.com/microsoft/TableProvider later.

Relational databases are the de facto standard for storing and querying structured data, and extracting insights from structured data requires advanced analytics. Deep neural networks (DNNs) have achieved super-human prediction performance in particular data types, e.g., images. However, existing DNNs may not produce meaningful results when applied to structured data. The reason is that there are correlations and dependencies across combinations of attribute values in a table, and these do not follow simple additive patterns that can be easily mimicked by a DNN. The number of possible such cross features is combinatorial, making them computationally prohibitive to model. Furthermore, the deployment of learning models in real-world applications has also highlighted the need for interpretability, especially for high-stakes applications, which remains another issue of concern to DNNs. In this paper, we present ARM-Net, an adaptive relation modeling network tailored for structured data, and a lightweight framework ARMOR based on ARM-Net for relational data analytics. The key idea is to model feature interactions with cross features selectively and dynamically, by first transforming the input features into exponential space, and then determining the interaction order and interaction weights adaptively for each cross feature. We propose a novel sparse attention mechanism to dynamically generate the interaction weights given the input tuple, so that we can explicitly model cross features of arbitrary orders with noisy features filtered selectively. Then during model inference, ARM-Net can specify the cross features being used for each prediction for higher accuracy and better interpretability. Our extensive experiments on real-world datasets demonstrate that ARM-Net consistently outperforms existing models and provides more interpretable predictions for data-driven decision making.

We introduce AutoGluon-Tabular, an open-source AutoML framework that requires only a single line of Python to train highly accurate machine learning models on an unprocessed tabular dataset such as a CSV file. Unlike existing AutoML frameworks that primarily focus on model/hyperparameter selection, AutoGluon-Tabular succeeds by ensembling multiple models and stacking them in multiple layers. Experiments reveal that our multi-layer combination of many models offers better use of allocated training time than seeking out the best. A second contribution is an extensive evaluation of public and commercial AutoML platforms including TPOT, H2O, AutoWEKA, auto-sklearn, AutoGluon, and Google AutoML Tables. Tests on a suite of 50 classification and regression tasks from Kaggle and the OpenML AutoML Benchmark reveal that AutoGluon is faster, more robust, and much more accurate. We find that AutoGluon often even outperforms the best-in-hindsight combination of all of its competitors. In two popular Kaggle competitions, AutoGluon beat 99% of the participating data scientists after merely 4h of training on the raw data.

Multimodal learning is a rapidly growing research field that has revolutionized multitasking and generative modeling in AI. While much of the research has focused on dealing with unstructured data (e.g., language, images, audio, or video), structured data (e.g., tabular data, time series, or signals) has received less attention. However, many industry-relevant use cases involve or can be benefited from both types of data. In this work, we propose a modular, end-to-end multimodal learning method called MAGNUM, which can natively handle both structured and unstructured data. MAGNUM is flexible enough to employ any specialized unimodal module to extract, compress, and fuse information from all available modalities.

Large Language Models (LLMs) pre-trained on massive corpora have exhibited remarkable performance on various NLP tasks. However, applying these models to specific domains still poses significant challenges, such as lack of domain knowledge, limited capacity to leverage domain knowledge and inadequate adaptation to domain-specific data formats. Considering the exorbitant cost of training LLMs from scratch and the scarcity of annotated data within particular domains, in this work, we focus on domain-specific continual pre-training of LLMs using E-commerce domain as an exemplar. Specifically, we explore the impact of continual pre-training on LLMs employing unlabeled general and E-commercial corpora. Furthermore, we design a mixing strategy among different data sources to better leverage E-commercial semi-structured data. We construct multiple tasks to assess LLMs' few-shot In-context Learning ability and their zero-shot performance after instruction tuning in E-commerce domain. Experimental results demonstrate the effectiveness of continual pre-training of E-commerce LLMs and the efficacy of our devised data mixing strategy.

Structured data sources, such as tables, graphs, and databases, are ubiquitous knowledge sources. Despite the demonstrated capabilities of large language models (LLMs) on plain text, their proficiency in interpreting and utilizing structured data remains limited. Our investigation reveals a notable deficiency in LLMs' ability to process structured data, e.g., ChatGPT lags behind state-of-the-art (SoTA) model by an average of 35%. To augment the Structured Knowledge Grounding (SKG) capabilities in LLMs, we have developed a comprehensive instruction tuning dataset comprising 1.1 million examples. Utilizing this dataset, we train a series of models, referred to as StructLM, based on the Code-LLaMA architecture, ranging from 7B to 34B parameters. Our StructLM series surpasses task-specific models on 14 out of 18 evaluated datasets and establishes new SoTA achievements on 7 SKG tasks. Furthermore, StructLM demonstrates exceptional generalization across 6 novel SKG tasks. Contrary to expectations, we observe that scaling model size offers marginal benefits, with StructLM-34B showing only slight improvements over StructLM-7B. This suggests that structured knowledge grounding is still a challenging task and requires more innovative design to push to a new level.

Background: This study aimed to evaluate and compare the performance of classical machine learning models (CMLs) and large language models (LLMs) in predicting mortality associated with COVID-19 by utilizing a high-dimensional tabular dataset. Materials and Methods: We analyzed data from 9,134 COVID-19 patients collected across four hospitals. Seven CML models, including XGBoost and random forest (RF), were trained and evaluated. The structured data was converted into text for zero-shot classification by eight LLMs, including GPT-4 and Mistral-7b. Additionally, Mistral-7b was fine-tuned using the QLoRA approach to enhance its predictive capabilities. Results: Among the CML models, XGBoost and RF achieved the highest accuracy, with F1 scores of 0.87 for internal validation and 0.83 for external validation. In the LLM category, GPT-4 was the top performer with an F1 score of 0.43. Fine-tuning Mistral-7b significantly improved its recall from 1% to 79%, resulting in an F1 score of 0.74, which was stable during external validation. Conclusion: While LLMs show moderate performance in zero-shot classification, fine-tuning can significantly enhance their effectiveness, potentially aligning them closer to CML models. However, CMLs still outperform LLMs in high-dimensional tabular data tasks.

In the U.S. historically, local newspapers drew their content largely from newswires like the Associated Press. Historians argue that newswires played a pivotal role in creating a national identity and shared understanding of the world, but there is no comprehensive archive of the content sent over newswires. We reconstruct such an archive by applying a customized deep learning pipeline to hundreds of terabytes of raw image scans from thousands of local newspapers. The resulting dataset contains 2.7 million unique public domain U.S. newswire articles, written between 1878 and 1977. Locations in these articles are georeferenced, topics are tagged using customized neural topic classification, named entities are recognized, and individuals are disambiguated to Wikipedia using a novel entity disambiguation model. To construct the Newswire dataset, we first recognize newspaper layouts and transcribe around 138 millions structured article texts from raw image scans. We then use a customized neural bi-encoder model to de-duplicate reproduced articles, in the presence of considerable abridgement and noise, quantifying how widely each article was reproduced. A text classifier is used to ensure that we only include newswire articles, which historically are in the public domain. The structured data that accompany the texts provide rich information about the who (disambiguated individuals), what (topics), and where (georeferencing) of the news that millions of Americans read over the course of a century. We also include Library of Congress metadata information about the newspapers that ran the articles on their front pages. The Newswire dataset is useful both for large language modeling - expanding training data beyond what is available from modern web texts - and for studying a diversity of questions in computational linguistics, social science, and the digital humanities.

Reliably generating structured outputs has become a critical capability for modern language model (LM) applications. Constrained decoding has emerged as the dominant technology across sectors for enforcing structured outputs during generation. Despite its growing adoption, little has been done with the systematic evaluation of the behaviors and performance of constrained decoding. Constrained decoding frameworks have standardized around JSON Schema as a structured data format, with most uses guaranteeing constraint compliance given a schema. However, there is poor understanding of the effectiveness of the methods in practice. We present an evaluation framework to assess constrained decoding approaches across three critical dimensions: efficiency in generating constraint-compliant outputs, coverage of diverse constraint types, and quality of the generated outputs. To facilitate this evaluation, we introduce JSONSchemaBench, a benchmark for constrained decoding comprising 10K real-world JSON schemas that encompass a wide range of constraints with varying complexity. We pair the benchmark with the existing official JSON Schema Test Suite and evaluate six state-of-the-art constrained decoding frameworks, including Guidance, Outlines, Llamacpp, XGrammar, OpenAI, and Gemini. Through extensive experiments, we gain insights into the capabilities and limitations of constrained decoding on structured generation with real-world JSON schemas. Our work provides actionable insights for improving constrained decoding frameworks and structured generation tasks, setting a new standard for evaluating constrained decoding and structured generation. We release JSONSchemaBench at https://github.com/guidance-ai/jsonschemabench

Entity linking is a prominent thread of research focused on structured data creation by linking spans of text to an ontology or knowledge source. We revisit the use of structured prediction for entity linking which classifies each individual input token as an entity, and aggregates the token predictions. Our system, called SpEL (Structured prediction for Entity Linking) is a state-of-the-art entity linking system that uses some new ideas to apply structured prediction to the task of entity linking including: two refined fine-tuning steps; a context sensitive prediction aggregation strategy; reduction of the size of the model's output vocabulary, and; we address a common problem in entity-linking systems where there is a training vs. inference tokenization mismatch. Our experiments show that we can outperform the state-of-the-art on the commonly used AIDA benchmark dataset for entity linking to Wikipedia. Our method is also very compute efficient in terms of number of parameters and speed of inference.

Document parsing is essential for converting unstructured and semi-structured documents-such as contracts, academic papers, and invoices-into structured, machine-readable data. Document parsing extract reliable structured data from unstructured inputs, providing huge convenience for numerous applications. Especially with recent achievements in Large Language Models, document parsing plays an indispensable role in both knowledge base construction and training data generation. This survey presents a comprehensive review of the current state of document parsing, covering key methodologies, from modular pipeline systems to end-to-end models driven by large vision-language models. Core components such as layout detection, content extraction (including text, tables, and mathematical expressions), and multi-modal data integration are examined in detail. Additionally, this paper discusses the challenges faced by modular document parsing systems and vision-language models in handling complex layouts, integrating multiple modules, and recognizing high-density text. It emphasizes the importance of developing larger and more diverse datasets and outlines future research directions.

While Deep Learning excels in structured data as encountered in vision and natural language processing, it failed to meet its expectations on tabular data. For tabular data, Support Vector Machines (SVMs), Random Forests, and Gradient Boosting are the best performing techniques with Gradient Boosting in the lead. Recently, we saw a surge of Deep Learning methods that were tailored to tabular data but still underperform compared to Gradient Boosting on small-sized datasets. We suggest "Hopular", a novel Deep Learning architecture for medium- and small-sized datasets, where each layer is equipped with continuous modern Hopfield networks. The modern Hopfield networks use stored data to identify feature-feature, feature-target, and sample-sample dependencies. Hopular's novelty is that every layer can directly access the original input as well as the whole training set via stored data in the Hopfield networks. Therefore, Hopular can step-wise update its current model and the resulting prediction at every layer like standard iterative learning algorithms. In experiments on small-sized tabular datasets with less than 1,000 samples, Hopular surpasses Gradient Boosting, Random Forests, SVMs, and in particular several Deep Learning methods. In experiments on medium-sized tabular data with about 10,000 samples, Hopular outperforms XGBoost, CatBoost, LightGBM and a state-of-the art Deep Learning method designed for tabular data. Thus, Hopular is a strong alternative to these methods on tabular data.

Graph Structure Learning (GSL) focuses on capturing intrinsic dependencies and interactions among nodes in graph-structured data by generating novel graph structures. Graph Neural Networks (GNNs) have emerged as promising GSL solutions, utilizing recursive message passing to encode node-wise inter-dependencies. However, many existing GSL methods heavily depend on explicit graph structural information as supervision signals, leaving them susceptible to challenges such as data noise and sparsity. In this work, we propose GraphEdit, an approach that leverages large language models (LLMs) to learn complex node relationships in graph-structured data. By enhancing the reasoning capabilities of LLMs through instruction-tuning over graph structures, we aim to overcome the limitations associated with explicit graph structural information and enhance the reliability of graph structure learning. Our approach not only effectively denoises noisy connections but also identifies node-wise dependencies from a global perspective, providing a comprehensive understanding of the graph structure. We conduct extensive experiments on multiple benchmark datasets to demonstrate the effectiveness and robustness of GraphEdit across various settings. We have made our model implementation available at: https://github.com/HKUDS/GraphEdit.

Large Language Models still struggle in challenging scenarios that leverage structured data, complex reasoning, or tool usage. In this paper, we propose Source2Synth: a new method that can be used for teaching LLMs new skills without relying on costly human annotations. Source2Synth takes as input a custom data source and produces synthetic data points with intermediate reasoning steps grounded in real-world sources. Source2Synth improves the dataset quality by discarding low-quality generations based on their answerability. We demonstrate the generality of this approach by applying it to two challenging domains: we test reasoning abilities in multi-hop question answering (MHQA), and tool usage in tabular question answering (TQA). Our method improves performance by 25.51% for TQA on WikiSQL and 22.57% for MHQA on HotPotQA compared to the fine-tuned baselines.

While advances in large language models (LLMs) have greatly improved the quality of synthetic text data in recent years, synthesizing tabular data has received relatively less attention. We address this disparity with Tabby, a simple but powerful post-training modification to the standard Transformer language model architecture, enabling its use for tabular dataset synthesis. Tabby enables the representation of differences across columns using Gated Mixture-of-Experts, with column-specific sets of parameters. Empirically, Tabby results in data quality near or equal to that of real data. By pairing our novel LLM table training technique, Plain, with Tabby, we observe up to a 44% improvement in quality over previous methods. We also show that Tabby extends beyond tables to more general structured data, reaching parity with real data on a nested JSON dataset as well.

The HuggingFace Datasets Hub hosts thousands of datasets. This provides exciting opportunities for language model training and evaluation. However, the datasets for a given type of task are stored with different schemas, and harmonization is harder than it seems (https://xkcd.com/927/). Multi-task training or evaluation requires manual work to fit data into task templates. Various initiatives independently address this problem by releasing the harmonized datasets or harmonization codes to preprocess datasets to the same format. We identify patterns across previous preprocessings, e.g. mapping of column names, and extraction of a specific sub-field from structured data in a column, and propose a structured annotation framework that makes our annotations fully exposed and not buried in unstructured code. We release a dataset annotation framework and dataset annotations for more than 400 English tasks (https://github.com/sileod/tasksource). These annotations provide metadata, like the name of the columns that should be used as input or labels for all datasets, and can save time for future dataset preprocessings, even if they do not use our framework. We fine-tune a multi-task text encoder on all tasksource tasks, outperforming every publicly available text encoder of comparable size on an external evaluation https://hf.co/sileod/deberta-v3-base-tasksource-nli.

Large Language Models (LLMs) are foundational to AI advancements, facilitating applications like predictive text generation. Nonetheless, they pose risks by potentially memorizing and disseminating sensitive, biased, or copyrighted information from their vast datasets. Machine unlearning emerges as a cutting-edge solution to mitigate these concerns, offering techniques for LLMs to selectively discard certain data. This paper reviews the latest in machine unlearning for LLMs, introducing methods for the targeted forgetting of information to address privacy, ethical, and legal challenges without necessitating full model retraining. It divides existing research into unlearning from unstructured/textual data and structured/classification data, showcasing the effectiveness of these approaches in removing specific data while maintaining model efficacy. Highlighting the practicality of machine unlearning, this analysis also points out the hurdles in preserving model integrity, avoiding excessive or insufficient data removal, and ensuring consistent outputs, underlining the role of machine unlearning in advancing responsible, ethical AI.

Extending Large Language Models (LLMs) to advanced applications requires reliable structured output generation. Existing methods which often rely on rigid JSON schemas, can lead to unreliable outputs, diminished reasoning capabilities, and increased computational overhead, limiting LLMs' adaptability for complex tasks. We introduce Meaning Typed Prompting (MTP), a technique for efficient structured output generation that integrates types, meanings, and abstractions, such as variables and classes, into the prompting process. By utilizing expressive type definitions, MTP enhances output clarity and reduces dependence on complex abstractions, simplifying development, and improving implementation efficiency. This enables LLMs to understand relationships and generate structured data more effectively. Empirical evaluations on multiple benchmarks demonstrate that MTP outperforms existing frameworks in accuracy, reliability, consistency, and token efficiency. We present Semantix, a framework that implements MTP, providing practical insights into its application.

Reasoning about real-life events is a unifying challenge in AI and NLP that has profound utility in a variety of domains, while fallacy in high-stake applications could be catastrophic. Able to work with diverse text in these domains, large language models (LLMs) have proven capable of answering questions and solving problems. However, I show that end-to-end LLMs still systematically fail to reason about complex events, and they lack interpretability due to their black-box nature. To address these issues, I propose three general approaches to use LLMs in conjunction with a structured representation of events. The first is a language-based representation involving relations of sub-events that can be learned by LLMs via fine-tuning. The second is a semi-symbolic representation involving states of entities that can be predicted and leveraged by LLMs via few-shot prompting. The third is a fully symbolic representation that can be predicted by LLMs trained with structured data and be executed by symbolic solvers. On a suite of event reasoning tasks spanning common-sense inference and planning, I show that each approach greatly outperforms end-to-end LLMs with more interpretability. These results suggest manners of synergy between LLMs and structured representations for event reasoning and beyond.

We present Semi-Structured Explanations for COPA (COPA-SSE), a new crowdsourced dataset of 9,747 semi-structured, English common sense explanations for Choice of Plausible Alternatives (COPA) questions. The explanations are formatted as a set of triple-like common sense statements with ConceptNet relations but freely written concepts. This semi-structured format strikes a balance between the high quality but low coverage of structured data and the lower quality but high coverage of free-form crowdsourcing. Each explanation also includes a set of human-given quality ratings. With their familiar format, the explanations are geared towards commonsense reasoners operating on knowledge graphs and serve as a starting point for ongoing work on improving such systems. The dataset is available at https://github.com/a-brassard/copa-sse.

