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Mar 11

Image2Struct: Benchmarking Structure Extraction for Vision-Language Models

We introduce Image2Struct, a benchmark to evaluate vision-language models (VLMs) on extracting structure from images. Our benchmark 1) captures real-world use cases, 2) is fully automatic and does not require human judgment, and 3) is based on a renewable stream of fresh data. In Image2Struct, VLMs are prompted to generate the underlying structure (e.g., LaTeX code or HTML) from an input image (e.g., webpage screenshot). The structure is then rendered to produce an output image (e.g., rendered webpage), which is compared against the input image to produce a similarity score. This round-trip evaluation allows us to quantitatively evaluate VLMs on tasks with multiple valid structures. We create a pipeline that downloads fresh data from active online communities upon execution and evaluates the VLMs without human intervention. We introduce three domains (Webpages, LaTeX, and Musical Scores) and use five image metrics (pixel similarity, cosine similarity between the Inception vectors, learned perceptual image patch similarity, structural similarity index measure, and earth mover similarity) that allow efficient and automatic comparison between pairs of images. We evaluate Image2Struct on 14 prominent VLMs and find that scores vary widely, indicating that Image2Struct can differentiate between the performances of different VLMs. Additionally, the best score varies considerably across domains (e.g., 0.402 on sheet music vs. 0.830 on LaTeX equations), indicating that Image2Struct contains tasks of varying difficulty. For transparency, we release the full results at https://crfm.stanford.edu/helm/image2struct/v1.0.1/.

TabSim: A Siamese Neural Network for Accurate Estimation of Table Similarity

Tables are a popular and efficient means of presenting structured information. They are used extensively in various kinds of documents including web pages. Tables display information as a two-dimensional matrix, the semantics of which is conveyed by a mixture of structure (rows, columns), headers, caption, and content. Recent research has started to consider tables as first class objects, not just as an addendum to texts, yielding interesting results for problems like table matching, table completion, or value imputation. All of these problems inherently rely on an accurate measure for the semantic similarity of two tables. We present TabSim, a novel method to compute table similarity scores using deep neural networks. Conceptually, TabSim represents a table as a learned concatenation of embeddings of its caption, its content, and its structure. Given two tables in this representation, a Siamese neural network is trained to compute a score correlating with the tables' semantic similarity. To train and evaluate our method, we created a gold standard corpus consisting of 1500 table pairs extracted from biomedical articles and manually scored regarding their degree of similarity, and adopted two other corpora originally developed for a different yet similar task. Our evaluation shows that TabSim outperforms other table similarity measures on average by app. 7% pp F1-score in a binary similarity classification setting and by app. 1.5% pp in a ranking scenario.

Attention-based Dynamic Subspace Learners for Medical Image Analysis

Learning similarity is a key aspect in medical image analysis, particularly in recommendation systems or in uncovering the interpretation of anatomical data in images. Most existing methods learn such similarities in the embedding space over image sets using a single metric learner. Images, however, have a variety of object attributes such as color, shape, or artifacts. Encoding such attributes using a single metric learner is inadequate and may fail to generalize. Instead, multiple learners could focus on separate aspects of these attributes in subspaces of an overarching embedding. This, however, implies the number of learners to be found empirically for each new dataset. This work, Dynamic Subspace Learners, proposes to dynamically exploit multiple learners by removing the need of knowing apriori the number of learners and aggregating new subspace learners during training. Furthermore, the visual interpretability of such subspace learning is enforced by integrating an attention module into our method. This integrated attention mechanism provides a visual insight of discriminative image features that contribute to the clustering of image sets and a visual explanation of the embedding features. The benefits of our attention-based dynamic subspace learners are evaluated in the application of image clustering, image retrieval, and weakly supervised segmentation. Our method achieves competitive results with the performances of multiple learners baselines and significantly outperforms the classification network in terms of clustering and retrieval scores on three different public benchmark datasets. Moreover, our attention maps offer a proxy-labels, which improves the segmentation accuracy up to 15% in Dice scores when compared to state-of-the-art interpretation techniques.

Domain and Function: A Dual-Space Model of Semantic Relations and Compositions

Given appropriate representations of the semantic relations between carpenter and wood and between mason and stone (for example, vectors in a vector space model), a suitable algorithm should be able to recognize that these relations are highly similar (carpenter is to wood as mason is to stone; the relations are analogous). Likewise, with representations of dog, house, and kennel, an algorithm should be able to recognize that the semantic composition of dog and house, dog house, is highly similar to kennel (dog house and kennel are synonymous). It seems that these two tasks, recognizing relations and compositions, are closely connected. However, up to now, the best models for relations are significantly different from the best models for compositions. In this paper, we introduce a dual-space model that unifies these two tasks. This model matches the performance of the best previous models for relations and compositions. The dual-space model consists of a space for measuring domain similarity and a space for measuring function similarity. Carpenter and wood share the same domain, the domain of carpentry. Mason and stone share the same domain, the domain of masonry. Carpenter and mason share the same function, the function of artisans. Wood and stone share the same function, the function of materials. In the composition dog house, kennel has some domain overlap with both dog and house (the domains of pets and buildings). The function of kennel is similar to the function of house (the function of shelters). By combining domain and function similarities in various ways, we can model relations, compositions, and other aspects of semantics.

Adaptive Multi-head Contrastive Learning

In contrastive learning, two views of an original image, generated by different augmentations, are considered a positive pair, and their similarity is required to be high. Similarly, two views of distinct images form a negative pair, with encouraged low similarity. Typically, a single similarity measure, provided by a lone projection head, evaluates positive and negative sample pairs. However, due to diverse augmentation strategies and varying intra-sample similarity, views from the same image may not always be similar. Additionally, owing to inter-sample similarity, views from different images may be more akin than those from the same image. Consequently, enforcing high similarity for positive pairs and low similarity for negative pairs may be unattainable, and in some cases, such enforcement could detrimentally impact performance. To address this challenge, we propose using multiple projection heads, each producing a distinct set of features. Our pre-training loss function emerges from a solution to the maximum likelihood estimation over head-wise posterior distributions of positive samples given observations. This loss incorporates the similarity measure over positive and negative pairs, each re-weighted by an individual adaptive temperature, regulated to prevent ill solutions. Our approach, Adaptive Multi-Head Contrastive Learning (AMCL), can be applied to and experimentally enhances several popular contrastive learning methods such as SimCLR, MoCo, and Barlow Twins. The improvement remains consistent across various backbones and linear probing epochs, and becomes more significant when employing multiple augmentation methods.

mPLUG-DocOwl 1.5: Unified Structure Learning for OCR-free Document Understanding

Structure information is critical for understanding the semantics of text-rich images, such as documents, tables, and charts. Existing Multimodal Large Language Models (MLLMs) for Visual Document Understanding are equipped with text recognition ability but lack general structure understanding abilities for text-rich document images. In this work, we emphasize the importance of structure information in Visual Document Understanding and propose the Unified Structure Learning to boost the performance of MLLMs. Our Unified Structure Learning comprises structure-aware parsing tasks and multi-grained text localization tasks across 5 domains: document, webpage, table, chart, and natural image. To better encode structure information, we design a simple and effective vision-to-text module H-Reducer, which can not only maintain the layout information but also reduce the length of visual features by merging horizontal adjacent patches through convolution, enabling the LLM to understand high-resolution images more efficiently. Furthermore, by constructing structure-aware text sequences and multi-grained pairs of texts and bounding boxes for publicly available text-rich images, we build a comprehensive training set DocStruct4M to support structure learning. Finally, we construct a small but high-quality reasoning tuning dataset DocReason25K to trigger the detailed explanation ability in the document domain. Our model DocOwl 1.5 achieves state-of-the-art performance on 10 visual document understanding benchmarks, improving the SOTA performance of MLLMs with a 7B LLM by more than 10 points in 5/10 benchmarks. Our codes, models, and datasets are publicly available at https://github.com/X-PLUG/mPLUG-DocOwl/tree/main/DocOwl1.5.