Tucker decomposition is a powerful tensor model to handle multi-aspect data. It demonstrates the low-rank property by decomposing the grid-structured data as interactions between a core tensor and a set of object representations (factors). A fundamental assumption of such decomposition is that there are finite objects in each aspect or mode, corresponding to discrete indexes of data entries. However, real-world data is often not naturally posed in this setting. For example, geographic data is represented as continuous indexes of latitude and longitude coordinates, and cannot fit tensor models directly. To generalize Tucker decomposition to such scenarios, we propose Functional Bayesian Tucker Decomposition (FunBaT). We treat the continuous-indexed data as the interaction between the Tucker core and a group of latent functions. We use Gaussian processes (GP) as functional priors to model the latent functions. Then, we convert each GP into a state-space prior by constructing an equivalent stochastic differential equation (SDE) to reduce computational cost. An efficient inference algorithm is developed for scalable posterior approximation based on advanced message-passing techniques. The advantage of our method is shown in both synthetic data and several real-world applications. We release the code of FunBaT at https://github.com/xuangu-fang/Functional-Bayesian-Tucker-Decomposition.

Electronic Health Records (EHRs) are integral for storing comprehensive patient medical records, combining structured data (e.g., medications) with detailed clinical notes (e.g., physician notes). These elements are essential for straightforward data retrieval and provide deep, contextual insights into patient care. However, they often suffer from discrepancies due to unintuitive EHR system designs and human errors, posing serious risks to patient safety. To address this, we developed EHRCon, a new dataset and task specifically designed to ensure data consistency between structured tables and unstructured notes in EHRs. EHRCon was crafted in collaboration with healthcare professionals using the MIMIC-III EHR dataset, and includes manual annotations of 3,943 entities across 105 clinical notes checked against database entries for consistency. EHRCon has two versions, one using the original MIMIC-III schema, and another using the OMOP CDM schema, in order to increase its applicability and generalizability. Furthermore, leveraging the capabilities of large language models, we introduce CheckEHR, a novel framework for verifying the consistency between clinical notes and database tables. CheckEHR utilizes an eight-stage process and shows promising results in both few-shot and zero-shot settings. The code is available at https://github.com/dustn1259/EHRCon.

The enduring legacy of Euclidean geometry underpins classical machine learning, which, for decades, has been primarily developed for data lying in Euclidean space. Yet, modern machine learning increasingly encounters richly structured data that is inherently nonEuclidean. This data can exhibit intricate geometric, topological and algebraic structure: from the geometry of the curvature of space-time, to topologically complex interactions between neurons in the brain, to the algebraic transformations describing symmetries of physical systems. Extracting knowledge from such non-Euclidean data necessitates a broader mathematical perspective. Echoing the 19th-century revolutions that gave rise to non-Euclidean geometry, an emerging line of research is redefining modern machine learning with non-Euclidean structures. Its goal: generalizing classical methods to unconventional data types with geometry, topology, and algebra. In this review, we provide an accessible gateway to this fast-growing field and propose a graphical taxonomy that integrates recent advances into an intuitive unified framework. We subsequently extract insights into current challenges and highlight exciting opportunities for future development in this field.

The task of annotating data into concise summaries poses a significant challenge across various domains, frequently requiring the allocation of significant time and specialized knowledge by human experts. Despite existing efforts to use large language models for annotation tasks, significant problems such as limited applicability to unlabeled data, the absence of self-supervised methods, and the lack of focus on complex structured data still persist. In this work, we propose a GPT self-supervision annotation method, which embodies a generating-recovering paradigm that leverages the one-shot learning capabilities of the Generative Pretrained Transformer (GPT). The proposed approach comprises a one-shot tuning phase followed by a generation phase. In the one-shot tuning phase, we sample a data from the support set as part of the prompt for GPT to generate a textual summary, which is then used to recover the original data. The alignment score between the recovered and original data serves as a self-supervision navigator to refine the process. In the generation stage, the optimally selected one-shot sample serves as a template in the prompt and is applied to generating summaries from challenging datasets. The annotation performance is evaluated by tuning several human feedback reward networks and by calculating alignment scores between original and recovered data at both sentence and structure levels. Our self-supervised annotation method consistently achieves competitive scores, convincingly demonstrating its robust strength in various data-to-summary annotation tasks.

We analyze the behaviors of open large language models (LLMs) on the task of data-to-text (D2T) generation, i.e., generating coherent and relevant text from structured data. To avoid the issue of LLM training data contamination with standard benchmarks, we design Quintd - a tool for collecting novel structured data records from public APIs. We find that open LLMs (Llama 2, Mistral, and Zephyr) can generate fluent and coherent texts in zero-shot settings from data in common formats collected with Quintd. However, we show that the semantic accuracy of the outputs is a major issue: both according to human annotators and our reference-free metric based on GPT-4, more than 80% of the outputs of open LLMs contain at least one semantic error. We publicly release the code, data, and model outputs.

Tables stored in databases and tables which are present in web pages and articles account for a large part of semi-structured data that is available on the internet. It then becomes pertinent to develop a modeling approach with large language models (LLMs) that can be used to solve diverse table tasks such as semantic parsing, question answering as well as classification problems. Traditionally, there existed separate models specialized for each task individually. It raises the question of how far can we go to build a unified model that works well on some table tasks without significant degradation on others. To that end, we attempt at creating a shared modeling approach in the pretraining stage with encoder-decoder style LLMs that can cater to diverse tasks. We evaluate our approach that continually pretrains and finetunes different model families of T5 with data from tables and surrounding context, on these downstream tasks at different model scales. Through multiple ablation studies, we observe that our pretraining with self-supervised objectives can significantly boost the performance of the models on these tasks. As an example of one improvement, we observe that the instruction finetuned public models which come specialized on text question answering (QA) and have been trained on table data still have room for improvement when it comes to table specific QA. Our work is the first attempt at studying the advantages of a unified approach to table specific pretraining when scaled from 770M to 11B sequence to sequence models while also comparing the instruction finetuned variants of the models.

We describe MGARD, a software providing MultiGrid Adaptive Reduction for floating-point scientific data on structured and unstructured grids. With exceptional data compression capability and precise error control, MGARD addresses a wide range of requirements, including storage reduction, high-performance I/O, and in-situ data analysis. It features a unified application programming interface (API) that seamlessly operates across diverse computing architectures. MGARD has been optimized with highly-tuned GPU kernels and efficient memory and device management mechanisms, ensuring scalable and rapid operations.

Diffusion models achieve state-of-the-art performance in various generation tasks. However, their theoretical foundations fall far behind. This paper studies score approximation, estimation, and distribution recovery of diffusion models, when data are supported on an unknown low-dimensional linear subspace. Our result provides sample complexity bounds for distribution estimation using diffusion models. We show that with a properly chosen neural network architecture, the score function can be both accurately approximated and efficiently estimated. Furthermore, the generated distribution based on the estimated score function captures the data geometric structures and converges to a close vicinity of the data distribution. The convergence rate depends on the subspace dimension, indicating that diffusion models can circumvent the curse of data ambient dimensionality.

Innovation is a major driver of economic and social development, and information about many kinds of innovation is embedded in semi-structured data from patents and patent applications. Although the impact and novelty of innovations expressed in patent data are difficult to measure through traditional means, ML offers a promising set of techniques for evaluating novelty, summarizing contributions, and embedding semantics. In this paper, we introduce the Harvard USPTO Patent Dataset (HUPD), a large-scale, well-structured, and multi-purpose corpus of English-language patent applications filed to the United States Patent and Trademark Office (USPTO) between 2004 and 2018. With more than 4.5 million patent documents, HUPD is two to three times larger than comparable corpora. Unlike previously proposed patent datasets in NLP, HUPD contains the inventor-submitted versions of patent applications--not the final versions of granted patents--thereby allowing us to study patentability at the time of filing using NLP methods for the first time. It is also novel in its inclusion of rich structured metadata alongside the text of patent filings: By providing each application's metadata along with all of its text fields, the dataset enables researchers to perform new sets of NLP tasks that leverage variation in structured covariates. As a case study on the types of research HUPD makes possible, we introduce a new task to the NLP community--namely, binary classification of patent decisions. We additionally show the structured metadata provided in the dataset enables us to conduct explicit studies of concept shifts for this task. Finally, we demonstrate how HUPD can be used for three additional tasks: multi-class classification of patent subject areas, language modeling, and summarization.

Graph-structured data are the commonly used and have wide application scenarios in the real world. For these diverse applications, the vast variety of learning tasks, graph domains, and complex graph learning procedures present challenges for human experts when designing versatile graph learning approaches. Facing these challenges, large language models (LLMs) offer a potential solution due to the extensive knowledge and the human-like intelligence. This paper proposes a novel conceptual prototype for designing versatile graph learning methods with LLMs, with a particular focus on the "where" and "how" perspectives. From the "where" perspective, we summarize four key graph learning procedures, including task definition, graph data feature engineering, model selection and optimization, deployment and serving. We then explore the application scenarios of LLMs in these procedures across a wider spectrum. In the "how" perspective, we align the abilities of LLMs with the requirements of each procedure. Finally, we point out the promising directions that could better leverage the strength of LLMs towards versatile graph learning methods.

As structured data are often insufficient, labels need to be extracted from free text in electronic health records when developing models for clinical information retrieval and decision support systems. One of the most important contextual properties in clinical text is negation, which indicates the absence of findings. We aimed to improve large scale extraction of labels by comparing three methods for negation detection in Dutch clinical notes. We used the Erasmus Medical Center Dutch Clinical Corpus to compare a rule-based method based on ContextD, a biLSTM model using MedCAT and (finetuned) RoBERTa-based models. We found that both the biLSTM and RoBERTa models consistently outperform the rule-based model in terms of F1 score, precision and recall. In addition, we systematically categorized the classification errors for each model, which can be used to further improve model performance in particular applications. Combining the three models naively was not beneficial in terms of performance. We conclude that the biLSTM and RoBERTa-based models in particular are highly accurate accurate in detecting clinical negations, but that ultimately all three approaches can be viable depending on the use case at hand.

Generating graph-structured data requires learning the underlying distribution of graphs. Yet, this is a challenging problem, and the previous graph generative methods either fail to capture the permutation-invariance property of graphs or cannot sufficiently model the complex dependency between nodes and edges, which is crucial for generating real-world graphs such as molecules. To overcome such limitations, we propose a novel score-based generative model for graphs with a continuous-time framework. Specifically, we propose a new graph diffusion process that models the joint distribution of the nodes and edges through a system of stochastic differential equations (SDEs). Then, we derive novel score matching objectives tailored for the proposed diffusion process to estimate the gradient of the joint log-density with respect to each component, and introduce a new solver for the system of SDEs to efficiently sample from the reverse diffusion process. We validate our graph generation method on diverse datasets, on which it either achieves significantly superior or competitive performance to the baselines. Further analysis shows that our method is able to generate molecules that lie close to the training distribution yet do not violate the chemical valency rule, demonstrating the effectiveness of the system of SDEs in modeling the node-edge relationships. Our code is available at https://github.com/harryjo97/GDSS.

We introduce Qwen2.5-VL, the latest flagship model of Qwen vision-language series, which demonstrates significant advancements in both foundational capabilities and innovative functionalities. Qwen2.5-VL achieves a major leap forward in understanding and interacting with the world through enhanced visual recognition, precise object localization, robust document parsing, and long-video comprehension. A standout feature of Qwen2.5-VL is its ability to localize objects using bounding boxes or points accurately. It provides robust structured data extraction from invoices, forms, and tables, as well as detailed analysis of charts, diagrams, and layouts. To handle complex inputs, Qwen2.5-VL introduces dynamic resolution processing and absolute time encoding, enabling it to process images of varying sizes and videos of extended durations (up to hours) with second-level event localization. This allows the model to natively perceive spatial scales and temporal dynamics without relying on traditional normalization techniques. By training a native dynamic-resolution Vision Transformer (ViT) from scratch and incorporating Window Attention, we reduce computational overhead while maintaining native resolution. As a result, Qwen2.5-VL excels not only in static image and document understanding but also as an interactive visual agent capable of reasoning, tool usage, and task execution in real-world scenarios such as operating computers and mobile devices. Qwen2.5-VL is available in three sizes, addressing diverse use cases from edge AI to high-performance computing. The flagship Qwen2.5-VL-72B model matches state-of-the-art models like GPT-4o and Claude 3.5 Sonnet, particularly excelling in document and diagram understanding. Additionally, Qwen2.5-VL maintains robust linguistic performance, preserving the core language competencies of the Qwen2.5 LLM.

Paywalls, licenses and copyright rules often restrict the broad dissemination and reuse of scientific knowledge. We take the position that it is both legally and technically feasible to extract the scientific knowledge in scholarly texts. Current methods, like text embeddings, fail to reliably preserve factual content, and simple paraphrasing may not be legally sound. We urge the community to adopt a new idea: convert scholarly documents into Knowledge Units using LLMs. These units use structured data capturing entities, attributes and relationships without stylistic content. We provide evidence that Knowledge Units: (1) form a legally defensible framework for sharing knowledge from copyrighted research texts, based on legal analyses of German copyright law and U.S. Fair Use doctrine, and (2) preserve most (~95%) factual knowledge from original text, measured by MCQ performance on facts from the original copyrighted text across four research domains. Freeing scientific knowledge from copyright promises transformative benefits for scientific research and education by allowing language models to reuse important facts from copyrighted text. To support this, we share open-source tools for converting research documents into Knowledge Units. Overall, our work posits the feasibility of democratizing access to scientific knowledge while respecting copyright.

Predicting disease trajectories from electronic health records (EHRs) is a complex task due to major challenges such as data non-stationarity, high granularity of medical codes, and integration of multimodal data. EHRs contain both structured data, such as diagnostic codes, and unstructured data, such as clinical notes, which hold essential information often overlooked. Current models, primarily based on structured data, struggle to capture the complete medical context of patients, resulting in a loss of valuable information. To address this issue, we propose an approach that integrates unstructured clinical notes into transformer-based deep learning models for sequential disease prediction. This integration enriches the representation of patients' medical histories, thereby improving the accuracy of diagnosis predictions. Experiments on MIMIC-IV datasets demonstrate that the proposed approach outperforms traditional models relying solely on structured data.

Associating unstructured data with structured information is crucial for real-world tasks that require relevance search. However, existing graph learning benchmarks often overlook the rich semantic information associate with each node. To bridge such gap, we introduce the Multimodal Graph Benchmark (MM-GRAPH), the first comprehensive multi-modal graph benchmark that incorporates both textual and visual information. MM-GRAPH surpasses previous efforts, which have primarily focused on text-attributed graphs with various connectivity patterns. MM-GRAPH consists of five graph learning datasets of various scales that are appropriate for different learning tasks. Their multimodal node features, enabling a more comprehensive evaluation of graph learning algorithms in real-world scenarios. To facilitate research on multimodal graph learning, we further provide an extensive study on the performance of various graph neural networks in the presence of features from various modalities. MM-GRAPH aims to foster research on multimodal graph learning and drive the development of more advanced and robust graph learning algorithms. By providing a diverse set of datasets and benchmarks, MM-GRAPH enables researchers to evaluate and compare their models in realistic settings, ultimately leading to improved performance on real-world applications that rely on multimodal graph data.

The successes of foundation models such as ChatGPT and AlphaFold have spurred significant interest in building similar models for electronic medical records (EMRs) to improve patient care and hospital operations. However, recent hype has obscured critical gaps in our understanding of these models' capabilities. We review over 80 foundation models trained on non-imaging EMR data (i.e. clinical text and/or structured data) and create a taxonomy delineating their architectures, training data, and potential use cases. We find that most models are trained on small, narrowly-scoped clinical datasets (e.g. MIMIC-III) or broad, public biomedical corpora (e.g. PubMed) and are evaluated on tasks that do not provide meaningful insights on their usefulness to health systems. In light of these findings, we propose an improved evaluation framework for measuring the benefits of clinical foundation models that is more closely grounded to metrics that matter in healthcare.

Foundation models, particularly those that incorporate Transformer architectures, have demonstrated exceptional performance in domains such as natural language processing and image processing. Adapting these models to structured data, like tables, however, introduces significant challenges. These difficulties are even more pronounced when addressing multi-table data linked via foreign key, which is prevalent in the enterprise realm and crucial for empowering business use cases. Despite its substantial impact, research focusing on such linked business tables within enterprise settings remains a significantly important yet underexplored domain. To address this, we introduce a curated dataset sourced from an Enterprise Resource Planning (ERP) system, featuring extensive linked tables. This dataset is specifically designed to support research endeavors in table representation learning. By providing access to authentic enterprise data, our goal is to potentially enhance the effectiveness and applicability of models for real-world business contexts.

Large Language Models (LLMs) stand at the forefront of a number of Natural Language Processing (NLP) tasks. Despite the widespread adoption of LLMs in NLP, much of their potential in broader fields remains largely unexplored, and significant limitations persist in their design and implementation. Notably, LLMs struggle with structured data, such as graphs, and often falter when tasked with answering domain-specific questions requiring deep expertise, such as those in biology and chemistry. In this paper, we explore a fundamental question: Can LLMs effectively handle molecule prediction tasks? Rather than pursuing top-tier performance, our goal is to assess how LLMs can contribute to diverse molecule tasks. We identify several classification and regression prediction tasks across six standard molecule datasets. Subsequently, we carefully design a set of prompts to query LLMs on these tasks and compare their performance with existing Machine Learning (ML) models, which include text-based models and those specifically designed for analysing the geometric structure of molecules. Our investigation reveals several key insights: Firstly, LLMs generally lag behind ML models in achieving competitive performance on molecule tasks, particularly when compared to models adept at capturing the geometric structure of molecules, highlighting the constrained ability of LLMs to comprehend graph data. Secondly, LLMs show promise in enhancing the performance of ML models when used collaboratively. Lastly, we engage in a discourse regarding the challenges and promising avenues to harness LLMs for molecule prediction tasks. The code and models are available at https://github.com/zhiqiangzhongddu/LLMaMol.