Unified Vision-Language Representation Modeling for E-Commerce Same-Style Products Retrieval

Same-style products retrieval plays an important role in e-commerce platforms, aiming to identify the same products which may have different text descriptions or images. It can be used for similar products retrieval from different suppliers or duplicate products detection of one supplier. Common methods use the image as the detected object, but they only consider the visual features and overlook the attribute information contained in the textual descriptions, and perform weakly for products in image less important industries like machinery, hardware tools and electronic component, even if an additional text matching module is added. In this paper, we propose a unified vision-language modeling method for e-commerce same-style products retrieval, which is designed to represent one product with its textual descriptions and visual contents. It contains one sampling skill to collect positive pairs from user click log with category and relevance constrained, and a novel contrastive loss unit to model the image, text, and image+text representations into one joint embedding space. It is capable of cross-modal product-to-product retrieval, as well as style transfer and user-interactive search. Offline evaluations on annotated data demonstrate its superior retrieval performance, and online testings show it can attract more clicks and conversions. Moreover, this model has already been deployed online for similar products retrieval in alibaba.com, the largest B2B e-commerce platform in the world.

ATLANTIC: Structure-Aware Retrieval-Augmented Language Model for Interdisciplinary Science

Large language models record impressive performance on many natural language processing tasks. However, their knowledge capacity is limited to the pretraining corpus. Retrieval augmentation offers an effective solution by retrieving context from external knowledge sources to complement the language model. However, existing retrieval augmentation techniques ignore the structural relationships between these documents. Furthermore, retrieval models are not explored much in scientific tasks, especially in regard to the faithfulness of retrieved documents. In this paper, we propose a novel structure-aware retrieval augmented language model that accommodates document structure during retrieval augmentation. We create a heterogeneous document graph capturing multiple types of relationships (e.g., citation, co-authorship, etc.) that connect documents from more than 15 scientific disciplines (e.g., Physics, Medicine, Chemistry, etc.). We train a graph neural network on the curated document graph to act as a structural encoder for the corresponding passages retrieved during the model pretraining. Particularly, along with text embeddings of the retrieved passages, we obtain structural embeddings of the documents (passages) and fuse them together before feeding them to the language model. We evaluate our model extensively on various scientific benchmarks that include science question-answering and scientific document classification tasks. Experimental results demonstrate that structure-aware retrieval improves retrieving more coherent, faithful and contextually relevant passages, while showing a comparable performance in the overall accuracy.

The Topology and Geometry of Neural Representations

A central question for neuroscience is how to characterize brain representations of perceptual and cognitive content. An ideal characterization should distinguish different functional regions with robustness to noise and idiosyncrasies of individual brains that do not correspond to computational differences. Previous studies have characterized brain representations by their representational geometry, which is defined by the representational dissimilarity matrix (RDM), a summary statistic that abstracts from the roles of individual neurons (or responses channels) and characterizes the discriminability of stimuli. Here we explore a further step of abstraction: from the geometry to the topology of brain representations. We propose topological representational similarity analysis (tRSA), an extension of representational similarity analysis (RSA) that uses a family of geo-topological summary statistics that generalizes the RDM to characterize the topology while de-emphasizing the geometry. We evaluate this new family of statistics in terms of the sensitivity and specificity for model selection using both simulations and functional MRI (fMRI) data. In the simulations, the ground truth is a data-generating layer representation in a neural network model and the models are the same and other layers in different model instances (trained from different random seeds). In fMRI, the ground truth is a visual area and the models are the same and other areas measured in different subjects. Results show that topology-sensitive characterizations of population codes are robust to noise and interindividual variability and maintain excellent sensitivity to the unique representational signatures of different neural network layers and brain regions.

Generating Drug Repurposing Hypotheses through the Combination of Disease-Specific Hypergraphs

The drug development pipeline for a new compound can last 10-20 years and cost over 10 billion. Drug repurposing offers a more time- and cost-effective alternative. Computational approaches based on biomedical knowledge graph representations have recently yielded new drug repurposing hypotheses. In this study, we present a novel, disease-specific hypergraph representation learning technique to derive contextual embeddings of biological pathways of various lengths but that all start at any given drug and all end at the disease of interest. Further, we extend this method to multi-disease hypergraphs. To determine the repurposing potential of each of the 1,522 drugs, we derive drug-specific distributions of cosine similarity values and ultimately consider the median for ranking. Cosine similarity values are computed between (1) all biological pathways starting at the considered drug and ending at the disease of interest and (2) all biological pathways starting at drugs currently prescribed against that disease and ending at the disease of interest. We illustrate our approach with Alzheimer's disease (AD) and two of its risk factors: hypertension (HTN) and type 2 diabetes (T2D). We compare each drug's rank across four hypergraph settings (single- or multi-disease): AD only, AD + HTN, AD + T2D, and AD + HTN + T2D. Notably, our framework led to the identification of two promising drugs whose repurposing potential was significantly higher in hypergraphs combining two diseases: dapagliflozin (antidiabetic; moved up, from top 32% to top 7%, across all considered drugs) and debrisoquine (antihypertensive; moved up, from top 76% to top 23%). Our approach serves as a hypothesis generation tool, to be paired with a validation pipeline relying on laboratory experiments and semi-automated parsing of the biomedical literature.

Simplicial Closure and higher-order link prediction

Networks provide a powerful formalism for modeling complex systems by using a model of pairwise interactions. But much of the structure within these systems involves interactions that take place among more than two nodes at once; for example, communication within a group rather than person-to person, collaboration among a team rather than a pair of coauthors, or biological interaction between a set of molecules rather than just two. Such higher-order interactions are ubiquitous, but their empirical study has received limited attention, and little is known about possible organizational principles of such structures. Here we study the temporal evolution of 19 datasets with explicit accounting for higher-order interactions. We show that there is a rich variety of structure in our datasets but datasets from the same system types have consistent patterns of higher-order structure. Furthermore, we find that tie strength and edge density are competing positive indicators of higher-order organization, and these trends are consistent across interactions involving differing numbers of nodes. To systematically further the study of theories for such higher-order structures, we propose higher-order link prediction as a benchmark problem to assess models and algorithms that predict higher-order structure. We find a fundamental differences from traditional pairwise link prediction, with a greater role for local rather than long-range information in predicting the appearance of new interactions.

Efficient and robust approximate nearest neighbor search using Hierarchical Navigable Small World graphs

We present a new approach for the approximate K-nearest neighbor search based on navigable small world graphs with controllable hierarchy (Hierarchical NSW, HNSW). The proposed solution is fully graph-based, without any need for additional search structures, which are typically used at the coarse search stage of the most proximity graph techniques. Hierarchical NSW incrementally builds a multi-layer structure consisting from hierarchical set of proximity graphs (layers) for nested subsets of the stored elements. The maximum layer in which an element is present is selected randomly with an exponentially decaying probability distribution. This allows producing graphs similar to the previously studied Navigable Small World (NSW) structures while additionally having the links separated by their characteristic distance scales. Starting search from the upper layer together with utilizing the scale separation boosts the performance compared to NSW and allows a logarithmic complexity scaling. Additional employment of a heuristic for selecting proximity graph neighbors significantly increases performance at high recall and in case of highly clustered data. Performance evaluation has demonstrated that the proposed general metric space search index is able to strongly outperform previous opensource state-of-the-art vector-only approaches. Similarity of the algorithm to the skip list structure allows straightforward balanced distributed implementation.

Towards Unified Benchmark and Models for Multi-Modal Perceptual Metrics

Human perception of similarity across uni- and multimodal inputs is highly complex, making it challenging to develop automated metrics that accurately mimic it. General purpose vision-language models, such as CLIP and large multi-modal models (LMMs), can be applied as zero-shot perceptual metrics, and several recent works have developed models specialized in narrow perceptual tasks. However, the extent to which existing perceptual metrics align with human perception remains unclear. To investigate this question, we introduce UniSim-Bench, a benchmark encompassing 7 multi-modal perceptual similarity tasks, with a total of 25 datasets. Our evaluation reveals that while general-purpose models perform reasonably well on average, they often lag behind specialized models on individual tasks. Conversely, metrics fine-tuned for specific tasks fail to generalize well to unseen, though related, tasks. As a first step towards a unified multi-task perceptual similarity metric, we fine-tune both encoder-based and generative vision-language models on a subset of the UniSim-Bench tasks. This approach yields the highest average performance, and in some cases, even surpasses taskspecific models. Nevertheless, these models still struggle with generalization to unseen tasks, highlighting the ongoing challenge of learning a robust, unified perceptual similarity metric capable of capturing the human notion of similarity. The code and models are available at https://github.com/SaraGhazanfari/UniSim.

Going Beyond Neural Network Feature Similarity: The Network Feature Complexity and Its Interpretation Using Category Theory

The behavior of neural networks still remains opaque, and a recently widely noted phenomenon is that networks often achieve similar performance when initialized with different random parameters. This phenomenon has attracted significant attention in measuring the similarity between features learned by distinct networks. However, feature similarity could be vague in describing the same feature since equivalent features hardly exist. In this paper, we expand the concept of equivalent feature and provide the definition of what we call functionally equivalent features. These features produce equivalent output under certain transformations. Using this definition, we aim to derive a more intrinsic metric for the so-called feature complexity regarding the redundancy of features learned by a neural network at each layer. We offer a formal interpretation of our approach through the lens of category theory, a well-developed area in mathematics. To quantify the feature complexity, we further propose an efficient algorithm named Iterative Feature Merging. Our experimental results validate our ideas and theories from various perspectives. We empirically demonstrate that the functionally equivalence widely exists among different features learned by the same neural network and we could reduce the number of parameters of the network without affecting the performance.The IFM shows great potential as a data-agnostic model prune method. We have also drawn several interesting empirical findings regarding the defined feature complexity.

Scalable Diffusion for Materials Generation

Generative models trained on internet-scale data are capable of generating novel and realistic texts, images, and videos. A natural next question is whether these models can advance science, for example by generating novel stable materials. Traditionally, models with explicit structures (e.g., graphs) have been used in modeling structural relationships in scientific data (e.g., atoms and bonds in crystals), but generating structures can be difficult to scale to large and complex systems. Another challenge in generating materials is the mismatch between standard generative modeling metrics and downstream applications. For instance, common metrics such as the reconstruction error do not correlate well with the downstream goal of discovering stable materials. In this work, we tackle the scalability challenge by developing a unified crystal representation that can represent any crystal structure (UniMat), followed by training a diffusion probabilistic model on these UniMat representations. Our empirical results suggest that despite the lack of explicit structure modeling, UniMat can generate high fidelity crystal structures from larger and more complex chemical systems, outperforming previous graph-based approaches under various generative modeling metrics. To better connect the generation quality of materials to downstream applications, such as discovering novel stable materials, we propose additional metrics for evaluating generative models of materials, including per-composition formation energy and stability with respect to convex hulls through decomposition energy from Density Function Theory (DFT). Lastly, we show that conditional generation with UniMat can scale to previously established crystal datasets with up to millions of crystals structures, outperforming random structure search (the current leading method for structure discovery) in discovering new stable materials.

Self-similarity Driven Scale-invariant Learning for Weakly Supervised Person Search

Weakly supervised person search aims to jointly detect and match persons with only bounding box annotations. Existing approaches typically focus on improving the features by exploring relations of persons. However, scale variation problem is a more severe obstacle and under-studied that a person often owns images with different scales (resolutions). On the one hand, small-scale images contain less information of a person, thus affecting the accuracy of the generated pseudo labels. On the other hand, the similarity of cross-scale images is often smaller than that of images with the same scale for a person, which will increase the difficulty of matching. In this paper, we address this problem by proposing a novel one-step framework, named Self-similarity driven Scale-invariant Learning (SSL). Scale invariance can be explored based on the self-similarity prior that it shows the same statistical properties of an image at different scales. To this end, we introduce a Multi-scale Exemplar Branch to guide the network in concentrating on the foreground and learning scale-invariant features by hard exemplars mining. To enhance the discriminative power of the features in an unsupervised manner, we introduce a dynamic multi-label prediction which progressively seeks true labels for training. It is adaptable to different types of unlabeled data and serves as a compensation for clustering based strategy. Experiments on PRW and CUHK-SYSU databases demonstrate the effectiveness of our method.

RDesign: Hierarchical Data-efficient Representation Learning for Tertiary Structure-based RNA Design

While artificial intelligence has made remarkable strides in revealing the relationship between biological macromolecules' primary sequence and tertiary structure, designing RNA sequences based on specified tertiary structures remains challenging. Though existing approaches in protein design have thoroughly explored structure-to-sequence dependencies in proteins, RNA design still confronts difficulties due to structural complexity and data scarcity. Moreover, direct transplantation of protein design methodologies into RNA design fails to achieve satisfactory outcomes although sharing similar structural components. In this study, we aim to systematically construct a data-driven RNA design pipeline. We crafted a large, well-curated benchmark dataset and designed a comprehensive structural modeling approach to represent the complex RNA tertiary structure. More importantly, we proposed a hierarchical data-efficient representation learning framework that learns structural representations through contrastive learning at both cluster-level and sample-level to fully leverage the limited data. By constraining data representations within a limited hyperspherical space, the intrinsic relationships between data points could be explicitly imposed. Moreover, we incorporated extracted secondary structures with base pairs as prior knowledge to facilitate the RNA design process. Extensive experiments demonstrate the effectiveness of our proposed method, providing a reliable baseline for future RNA design tasks. The source code and benchmark dataset are available at https://github.com/A4Bio/RDesign.