The rise in loosely-structured data available through text, images, and other modalities has called for new ways of querying them. Multimedia Information Retrieval has filled this gap and has witnessed exciting progress in recent years. Tasks such as search and retrieval of extensive multimedia archives have undergone massive performance improvements, driven to a large extent by recent developments in multimodal deep learning. However, methods in this field remain limited in the kinds of queries they support and, in particular, their inability to answer database-like queries. For this reason, inspired by recent work on neural databases, we propose a new framework, which we name Multimodal Neural Databases (MMNDBs). MMNDBs can answer complex database-like queries that involve reasoning over different input modalities, such as text and images, at scale. In this paper, we present the first architecture able to fulfill this set of requirements and test it with several baselines, showing the limitations of currently available models. The results show the potential of these new techniques to process unstructured data coming from different modalities, paving the way for future research in the area. Code to replicate the experiments will be released at https://github.com/GiovanniTRA/MultimodalNeuralDatabases

Choropleth maps are a common visual representation for region-specific tabular data and are used in a number of different venues (newspapers, articles, etc). These maps are human-readable but are often challenging to deal with when trying to extract data for screen readers, analyses, or other related tasks. Recent research into Visual-Question Answering (VQA) has studied question answering on human-generated charts (ChartQA), such as bar, line, and pie charts. However, little work has paid attention to understanding maps; general VQA models, and ChartQA models, suffer when asked to perform this task. To facilitate and encourage research in this area, we present MapQA, a large-scale dataset of ~800K question-answer pairs over ~60K map images. Our task tests various levels of map understanding, from surface questions about map styles to complex questions that require reasoning on the underlying data. We present the unique challenges of MapQA that frustrate most strong baseline algorithms designed for ChartQA and general VQA tasks. We also present a novel algorithm, Visual Multi-Output Data Extraction based QA (V-MODEQA) for MapQA. V-MODEQA extracts the underlying structured data from a map image with a multi-output model and then performs reasoning on the extracted data. Our experimental results show that V-MODEQA has better overall performance and robustness on MapQA than the state-of-the-art ChartQA and VQA algorithms by capturing the unique properties in map question answering.

Modern sequence models (e.g., Transformers, linear RNNs, etc.) emerged as dominant backbones of recent deep learning frameworks, mainly due to their efficiency, representational power, and/or ability to capture long-range dependencies. Adopting these sequence models for graph-structured data has recently gained popularity as the alternative to Message Passing Neural Networks (MPNNs). There is, however, a lack of a common foundation about what constitutes a good graph sequence model, and a mathematical description of the benefits and deficiencies in adopting different sequence models for learning on graphs. To this end, we first present Graph Sequence Model (GSM), a unifying framework for adopting sequence models for graphs, consisting of three main steps: (1) Tokenization, which translates the graph into a set of sequences; (2) Local Encoding, which encodes local neighborhoods around each node; and (3) Global Encoding, which employs a scalable sequence model to capture long-range dependencies within the sequences. This framework allows us to understand, evaluate, and compare the power of different sequence model backbones in graph tasks. Our theoretical evaluations of the representation power of Transformers and modern recurrent models through the lens of global and local graph tasks show that there are both negative and positive sides for both types of models. Building on this observation, we present GSM++, a fast hybrid model that uses the Hierarchical Affinity Clustering (HAC) algorithm to tokenize the graph into hierarchical sequences, and then employs a hybrid architecture of Transformer to encode these sequences. Our theoretical and experimental results support the design of GSM++, showing that GSM++ outperforms baselines in most benchmark evaluations.

The widespread adoption of REST APIs, coupled with their growing complexity and size, has led to the need for automated REST API testing tools. Current testing tools focus on the structured data in REST API specifications but often neglect valuable insights available in unstructured natural-language descriptions in the specifications, which leads to suboptimal test coverage. Recently, to address this gap, researchers have developed techniques that extract rules from these human-readable descriptions and query knowledge bases to derive meaningful input values. However, these techniques are limited in the types of rules they can extract and can produce inaccurate results. This paper presents RESTGPT, an innovative approach that leverages the power and intrinsic context-awareness of Large Language Models (LLMs) to improve REST API testing. RESTGPT takes as input an API specification, extracts machine-interpretable rules, and generates example parameter values from natural-language descriptions in the specification. It then augments the original specification with these rules and values. Our preliminary evaluation suggests that RESTGPT outperforms existing techniques in both rule extraction and value generation. Given these encouraging results, we outline future research directions for leveraging LLMs more broadly for improving REST API testing.

Generating natural language text from graph-structured data is essential for conversational information seeking. Semantic triples derived from knowledge graphs can serve as a valuable source for grounding responses from conversational agents by providing a factual basis for the information they communicate. This is especially relevant in the context of large language models, which offer great potential for conversational interaction but are prone to hallucinating, omitting, or producing conflicting information. In this study, we conduct an empirical analysis of conversational large language models in generating natural language text from semantic triples. We compare four large language models of varying sizes with different prompting techniques. Through a series of benchmark experiments on the WebNLG dataset, we analyze the models' performance and identify the most common issues in the generated predictions. Our findings show that the capabilities of large language models in triple verbalization can be significantly improved through few-shot prompting, post-processing, and efficient fine-tuning techniques, particularly for smaller models that exhibit lower zero-shot performance.

Machine-based prediction of real-world events is garnering attention due to its potential for informed decision-making. Whereas traditional forecasting predominantly hinges on structured data like time-series, recent breakthroughs in language models enable predictions using unstructured text. In particular, (Zou et al., 2022) unveils AutoCast, a new benchmark that employs news articles for answering forecasting queries. Nevertheless, existing methods still trail behind human performance. The cornerstone of accurate forecasting, we argue, lies in identifying a concise, yet rich subset of news snippets from a vast corpus. With this motivation, we introduce AutoCast++, a zero-shot ranking-based context retrieval system, tailored to sift through expansive news document collections for event forecasting. Our approach first re-ranks articles based on zero-shot question-passage relevance, honing in on semantically pertinent news. Following this, the chosen articles are subjected to zero-shot summarization to attain succinct context. Leveraging a pre-trained language model, we conduct both the relevance evaluation and article summarization without needing domain-specific training. Notably, recent articles can sometimes be at odds with preceding ones due to new facts or unanticipated incidents, leading to fluctuating temporal dynamics. To tackle this, our re-ranking mechanism gives preference to more recent articles, and we further regularize the multi-passage representation learning to align with human forecaster responses made on different dates. Empirical results underscore marked improvements across multiple metrics, improving the performance for multiple-choice questions (MCQ) by 48% and true/false (TF) questions by up to 8%.

Enterprises often own large collections of structured data in the form of large databases or an enterprise data lake. Such data collections come with limited metadata and strict access policies that could limit access to the data contents and, therefore, limit the application of classic retrieval and analysis solutions. As a result, there is a need for solutions that can effectively utilize the available metadata. In this paper, we study the problem of matching table metadata to a business glossary containing data labels and descriptions. The resulting matching enables the use of an available or curated business glossary for retrieval and analysis without or before requesting access to the data contents. One solution to this problem is to use manually-defined rules or similarity measures on column names and glossary descriptions (or their vector embeddings) to find the closest match. However, such approaches need to be tuned through manual labeling and cannot handle many business glossaries that contain a combination of simple as well as complex and long descriptions. In this work, we leverage the power of large language models (LLMs) to design generic matching methods that do not require manual tuning and can identify complex relations between column names and glossaries. We propose methods that utilize LLMs in two ways: a) by generating additional context for column names that can aid with matching b) by using LLMs to directly infer if there is a relation between column names and glossary descriptions. Our preliminary experimental results show the effectiveness of our proposed methods.

This study presents an innovative enhancement to retrieval-augmented generation (RAG) systems by seamlessly integrating fine-tuned large language models (LLMs) with vector databases. This integration capitalizes on the combined strengths of structured data retrieval and the nuanced comprehension provided by advanced LLMs. Central to our approach are the LoRA and QLoRA methodologies, which stand at the forefront of model refinement through parameter-efficient fine-tuning and memory optimization. A novel feature of our research is the incorporation of user feedback directly into the training process, ensuring the model's continuous adaptation to user expectations and thus, improving its performance and applicability. Additionally, we introduce a Quantized Influence Measure (QIM) as an innovative "AI Judge" mechanism to enhance the precision of result selection, further refining the system's accuracy. Accompanied by an executive diagram and a detailed algorithm for fine-tuning QLoRA, our work provides a comprehensive framework for implementing these advancements within chatbot technologies. This research contributes significant insights into LLM optimization for specific uses and heralds new directions for further development in retrieval-augmented models. Through extensive experimentation and analysis, our findings lay a robust foundation for future advancements in chatbot technology and retrieval systems, marking a significant step forward in the creation of more sophisticated, precise, and user-centric conversational AI systems.

Large language models (LLMs) such as GPT-4 have emerged as frontrunners, showcasing unparalleled prowess in diverse applications, including answering queries, code generation, and more. Parallelly, graph-structured data, an intrinsic data type, is pervasive in real-world scenarios. Merging the capabilities of LLMs with graph-structured data has been a topic of keen interest. This paper bifurcates such integrations into two predominant categories. The first leverages LLMs for graph learning, where LLMs can not only augment existing graph algorithms but also stand as prediction models for various graph tasks. Conversely, the second category underscores the pivotal role of graphs in advancing LLMs. Mirroring human cognition, we solve complex tasks by adopting graphs in either reasoning or collaboration. Integrating with such structures can significantly boost the performance of LLMs in various complicated tasks. We also discuss and propose open questions for integrating LLMs with graph-structured data for the future direction of the field.

E-commerce search and recommendation usually operate on structured data such as product catalogs and taxonomies. However, creating better search and recommendation systems often requires a large variety of unstructured data including customer reviews and articles on the web. Traditionally, the solution has always been converting unstructured data into structured data through information extraction, and conducting search over the structured data. However, this is a costly approach that often has low quality. In this paper, we envision a solution that does entirely the opposite. Instead of converting unstructured data (web pages, customer reviews, etc) to structured data, we instead convert structured data (product inventory, catalogs, taxonomies, etc) into textual data, which can be easily integrated into the text corpus that trains LLMs. Then, search and recommendation can be performed through a Q/A mechanism through an LLM instead of using traditional information retrieval methods over structured data.

Understanding visually-rich business documents to extract structured data and automate business workflows has been receiving attention both in academia and industry. Although recent multi-modal language models have achieved impressive results, we find that existing benchmarks do not reflect the complexity of real documents seen in industry. In this work, we identify the desiderata for a more comprehensive benchmark and propose one we call Visually Rich Document Understanding (VRDU). VRDU contains two datasets that represent several challenges: rich schema including diverse data types as well as hierarchical entities, complex templates including tables and multi-column layouts, and diversity of different layouts (templates) within a single document type. We design few-shot and conventional experiment settings along with a carefully designed matching algorithm to evaluate extraction results. We report the performance of strong baselines and offer three observations: (1) generalizing to new document templates is still very challenging, (2) few-shot performance has a lot of headroom, and (3) models struggle with hierarchical fields such as line-items in an invoice. We plan to open source the benchmark and the evaluation toolkit. We hope this helps the community make progress on these challenging tasks in extracting structured data from visually rich documents.

As the use of interactive machines grow, the task of Emotion Recognition in Conversation (ERC) became more important. If the machine-generated sentences reflect emotion, more human-like sympathetic conversations are possible. Since emotion recognition in conversation is inaccurate if the previous utterances are not taken into account, many studies reflect the dialogue context to improve the performances. Many recent approaches show performance improvement by combining knowledge into modules learned from external structured data. However, structured data is difficult to access in non-English languages, making it difficult to extend to other languages. Therefore, we extract the pre-trained memory using the pre-trained language model as an extractor of external knowledge. We introduce CoMPM, which combines the speaker's pre-trained memory with the context model, and find that the pre-trained memory significantly improves the performance of the context model. CoMPM achieves the first or second performance on all data and is state-of-the-art among systems that do not leverage structured data. In addition, our method shows that it can be extended to other languages because structured knowledge is not required, unlike previous methods. Our code is available on github (https://github.com/rungjoo/CoMPM).

Employing a machine learning approach we predict, up to 24 hours prior, a diagnosis of severe sepsis. Strongly predictive models are possible that use only text reports from the Electronic Health Record (EHR), and omit structured numerical data. Unstructured text alone gives slightly better performance than structured data alone, and the combination further improves performance. We also discuss advantages of using unstructured EHR text for modeling, as compared to structured EHR data.

Program source code contains complex structure information, which can be represented in structured data forms like trees or graphs. To acquire the structural information in source code, most existing researches use abstract syntax trees (AST). A group of works add additional edges to ASTs to convert source code into graphs and use graph neural networks to learn representations for program graphs. Although these works provide additional control or data flow information to ASTs for downstream tasks, they neglect an important aspect of structure information in AST itself: the different types of nodes and edges. In ASTs, different nodes contain different kinds of information like variables or control flow, and the relation between a node and all its children can also be different. To address the information of node and edge types, we bring the idea of heterogeneous graphs to learning on source code and present a new formula of building heterogeneous program graphs from ASTs with additional type information for nodes and edges. We use the ASDL grammar of programming language to define the node and edge types of program graphs. Then we use heterogeneous graph neural networks to learn on these graphs. We evaluate our approach on two tasks: code comment generation and method naming. Both tasks require reasoning on the semantics of complete code snippets. Experiment results show that our approach outperforms baseline models, including homogeneous graph-based models, showing that leveraging the type information of nodes and edges in program graphs can help in learning program semantics.

Graphical User Interface (GUI) agents are designed to automate complex tasks on digital devices, such as smartphones and desktops. Most existing GUI agents interact with the environment through extracted structured data, which can be notably lengthy (e.g., HTML) and occasionally inaccessible (e.g., on desktops). To alleviate this issue, we propose a visual GUI agent -- SeeClick, which only relies on screenshots for task automation. In our preliminary study, we have discovered a key challenge in developing visual GUI agents: GUI grounding -- the capacity to accurately locate screen elements based on instructions. To tackle this challenge, we propose to enhance SeeClick with GUI grounding pre-training and devise a method to automate the curation of GUI grounding data. Along with the efforts above, we have also created ScreenSpot, the first realistic GUI grounding dataset that encompasses mobile, desktop, and web environments. After pre-training, SeeClick demonstrates significant improvement in ScreenSpot over various baselines. Moreover, comprehensive evaluations on three widely used benchmarks consistently support our finding that advancements in GUI grounding directly correlate with enhanced performance in downstream GUI agent tasks. The model, data and code are available at https://github.com/njucckevin/SeeClick.

Graph neural networks (GNNs) learn the representation of graph-structured data, and their expressiveness can be further enhanced by inferring node relations for propagation. Attention-based GNNs infer neighbor importance to manipulate the weight of its propagation. Despite their popularity, the discussion on deep graph attention and its unique challenges has been limited. In this work, we investigate some problematic phenomena related to deep graph attention, including vulnerability to over-smoothed features and smooth cumulative attention. Through theoretical and empirical analyses, we show that various attention-based GNNs suffer from these problems. Motivated by our findings, we propose AEROGNN, a novel GNN architecture designed for deep graph attention. AERO-GNN provably mitigates the proposed problems of deep graph attention, which is further empirically demonstrated with (a) its adaptive and less smooth attention functions and (b) higher performance at deep layers (up to 64). On 9 out of 12 node classification benchmarks, AERO-GNN outperforms the baseline GNNs, highlighting the advantages of deep graph attention. Our code is available at https://github.com/syleeheal/AERO-GNN.

Recent advances in Graph Neural Networks (GNNs) have revolutionized graph-structured data modeling, yet traditional GNNs struggle with complex heterogeneous structures prevalent in real-world scenarios. Despite progress in handling heterogeneous interactions, two fundamental challenges persist: noisy data significantly compromising embedding quality and learning performance, and existing methods' inability to capture intricate semantic transitions among heterogeneous relations, which impacts downstream predictions. To address these fundamental issues, we present the Heterogeneous Graph Diffusion Model (DiffGraph), a pioneering framework that introduces an innovative cross-view denoising strategy. This advanced approach transforms auxiliary heterogeneous data into target semantic spaces, enabling precise distillation of task-relevant information. At its core, DiffGraph features a sophisticated latent heterogeneous graph diffusion mechanism, implementing a novel forward and backward diffusion process for superior noise management. This methodology achieves simultaneous heterogeneous graph denoising and cross-type transition, while significantly simplifying graph generation through its latent-space diffusion capabilities. Through rigorous experimental validation on both public and industrial datasets, we demonstrate that DiffGraph consistently surpasses existing methods in link prediction and node classification tasks, establishing new benchmarks for robustness and efficiency in heterogeneous graph processing. The model implementation is publicly available at: https://github.com/HKUDS/DiffGraph.

The need to analyze graphs is ubiquitous across various fields, from social networks to biological research and recommendation systems. Therefore, enabling the ability of large language models (LLMs) to process graphs is an important step toward more advanced general intelligence. However, current LLM benchmarks on graph analysis require models to directly reason over the prompts describing graph topology, and are thus limited to small graphs with only a few dozens of nodes. In contrast, human experts typically write programs based on popular libraries for task solving, and can thus handle graphs with different scales. To this end, a question naturally arises: can LLMs analyze graphs like professionals? In this paper, we introduce ProGraph, a manually crafted benchmark containing 3 categories of graph tasks. The benchmark expects solutions based on programming instead of directly reasoning over raw inputs. Our findings reveal that the performance of current LLMs is unsatisfactory, with the best model achieving only 36% accuracy. To bridge this gap, we propose LLM4Graph datasets, which include crawled documents and auto-generated codes based on 6 widely used graph libraries. By augmenting closed-source LLMs with document retrieval and fine-tuning open-source ones on the codes, we show 11-32% absolute improvements in their accuracies. Our results underscore that the capabilities of LLMs in handling structured data are still under-explored, and show the effectiveness of LLM4Graph in enhancing LLMs' proficiency of graph analysis. The benchmark, datasets and enhanced open-source models are available at https://github.com/BUPT-GAMMA/ProGraph.

Information Extraction (IE) is crucial for converting unstructured data into structured formats like Knowledge Graphs (KGs). A key task within IE is Relation Extraction (RE), which identifies relationships between entities in text. Various RE methods exist, including supervised, unsupervised, weakly supervised, and rule-based approaches. Recent studies leveraging pre-trained language models (PLMs) have shown significant success in this area. In the current era dominated by Large Language Models (LLMs), fine-tuning these models can overcome limitations associated with zero-shot LLM prompting-based RE methods, especially regarding domain adaptation challenges and identifying implicit relations between entities in sentences. These implicit relations, which cannot be easily extracted from a sentence's dependency tree, require logical inference for accurate identification. This work explores the performance of fine-tuned LLMs and their integration into the Retrieval Augmented-based (RAG) RE approach to address the challenges of identifying implicit relations at the sentence level, particularly when LLMs act as generators within the RAG framework. Empirical evaluations on the TACRED, TACRED-Revisited (TACREV), Re-TACRED, and SemEVAL datasets show significant performance improvements with fine-tuned LLMs, including Llama2-7B, Mistral-7B, and T5 (Large). Notably, our approach achieves substantial gains on SemEVAL, where implicit relations are common, surpassing previous results on this dataset. Additionally, our method outperforms previous works on TACRED, TACREV, and Re-TACRED, demonstrating exceptional performance across diverse evaluation scenarios.

Real-world multi-modal problems are rarely solved by a single machine learning model, and often require multi-step computational plans that involve stitching several models. Tool-augmented LLMs hold tremendous promise for automating the generation of such computational plans. However, the lack of standardized benchmarks for evaluating LLMs as planners for multi-step multi-modal tasks has prevented a systematic study of planner design decisions. Should LLMs generate a full plan in a single shot or step-by-step? Should they invoke tools directly with Python code or through structured data formats like JSON? Does feedback improve planning? To answer these questions and more, we introduce m&m's: a benchmark containing 4K+ multi-step multi-modal tasks involving 33 tools that include multi-modal models, (free) public APIs, and image processing modules. For each of these task queries, we provide automatically generated plans using this realistic toolset. We further provide a high-quality subset of 1,565 task plans that are human-verified and correctly executable. With m&m's, we evaluate 6 popular LLMs with 2 planning strategies (multi-step vs. step-by-step planning), 2 plan formats (JSON vs. code), and 3 types of feedback (parsing/verification/execution). Finally, we summarize takeaways from our extensive experiments. Our dataset and code are available on HuggingFace (https://huggingface.co/datasets/zixianma/mnms) and Github (https://github.com/RAIVNLab/mnms).

Graph Neural Networks (GNNs) are neural models that leverage the dependency structure in graphical data via message passing among the graph nodes. GNNs have emerged as pivotal architectures in analyzing graph-structured data, and their expansive application in sensitive domains requires a comprehensive understanding of their decision-making processes -- necessitating a framework for GNN explainability. An explanation function for GNNs takes a pre-trained GNN along with a graph as input, to produce a `sufficient statistic' subgraph with respect to the graph label. A main challenge in studying GNN explainability is to provide fidelity measures that evaluate the performance of these explanation functions. This paper studies this foundational challenge, spotlighting the inherent limitations of prevailing fidelity metrics, including Fid_+, Fid_-, and Fid_Delta. Specifically, a formal, information-theoretic definition of explainability is introduced and it is shown that existing metrics often fail to align with this definition across various statistical scenarios. The reason is due to potential distribution shifts when subgraphs are removed in computing these fidelity measures. Subsequently, a robust class of fidelity measures are introduced, and it is shown analytically that they are resilient to distribution shift issues and are applicable in a wide range of scenarios. Extensive empirical analysis on both synthetic and real datasets are provided to illustrate that the proposed metrics are more coherent with gold standard metrics. The source code is available at https://trustai4s-lab.github.io/fidelity.

This presentation focuses on the importance of web crawling and page ranking algorithms in dealing with the massive amount of data present on the World Wide Web. As the web continues to grow exponentially, efficient search and retrieval methods become crucial. Web crawling is a process that converts unstructured data into structured data, enabling effective information retrieval. Additionally, page ranking algorithms play a significant role in assessing the quality and popularity of web pages. The presentation explores the background of these algorithms and evaluates five different crawling algorithms: Shark Search, Priority-Based Queue, Naive Bayes, Breadth-First, and Depth-First. The goal is to identify the most effective algorithm for crawling web pages. By understanding these algorithms, we can enhance our ability to navigate the web and extract valuable information efficiently.

Graph neural networks aim to learn representations for graph-structured data and show impressive performance, particularly in node classification. Recently, many methods have studied the representations of GNNs from the perspective of optimization goals and spectral graph theory. However, the feature space that dominates representation learning has not been systematically studied in graph neural networks. In this paper, we propose to fill this gap by analyzing the feature space of both spatial and spectral models. We decompose graph neural networks into determined feature spaces and trainable weights, providing the convenience of studying the feature space explicitly using matrix space analysis. In particular, we theoretically find that the feature space tends to be linearly correlated due to repeated aggregations. Motivated by these findings, we propose 1) feature subspaces flattening and 2) structural principal components to expand the feature space. Extensive experiments verify the effectiveness of our proposed more comprehensive feature space, with comparable inference time to the baseline, and demonstrate its efficient convergence capability.

Pretrained contextualized text representation models learn an effective representation of a natural language to make it machine understandable. After the breakthrough of the attention mechanism, a new generation of pretrained models have been proposed achieving good performances since the introduction of the Transformer. Bidirectional Encoder Representations from Transformers (BERT) has become the state-of-the-art model for language understanding. Despite their success, most of the available models have been trained on Indo-European languages however similar research for under-represented languages and dialects remains sparse. In this paper, we investigate the feasibility of training monolingual Transformer-based language models for under represented languages, with a specific focus on the Tunisian dialect. We evaluate our language model on sentiment analysis task, dialect identification task and reading comprehension question-answering task. We show that the use of noisy web crawled data instead of structured data (Wikipedia, articles, etc.) is more convenient for such non-standardized language. Moreover, results indicate that a relatively small web crawled dataset leads to performances that are as good as those obtained using larger datasets. Finally, our best performing TunBERT model reaches or improves the state-of-the-art in all three downstream tasks. We release the TunBERT pretrained model and the datasets used for fine-tuning.

Clinical notes contain information about patients that goes beyond structured data like lab values and medications. However, clinical notes have been underused relative to structured data, because notes are high-dimensional and sparse. This work develops and evaluates representations of clinical notes using bidirectional transformers (ClinicalBERT). ClinicalBERT uncovers high-quality relationships between medical concepts as judged by humans. ClinicalBert outperforms baselines on 30-day hospital readmission prediction using both discharge summaries and the first few days of notes in the intensive care unit. Code and model parameters are available.

Graph Neural Networks (GNNs) have shown promising potential in graph representation learning. The majority of GNNs define a local message-passing mechanism, propagating information over the graph by stacking multiple layers. These methods, however, are known to suffer from two major limitations: over-squashing and poor capturing of long-range dependencies. Recently, Graph Transformers (GTs) emerged as a powerful alternative to Message-Passing Neural Networks (MPNNs). GTs, however, have quadratic computational cost, lack inductive biases on graph structures, and rely on complex Positional/Structural Encodings (SE/PE). In this paper, we show that while Transformers, complex message-passing, and SE/PE are sufficient for good performance in practice, neither is necessary. Motivated by the recent success of State Space Models (SSMs), such as Mamba, we present Graph Mamba Networks (GMNs), a general framework for a new class of GNNs based on selective SSMs. We discuss and categorize the new challenges when adopting SSMs to graph-structured data, and present four required and one optional steps to design GMNs, where we choose (1) Neighborhood Tokenization, (2) Token Ordering, (3) Architecture of Bidirectional Selective SSM Encoder, (4) Local Encoding, and dispensable (5) PE and SE. We further provide theoretical justification for the power of GMNs. Experiments demonstrate that despite much less computational cost, GMNs attain an outstanding performance in long-range, small-scale, large-scale, and heterophilic benchmark datasets.

While the general machine learning (ML) community has benefited from public datasets, tasks, and models, the progress of ML in healthcare has been hampered by a lack of such shared assets. The success of foundation models creates new challenges for healthcare ML by requiring access to shared pretrained models to validate performance benefits. We help address these challenges through three contributions. First, we publish a new dataset, EHRSHOT, which contains deidentified structured data from the electronic health records (EHRs) of 6,739 patients from Stanford Medicine. Unlike MIMIC-III/IV and other popular EHR datasets, EHRSHOT is longitudinal and not restricted to ICU/ED patients. Second, we publish the weights of CLMBR-T-base, a 141M parameter clinical foundation model pretrained on the structured EHR data of 2.57M patients. We are one of the first to fully release such a model for coded EHR data; in contrast, most prior models released for clinical data (e.g. GatorTron, ClinicalBERT) only work with unstructured text and cannot process the rich, structured data within an EHR. We provide an end-to-end pipeline for the community to validate and build upon its performance. Third, we define 15 few-shot clinical prediction tasks, enabling evaluation of foundation models on benefits such as sample efficiency and task adaptation. Our model and dataset are available via a research data use agreement from the Stanford AIMI Center. Code to reproduce our results are available at our Github repo: https://github.com/som-shahlab/ehrshot-benchmark

Electronic health records contain an enormous amount of valuable information, but many are recorded in free text. Information extraction is the strategy to transform the sequence of characters into structured data, which can be employed for secondary analysis. However, the traditional information extraction components, such as named entity recognition and relation extraction, require annotated data to optimize the model parameters, which has become one of the major bottlenecks in building information extraction systems. With the large language models achieving good performances on various downstream NLP tasks without parameter tuning, it becomes possible to use large language models for zero-shot information extraction. In this study, we aim to explore whether the most popular large language model, ChatGPT, can extract useful information from the radiological reports. We first design the prompt template for the interested information in the CT reports. Then, we generate the prompts by combining the prompt template with the CT reports as the inputs of ChatGPT to obtain the responses. A post-processing module is developed to transform the responses into structured extraction results. We conducted the experiments with 847 CT reports collected from Peking University Cancer Hospital. The experimental results indicate that ChatGPT can achieve competitive performances for some extraction tasks compared with the baseline information extraction system, but some limitations need to be further improved.

Graph neural networks (GNNs) are the most widely adopted model in graph-structured data oriented learning and representation. Despite their extraordinary success in real-world applications, understanding their working mechanism by theory is still on primary stage. In this paper, we move towards this goal from the perspective of generalization. To be specific, we first establish high probability bounds of generalization gap and gradients in transductive learning with consideration of stochastic optimization. After that, we provide high probability bounds of generalization gap for popular GNNs. The theoretical results reveal the architecture specific factors affecting the generalization gap. Experimental results on benchmark datasets show the consistency between theoretical results and empirical evidence. Our results provide new insights in understanding the generalization of GNNs.

Graph Neural Networks (GNNs) are a popular technique for modelling graph-structured data and computing node-level representations via aggregation of information from the neighborhood of each node. However, this aggregation implies an increased risk of revealing sensitive information, as a node can participate in the inference for multiple nodes. This implies that standard privacy-preserving machine learning techniques, such as differentially private stochastic gradient descent (DP-SGD) - which are designed for situations where each data point participates in the inference for one point only - either do not apply, or lead to inaccurate models. In this work, we formally define the problem of learning GNN parameters with node-level privacy, and provide an algorithmic solution with a strong differential privacy guarantee. We employ a careful sensitivity analysis and provide a non-trivial extension of the privacy-by-amplification technique to the GNN setting. An empirical evaluation on standard benchmark datasets demonstrates that our method is indeed able to learn accurate privacy-preserving GNNs which outperform both private and non-private methods that completely ignore graph information.

The current state of adoption of well-structured electronic health records and integration of digital methods for storing medical patient data in structured formats can often considered as inferior compared to the use of traditional, unstructured text based patient data documentation. Data mining in the field of medical data analysis often needs to rely solely on processing of unstructured data to retrieve relevant data. In natural language processing (NLP), statistical models have been shown successful in various tasks like part-of-speech tagging, relation extraction (RE) and named entity recognition (NER). In this work, we present GERNERMED, the first open, neural NLP model for NER tasks dedicated to detect medical entity types in German text data. Here, we avoid the conflicting goals of protection of sensitive patient data from training data extraction and the publication of the statistical model weights by training our model on a custom dataset that was translated from publicly available datasets in foreign language by a pretrained neural machine translation model. The sample code and the statistical model is available at: https://github.com/frankkramer-lab/GERNERMED

Relation linking is essential to enable question answering over knowledge bases. Although there are various efforts to improve relation linking performance, the current state-of-the-art methods do not achieve optimal results, therefore, negatively impacting the overall end-to-end question answering performance. In this work, we propose a novel approach for relation linking framing it as a generative problem facilitating the use of pre-trained sequence-to-sequence models. We extend such sequence-to-sequence models with the idea of infusing structured data from the target knowledge base, primarily to enable these models to handle the nuances of the knowledge base. Moreover, we train the model with the aim to generate a structured output consisting of a list of argument-relation pairs, enabling a knowledge validation step. We compared our method against the existing relation linking systems on four different datasets derived from DBpedia and Wikidata. Our method reports large improvements over the state-of-the-art while using a much simpler model that can be easily adapted to different knowledge bases.

Graph neural networks have recently achieved remarkable success in representing graph-structured data, with rapid progress in both the node embedding and graph pooling methods. Yet, they mostly focus on capturing information from the nodes considering their connectivity, and not much work has been done in representing the edges, which are essential components of a graph. However, for tasks such as graph reconstruction and generation, as well as graph classification tasks for which the edges are important for discrimination, accurately representing edges of a given graph is crucial to the success of the graph representation learning. To this end, we propose a novel edge representation learning framework based on Dual Hypergraph Transformation (DHT), which transforms the edges of a graph into the nodes of a hypergraph. This dual hypergraph construction allows us to apply message-passing techniques for node representations to edges. After obtaining edge representations from the hypergraphs, we then cluster or drop edges to obtain holistic graph-level edge representations. We validate our edge representation learning method with hypergraphs on diverse graph datasets for graph representation and generation performance, on which our method largely outperforms existing graph representation learning methods. Moreover, our edge representation learning and pooling method also largely outperforms state-of-the-art graph pooling methods on graph classification, not only because of its accurate edge representation learning, but also due to its lossless compression of the nodes and removal of irrelevant edges for effective message-passing.

The problem of verifying whether a textual hypothesis holds based on the given evidence, also known as fact verification, plays an important role in the study of natural language understanding and semantic representation. However, existing studies are mainly restricted to dealing with unstructured evidence (e.g., natural language sentences and documents, news, etc), while verification under structured evidence, such as tables, graphs, and databases, remains under-explored. This paper specifically aims to study the fact verification given semi-structured data as evidence. To this end, we construct a large-scale dataset called TabFact with 16k Wikipedia tables as the evidence for 118k human-annotated natural language statements, which are labeled as either ENTAILED or REFUTED. TabFact is challenging since it involves both soft linguistic reasoning and hard symbolic reasoning. To address these reasoning challenges, we design two different models: Table-BERT and Latent Program Algorithm (LPA). Table-BERT leverages the state-of-the-art pre-trained language model to encode the linearized tables and statements into continuous vectors for verification. LPA parses statements into programs and executes them against the tables to obtain the returned binary value for verification. Both methods achieve similar accuracy but still lag far behind human performance. We also perform a comprehensive analysis to demonstrate great future opportunities. The data and code of the dataset are provided in https://github.com/wenhuchen/Table-Fact-Checking.

We introduce the variational graph auto-encoder (VGAE), a framework for unsupervised learning on graph-structured data based on the variational auto-encoder (VAE). This model makes use of latent variables and is capable of learning interpretable latent representations for undirected graphs. We demonstrate this model using a graph convolutional network (GCN) encoder and a simple inner product decoder. Our model achieves competitive results on a link prediction task in citation networks. In contrast to most existing models for unsupervised learning on graph-structured data and link prediction, our model can naturally incorporate node features, which significantly improves predictive performance on a number of benchmark datasets.

Scientific documents record research findings and valuable human knowledge, comprising a vast corpus of high-quality data. Leveraging multi-modality data extracted from these documents and assessing large models' abilities to handle scientific document-oriented tasks is therefore meaningful. Despite promising advancements, large models still perform poorly on multi-page scientific document extraction and understanding tasks, and their capacity to process within-document data formats such as charts and equations remains under-explored. To address these issues, we present DocGenome, a structured document benchmark constructed by annotating 500K scientific documents from 153 disciplines in the arXiv open-access community, using our custom auto-labeling pipeline. DocGenome features four key characteristics: 1) Completeness: It is the first dataset to structure data from all modalities including 13 layout attributes along with their LaTeX source codes. 2) Logicality: It provides 6 logical relationships between different entities within each scientific document. 3) Diversity: It covers various document-oriented tasks, including document classification, visual grounding, document layout detection, document transformation, open-ended single-page QA and multi-page QA. 4) Correctness: It undergoes rigorous quality control checks conducted by a specialized team. We conduct extensive experiments to demonstrate the advantages of DocGenome and objectively evaluate the performance of large models on our benchmark.

Large language models (LLMs) have made impressive progress in chemistry applications, including molecular property prediction, molecular generation, experimental protocol design, etc. However, the community lacks a dialogue-based model specifically designed for chemistry. The challenge arises from the fact that most chemical data and scientific knowledge are primarily stored in structured databases, and the direct use of these structured data compromises the model's ability to maintain coherent dialogue. To tackle this issue, we develop a novel template-based instruction construction method that transforms structured knowledge into plain dialogue, making it suitable for language model training. By leveraging this approach, we develop ChemLLM, the first large language model dedicated to chemistry, capable of performing various tasks across chemical disciplines with smooth dialogue interaction. ChemLLM beats GPT-3.5 on all three principal tasks in chemistry, i.e., name conversion, molecular caption, and reaction prediction, and surpasses GPT-4 on two of them. Remarkably, ChemLLM also shows exceptional adaptability to related mathematical and physical tasks despite being trained mainly on chemical-centric corpora. Furthermore, ChemLLM demonstrates proficiency in specialized NLP tasks within chemistry, such as literature translation and cheminformatic programming. ChemLLM opens up a new avenue for exploration within chemical studies, while our method of integrating structured chemical knowledge into dialogue systems sets a new frontier for developing LLMs across various scientific fields. Codes, Datasets, and Model weights are publicly accessible at hf.co/AI4Chem/ChemLLM-7B-Chat.