Rethinking Symbolic Regression Datasets and Benchmarks for Scientific Discovery

This paper revisits datasets and evaluation criteria for Symbolic Regression, a task of expressing given data using mathematical equations, specifically focused on its potential for scientific discovery. Focused on a set of formulas used in the existing datasets based on Feynman Lectures on Physics, we recreate 120 datasets to discuss the performance of symbolic regression for scientific discovery (SRSD). For each of the 120 SRSD datasets, we carefully review the properties of the formula and its variables to design reasonably realistic sampling range of values so that our new SRSD datasets can be used for evaluating the potential of SRSD such as whether or not an SR method can (re)discover physical laws from such datasets. As an evaluation metric, we also propose to use normalized edit distances between a predicted equation and the ground-truth equation trees. While existing metrics are either binary or errors between the target values and an SR model's predicted values for a given input, normalized edit distances evaluate a sort of similarity between the ground-truth and predicted equation trees. We have conducted experiments on our new SRSD datasets using five state-of-the-art SR methods in SRBench and a simple baseline based on a recent Transformer architecture. The results show that we provide a more realistic performance evaluation and open up a new machine learning-based approach for scientific discovery. Our datasets and code repository are publicly available.

Fast and Accurate Network Embeddings via Very Sparse Random Projection

We present FastRP, a scalable and performant algorithm for learning distributed node representations in a graph. FastRP is over 4,000 times faster than state-of-the-art methods such as DeepWalk and node2vec, while achieving comparable or even better performance as evaluated on several real-world networks on various downstream tasks. We observe that most network embedding methods consist of two components: construct a node similarity matrix and then apply dimension reduction techniques to this matrix. We show that the success of these methods should be attributed to the proper construction of this similarity matrix, rather than the dimension reduction method employed. FastRP is proposed as a scalable algorithm for network embeddings. Two key features of FastRP are: 1) it explicitly constructs a node similarity matrix that captures transitive relationships in a graph and normalizes matrix entries based on node degrees; 2) it utilizes very sparse random projection, which is a scalable optimization-free method for dimension reduction. An extra benefit from combining these two design choices is that it allows the iterative computation of node embeddings so that the similarity matrix need not be explicitly constructed, which further speeds up FastRP. FastRP is also advantageous for its ease of implementation, parallelization and hyperparameter tuning. The source code is available at https://github.com/GTmac/FastRP.

GeneCIS: A Benchmark for General Conditional Image Similarity

We argue that there are many notions of 'similarity' and that models, like humans, should be able to adapt to these dynamically. This contrasts with most representation learning methods, supervised or self-supervised, which learn a fixed embedding function and hence implicitly assume a single notion of similarity. For instance, models trained on ImageNet are biased towards object categories, while a user might prefer the model to focus on colors, textures or specific elements in the scene. In this paper, we propose the GeneCIS ('genesis') benchmark, which measures models' ability to adapt to a range of similarity conditions. Extending prior work, our benchmark is designed for zero-shot evaluation only, and hence considers an open-set of similarity conditions. We find that baselines from powerful CLIP models struggle on GeneCIS and that performance on the benchmark is only weakly correlated with ImageNet accuracy, suggesting that simply scaling existing methods is not fruitful. We further propose a simple, scalable solution based on automatically mining information from existing image-caption datasets. We find our method offers a substantial boost over the baselines on GeneCIS, and further improves zero-shot performance on related image retrieval benchmarks. In fact, though evaluated zero-shot, our model surpasses state-of-the-art supervised models on MIT-States. Project page at https://sgvaze.github.io/genecis/.

Signal-to-Noise Ratio: A Robust Distance Metric for Deep Metric Learning

Deep metric learning, which learns discriminative features to process image clustering and retrieval tasks, has attracted extensive attention in recent years. A number of deep metric learning methods, which ensure that similar examples are mapped close to each other and dissimilar examples are mapped farther apart, have been proposed to construct effective structures for loss functions and have shown promising results. In this paper, different from the approaches on learning the loss structures, we propose a robust SNR distance metric based on Signal-to-Noise Ratio (SNR) for measuring the similarity of image pairs for deep metric learning. By exploring the properties of our SNR distance metric from the view of geometry space and statistical theory, we analyze the properties of our metric and show that it can preserve the semantic similarity between image pairs, which well justify its suitability for deep metric learning. Compared with Euclidean distance metric, our SNR distance metric can further jointly reduce the intra-class distances and enlarge the inter-class distances for learned features. Leveraging our SNR distance metric, we propose Deep SNR-based Metric Learning (DSML) to generate discriminative feature embeddings. By extensive experiments on three widely adopted benchmarks, including CARS196, CUB200-2011 and CIFAR10, our DSML has shown its superiority over other state-of-the-art methods. Additionally, we extend our SNR distance metric to deep hashing learning, and conduct experiments on two benchmarks, including CIFAR10 and NUS-WIDE, to demonstrate the effectiveness and generality of our SNR distance metric.

Extending Bootstrap AMG for Clustering of Attributed Graphs

In this paper we propose a new approach to detect clusters in undirected graphs with attributed vertices. We incorporate structural and attribute similarities between the vertices in an augmented graph by creating additional vertices and edges as proposed in [1, 2]. The augmented graph is then embedded in a Euclidean space associated to its Laplacian and we cluster vertices via a modified K-means algorithm, using a new vector-valued distance in the embedding space. Main novelty of our method, which can be classified as an early fusion method, i.e., a method in which additional information on vertices are fused to the structure information before applying clustering, is the interpretation of attributes as new realizations of graph vertices, which can be dealt with as coordinate vectors in a related Euclidean space. This allows us to extend a scalable generalized spectral clustering procedure which substitutes graph Laplacian eigenvectors with some vectors, named algebraically smooth vectors, obtained by a linear-time complexity Algebraic MultiGrid (AMG) method. We discuss the performance of our proposed clustering method by comparison with recent literature approaches and public available results. Extensive experiments on different types of synthetic datasets and real-world attributed graphs show that our new algorithm, embedding attributes information in the clustering, outperforms structure-only-based methods, when the attributed network has an ambiguous structure. Furthermore, our new method largely outperforms the method which originally proposed the graph augmentation, showing that our embedding strategy and vector-valued distance are very effective in taking advantages from the augmented-graph representation.

Linking Representations with Multimodal Contrastive Learning

Many applications require grouping instances contained in diverse document datasets into classes. Most widely used methods do not employ deep learning and do not exploit the inherently multimodal nature of documents. Notably, record linkage is typically conceptualized as a string-matching problem. This study develops CLIPPINGS, (Contrastively Linking Pooled Pre-trained Embeddings), a multimodal framework for record linkage. CLIPPINGS employs end-to-end training of symmetric vision and language bi-encoders, aligned through contrastive language-image pre-training, to learn a metric space where the pooled image-text representation for a given instance is close to representations in the same class and distant from representations in different classes. At inference time, instances can be linked by retrieving their nearest neighbor from an offline exemplar embedding index or by clustering their representations. The study examines two challenging applications: constructing comprehensive supply chains for mid-20th century Japan through linking firm level financial records - with each firm name represented by its crop in the document image and the corresponding OCR - and detecting which image-caption pairs in a massive corpus of historical U.S. newspapers came from the same underlying photo wire source. CLIPPINGS outperforms widely used string matching methods by a wide margin and also outperforms unimodal methods. Moreover, a purely self-supervised model trained on only image-OCR pairs also outperforms popular string-matching methods without requiring any labels.

MagicLens: Self-Supervised Image Retrieval with Open-Ended Instructions

Image retrieval, i.e., finding desired images given a reference image, inherently encompasses rich, multi-faceted search intents that are difficult to capture solely using image-based measures. Recent work leverages text instructions to allow users to more freely express their search intents. However, existing work primarily focuses on image pairs that are visually similar and/or can be characterized by a small set of pre-defined relations. The core thesis of this paper is that text instructions can enable retrieving images with richer relations beyond visual similarity. To show this, we introduce MagicLens, a series of self-supervised image retrieval models that support open-ended instructions. MagicLens is built on a key novel insight: image pairs that naturally occur on the same web pages contain a wide range of implicit relations (e.g., inside view of), and we can bring those implicit relations explicit by synthesizing instructions via large multimodal models (LMMs) and large language models (LLMs). Trained on 36.7M (query image, instruction, target image) triplets with rich semantic relations mined from the web, MagicLens achieves comparable or better results on eight benchmarks of various image retrieval tasks than prior state-of-the-art (SOTA) methods. Remarkably, it outperforms previous SOTA but with a 50X smaller model size on multiple benchmarks. Additional human analyses on a 1.4M-image unseen corpus further demonstrate the diversity of search intents supported by MagicLens.

Multimodal Molecular Pretraining via Modality Blending

Self-supervised learning has recently gained growing interest in molecular modeling for scientific tasks such as AI-assisted drug discovery. Current studies consider leveraging both 2D and 3D molecular structures for representation learning. However, relying on straightforward alignment strategies that treat each modality separately, these methods fail to exploit the intrinsic correlation between 2D and 3D representations that reflect the underlying structural characteristics of molecules, and only perform coarse-grained molecule-level alignment. To derive fine-grained alignment and promote structural molecule understanding, we introduce an atomic-relation level "blend-then-predict" self-supervised learning approach, MoleBLEND, which first blends atom relations represented by different modalities into one unified relation matrix for joint encoding, then recovers modality-specific information for 2D and 3D structures individually. By treating atom relationships as anchors, MoleBLEND organically aligns and integrates visually dissimilar 2D and 3D modalities of the same molecule at fine-grained atomic level, painting a more comprehensive depiction of each molecule. Extensive experiments show that MoleBLEND achieves state-of-the-art performance across major 2D/3D molecular benchmarks. We further provide theoretical insights from the perspective of mutual-information maximization, demonstrating that our method unifies contrastive, generative (cross-modality prediction) and mask-then-predict (single-modality prediction) objectives into one single cohesive framework.

Words are all you need? Language as an approximation for human similarity judgments

Human similarity judgments are a powerful supervision signal for machine learning applications based on techniques such as contrastive learning, information retrieval, and model alignment, but classical methods for collecting human similarity judgments are too expensive to be used at scale. Recent methods propose using pre-trained deep neural networks (DNNs) to approximate human similarity, but pre-trained DNNs may not be available for certain domains (e.g., medical images, low-resource languages) and their performance in approximating human similarity has not been extensively tested. We conducted an evaluation of 611 pre-trained models across three domains -- images, audio, video -- and found that there is a large gap in performance between human similarity judgments and pre-trained DNNs. To address this gap, we propose a new class of similarity approximation methods based on language. To collect the language data required by these new methods, we also developed and validated a novel adaptive tag collection pipeline. We find that our proposed language-based methods are significantly cheaper, in the number of human judgments, than classical methods, but still improve performance over the DNN-based methods. Finally, we also develop `stacked' methods that combine language embeddings with DNN embeddings, and find that these consistently provide the best approximations for human similarity across all three of our modalities. Based on the results of this comprehensive study, we provide a concise guide for researchers interested in collecting or approximating human similarity data. To accompany this guide, we also release all of the similarity and language data, a total of 206,339 human judgments, that we collected in our experiments, along with a detailed breakdown of all modeling results.

MUSER: A Multi-View Similar Case Retrieval Dataset

Similar case retrieval (SCR) is a representative legal AI application that plays a pivotal role in promoting judicial fairness. However, existing SCR datasets only focus on the fact description section when judging the similarity between cases, ignoring other valuable sections (e.g., the court's opinion) that can provide insightful reasoning process behind. Furthermore, the case similarities are typically measured solely by the textual semantics of the fact descriptions, which may fail to capture the full complexity of legal cases from the perspective of legal knowledge. In this work, we present MUSER, a similar case retrieval dataset based on multi-view similarity measurement and comprehensive legal element with sentence-level legal element annotations. Specifically, we select three perspectives (legal fact, dispute focus, and law statutory) and build a comprehensive and structured label schema of legal elements for each of them, to enable accurate and knowledgeable evaluation of case similarities. The constructed dataset originates from Chinese civil cases and contains 100 query cases and 4,024 candidate cases. We implement several text classification algorithms for legal element prediction and various retrieval methods for retrieving similar cases on MUSER. The experimental results indicate that incorporating legal elements can benefit the performance of SCR models, but further efforts are still required to address the remaining challenges posed by MUSER. The source code and dataset are released at https://github.com/THUlawtech/MUSER.

A Named Entity Based Approach to Model Recipes

Traditional cooking recipes follow a structure which can be modelled very well if the rules and semantics of the different sections of the recipe text are analyzed and represented accurately. We propose a structure that can accurately represent the recipe as well as a pipeline to infer the best representation of the recipe in this uniform structure. The Ingredients section in a recipe typically lists down the ingredients required and corresponding attributes such as quantity, temperature, and processing state. This can be modelled by defining these attributes and their values. The physical entities which make up a recipe can be broadly classified into utensils, ingredients and their combinations that are related by cooking techniques. The instruction section lists down a series of events in which a cooking technique or process is applied upon these utensils and ingredients. We model these relationships in the form of tuples. Thus, using a combination of these methods we model cooking recipe in the dataset RecipeDB to show the efficacy of our method. This mined information model can have several applications which include translating recipes between languages, determining similarity between recipes, generation of novel recipes and estimation of the nutritional profile of recipes. For the purpose of recognition of ingredient attributes, we train the Named Entity Relationship (NER) models and analyze the inferences with the help of K-Means clustering. Our model presented with an F1 score of 0.95 across all datasets. We use a similar NER tagging model for labelling cooking techniques (F1 score = 0.88) and utensils (F1 score = 0.90) within the instructions section. Finally, we determine the temporal sequence of relationships between ingredients, utensils and cooking techniques for modeling the instruction steps.

LeanVec: Search your vectors faster by making them fit

Modern deep learning models have the ability to generate high-dimensional vectors whose similarity reflects semantic resemblance. Thus, similarity search, i.e., the operation of retrieving those vectors in a large collection that are similar to a given query, has become a critical component of a wide range of applications that demand highly accurate and timely answers. In this setting, the high vector dimensionality puts similarity search systems under compute and memory pressure, leading to subpar performance. Additionally, cross-modal retrieval tasks have become increasingly common, e.g., where a user inputs a text query to find the most relevant images for that query. However, these queries often have different distributions than the database embeddings, making it challenging to achieve high accuracy. In this work, we present LeanVec, a framework that combines linear dimensionality reduction with vector quantization to accelerate similarity search on high-dimensional vectors while maintaining accuracy. We present LeanVec variants for in-distribution (ID) and out-of-distribution (OOD) queries. LeanVec-ID yields accuracies on par with those from recently introduced deep learning alternatives whose computational overhead precludes their usage in practice. LeanVec-OOD uses a novel technique for dimensionality reduction that considers the query and database distributions to simultaneously boost the accuracy and the performance of the framework even further (even presenting competitive results when the query and database distributions match). All in all, our extensive and varied experimental results show that LeanVec produces state-of-the-art results, with up to 3.7x improvement in search throughput and up to 4.9x faster index build time over the state of the art.