Retrieval-augmented Generation (RAG) enhances Large Language Models (LLMs) by integrating external knowledge to reduce hallucinations and incorporate up-to-date information without retraining. As an essential part of RAG, external knowledge bases are commonly built by extracting structured data from unstructured PDF documents using Optical Character Recognition (OCR). However, given the imperfect prediction of OCR and the inherent non-uniform representation of structured data, knowledge bases inevitably contain various OCR noises. In this paper, we introduce OHRBench, the first benchmark for understanding the cascading impact of OCR on RAG systems. OHRBench includes 350 carefully selected unstructured PDF documents from six real-world RAG application domains, along with Q&As derived from multimodal elements in documents, challenging existing OCR solutions used for RAG To better understand OCR's impact on RAG systems, we identify two primary types of OCR noise: Semantic Noise and Formatting Noise and apply perturbation to generate a set of structured data with varying degrees of each OCR noise. Using OHRBench, we first conduct a comprehensive evaluation of current OCR solutions and reveal that none is competent for constructing high-quality knowledge bases for RAG systems. We then systematically evaluate the impact of these two noise types and demonstrate the vulnerability of RAG systems. Furthermore, we discuss the potential of employing Vision-Language Models (VLMs) without OCR in RAG systems. Code: https://github.com/opendatalab/OHR-Bench

Graph Neural Networks (GNNs) are a powerful technique for machine learning on graph-structured data, yet they pose challenges in interpretability. Existing GNN explanation methods usually yield technical outputs, such as subgraphs and feature importance scores, that are difficult for non-data scientists to understand and thereby violate the purpose of explanations. Motivated by recent Explainable AI (XAI) research, we propose GraphXAIN, a method that generates natural language narratives explaining GNN predictions. GraphXAIN is a model- and explainer-agnostic method that uses Large Language Models (LLMs) to translate explanatory subgraphs and feature importance scores into coherent, story-like explanations of GNN decision-making processes. Evaluations on real-world datasets demonstrate GraphXAIN's ability to improve graph explanations. A survey of machine learning researchers and practitioners reveals that GraphXAIN enhances four explainability dimensions: understandability, satisfaction, convincingness, and suitability for communicating model predictions. When combined with another graph explainer method, GraphXAIN further improves trustworthiness, insightfulness, confidence, and usability. Notably, 95% of participants found GraphXAIN to be a valuable addition to the GNN explanation method. By incorporating natural language narratives, our approach serves both graph practitioners and non-expert users by providing clearer and more effective explanations.

In many real-world applications, graph-structured data used for training and testing have differences in distribution, such as in high energy physics (HEP) where simulation data used for training may not match real experiments. Graph domain adaptation (GDA) is a method used to address these differences. However, current GDA primarily works by aligning the distributions of node representations output by a single graph neural network encoder shared across the training and testing domains, which may often yield sub-optimal solutions. This work examines different impacts of distribution shifts caused by either graph structure or node attributes and identifies a new type of shift, named conditional structure shift (CSS), which current GDA approaches are provably sub-optimal to deal with. A novel approach, called structural reweighting (StruRW), is proposed to address this issue and is tested on synthetic graphs, four benchmark datasets, and a new application in HEP. StruRW has shown significant performance improvement over the baselines in the settings with large graph structure shifts, and reasonable performance improvement when node attribute shift dominates.

The field of deep generative modeling has grown rapidly and consistently over the years. With the availability of massive amounts of training data coupled with advances in scalable unsupervised learning paradigms, recent large-scale generative models show tremendous promise in synthesizing high-resolution images and text, as well as structured data such as videos and molecules. However, we argue that current large-scale generative AI models do not sufficiently address several fundamental issues that hinder their widespread adoption across domains. In this work, we aim to identify key unresolved challenges in modern generative AI paradigms that should be tackled to further enhance their capabilities, versatility, and reliability. By identifying these challenges, we aim to provide researchers with valuable insights for exploring fruitful research directions, thereby fostering the development of more robust and accessible generative AI solutions.

This study presents the first investigation of pedestrian crash severity using the TabNet model, a novel tabular deep learning method exceptionally suited for analyzing the tabular data inherent in transportation safety research. Through the application of TabNet to a comprehensive dataset from Utah covering the years 2010 to 2022, we uncover intricate factors contributing to pedestrian crash severity. The TabNet model, capitalizing on its compatibility with structured data, demonstrates remarkable predictive accuracy, eclipsing that of traditional models. It identifies critical variables, such as pedestrian age, involvement in left or right turns, lighting conditions, and alcohol consumption, which significantly influence crash outcomes. The utilization of SHapley Additive exPlanations (SHAP) enhances our ability to interpret the TabNet model's predictions, ensuring transparency and understandability in our deep learning approach. The insights derived from our analysis provide a valuable compass for transportation safety engineers and policymakers, enabling the identification of pivotal factors that affect pedestrian crash severity. Such knowledge is instrumental in formulating precise, data-driven interventions aimed at bolstering pedestrian safety across diverse urban and rural settings.

Two lines of work are taking the central stage in AI research. On the one hand, the community is making increasing efforts to build models that discard spurious correlations and generalize better in novel test environments. Unfortunately, the bitter lesson so far is that no proposal convincingly outperforms a simple empirical risk minimization baseline. On the other hand, large language models (LLMs) have erupted as algorithms able to learn in-context, generalizing on-the-fly to eclectic contextual circumstances that users enforce by means of prompting. In this paper, we argue that context is environment, and posit that in-context learning holds the key to better domain generalization. Via extensive theory and experiments, we show that paying attention to contextx2013x2013unlabeled examples as they arrivex2013x2013allows our proposed In-Context Risk Minimization (ICRM) algorithm to zoom-in on the test environment risk minimizer, leading to significant out-of-distribution performance improvements. From all of this, two messages are worth taking home. Researchers in domain generalization should consider environment as context, and harness the adaptive power of in-context learning. Researchers in LLMs should consider context as environment, to better structure data towards generalization.

Graphs are a powerful tool for representing and analyzing complex relationships in real-world applications such as social networks, recommender systems, and computational finance. Reasoning on graphs is essential for drawing inferences about the relationships between entities in a complex system, and to identify hidden patterns and trends. Despite the remarkable progress in automated reasoning with natural text, reasoning on graphs with large language models (LLMs) remains an understudied problem. In this work, we perform the first comprehensive study of encoding graph-structured data as text for consumption by LLMs. We show that LLM performance on graph reasoning tasks varies on three fundamental levels: (1) the graph encoding method, (2) the nature of the graph task itself, and (3) interestingly, the very structure of the graph considered. These novel results provide valuable insight on strategies for encoding graphs as text. Using these insights we illustrate how the correct choice of encoders can boost performance on graph reasoning tasks inside LLMs by 4.8% to 61.8%, depending on the task.

The ability to generate SPARQL queries from natural language questions is crucial for ensuring efficient and accurate retrieval of structured data from knowledge graphs (KG). While large language models (LLMs) have been widely adopted for SPARQL query generation, they are often susceptible to hallucinations and out-of-distribution errors when producing KG elements like Uniform Resource Identifiers (URIs) based on internal parametric knowledge. This often results in content that appears plausible but is factually incorrect, posing significant challenges for their use in real-world information retrieval (IR) applications. This has led to increased research aimed at detecting and mitigating such errors. In this paper, we introduce PGMR (Post-Generation Memory Retrieval), a modular framework that incorporates a non-parametric memory module to retrieve KG elements and enhance LLM-based SPARQL query generation. Our experimental results indicate that PGMR consistently delivers strong performance across diverse datasets, data distributions, and LLMs. Notably, PGMR significantly mitigates URI hallucinations, nearly eliminating the problem in several scenarios.

This study explores the use of Large Language Models (LLMs) for automatic evaluation of knowledge graph (KG) completion models. Historically, validating information in KGs has been a challenging task, requiring large-scale human annotation at prohibitive cost. With the emergence of general-purpose generative AI and LLMs, it is now plausible that human-in-the-loop validation could be replaced by a generative agent. We introduce a framework for consistency and validation when using generative models to validate knowledge graphs. Our framework is based upon recent open-source developments for structural and semantic validation of LLM outputs, and upon flexible approaches to fact checking and verification, supported by the capacity to reference external knowledge sources of any kind. The design is easy to adapt and extend, and can be used to verify any kind of graph-structured data through a combination of model-intrinsic knowledge, user-supplied context, and agents capable of external knowledge retrieval.

Diffusion models have established themselves as state-of-the-art generative models across various data modalities, including images and videos, due to their ability to accurately approximate complex data distributions. Unlike traditional generative approaches such as VAEs and GANs, diffusion models employ a progressive denoising process that transforms noise into meaningful data over multiple iterative steps. This gradual approach enhances their expressiveness and generation quality. Not only that, diffusion models have also been shown to extract meaningful representations from data while learning to generate samples. Despite their success, the application of diffusion models to graph-structured data remains relatively unexplored, primarily due to the discrete nature of graphs, which necessitates discrete diffusion processes distinct from the continuous methods used in other domains. In this work, we leverage the representational capabilities of diffusion models to learn meaningful embeddings for graph data. By training a discrete diffusion model within an autoencoder framework, we enable both effective autoencoding and representation learning tailored to the unique characteristics of graph-structured data. We only need the encoder at the end to extract representations. Our approach demonstrates the potential of discrete diffusion models to be used for graph representation learning.

Tumor documentation in Germany is largely done manually, requiring reading patient records and entering data into structured databases. Large language models (LLMs) could potentially enhance this process by improving efficiency and reliability. This evaluation tests eleven different open source LLMs with sizes ranging from 1-70 billion model parameters on three basic tasks of the tumor documentation process: identifying tumor diagnoses, assigning ICD-10 codes, and extracting the date of first diagnosis. For evaluating the LLMs on these tasks, a dataset of annotated text snippets based on anonymized doctors' notes from urology was prepared. Different prompting strategies were used to investigate the effect of the number of examples in few-shot prompting and to explore the capabilities of the LLMs in general. The models Llama 3.1 8B, Mistral 7B, and Mistral NeMo 12 B performed comparably well in the tasks. Models with less extensive training data or having fewer than 7 billion parameters showed notably lower performance, while larger models did not display performance gains. Examples from a different medical domain than urology could also improve the outcome in few-shot prompting, which demonstrates the ability of LLMs to handle tasks needed for tumor documentation. Open source LLMs show a strong potential for automating tumor documentation. Models from 7-12 billion parameters could offer an optimal balance between performance and resource efficiency. With tailored fine-tuning and well-designed prompting, these models might become important tools for clinical documentation in the future. The code for the evaluation is available from https://github.com/stefan-m-lenz/UroLlmEval. We also release the dataset as a new valuable resource that addresses the shortage of authentic and easily accessible benchmarks in German-language medical NLP.

Advances in natural language processing techniques, such as named entity recognition and normalization to widely used standardized terminologies like UMLS or SNOMED-CT, along with the digitalization of electronic health records, have significantly advanced clinical text analysis. This study presents ClinLinker, a novel approach employing a two-phase pipeline for medical entity linking that leverages the potential of in-domain adapted language models for biomedical text mining: initial candidate retrieval using a SapBERT-based bi-encoder and subsequent re-ranking with a cross-encoder, trained by following a contrastive-learning strategy to be tailored to medical concepts in Spanish. This methodology, focused initially on content in Spanish, substantially outperforming multilingual language models designed for the same purpose. This is true even for complex scenarios involving heterogeneous medical terminologies and being trained on a subset of the original data. Our results, evaluated using top-k accuracy at 25 and other top-k metrics, demonstrate our approach's performance on two distinct clinical entity linking Gold Standard corpora, DisTEMIST (diseases) and MedProcNER (clinical procedures), outperforming previous benchmarks by 40 points in DisTEMIST and 43 points in MedProcNER, both normalized to SNOMED-CT codes. These findings highlight our approach's ability to address language-specific nuances and set a new benchmark in entity linking, offering a potent tool for enhancing the utility of digital medical records. The resulting system is of practical value, both for large scale automatic generation of structured data derived from clinical records, as well as for exhaustive extraction and harmonization of predefined clinical variables of interest.

Molecular property prediction has gained significant attention due to its transformative potential in multiple scientific disciplines. Conventionally, a molecule graph can be represented either as a graph-structured data or a SMILES text. Recently, the rapid development of Large Language Models (LLMs) has revolutionized the field of NLP. Although it is natural to utilize LLMs to assist in understanding molecules represented by SMILES, the exploration of how LLMs will impact molecular property prediction is still in its early stage. In this work, we advance towards this objective through two perspectives: zero/few-shot molecular classification, and using the new explanations generated by LLMs as representations of molecules. To be specific, we first prompt LLMs to do in-context molecular classification and evaluate their performance. After that, we employ LLMs to generate semantically enriched explanations for the original SMILES and then leverage that to fine-tune a small-scale LM model for multiple downstream tasks. The experimental results highlight the superiority of text explanations as molecular representations across multiple benchmark datasets, and confirm the immense potential of LLMs in molecular property prediction tasks. Codes are available at https://github.com/ChnQ/LLM4Mol.

In this paper, we explore the question of whether large language models can support cost-efficient information extraction from tables. We introduce schema-driven information extraction, a new task that transforms tabular data into structured records following a human-authored schema. To assess various LLM's capabilities on this task, we present a benchmark comprised of tables from four diverse domains: machine learning papers, chemistry literature, material science journals, and webpages. We use this collection of annotated tables to evaluate the ability of open-source and API-based language models to extract information from tables covering diverse domains and data formats. Our experiments demonstrate that surprisingly competitive performance can be achieved without requiring task-specific pipelines or labels, achieving F1 scores ranging from 74.2 to 96.1, while maintaining cost efficiency. Moreover, through detailed ablation studies and analyses, we investigate the factors contributing to model success and validate the practicality of distilling compact models to reduce API reliance.

Graph neural networks (GNNs) are one of the most popular approaches to using deep learning on graph-structured data, and they have shown state-of-the-art performances on a variety of tasks. However, according to a recent study, a careful choice of pooling functions, which are used for the aggregation and readout operations in GNNs, is crucial for enabling GNNs to extrapolate. Without proper choices of pooling functions, which varies across tasks, GNNs completely fail to generalize to out-of-distribution data, while the number of possible choices grows exponentially with the number of layers. In this paper, we present GNP, a L^p norm-like pooling function that is trainable end-to-end for any given task. Notably, GNP generalizes most of the widely-used pooling functions. We verify experimentally that simply using GNP for every aggregation and readout operation enables GNNs to extrapolate well on many node-level, graph-level, and set-related tasks; and GNP sometimes performs even better than the best-performing choices among existing pooling functions.

It is challenging for humans -- particularly those living with physical disabilities -- to control high-dimensional, dexterous robots. Prior work explores learning embedding functions that map a human's low-dimensional inputs (e.g., via a joystick) to complex, high-dimensional robot actions for assistive teleoperation; however, a central problem is that there are many more high-dimensional actions than available low-dimensional inputs. To extract the correct action and maximally assist their human controller, robots must reason over their context: for example, pressing a joystick down when interacting with a coffee cup indicates a different action than when interacting with knife. In this work, we develop assistive robots that condition their latent embeddings on visual inputs. We explore a spectrum of visual encoders and show that incorporating object detectors pretrained on small amounts of cheap, easy-to-collect structured data enables i) accurately and robustly recognizing the current context and ii) generalizing control embeddings to new objects and tasks. In user studies with a high-dimensional physical robot arm, participants leverage this approach to perform new tasks with unseen objects. Our results indicate that structured visual representations improve few-shot performance and are subjectively preferred by users.

Generalizable, transferrable, and robust representation learning on graph-structured data remains a challenge for current graph neural networks (GNNs). Unlike what has been developed for convolutional neural networks (CNNs) for image data, self-supervised learning and pre-training are less explored for GNNs. In this paper, we propose a graph contrastive learning (GraphCL) framework for learning unsupervised representations of graph data. We first design four types of graph augmentations to incorporate various priors. We then systematically study the impact of various combinations of graph augmentations on multiple datasets, in four different settings: semi-supervised, unsupervised, and transfer learning as well as adversarial attacks. The results show that, even without tuning augmentation extents nor using sophisticated GNN architectures, our GraphCL framework can produce graph representations of similar or better generalizability, transferrability, and robustness compared to state-of-the-art methods. We also investigate the impact of parameterized graph augmentation extents and patterns, and observe further performance gains in preliminary experiments. Our codes are available at https://github.com/Shen-Lab/GraphCL.

We present graph attention networks (GATs), novel neural network architectures that operate on graph-structured data, leveraging masked self-attentional layers to address the shortcomings of prior methods based on graph convolutions or their approximations. By stacking layers in which nodes are able to attend over their neighborhoods' features, we enable (implicitly) specifying different weights to different nodes in a neighborhood, without requiring any kind of costly matrix operation (such as inversion) or depending on knowing the graph structure upfront. In this way, we address several key challenges of spectral-based graph neural networks simultaneously, and make our model readily applicable to inductive as well as transductive problems. Our GAT models have achieved or matched state-of-the-art results across four established transductive and inductive graph benchmarks: the Cora, Citeseer and Pubmed citation network datasets, as well as a protein-protein interaction dataset (wherein test graphs remain unseen during training).

We introduce Zep, a novel memory layer service for AI agents that outperforms the current state-of-the-art system, MemGPT, in the Deep Memory Retrieval (DMR) benchmark. Additionally, Zep excels in more comprehensive and challenging evaluations than DMR that better reflect real-world enterprise use cases. While existing retrieval-augmented generation (RAG) frameworks for large language model (LLM)-based agents are limited to static document retrieval, enterprise applications demand dynamic knowledge integration from diverse sources including ongoing conversations and business data. Zep addresses this fundamental limitation through its core component Graphiti -- a temporally-aware knowledge graph engine that dynamically synthesizes both unstructured conversational data and structured business data while maintaining historical relationships. In the DMR benchmark, which the MemGPT team established as their primary evaluation metric, Zep demonstrates superior performance (94.8% vs 93.4%). Beyond DMR, Zep's capabilities are further validated through the more challenging LongMemEval benchmark, which better reflects enterprise use cases through complex temporal reasoning tasks. In this evaluation, Zep achieves substantial results with accuracy improvements of up to 18.5% while simultaneously reducing response latency by 90% compared to baseline implementations. These results are particularly pronounced in enterprise-critical tasks such as cross-session information synthesis and long-term context maintenance, demonstrating Zep's effectiveness for deployment in real-world applications.