Graph Self-supervised Learning with Accurate Discrepancy Learning

Self-supervised learning of graph neural networks (GNNs) aims to learn an accurate representation of the graphs in an unsupervised manner, to obtain transferable representations of them for diverse downstream tasks. Predictive learning and contrastive learning are the two most prevalent approaches for graph self-supervised learning. However, they have their own drawbacks. While the predictive learning methods can learn the contextual relationships between neighboring nodes and edges, they cannot learn global graph-level similarities. Contrastive learning, while it can learn global graph-level similarities, its objective to maximize the similarity between two differently perturbed graphs may result in representations that cannot discriminate two similar graphs with different properties. To tackle such limitations, we propose a framework that aims to learn the exact discrepancy between the original and the perturbed graphs, coined as Discrepancy-based Self-supervised LeArning (D-SLA). Specifically, we create multiple perturbations of the given graph with varying degrees of similarity, and train the model to predict whether each graph is the original graph or the perturbed one. Moreover, we further aim to accurately capture the amount of discrepancy for each perturbed graph using the graph edit distance. We validate our D-SLA on various graph-related downstream tasks, including molecular property prediction, protein function prediction, and link prediction tasks, on which ours largely outperforms relevant baselines.

From Graphs to Hypergraphs: Hypergraph Projection and its Remediation

We study the implications of the modeling choice to use a graph, instead of a hypergraph, to represent real-world interconnected systems whose constituent relationships are of higher order by nature. Such a modeling choice typically involves an underlying projection process that maps the original hypergraph onto a graph, and is common in graph-based analysis. While hypergraph projection can potentially lead to loss of higher-order relations, there exists very limited studies on the consequences of doing so, as well as its remediation. This work fills this gap by doing two things: (1) we develop analysis based on graph and set theory, showing two ubiquitous patterns of hyperedges that are root to structural information loss in all hypergraph projections; we also quantify the combinatorial impossibility of recovering the lost higher-order structures if no extra help is provided; (2) we still seek to recover the lost higher-order structures in hypergraph projection, and in light of (1)'s findings we propose to relax the problem into a learning-based setting. Under this setting, we develop a learning-based hypergraph reconstruction method based on an important statistic of hyperedge distributions that we find. Our reconstruction method is evaluated on 8 real-world datasets under different settings, and exhibits consistently good performance. We also demonstrate benefits of the reconstructed hypergraphs via use cases of protein rankings and link predictions.

Homeomorphism Prior for False Positive and Negative Problem in Medical Image Dense Contrastive Representation Learning

Dense contrastive representation learning (DCRL) has greatly improved the learning efficiency for image-dense prediction tasks, showing its great potential to reduce the large costs of medical image collection and dense annotation. However, the properties of medical images make unreliable correspondence discovery, bringing an open problem of large-scale false positive and negative (FP&N) pairs in DCRL. In this paper, we propose GEoMetric vIsual deNse sImilarity (GEMINI) learning which embeds the homeomorphism prior to DCRL and enables a reliable correspondence discovery for effective dense contrast. We propose a deformable homeomorphism learning (DHL) which models the homeomorphism of medical images and learns to estimate a deformable mapping to predict the pixels' correspondence under topological preservation. It effectively reduces the searching space of pairing and drives an implicit and soft learning of negative pairs via a gradient. We also propose a geometric semantic similarity (GSS) which extracts semantic information in features to measure the alignment degree for the correspondence learning. It will promote the learning efficiency and performance of deformation, constructing positive pairs reliably. We implement two practical variants on two typical representation learning tasks in our experiments. Our promising results on seven datasets which outperform the existing methods show our great superiority. We will release our code on a companion link: https://github.com/YutingHe-list/GEMINI.

Relative representations enable zero-shot latent space communication

Neural networks embed the geometric structure of a data manifold lying in a high-dimensional space into latent representations. Ideally, the distribution of the data points in the latent space should depend only on the task, the data, the loss, and other architecture-specific constraints. However, factors such as the random weights initialization, training hyperparameters, or other sources of randomness in the training phase may induce incoherent latent spaces that hinder any form of reuse. Nevertheless, we empirically observe that, under the same data and modeling choices, the angles between the encodings within distinct latent spaces do not change. In this work, we propose the latent similarity between each sample and a fixed set of anchors as an alternative data representation, demonstrating that it can enforce the desired invariances without any additional training. We show how neural architectures can leverage these relative representations to guarantee, in practice, invariance to latent isometries and rescalings, effectively enabling latent space communication: from zero-shot model stitching to latent space comparison between diverse settings. We extensively validate the generalization capability of our approach on different datasets, spanning various modalities (images, text, graphs), tasks (e.g., classification, reconstruction) and architectures (e.g., CNNs, GCNs, transformers).

A Framework for Fast and Stable Representations of Multiparameter Persistent Homology Decompositions

Topological data analysis (TDA) is an area of data science that focuses on using invariants from algebraic topology to provide multiscale shape descriptors for geometric data sets such as point clouds. One of the most important such descriptors is {\em persistent homology}, which encodes the change in shape as a filtration parameter changes; a typical parameter is the feature scale. For many data sets, it is useful to simultaneously vary multiple filtration parameters, for example feature scale and density. While the theoretical properties of single parameter persistent homology are well understood, less is known about the multiparameter case. In particular, a central question is the problem of representing multiparameter persistent homology by elements of a vector space for integration with standard machine learning algorithms. Existing approaches to this problem either ignore most of the multiparameter information to reduce to the one-parameter case or are heuristic and potentially unstable in the face of noise. In this article, we introduce a new general representation framework that leverages recent results on {\em decompositions} of multiparameter persistent homology. This framework is rich in information, fast to compute, and encompasses previous approaches. Moreover, we establish theoretical stability guarantees under this framework as well as efficient algorithms for practical computation, making this framework an applicable and versatile tool for analyzing geometric and point cloud data. We validate our stability results and algorithms with numerical experiments that demonstrate statistical convergence, prediction accuracy, and fast running times on several real data sets.

RREH: Reconstruction Relations Embedded Hashing for Semi-Paired Cross-Modal Retrieval

Known for efficient computation and easy storage, hashing has been extensively explored in cross-modal retrieval. The majority of current hashing models are predicated on the premise of a direct one-to-one mapping between data points. However, in real practice, data correspondence across modalities may be partially provided. In this research, we introduce an innovative unsupervised hashing technique designed for semi-paired cross-modal retrieval tasks, named Reconstruction Relations Embedded Hashing (RREH). RREH assumes that multi-modal data share a common subspace. For paired data, RREH explores the latent consistent information of heterogeneous modalities by seeking a shared representation. For unpaired data, to effectively capture the latent discriminative features, the high-order relationships between unpaired data and anchors are embedded into the latent subspace, which are computed by efficient linear reconstruction. The anchors are sampled from paired data, which improves the efficiency of hash learning. The RREH trains the underlying features and the binary encodings in a unified framework with high-order reconstruction relations preserved. With the well devised objective function and discrete optimization algorithm, RREH is designed to be scalable, making it suitable for large-scale datasets and facilitating efficient cross-modal retrieval. In the evaluation process, the proposed is tested with partially paired data to establish its superiority over several existing methods.