Webpages have been a rich resource for language and vision-language tasks. Yet only pieces of webpages are kept: image-caption pairs, long text articles, or raw HTML, never all in one place. Webpage tasks have resultingly received little attention and structured image-text data underused. To study multimodal webpage understanding, we introduce the Wikipedia Webpage 2M (WikiWeb2M) suite; the first to retain the full set of images, text, and structure data available in a page. WikiWeb2M can be used for tasks like page description generation, section summarization, and contextual image captioning.

Graph Convolutional Networks (GCNs) have shown strong performance in learning text representations for various tasks such as text classification, due to its expressive power in modeling graph structure data (e.g., a literature citation network). Most existing GCNs are limited to deal with documents included in a pre-defined graph, i.e., it cannot be generalized to out-of-graph documents. To address this issue, we propose to transform the document graph into a word graph, to decouple data samples (i.e., documents in training and test sets) and a GCN model by using a document-independent graph. Such word-level GCN could therefore naturally inference out-of-graph documents in an inductive way. The proposed Word-level Graph (WGraph) can not only implicitly learning word presentation with commonly-used word co-occurrences in corpora, but also incorporate extra global semantic dependency derived from inter-document relationships (e.g., literature citations). An inductive Word-grounded Graph Convolutional Network (WGCN) is proposed to learn word and document representations based on WGraph in a supervised manner. Experiments on text classification with and without citation networks evidence that the proposed WGCN model outperforms existing methods in terms of effectiveness and efficiency.

While many contemporary large language models (LLMs) can process lengthy input, they still struggle to fully utilize information within the long context, known as the lost-in-the-middle challenge. We hypothesize that it stems from insufficient explicit supervision during the long-context training, which fails to emphasize that any position in a long context can hold crucial information. Based on this intuition, our study presents information-intensive (IN2) training, a purely data-driven solution to overcome lost-in-the-middle. Specifically, IN2 training leverages a synthesized long-context question-answer dataset, where the answer requires (1) fine-grained information awareness on a short segment (~128 tokens) within a synthesized long context (4K-32K tokens), and (2) the integration and reasoning of information from two or more short segments. Through applying this information-intensive training on Mistral-7B, we present FILM-7B (FILl-in-the-Middle). To thoroughly assess the ability of FILM-7B for utilizing long contexts, we design three probing tasks that encompass various context styles (document, code, and structured-data context) and information retrieval patterns (forward, backward, and bi-directional retrieval). The probing results demonstrate that FILM-7B can robustly retrieve information from different positions in its 32K context window. Beyond these probing tasks, FILM-7B significantly improves the performance on real-world long-context tasks (e.g., 23.5->26.9 F1 score on NarrativeQA), while maintaining a comparable performance on short-context tasks (e.g., 59.3->59.2 accuracy on MMLU). Github Link: https://github.com/microsoft/FILM.

Current multimodal and multitask foundation models like 4M or UnifiedIO show promising results, but in practice their out-of-the-box abilities to accept diverse inputs and perform diverse tasks are limited by the (usually rather small) number of modalities and tasks they are trained on. In this paper, we expand upon the capabilities of them by training a single model on tens of highly diverse modalities and by performing co-training on large-scale multimodal datasets and text corpora. This includes training on several semantic and geometric modalities, feature maps from recent state of the art models like DINOv2 and ImageBind, pseudo labels of specialist models like SAM and 4DHumans, and a range of new modalities that allow for novel ways to interact with the model and steer the generation, for example image metadata or color palettes. A crucial step in this process is performing discrete tokenization on various modalities, whether they are image-like, neural network feature maps, vectors, structured data like instance segmentation or human poses, or data that can be represented as text. Through this, we expand on the out-of-the-box capabilities of multimodal models and specifically show the possibility of training one model to solve at least 3x more tasks/modalities than existing ones and doing so without a loss in performance. This enables more fine-grained and controllable multimodal generation capabilities and allows us to study the distillation of models trained on diverse data and objectives into a unified model. We successfully scale the training to a three billion parameter model using tens of modalities and different datasets. The resulting models and training code are open sourced at 4m.epfl.ch.

Multimodal Retrieval-Augmented Generation (MRAG) enhances reasoning capabilities by integrating external knowledge. However, existing benchmarks primarily focus on simple image-text interactions, overlooking complex visual formats like charts that are prevalent in real-world applications. In this work, we introduce a novel task, Chart-based MRAG, to address this limitation. To semi-automatically generate high-quality evaluation samples, we propose CHARt-based document question-answering GEneration (CHARGE), a framework that produces evaluation data through structured keypoint extraction, crossmodal verification, and keypoint-based generation. By combining CHARGE with expert validation, we construct Chart-MRAG Bench, a comprehensive benchmark for chart-based MRAG evaluation, featuring 4,738 question-answering pairs across 8 domains from real-world documents. Our evaluation reveals three critical limitations in current approaches: (1) unified multimodal embedding retrieval methods struggles in chart-based scenarios, (2) even with ground-truth retrieval, state-of-the-art MLLMs achieve only 58.19% Correctness and 73.87% Coverage scores, and (3) MLLMs demonstrate consistent text-over-visual modality bias during Chart-based MRAG reasoning. The CHARGE and Chart-MRAG Bench are released at https://github.com/Nomothings/CHARGE.git.

Large Language Models (LLMs) have demonstrated unprecedented prowess across various natural language processing tasks in various application domains. Recent studies show that LLMs can be leveraged to perform lexical semantic tasks, such as Knowledge Base Completion (KBC) or Ontology Learning (OL). However, it has not effectively been verified whether their success is due to their ability to reason over unstructured or semi-structured data, or their effective learning of linguistic patterns and senses alone. This unresolved question is particularly crucial when dealing with domain-specific data, where the lexical senses and their meaning can completely differ from what a LLM has learned during its training stage. This paper investigates the following question: Do LLMs really adapt to domains and remain consistent in the extraction of structured knowledge, or do they only learn lexical senses instead of reasoning? To answer this question and, we devise a controlled experiment setup that uses WordNet to synthesize parallel corpora, with English and gibberish terms. We examine the differences in the outputs of LLMs for each corpus in two OL tasks: relation extraction and taxonomy discovery. Empirical results show that, while adapting to the gibberish corpora, off-the-shelf LLMs do not consistently reason over semantic relationships between concepts, and instead leverage senses and their frame. However, fine-tuning improves the performance of LLMs on lexical semantic tasks even when the domain-specific terms are arbitrary and unseen during pre-training, hinting at the applicability of pre-trained LLMs for OL.

The statistical analysis of large scale legal corpus can provide valuable legal insights. For such analysis one needs to (1) select a subset of the corpus using document retrieval tools, (2) structuralize text using information extraction (IE) systems, and (3) visualize the data for the statistical analysis. Each process demands either specialized tools or programming skills whereas no comprehensive unified "no-code" tools have been available. Especially for IE, if the target information is not predefined in the ontology of the IE system, one needs to build their own system. Here we provide NESTLE, a no code tool for large-scale statistical analysis of legal corpus. With NESTLE, users can search target documents, extract information, and visualize the structured data all via the chat interface with accompanying auxiliary GUI for the fine-level control. NESTLE consists of three main components: a search engine, an end-to-end IE system, and a Large Language Model (LLM) that glues the whole components together and provides the chat interface. Powered by LLM and the end-to-end IE system, NESTLE can extract any type of information that has not been predefined in the IE system opening up the possibility of unlimited customizable statistical analysis of the corpus without writing a single line of code. The use of the custom end-to-end IE system also enables faster and low-cost IE on large scale corpus. We validate our system on 15 Korean precedent IE tasks and 3 legal text classification tasks from LEXGLUE. The comprehensive experiments reveal NESTLE can achieve GPT-4 comparable performance by training the internal IE module with 4 human-labeled, and 192 LLM-labeled examples. The detailed analysis provides the insight on the trade-off between accuracy, time, and cost in building such system.

The progress in modelling time series and, more generally, sequences of structured data has recently revamped research in anomaly detection. The task stands for identifying abnormal behaviors in financial series, IT systems, aerospace measurements, and the medical domain, where anomaly detection may aid in isolating cases of depression and attend the elderly. Anomaly detection in time series is a complex task since anomalies are rare due to highly non-linear temporal correlations and since the definition of anomalous is sometimes subjective. Here we propose the novel use of Hyperbolic uncertainty for Anomaly Detection (HypAD). HypAD learns self-supervisedly to reconstruct the input signal. We adopt best practices from the state-of-the-art to encode the sequence by an LSTM, jointly learned with a decoder to reconstruct the signal, with the aid of GAN critics. Uncertainty is estimated end-to-end by means of a hyperbolic neural network. By using uncertainty, HypAD may assess whether it is certain about the input signal but it fails to reconstruct it because this is anomalous; or whether the reconstruction error does not necessarily imply anomaly, as the model is uncertain, e.g. a complex but regular input signal. The novel key idea is that a detectable anomaly is one where the model is certain but it predicts wrongly. HypAD outperforms the current state-of-the-art for univariate anomaly detection on established benchmarks based on data from NASA, Yahoo, Numenta, Amazon, and Twitter. It also yields state-of-the-art performance on a multivariate dataset of anomaly activities in elderly home residences, and it outperforms the baseline on SWaT. Overall, HypAD yields the lowest false alarms at the best performance rate, thanks to successfully identifying detectable anomalies.

With the rise of software-as-a-service and microservice architectures, RESTful APIs are now ubiquitous in mobile and web applications. A service can have tens or hundreds of API methods, making it a challenge for programmers to find the right combination of methods to solve their task. We present APIphany, a component-based synthesizer for programs that compose calls to RESTful APIs. The main innovation behind APIphany is the use of precise semantic types, both to specify user intent and to direct the search. APIphany contributes three novel mechanisms to overcome challenges in adapting component-based synthesis to the REST domain: (1) a type inference algorithm for augmenting REST specifications with semantic types; (2) an efficient synthesis technique for "wrangling" semi-structured data, which is commonly required in working with RESTful APIs; and (3) a new form of simulated execution to avoid executing APIs calls during synthesis. We evaluate APIphany on three real-world APIs and 32 tasks extracted from GitHub repositories and StackOverflow. In our experiments, APIphany found correct solutions to 29 tasks, with 23 of them reported among top ten synthesis results.

Machine learning (ML) approaches have demonstrated promising results in a wide range of healthcare applications. Data plays a crucial role in developing ML-based healthcare systems that directly affect people's lives. Many of the ethical issues surrounding the use of ML in healthcare stem from structural inequalities underlying the way we collect, use, and handle data. Developing guidelines to improve documentation practices regarding the creation, use, and maintenance of ML healthcare datasets is therefore of critical importance. In this work, we introduce Healthsheet, a contextualized adaptation of the original datasheet questionnaire ~gebru2018datasheets for health-specific applications. Through a series of semi-structured interviews, we adapt the datasheets for healthcare data documentation. As part of the Healthsheet development process and to understand the obstacles researchers face in creating datasheets, we worked with three publicly-available healthcare datasets as our case studies, each with different types of structured data: Electronic health Records (EHR), clinical trial study data, and smartphone-based performance outcome measures. Our findings from the interviewee study and case studies show 1) that datasheets should be contextualized for healthcare, 2) that despite incentives to adopt accountability practices such as datasheets, there is a lack of consistency in the broader use of these practices 3) how the ML for health community views datasheets and particularly Healthsheets as diagnostic tool to surface the limitations and strength of datasets and 4) the relative importance of different fields in the datasheet to healthcare concerns.

Systematic literature reviews and meta-analyses are essential for synthesizing research insights, but they remain time-intensive and labor-intensive due to the iterative processes of screening, evaluation, and data extraction. This paper introduces and evaluates LatteReview, a Python-based framework that leverages large language models (LLMs) and multi-agent systems to automate key elements of the systematic review process. Designed to streamline workflows while maintaining rigor, LatteReview utilizes modular agents for tasks such as title and abstract screening, relevance scoring, and structured data extraction. These agents operate within orchestrated workflows, supporting sequential and parallel review rounds, dynamic decision-making, and iterative refinement based on user feedback. LatteReview's architecture integrates LLM providers, enabling compatibility with both cloud-based and locally hosted models. The framework supports features such as Retrieval-Augmented Generation (RAG) for incorporating external context, multimodal reviews, Pydantic-based validation for structured inputs and outputs, and asynchronous programming for handling large-scale datasets. The framework is available on the GitHub repository, with detailed documentation and an installable package.

Retrieval-augmented generation (RAG) is a powerful technique that enhances downstream task execution by retrieving additional information, such as knowledge, skills, and tools from external sources. Graph, by its intrinsic "nodes connected by edges" nature, encodes massive heterogeneous and relational information, making it a golden resource for RAG in tremendous real-world applications. As a result, we have recently witnessed increasing attention on equipping RAG with Graph, i.e., GraphRAG. However, unlike conventional RAG, where the retriever, generator, and external data sources can be uniformly designed in the neural-embedding space, the uniqueness of graph-structured data, such as diverse-formatted and domain-specific relational knowledge, poses unique and significant challenges when designing GraphRAG for different domains. Given the broad applicability, the associated design challenges, and the recent surge in GraphRAG, a systematic and up-to-date survey of its key concepts and techniques is urgently desired. Following this motivation, we present a comprehensive and up-to-date survey on GraphRAG. Our survey first proposes a holistic GraphRAG framework by defining its key components, including query processor, retriever, organizer, generator, and data source. Furthermore, recognizing that graphs in different domains exhibit distinct relational patterns and require dedicated designs, we review GraphRAG techniques uniquely tailored to each domain. Finally, we discuss research challenges and brainstorm directions to inspire cross-disciplinary opportunities. Our survey repository is publicly maintained at https://github.com/Graph-RAG/GraphRAG/.

Retrieving and extracting knowledge from extensive research documents and large databases presents significant challenges for researchers, students, and professionals in today's information-rich era. Existing retrieval systems, which rely on general-purpose Large Language Models (LLMs), often fail to provide accurate responses to domain-specific inquiries. Additionally, the high cost of pretraining or fine-tuning LLMs for specific domains limits their widespread adoption. To address these limitations, we propose a novel methodology that combines the generative capabilities of LLMs with the fast and accurate retrieval capabilities of vector databases. This advanced retrieval system can efficiently handle both tabular and non-tabular data, understand natural language user queries, and retrieve relevant information without fine-tuning. The developed model, Generative Text Retrieval (GTR), is adaptable to both unstructured and structured data with minor refinement. GTR was evaluated on both manually annotated and public datasets, achieving over 90% accuracy and delivering truthful outputs in 87% of cases. Our model achieved state-of-the-art performance with a Rouge-L F1 score of 0.98 on the MSMARCO dataset. The refined model, Generative Tabular Text Retrieval (GTR-T), demonstrated its efficiency in large database querying, achieving an Execution Accuracy (EX) of 0.82 and an Exact-Set-Match (EM) accuracy of 0.60 on the Spider dataset, using an open-source LLM. These efforts leverage Generative AI and In-Context Learning to enhance human-text interaction and make advanced AI capabilities more accessible. By integrating robust retrieval systems with powerful LLMs, our approach aims to democratize access to sophisticated AI tools, improving the efficiency, accuracy, and scalability of AI-driven information retrieval and database querying.

Safe deployment of graph neural networks (GNNs) under distribution shift requires models to provide accurate confidence indicators (CI). However, while it is well-known in computer vision that CI quality diminishes under distribution shift, this behavior remains understudied for GNNs. Hence, we begin with a case study on CI calibration under controlled structural and feature distribution shifts and demonstrate that increased expressivity or model size do not always lead to improved CI performance. Consequently, we instead advocate for the use of epistemic uncertainty quantification (UQ) methods to modulate CIs. To this end, we propose G-DeltaUQ, a new single model UQ method that extends the recently proposed stochastic centering framework to support structured data and partial stochasticity. Evaluated across covariate, concept, and graph size shifts, G-DeltaUQ not only outperforms several popular UQ methods in obtaining calibrated CIs, but also outperforms alternatives when CIs are used for generalization gap prediction or OOD detection. Overall, our work not only introduces a new, flexible GNN UQ method, but also provides novel insights into GNN CIs on safety-critical tasks.

Log data have facilitated various tasks of software development and maintenance, such as testing, debugging and diagnosing. Due to the unstructured nature of logs, log parsing is typically required to transform log messages into structured data for automated log analysis. Given the abundance of log parsers that employ various techniques, evaluating these tools to comprehend their characteristics and performance becomes imperative. Loghub serves as a commonly used dataset for benchmarking log parsers, but it suffers from limited scale and representativeness, posing significant challenges for studies to comprehensively evaluate existing log parsers or develop new methods. This limitation is particularly pronounced when assessing these log parsers for production use. To address these limitations, we provide a new collection of annotated log datasets, denoted Loghub-2.0, which can better reflect the characteristics of log data in real-world software systems. Loghub-2.0 comprises 14 datasets with an average of 3.6 million log lines in each dataset. Based on Loghub-2.0, we conduct a thorough re-evaluation of 15 state-of-the-art log parsers in a more rigorous and practical setting. Particularly, we introduce a new evaluation metric to mitigate the sensitivity of existing metrics to imbalanced data distributions. We are also the first to investigate the granular performance of log parsers on logs that represent rare system events, offering in-depth details for software diagnosis. Accurately parsing such logs is essential, yet it remains a challenge. We believe this work could shed light on the evaluation and design of log parsers in practical settings, thereby facilitating their deployment in production systems.

Much of the previous work towards digital agents for graphical user interfaces (GUIs) has relied on text-based representations (derived from HTML or other structured data sources), which are not always readily available. These input representations have been often coupled with custom, task-specific action spaces. This paper focuses on creating agents that interact with the digital world using the same conceptual interface that humans commonly use -- via pixel-based screenshots and a generic action space corresponding to keyboard and mouse actions. Building upon recent progress in pixel-based pretraining, we show, for the first time, that it is possible for such agents to outperform human crowdworkers on the MiniWob++ benchmark of GUI-based instruction following tasks.