PMC-Patients: A Large-scale Dataset of Patient Notes and Relations Extracted from Case Reports in PubMed Central

Objective: Data unavailability has been one of the biggest barriers in clinical natural language processing. This paper is aimed at providing a large-scale and publicly available patient note dataset, named PMC-Patients, with relevant articles and similar patients annotations. The ultimate goal of PMC-Patients is to facilitate the development of retrieval-based clinical decision support systems. Materials and Methods: To collect PMC-Patients, we extract patient notes from case reports in PubMed Central by recognizing certain section patterns. Patient-article relevance and patient-patient similarity are annotated by citation relationships in PubMed. In addition, we perform three tasks with PMC-Patients to demonstrate its utility in providing clinical decision support for a given patient, including (1) classifying whether another patient is similar, (2) retrieving similar patients in PMC-Patients, and (3) retrieving relevant articles in PubMed. Results: We collect and release PMC-Patients under the CC BY-NC-SA license, which becomes the largest publicly available patient note dataset so far. PMC-Patients contains 167k patient notes that are annotated with 3.1M relevant articles and 293k similar patients. Qualitative and quantitative analyses reveal the high quality and richness of our dataset. Experiments show that classifying the similarity of patient pairs is relatively easy, but it is hard to retrieve similar patients or relevant articles for a given patient from a large set of candidates. Conclusion: We present PMC-Patients, a large-scale dataset of patient notes with high quality, easy access, diverse conditions, and rich annotations. The proposed dataset can also serve as a hard benchmark for evaluating retrieval-based clinical decision support systems.

Efficient Nearest Neighbor Search for Cross-Encoder Models using Matrix Factorization

Efficient k-nearest neighbor search is a fundamental task, foundational for many problems in NLP. When the similarity is measured by dot-product between dual-encoder vectors or ell_2-distance, there already exist many scalable and efficient search methods. But not so when similarity is measured by more accurate and expensive black-box neural similarity models, such as cross-encoders, which jointly encode the query and candidate neighbor. The cross-encoders' high computational cost typically limits their use to reranking candidates retrieved by a cheaper model, such as dual encoder or TF-IDF. However, the accuracy of such a two-stage approach is upper-bounded by the recall of the initial candidate set, and potentially requires additional training to align the auxiliary retrieval model with the cross-encoder model. In this paper, we present an approach that avoids the use of a dual-encoder for retrieval, relying solely on the cross-encoder. Retrieval is made efficient with CUR decomposition, a matrix decomposition approach that approximates all pairwise cross-encoder distances from a small subset of rows and columns of the distance matrix. Indexing items using our approach is computationally cheaper than training an auxiliary dual-encoder model through distillation. Empirically, for k > 10, our approach provides test-time recall-vs-computational cost trade-offs superior to the current widely-used methods that re-rank items retrieved using a dual-encoder or TF-IDF.

Matching Table Metadata with Business Glossaries Using Large Language Models

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.

Coarse-to-Fine: Learning Compact Discriminative Representation for Single-Stage Image Retrieval

Image retrieval targets to find images from a database that are visually similar to the query image. Two-stage methods following retrieve-and-rerank paradigm have achieved excellent performance, but their separate local and global modules are inefficient to real-world applications. To better trade-off retrieval efficiency and accuracy, some approaches fuse global and local feature into a joint representation to perform single-stage image retrieval. However, they are still challenging due to various situations to tackle, e.g., background, occlusion and viewpoint. In this work, we design a Coarse-to-Fine framework to learn Compact Discriminative representation (CFCD) for end-to-end single-stage image retrieval-requiring only image-level labels. Specifically, we first design a novel adaptive softmax-based loss which dynamically tunes its scale and margin within each mini-batch and increases them progressively to strengthen supervision during training and intra-class compactness. Furthermore, we propose a mechanism which attentively selects prominent local descriptors and infuse fine-grained semantic relations into the global representation by a hard negative sampling strategy to optimize inter-class distinctiveness at a global scale. Extensive experimental results have demonstrated the effectiveness of our method, which achieves state-of-the-art single-stage image retrieval performance on benchmarks such as Revisited Oxford and Revisited Paris. Code is available at https://github.com/bassyess/CFCD.

Linking Datasets on Organizations Using Half A Billion Open Collaborated Records

Scholars studying organizations often work with multiple datasets lacking shared unique identifiers or covariates. In such situations, researchers may turn to approximate string matching methods to combine datasets. String matching, although useful, faces fundamental challenges. Even when two strings appear similar to humans, fuzzy matching often does not work because it fails to adapt to the informativeness of the character combinations presented. Worse, many entities have multiple names that are dissimilar (e.g., "Fannie Mae" and "Federal National Mortgage Association"), a case where string matching has little hope of succeeding. This paper introduces data from a prominent employment-related networking site (LinkedIn) as a tool to address these problems. We propose interconnected approaches to leveraging the massive amount of information from LinkedIn regarding organizational name-to-name links. The first approach builds a machine learning model for predicting matches from character strings, treating the trillions of user-contributed organizational name pairs as a training corpus: this approach constructs a string matching metric that explicitly maximizes match probabilities. A second approach identifies relationships between organization names using network representations of the LinkedIn data. A third approach combines the first and second. We document substantial improvements over fuzzy matching in applications, making all methods accessible in open-source software ("LinkOrgs").

Hierarchical Pretraining for Biomedical Term Embeddings

Electronic health records (EHR) contain narrative notes that provide extensive details on the medical condition and management of patients. Natural language processing (NLP) of clinical notes can use observed frequencies of clinical terms as predictive features for downstream applications such as clinical decision making and patient trajectory prediction. However, due to the vast number of highly similar and related clinical concepts, a more effective modeling strategy is to represent clinical terms as semantic embeddings via representation learning and use the low dimensional embeddings as feature vectors for predictive modeling. To achieve efficient representation, fine-tuning pretrained language models with biomedical knowledge graphs may generate better embeddings for biomedical terms than those from standard language models alone. These embeddings can effectively discriminate synonymous pairs of from those that are unrelated. However, they often fail to capture different degrees of similarity or relatedness for concepts that are hierarchical in nature. To overcome this limitation, we propose HiPrBERT, a novel biomedical term representation model trained on additionally complied data that contains hierarchical structures for various biomedical terms. We modify an existing contrastive loss function to extract information from these hierarchies. Our numerical experiments demonstrate that HiPrBERT effectively learns the pair-wise distance from hierarchical information, resulting in a substantially more informative embeddings for further biomedical applications

Accelerating Scientific Discovery with Generative Knowledge Extraction, Graph-Based Representation, and Multimodal Intelligent Graph Reasoning