Attention-based graph neural networks (GNNs), such as graph attention networks (GATs), have become popular neural architectures for processing graph-structured data and learning node embeddings. Despite their empirical success, these models rely on labeled data and the theoretical properties of these models have yet to be fully understood. In this work, we propose a novel attention-based node embedding framework for graphs. Our framework builds upon a hierarchical kernel for multisets of subgraphs around nodes (e.g. neighborhoods) and each kernel leverages the geometry of a smooth statistical manifold to compare pairs of multisets, by "projecting" the multisets onto the manifold. By explicitly computing node embeddings with a manifold of Gaussian mixtures, our method leads to a new attention mechanism for neighborhood aggregation. We provide theoretical insights into generalizability and expressivity of our embeddings, contributing to a deeper understanding of attention-based GNNs. We propose both efficient unsupervised and supervised methods for learning the embeddings. Through experiments on several node classification benchmarks, we demonstrate that our proposed method outperforms existing attention-based graph models like GATs. Our code is available at https://github.com/BorgwardtLab/fisher_information_embedding.

It has been shown that a message passing neural networks (MPNNs), a popular family of neural networks for graph-structured data, are at most as expressive as the first-order Weisfeiler-Leman (1-WL) graph isomorphism test, which has motivated the development of more expressive architectures. In this work, we analyze if the limited expressiveness is actually a limiting factor for MPNNs and other WL-based models in standard graph datasets. Interestingly, we find that the expressiveness of WL is sufficient to identify almost all graphs in most datasets. Moreover, we find that the classification accuracy upper bounds are often close to 100\%. Furthermore, we find that simple WL-based neural networks and several MPNNs can be fitted to several datasets. In sum, we conclude that the performance of WL/MPNNs is not limited by their expressiveness in practice.

Radiology reports are one of the main forms of communication between radiologists and other clinicians and contain important information for patient care. In order to use this information for research and automated patient care programs, it is necessary to convert the raw text into structured data suitable for analysis. State-of-the-art natural language processing (NLP) domain-specific contextual word embeddings have been shown to achieve impressive accuracy for these tasks in medicine, but have yet to be utilized for section structure segmentation. In this work, we pre-trained a contextual embedding BERT model using breast radiology reports and developed a classifier that incorporated the embedding with auxiliary global textual features in order to perform section segmentation. This model achieved a 98% accuracy at segregating free text reports sentence by sentence into sections of information outlined in the Breast Imaging Reporting and Data System (BI-RADS) lexicon, a significant improvement over the Classic BERT model without auxiliary information. We then evaluated whether using section segmentation improved the downstream extraction of clinically relevant information such as modality/procedure, previous cancer, menopausal status, the purpose of the exam, breast density, and breast MRI background parenchymal enhancement. Using the BERT model pre-trained on breast radiology reports combined with section segmentation resulted in an overall accuracy of 95.9% in the field extraction tasks. This is a 17% improvement compared to an overall accuracy of 78.9% for field extraction with models using Classic BERT embeddings and not using section segmentation. Our work shows the strength of using BERT in radiology report analysis and the advantages of section segmentation in identifying key features of patient factors recorded in breast radiology reports.

The variational autoencoder (VAE) framework remains a popular option for training unsupervised generative models, especially for discrete data where generative adversarial networks (GANs) require workaround to create gradient for the generator. In our work modeling US postal addresses, we show that our discrete VAE with tree recursive architecture demonstrates limited capability of capturing field correlations within structured data, even after overcoming the challenge of posterior collapse with scheduled sampling and tuning of the KL-divergence weight beta. Worse, VAE seems to have difficulty mapping its generated samples to the latent space, as their VAE loss lags behind or even increases during the training process. Motivated by this observation, we show that augmenting training data with generated variants (augmented training) and training a VAE with multiple values of beta simultaneously (multiscale VAE) both improve the generation quality of VAE. Despite their differences in motivation and emphasis, we show that augmented training and multiscale VAE are actually connected and have similar effects on the model.

This paper introduces LongBench v2, a benchmark designed to assess the ability of LLMs to handle long-context problems requiring deep understanding and reasoning across real-world multitasks. LongBench v2 consists of 503 challenging multiple-choice questions, with contexts ranging from 8k to 2M words, across six major task categories: single-document QA, multi-document QA, long in-context learning, long-dialogue history understanding, code repository understanding, and long structured data understanding. To ensure the breadth and the practicality, we collect data from nearly 100 highly educated individuals with diverse professional backgrounds. We employ both automated and manual review processes to maintain high quality and difficulty, resulting in human experts achieving only 53.7% accuracy under a 15-minute time constraint. Our evaluation reveals that the best-performing model, when directly answers the questions, achieves only 50.1% accuracy. In contrast, the o1-preview model, which includes longer reasoning, achieves 57.7%, surpassing the human baseline by 4%. These results highlight the importance of enhanced reasoning ability and scaling inference-time compute to tackle the long-context challenges in LongBench v2. The project is available at https://longbench2.github.io.

We present MapReader, a free, open-source software library written in Python for analyzing large map collections (scanned or born-digital). This library transforms the way historians can use maps by turning extensive, homogeneous map sets into searchable primary sources. MapReader allows users with little or no computer vision expertise to i) retrieve maps via web-servers; ii) preprocess and divide them into patches; iii) annotate patches; iv) train, fine-tune, and evaluate deep neural network models; and v) create structured data about map content. We demonstrate how MapReader enables historians to interpret a collection of approx16K nineteenth-century Ordnance Survey map sheets (approx30.5M patches), foregrounding the challenge of translating visual markers into machine-readable data. We present a case study focusing on British rail infrastructure and buildings as depicted on these maps. We also show how the outputs from the MapReader pipeline can be linked to other, external datasets, which we use to evaluate as well as enrich and interpret the results. We release approx62K manually annotated patches used here for training and evaluating the models.

Large language models (LLMs) have achieved significant progress across various domains, but their increasing scale results in high computational and memory costs. Recent studies have revealed that LLMs exhibit sparsity, providing the potential to reduce model size through pruning techniques. However, existing pruning methods typically follow a prune-then-finetune paradigm. Since the pruned components still contain valuable information, their direct removal often leads to irreversible performance degradation, imposing a substantial computational burden to recover performance during finetuning. In this paper, we propose a novel paradigm that first applies regularization, then prunes, and finally finetunes. Based on this paradigm, we introduce DReSS, a simple and effective Data-driven Regularized Structured Streamlining method for LLMs. By leveraging a small amount of data to regularize the components to be pruned, DReSS explicitly transfers the important information to the remaining parts of the model in advance. Compared to direct pruning, this can reduce the information loss caused by parameter removal, thereby enhancing its language modeling capabilities. Experimental results demonstrate that DReSS significantly outperforms existing pruning methods even under extreme pruning ratios, significantly reducing latency and increasing throughput.

Even for known nonlinear dynamical systems, feedback controller synthesis is a difficult problem that often requires leveraging the particular structure of the dynamics to induce a stable closed-loop system. For general nonlinear models, including those fit to data, there may not be enough known structure to reliably synthesize a stabilizing feedback controller. In this paper, we discuss a state-dependent nonlinear tracking controller formulation based on a state-dependent Riccati equation for general nonlinear control-affine systems. This formulation depends on a nonlinear factorization of the system of vector fields defining the control-affine dynamics, which always exists under mild smoothness assumptions. We propose a method for learning this factorization from a finite set of data. On a variety of simulated nonlinear dynamical systems, we empirically demonstrate the efficacy of learned versions of this controller in stable trajectory tracking. Alongside our learning method, we evaluate recent ideas in jointly learning a controller and stabilizability certificate for known dynamical systems; we show experimentally that such methods can be frail in comparison.

Procedures are inherently hierarchical. To "make videos", one may need to "purchase a camera", which in turn may require one to "set a budget". While such hierarchical knowledge is critical for reasoning about complex procedures, most existing work has treated procedures as shallow structures without modeling the parent-child relation. In this work, we attempt to construct an open-domain hierarchical knowledge-base (KB) of procedures based on wikiHow, a website containing more than 110k instructional articles, each documenting the steps to carry out a complex procedure. To this end, we develop a simple and efficient method that links steps (e.g., "purchase a camera") in an article to other articles with similar goals (e.g., "how to choose a camera"), recursively constructing the KB. Our method significantly outperforms several strong baselines according to automatic evaluation, human judgment, and application to downstream tasks such as instructional video retrieval. A demo with partial data can be found at https://wikihow-hierarchy.github.io. The code and the data are at https://github.com/shuyanzhou/wikihow_hierarchy.

Non-coding RNA structure and function are essential to understanding various biological processes, such as cell signaling, gene expression, and post-transcriptional regulations. These are all among the core problems in the RNA field. With the rapid growth of sequencing technology, we have accumulated a massive amount of unannotated RNA sequences. On the other hand, expensive experimental observatory results in only limited numbers of annotated data and 3D structures. Hence, it is still challenging to design computational methods for predicting their structures and functions. The lack of annotated data and systematic study causes inferior performance. To resolve the issue, we propose a novel RNA foundation model (RNA-FM) to take advantage of all the 23 million non-coding RNA sequences through self-supervised learning. Within this approach, we discover that the pre-trained RNA-FM could infer sequential and evolutionary information of non-coding RNAs without using any labels. Furthermore, we demonstrate RNA-FM's effectiveness by applying it to the downstream secondary/3D structure prediction, SARS-CoV-2 genome structure and evolution prediction, protein-RNA binding preference modeling, and gene expression regulation modeling. The comprehensive experiments show that the proposed method improves the RNA structural and functional modelling results significantly and consistently. Despite only being trained with unlabelled data, RNA-FM can serve as the foundational model for the field.

As research and industry moves towards large-scale models capable of numerous downstream tasks, the complexity of understanding multi-modal datasets that give nuance to models rapidly increases. A clear and thorough understanding of a dataset's origins, development, intent, ethical considerations and evolution becomes a necessary step for the responsible and informed deployment of models, especially those in people-facing contexts and high-risk domains. However, the burden of this understanding often falls on the intelligibility, conciseness, and comprehensiveness of the documentation. It requires consistency and comparability across the documentation of all datasets involved, and as such documentation must be treated as a user-centric product in and of itself. In this paper, we propose Data Cards for fostering transparent, purposeful and human-centered documentation of datasets within the practical contexts of industry and research. Data Cards are structured summaries of essential facts about various aspects of ML datasets needed by stakeholders across a dataset's lifecycle for responsible AI development. These summaries provide explanations of processes and rationales that shape the data and consequently the models, such as upstream sources, data collection and annotation methods; training and evaluation methods, intended use; or decisions affecting model performance. We also present frameworks that ground Data Cards in real-world utility and human-centricity. Using two case studies, we report on desirable characteristics that support adoption across domains, organizational structures, and audience groups. Finally, we present lessons learned from deploying over 20 Data Cards.

We investigate compositional structures in data embeddings from pre-trained vision-language models (VLMs). Traditionally, compositionality has been associated with algebraic operations on embeddings of words from a pre-existing vocabulary. In contrast, we seek to approximate representations from an encoder as combinations of a smaller set of vectors in the embedding space. These vectors can be seen as "ideal words" for generating concepts directly within the embedding space of the model. We first present a framework for understanding compositional structures from a geometric perspective. We then explain what these compositional structures entail probabilistically in the case of VLM embeddings, providing intuitions for why they arise in practice. Finally, we empirically explore these structures in CLIP's embeddings and we evaluate their usefulness for solving different vision-language tasks such as classification, debiasing, and retrieval. Our results show that simple linear algebraic operations on embedding vectors can be used as compositional and interpretable methods for regulating the behavior of VLMs.

Tensor Networks (TN) offer a powerful framework to efficiently represent very high-dimensional objects. TN have recently shown their potential for machine learning applications and offer a unifying view of common tensor decomposition models such as Tucker, tensor train (TT) and tensor ring (TR). However, identifying the best tensor network structure from data for a given task is challenging. In this work, we leverage the TN formalism to develop a generic and efficient adaptive algorithm to jointly learn the structure and the parameters of a TN from data. Our method is based on a simple greedy approach starting from a rank one tensor and successively identifying the most promising tensor network edges for small rank increments. Our algorithm can adaptively identify TN structures with small number of parameters that effectively optimize any differentiable objective function. Experiments on tensor decomposition, tensor completion and model compression tasks demonstrate the effectiveness of the proposed algorithm. In particular, our method outperforms the state-of-the-art evolutionary topology search [Li and Sun, 2020] for tensor decomposition of images (while being orders of magnitude faster) and finds efficient tensor network structures to compress neural networks outperforming popular TT based approaches [Novikov et al., 2015].

Generative models are a class of machine learning models that aim to learn the underlying probability distribution of data. Unlike discriminative models, generative models focus on capturing the data's inherent structure, allowing them to generate new samples that resemble the original data. To fully exploit the potential of modeling probability distributions using quantum physics, a quantum-inspired generative model known as the Born machines have shown great advancements in learning classical and quantum data over matrix product state(MPS) framework. The Born machines support tractable log-likelihood, autoregressive and mask sampling, and have shown outstanding performance in various unsupervised learning tasks. However, much of the current research has been centered on improving the expressive power of MPS, predominantly embedding each token directly by a corresponding tensor index. In this study, we generalize the embedding method into trainable quantum measurement operators that can be simultaneously honed with MPS. Our study indicated that combined with trainable embedding, Born machines can exhibit better performance and learn deeper correlations from the dataset.

Machine learning frameworks such as graph neural networks typically rely on a given, fixed graph to exploit relational inductive biases and thus effectively learn from network data. However, when said graphs are (partially) unobserved, noisy, or dynamic, the problem of inferring graph structure from data becomes relevant. In this paper, we postulate a graph convolutional relationship between the observed and latent graphs, and formulate the graph learning task as a network inverse (deconvolution) problem. In lieu of eigendecomposition-based spectral methods or iterative optimization solutions, we unroll and truncate proximal gradient iterations to arrive at a parameterized neural network architecture that we call a Graph Deconvolution Network (GDN). GDNs can learn a distribution of graphs in a supervised fashion, perform link prediction or edge-weight regression tasks by adapting the loss function, and they are inherently inductive. We corroborate GDN's superior graph recovery performance and its generalization to larger graphs using synthetic data in supervised settings. Furthermore, we demonstrate the robustness and representation power of GDNs on real world neuroimaging and social network datasets.

Diagnosing and cleaning data is a crucial step for building robust machine learning systems. However, identifying problems within large-scale datasets with real-world distributions is challenging due to the presence of complex issues such as label errors, under-representation, and outliers. In this paper, we propose a unified approach for identifying the problematic data by utilizing a largely ignored source of information: a relational structure of data in the feature-embedded space. To this end, we present scalable and effective algorithms for detecting label errors and outlier data based on the relational graph structure of data. We further introduce a visualization tool that provides contextual information of a data point in the feature-embedded space, serving as an effective tool for interactively diagnosing data. We evaluate the label error and outlier/out-of-distribution (OOD) detection performances of our approach on the large-scale image, speech, and language domain tasks, including ImageNet, ESC-50, and SST2. Our approach achieves state-of-the-art detection performance on all tasks considered and demonstrates its effectiveness in debugging large-scale real-world datasets across various domains. We release codes at https://github.com/snu-mllab/Neural-Relation-Graph.

Electronic Health Records (EHRs) hold immense potential for advancing healthcare, offering rich, longitudinal data that combines structured information with valuable insights from unstructured clinical notes. However, the unstructured nature of clinical text poses significant challenges for secondary applications. Traditional methods for structuring EHR free-text data, such as rule-based systems and multi-stage pipelines, are often limited by their time-consuming configurations and inability to adapt across clinical notes from diverse healthcare settings. Few systems provide a comprehensive attribute extraction for terminologies. While giant large language models (LLMs) like GPT-4 and LLaMA 405B excel at structuring tasks, they are slow, costly, and impractical for large-scale use. To overcome these limitations, we introduce GENIE, a Generative Note Information Extraction system that leverages LLMs to streamline the structuring of unstructured clinical text into usable data with standardized format. GENIE processes entire paragraphs in a single pass, extracting entities, assertion statuses, locations, modifiers, values, and purposes with high accuracy. Its unified, end-to-end approach simplifies workflows, reduces errors, and eliminates the need for extensive manual intervention. Using a robust data preparation pipeline and fine-tuned small scale LLMs, GENIE achieves competitive performance across multiple information extraction tasks, outperforming traditional tools like cTAKES and MetaMap and can handle extra attributes to be extracted. GENIE strongly enhances real-world applicability and scalability in healthcare systems. By open-sourcing the model and test data, we aim to encourage collaboration and drive further advancements in EHR structurization.

In a rapidly evolving knowledge landscape and the increasing adoption of large language models, a need has emerged to keep these models continuously updated with current events. While existing benchmarks evaluate general factual recall, they often overlook two critical aspects: the ability of models to integrate evolving knowledge through continual learning and the significant regional disparities in their performance. To address these gaps, we introduce the Timely Events Benchmark (TiEBe), a dataset containing over 11,000 question-answer pairs focused on globally and regionally significant events. TiEBe leverages structured retrospective data from Wikipedia, enabling continuous updates to assess LLMs' knowledge of evolving global affairs and their understanding of events across different regions. Our benchmark demonstrates that LLMs exhibit substantial geographic disparities in factual recall, emphasizing the need for more balanced global knowledge representation. Furthermore, TiEBe serves as a tool for evaluating continual learning strategies, providing insights into models' ability to acquire new information without forgetting past knowledge.

Discovering causal structures from data is a challenging inference problem of fundamental importance in all areas of science. The appealing properties of neural networks have recently led to a surge of interest in differentiable neural network-based methods for learning causal structures from data. So far, differentiable causal discovery has focused on static datasets of observational or fixed interventional origin. In this work, we introduce an active intervention targeting (AIT) method which enables a quick identification of the underlying causal structure of the data-generating process. Our method significantly reduces the required number of interactions compared with random intervention targeting and is applicable for both discrete and continuous optimization formulations of learning the underlying directed acyclic graph (DAG) from data. We examine the proposed method across multiple frameworks in a wide range of settings and demonstrate superior performance on multiple benchmarks from simulated to real-world data.

Recent 3D face reconstruction methods have made remarkable advancements, yet there remain huge challenges in monocular high-quality facial reflectance reconstruction. Existing methods rely on a large amount of light-stage captured data to learn facial reflectance models. However, the lack of subject diversity poses challenges in achieving good generalization and widespread applicability. In this paper, we learn the reflectance prior in image space rather than UV space and present a framework named ID2Reflectance. Our framework can directly estimate the reflectance maps of a single image while using limited reflectance data for training. Our key insight is that reflectance data shares facial structures with RGB faces, which enables obtaining expressive facial prior from inexpensive RGB data thus reducing the dependency on reflectance data. We first learn a high-quality prior for facial reflectance. Specifically, we pretrain multi-domain facial feature codebooks and design a codebook fusion method to align the reflectance and RGB domains. Then, we propose an identity-conditioned swapping module that injects facial identity from the target image into the pre-trained autoencoder to modify the identity of the source reflectance image. Finally, we stitch multi-view swapped reflectance images to obtain renderable assets. Extensive experiments demonstrate that our method exhibits excellent generalization capability and achieves state-of-the-art facial reflectance reconstruction results for in-the-wild faces. Our project page is https://xingyuren.github.io/id2reflectance/.

We present a new text-to-SQL dataset for electronic health records (EHRs). The utterances were collected from 222 hospital staff members, including physicians, nurses, and insurance review and health records teams. To construct the QA dataset on structured EHR data, we conducted a poll at a university hospital and used the responses to create seed questions. We then manually linked these questions to two open-source EHR databases, MIMIC-III and eICU, and included various time expressions and held-out unanswerable questions in the dataset, which were also collected from the poll. Our dataset poses a unique set of challenges: the model needs to 1) generate SQL queries that reflect a wide range of needs in the hospital, including simple retrieval and complex operations such as calculating survival rate, 2) understand various time expressions to answer time-sensitive questions in healthcare, and 3) distinguish whether a given question is answerable or unanswerable. We believe our dataset, EHRSQL, can serve as a practical benchmark for developing and assessing QA models on structured EHR data and take a step further towards bridging the gap between text-to-SQL research and its real-life deployment in healthcare. EHRSQL is available at https://github.com/glee4810/EHRSQL.

A central problem in machine learning involves modeling complex data-sets using highly flexible families of probability distributions in which learning, sampling, inference, and evaluation are still analytically or computationally tractable. Here, we develop an approach that simultaneously achieves both flexibility and tractability. The essential idea, inspired by non-equilibrium statistical physics, is to systematically and slowly destroy structure in a data distribution through an iterative forward diffusion process. We then learn a reverse diffusion process that restores structure in data, yielding a highly flexible and tractable generative model of the data. This approach allows us to rapidly learn, sample from, and evaluate probabilities in deep generative models with thousands of layers or time steps, as well as to compute conditional and posterior probabilities under the learned model. We additionally release an open source reference implementation of the algorithm.

While multi-modal models have successfully integrated information from image, video, and audio modalities, integrating graph modality into large language models (LLMs) remains unexplored. This discrepancy largely stems from the inherent divergence between structured graph data and unstructured text data. Incorporating graph knowledge provides a reliable source of information, enabling potential solutions to address issues in text generation, e.g., hallucination, and lack of domain knowledge. To evaluate the integration of graph knowledge into language models, a dedicated dataset is needed. However, there is currently no benchmark dataset specifically designed for multimodal graph-language models. To address this gap, we propose GraphextQA, a question answering dataset with paired subgraphs, retrieved from Wikidata, to facilitate the evaluation and future development of graph-language models. Additionally, we introduce a baseline model called CrossGNN, which conditions answer generation on the paired graphs by cross-attending question-aware graph features at decoding. The proposed dataset is designed to evaluate graph-language models' ability to understand graphs and make use of it for answer generation. We perform experiments with language-only models and the proposed graph-language model to validate the usefulness of the paired graphs and to demonstrate the difficulty of the task.

Diffusion-based manifold learning methods have proven useful in representation learning and dimensionality reduction of modern high dimensional, high throughput, noisy datasets. Such datasets are especially present in fields like biology and physics. While it is thought that these methods preserve underlying manifold structure of data by learning a proxy for geodesic distances, no specific theoretical links have been established. Here, we establish such a link via results in Riemannian geometry explicitly connecting heat diffusion to manifold distances. In this process, we also formulate a more general heat kernel based manifold embedding method that we call heat geodesic embeddings. This novel perspective makes clearer the choices available in manifold learning and denoising. Results show that our method outperforms existing state of the art in preserving ground truth manifold distances, and preserving cluster structure in toy datasets. We also showcase our method on single cell RNA-sequencing datasets with both continuum and cluster structure, where our method enables interpolation of withheld timepoints of data. Finally, we show that parameters of our more general method can be configured to give results similar to PHATE (a state-of-the-art diffusion based manifold learning method) as well as SNE (an attraction/repulsion neighborhood based method that forms the basis of t-SNE).

Distinguishing spatial relations is a basic part of human cognition which requires fine-grained perception on cross-instance. Although benchmarks like MME, MMBench and SEED comprehensively have evaluated various capabilities which already include visual spatial reasoning(VSR). There is still a lack of sufficient quantity and quality evaluation and optimization datasets for Vision Large Language Models(VLLMs) specifically targeting visual positional reasoning. To handle this, we first diagnosed current VLLMs with the VSR dataset and proposed a unified test set. We found current VLLMs to exhibit a contradiction of over-sensitivity to language instructions and under-sensitivity to visual positional information. By expanding the original benchmark from two aspects of tunning data and model structure, we mitigated this phenomenon. To our knowledge, we expanded spatially positioned image data controllably using diffusion models for the first time and integrated original visual encoding(CLIP) with other 3 powerful visual encoders(SigLIP, SAM and DINO). After conducting combination experiments on scaling data and models, we obtained a VLLM VSR Expert(VSRE) that not only generalizes better to different instructions but also accurately distinguishes differences in visual positional information. VSRE achieved over a 27\% increase in accuracy on the VSR test set. It becomes a performant VLLM on the position reasoning of both the VSR dataset and relevant subsets of other evaluation benchmarks. We open-sourced the expanded model with data and Appendix at https://github.com/peijin360/vsre and hope it will accelerate advancements in VLLM on VSR learning.

Large Language Models (LLMs) demonstrate enhanced capabilities and reliability by reasoning more, evolving from Chain-of-Thought prompting to product-level solutions like OpenAI o1. Despite various efforts to improve LLM reasoning, high-quality long-chain reasoning data and optimized training pipelines still remain inadequately explored in vision-language tasks. In this paper, we present Insight-V, an early effort to 1) scalably produce long and robust reasoning data for complex multi-modal tasks, and 2) an effective training pipeline to enhance the reasoning capabilities of multi-modal large language models (MLLMs). Specifically, to create long and structured reasoning data without human labor, we design a two-step pipeline with a progressive strategy to generate sufficiently long and diverse reasoning paths and a multi-granularity assessment method to ensure data quality. We observe that directly supervising MLLMs with such long and complex reasoning data will not yield ideal reasoning ability. To tackle this problem, we design a multi-agent system consisting of a reasoning agent dedicated to performing long-chain reasoning and a summary agent trained to judge and summarize reasoning results. We further incorporate an iterative DPO algorithm to enhance the reasoning agent's generation stability and quality. Based on the popular LLaVA-NeXT model and our stronger base MLLM, we demonstrate significant performance gains across challenging multi-modal benchmarks requiring visual reasoning. Benefiting from our multi-agent system, Insight-V can also easily maintain or improve performance on perception-focused multi-modal tasks.

Information Extraction (IE) is a transformative process that converts unstructured text data into a structured format by employing entity and relation extraction (RE) methodologies. The identification of the relation between a pair of entities plays a crucial role within this framework. Despite the existence of various techniques for relation extraction, their efficacy heavily relies on access to labeled data and substantial computational resources. In addressing these challenges, Large Language Models (LLMs) emerge as promising solutions; however, they might return hallucinating responses due to their own training data. To overcome these limitations, Retrieved-Augmented Generation-based Relation Extraction (RAG4RE) in this work is proposed, offering a pathway to enhance the performance of relation extraction tasks. This work evaluated the effectiveness of our RAG4RE approach utilizing different LLMs. Through the utilization of established benchmarks, such as TACRED, TACREV, Re-TACRED, and SemEval RE datasets, our aim is to comprehensively evaluate the efficacy of our RAG4RE approach. In particularly, we leverage prominent LLMs including Flan T5, Llama2, and Mistral in our investigation. The results of our study demonstrate that our RAG4RE approach surpasses performance of traditional RE approaches based solely on LLMs, particularly evident in the TACRED dataset and its variations. Furthermore, our approach exhibits remarkable performance compared to previous RE methodologies across both TACRED and TACREV datasets, underscoring its efficacy and potential for advancing RE tasks in natural language processing.

Understanding causal narratives communicated in clinical notes can help make strides towards personalized healthcare. Extracted causal information from clinical notes can be combined with structured EHR data such as patients' demographics, diagnoses, and medications. This will enhance healthcare providers' ability to identify aspects of a patient's story communicated in the clinical notes and help make more informed decisions. In this work, we propose annotation guidelines, develop an annotated corpus and provide baseline scores to identify types and direction of causal relations between a pair of biomedical concepts in clinical notes; communicated implicitly or explicitly, identified either in a single sentence or across multiple sentences. We annotate a total of 2714 de-identified examples sampled from the 2018 n2c2 shared task dataset and train four different language model based architectures. Annotation based on our guidelines achieved a high inter-annotator agreement i.e. Fleiss' kappa (kappa) score of 0.72, and our model for identification of causal relations achieved a macro F1 score of 0.56 on the test data. The high inter-annotator agreement for clinical text shows the quality of our annotation guidelines while the provided baseline F1 score sets the direction for future research towards understanding narratives in clinical texts.

Symmetry learning has proven to be an effective approach for extracting the hidden structure of data, with the concept of equivariance relation playing the central role. However, most of the current studies are built on architectural theory and corresponding assumptions on the form of data. We propose Neural Fourier Transform (NFT), a general framework of learning the latent linear action of the group without assuming explicit knowledge of how the group acts on data. We present the theoretical foundations of NFT and show that the existence of a linear equivariant feature, which has been assumed ubiquitously in equivariance learning, is equivalent to the existence of a group invariant kernel on the dataspace. We also provide experimental results to demonstrate the application of NFT in typical scenarios with varying levels of knowledge about the acting group.

We present a principled approach to uncover the structure of visual data by solving a novel deep learning task coined visual permutation learning. The goal of this task is to find the permutation that recovers the structure of data from shuffled versions of it. In the case of natural images, this task boils down to recovering the original image from patches shuffled by an unknown permutation matrix. Unfortunately, permutation matrices are discrete, thereby posing difficulties for gradient-based methods. To this end, we resort to a continuous approximation of these matrices using doubly-stochastic matrices which we generate from standard CNN predictions using Sinkhorn iterations. Unrolling these iterations in a Sinkhorn network layer, we propose DeepPermNet, an end-to-end CNN model for this task. The utility of DeepPermNet is demonstrated on two challenging computer vision problems, namely, (i) relative attributes learning and (ii) self-supervised representation learning. Our results show state-of-the-art performance on the Public Figures and OSR benchmarks for (i) and on the classification and segmentation tasks on the PASCAL VOC dataset for (ii).

In recent years, exploiting the domain-specific underlying structure of data and its generative factors for representation learning has shown success in various use-case agnostic applications. However, the diversity and complexity of tabular data have made it challenging to represent these structures in a latent space through multi-dimensional vectors. We design an autoencoder-based framework for building general purpose embeddings, we assess the performance of different autoencoder architectures, and show simpler models outperform complex ones in embedding highly complex tabular data. We apply our framework to produce plug-and-play, rich, and anonymized embeddings representing AWS customers for usage in any model, saving up to 45% of development time, and observe significant improvements in downstream models. Moreover, we propose a significant improvement to the calculation of reconstruction loss for multi-layer contractive autoencoders (CAE) by calculating the Jacobian of the entire encoder leading to a 15% improvement in reconstruction quality when compared to a stacked CAE.

Deep generative diffusion models are a promising avenue for 3D de novo molecular design in materials science and drug discovery. However, their utility is still limited by suboptimal performance on large molecular structures and limited training data. To address this gap, we explore the design space of E(3)-equivariant diffusion models, focusing on previously unexplored areas. Our extensive comparative analysis evaluates the interplay between continuous and discrete state spaces. From this investigation, we present the EQGAT-diff model, which consistently outperforms established models for the QM9 and GEOM-Drugs datasets. Significantly, EQGAT-diff takes continuous atom positions, while chemical elements and bond types are categorical and uses time-dependent loss weighting, substantially increasing training convergence, the quality of generated samples, and inference time. We also showcase that including chemically motivated additional features like hybridization states in the diffusion process enhances the validity of generated molecules. To further strengthen the applicability of diffusion models to limited training data, we investigate the transferability of EQGAT-diff trained on the large PubChem3D dataset with implicit hydrogen atoms to target different data distributions. Fine-tuning EQGAT-diff for just a few iterations shows an efficient distribution shift, further improving performance throughout data sets. Finally, we test our model on the Crossdocked data set for structure-based de novo ligand generation, underlining the importance of our findings showing state-of-the-art performance on Vina docking scores.

Similarity metrics such as representational similarity analysis (RSA) and centered kernel alignment (CKA) have been used to compare layer-wise representations between neural networks. However, these metrics are confounded by the population structure of data items in the input space, leading to spuriously high similarity for even completely random neural networks and inconsistent domain relations in transfer learning. We introduce a simple and generally applicable fix to adjust for the confounder with covariate adjustment regression, which retains the intuitive invariance properties of the original similarity measures. We show that deconfounding the similarity metrics increases the resolution of detecting semantically similar neural networks. Moreover, in real-world applications, deconfounding improves the consistency of representation similarities with domain similarities in transfer learning, and increases correlation with out-of-distribution accuracy.

In generative modeling, tokenization simplifies complex data into compact, structured representations, creating a more efficient, learnable space. For high-dimensional visual data, it reduces redundancy and emphasizes key features for high-quality generation. Current visual tokenization methods rely on a traditional autoencoder framework, where the encoder compresses data into latent representations, and the decoder reconstructs the original input. In this work, we offer a new perspective by proposing denoising as decoding, shifting from single-step reconstruction to iterative refinement. Specifically, we replace the decoder with a diffusion process that iteratively refines noise to recover the original image, guided by the latents provided by the encoder. We evaluate our approach by assessing both reconstruction (rFID) and generation quality (FID), comparing it to state-of-the-art autoencoding approach. We hope this work offers new insights into integrating iterative generation and autoencoding for improved compression and generation.

We present DRESS, a large vision language model (LVLM) that innovatively exploits Natural Language feedback (NLF) from Large Language Models to enhance its alignment and interactions by addressing two key limitations in the state-of-the-art LVLMs. First, prior LVLMs generally rely only on the instruction finetuning stage to enhance alignment with human preferences. Without incorporating extra feedback, they are still prone to generate unhelpful, hallucinated, or harmful responses. Second, while the visual instruction tuning data is generally structured in a multi-turn dialogue format, the connections and dependencies among consecutive conversational turns are weak. This reduces the capacity for effective multi-turn interactions. To tackle these, we propose a novel categorization of the NLF into two key types: critique and refinement. The critique NLF identifies the strengths and weaknesses of the responses and is used to align the LVLMs with human preferences. The refinement NLF offers concrete suggestions for improvement and is adopted to improve the interaction ability of the LVLMs-- which focuses on LVLMs' ability to refine responses by incorporating feedback in multi-turn interactions. To address the non-differentiable nature of NLF, we generalize conditional reinforcement learning for training. Our experimental results demonstrate that DRESS can generate more helpful (9.76%), honest (11.52%), and harmless (21.03%) responses, and more effectively learn from feedback during multi-turn interactions compared to SOTA LVMLs.

Recent progress in language model pre-training has achieved a great success via leveraging large-scale unstructured textual data. However, it is still a challenge to apply pre-training on structured tabular data due to the absence of large-scale high-quality tabular data. In this paper, we propose TAPEX to show that table pre-training can be achieved by learning a neural SQL executor over a synthetic corpus, which is obtained by automatically synthesizing executable SQL queries and their execution outputs. TAPEX addresses the data scarcity challenge via guiding the language model to mimic a SQL executor on the diverse, large-scale and high-quality synthetic corpus. We evaluate TAPEX on four benchmark datasets. Experimental results demonstrate that TAPEX outperforms previous table pre-training approaches by a large margin and achieves new state-of-the-art results on all of them. This includes the improvements on the weakly-supervised WikiSQL denotation accuracy to 89.5% (+2.3%), the WikiTableQuestions denotation accuracy to 57.5% (+4.8%), the SQA denotation accuracy to 74.5% (+3.5%), and the TabFact accuracy to 84.2% (+3.2%). To our knowledge, this is the first work to exploit table pre-training via synthetic executable programs and to achieve new state-of-the-art results on various downstream tasks. Our code can be found at https://github.com/microsoft/Table-Pretraining.

Machine learning (ML) has become crucial in modern life, with growing interest from researchers and the public. Despite its potential, a significant entry barrier prevents widespread adoption, making it challenging for non-experts to understand and implement ML techniques. The increasing desire to leverage ML is counterbalanced by its technical complexity, creating a gap between potential and practical application. This work introduces asanAI, an offline-first, open-source, no-code machine learning toolkit designed for users of all skill levels. It allows individuals to design, debug, train, and test ML models directly in a web browser, eliminating the need for software installations and coding. The toolkit runs on any device with a modern web browser, including smartphones, and ensures user privacy through local computations while utilizing WebGL for enhanced GPU performance. Users can quickly experiment with neural networks and train custom models using various data sources, supported by intuitive visualizations of network structures and data flows. asanAI simplifies the teaching of ML concepts in educational settings and is released under an open-source MIT license, encouraging modifications. It also supports exporting models in industry-ready formats, empowering a diverse range of users to effectively learn and apply machine learning in their projects. The proposed toolkit is successfully utilized by researchers of ScaDS.AI to swiftly draft and test machine learning ideas, by trainers to effectively educate enthusiasts, and by teachers to introduce contemporary ML topics in classrooms with minimal effort and high clarity.