Leveraging generative Artificial Intelligence (AI), we have transformed a dataset comprising 1,000 scientific papers into an ontological knowledge graph. Through an in-depth structural analysis, we have calculated node degrees, identified communities and connectivities, and evaluated clustering coefficients and betweenness centrality of pivotal nodes, uncovering fascinating knowledge architectures. The graph has an inherently scale-free nature, is highly connected, and can be used for graph reasoning by taking advantage of transitive and isomorphic properties that reveal unprecedented interdisciplinary relationships that can be used to answer queries, identify gaps in knowledge, propose never-before-seen material designs, and predict material behaviors. We compute deep node embeddings for combinatorial node similarity ranking for use in a path sampling strategy links dissimilar concepts that have previously not been related. One comparison revealed structural parallels between biological materials and Beethoven's 9th Symphony, highlighting shared patterns of complexity through isomorphic mapping. In another example, the algorithm proposed a hierarchical mycelium-based composite based on integrating path sampling with principles extracted from Kandinsky's 'Composition VII' painting. The resulting material integrates an innovative set of concepts that include a balance of chaos/order, adjustable porosity, mechanical strength, and complex patterned chemical functionalization. We uncover other isomorphisms across science, technology and art, revealing a nuanced ontology of immanence that reveal a context-dependent heterarchical interplay of constituents. Graph-based generative AI achieves a far higher degree of novelty, explorative capacity, and technical detail, than conventional approaches and establishes a widely useful framework for innovation by revealing hidden connections.

X-Pool: Cross-Modal Language-Video Attention for Text-Video Retrieval

In text-video retrieval, the objective is to learn a cross-modal similarity function between a text and a video that ranks relevant text-video pairs higher than irrelevant pairs. However, videos inherently express a much wider gamut of information than texts. Instead, texts often capture sub-regions of entire videos and are most semantically similar to certain frames within videos. Therefore, for a given text, a retrieval model should focus on the text's most semantically similar video sub-regions to make a more relevant comparison. Yet, most existing works aggregate entire videos without directly considering text. Common text-agnostic aggregations schemes include mean-pooling or self-attention over the frames, but these are likely to encode misleading visual information not described in the given text. To address this, we propose a cross-modal attention model called X-Pool that reasons between a text and the frames of a video. Our core mechanism is a scaled dot product attention for a text to attend to its most semantically similar frames. We then generate an aggregated video representation conditioned on the text's attention weights over the frames. We evaluate our method on three benchmark datasets of MSR-VTT, MSVD and LSMDC, achieving new state-of-the-art results by up to 12% in relative improvement in Recall@1. Our findings thereby highlight the importance of joint text-video reasoning to extract important visual cues according to text. Full code and demo can be found at: https://layer6ai-labs.github.io/xpool/

VacancySBERT: the approach for representation of titles and skills for semantic similarity search in the recruitment domain

The paper focuses on deep learning semantic search algorithms applied in the HR domain. The aim of the article is developing a novel approach to training a Siamese network to link the skills mentioned in the job ad with the title. It has been shown that the title normalization process can be based either on classification or similarity comparison approaches. While classification algorithms strive to classify a sample into predefined set of categories, similarity search algorithms take a more flexible approach, since they are designed to find samples that are similar to a given query sample, without requiring pre-defined classes and labels. In this article semantic similarity search to find candidates for title normalization has been used. A pre-trained language model has been adapted while teaching it to match titles and skills based on co-occurrence information. For the purpose of this research fifty billion title-descriptions pairs had been collected for training the model and thirty three thousand title-description-normalized title triplets, where normalized job title was picked up manually by job ad creator for testing purposes. As baselines FastText, BERT, SentenceBert and JobBert have been used. As a metric of the accuracy of the designed algorithm is Recall in top one, five and ten model's suggestions. It has been shown that the novel training objective lets it achieve significant improvement in comparison to other generic and specific text encoders. Two settings with treating titles as standalone strings, and with included skills as additional features during inference have been used and the results have been compared in this article. Improvements by 10% and 21.5% have been achieved using VacancySBERT and VacancySBERT (with skills) respectively. The benchmark has been developed as open-source to foster further research in the area.

GeAR: Generation Augmented Retrieval

Document retrieval techniques form the foundation for the development of large-scale information systems. The prevailing methodology is to construct a bi-encoder and compute the semantic similarity. However, such scalar similarity is difficult to reflect enough information and impedes our comprehension of the retrieval results. In addition, this computational process mainly emphasizes the global semantics and ignores the fine-grained semantic relationship between the query and the complex text in the document. In this paper, we propose a new method called Generation Augmented Retrieval (GeAR) that incorporates well-designed fusion and decoding modules. This enables GeAR to generate the relevant text from documents based on the fused representation of the query and the document, thus learning to "focus on" the fine-grained information. Also when used as a retriever, GeAR does not add any computational burden over bi-encoders. To support the training of the new framework, we have introduced a pipeline to efficiently synthesize high-quality data by utilizing large language models. GeAR exhibits competitive retrieval and localization performance across diverse scenarios and datasets. Moreover, the qualitative analysis and the results generated by GeAR provide novel insights into the interpretation of retrieval results. The code, data, and models will be released after completing technical review to facilitate future research.

3D-MolT5: Towards Unified 3D Molecule-Text Modeling with 3D Molecular Tokenization

The integration of molecule and language has garnered increasing attention in molecular science. Recent advancements in Language Models (LMs) have demonstrated potential for the comprehensive modeling of molecule and language. However, existing works exhibit notable limitations. Most existing works overlook the modeling of 3D information, which is crucial for understanding molecular structures and also functions. While some attempts have been made to leverage external structure encoding modules to inject the 3D molecular information into LMs, there exist obvious difficulties that hinder the integration of molecular structure and language text, such as modality alignment and separate tuning. To bridge this gap, we propose 3D-MolT5, a unified framework designed to model both 1D molecular sequence and 3D molecular structure. The key innovation lies in our methodology for mapping fine-grained 3D substructure representations (based on 3D molecular fingerprints) to a specialized 3D token vocabulary for 3D-MolT5. This 3D structure token vocabulary enables the seamless combination of 1D sequence and 3D structure representations in a tokenized format, allowing 3D-MolT5 to encode molecular sequence (SELFIES), molecular structure, and text sequences within a unified architecture. Alongside, we further introduce 1D and 3D joint pre-training to enhance the model's comprehension of these diverse modalities in a joint representation space and better generalize to various tasks for our foundation model. Through instruction tuning on multiple downstream datasets, our proposed 3D-MolT5 shows superior performance than existing methods in molecular property prediction, molecule captioning, and text-based molecule generation tasks. Our code will be available on GitHub soon.

Disentangled Structural and Featural Representation for Task-Agnostic Graph Valuation

With the emergence of data marketplaces, the demand for methods to assess the value of data has increased significantly. While numerous techniques have been proposed for this purpose, none have specifically addressed graphs as the main data modality. Graphs are widely used across various fields, ranging from chemical molecules to social networks. In this study, we break down graphs into two main components: structural and featural, and we focus on evaluating data without relying on specific task-related metrics, making it applicable in practical scenarios where validation requirements may be lacking. We introduce a novel framework called blind message passing, which aligns the seller's and buyer's graphs using a shared node permutation based on graph matching. This allows us to utilize the graph Wasserstein distance to quantify the differences in the structural distribution of graph datasets, called the structural disparities. We then consider featural aspects of buyers' and sellers' graphs for data valuation and capture their statistical similarities and differences, referred to as relevance and diversity, respectively. Our approach ensures that buyers and sellers remain unaware of each other's datasets. Our experiments on real datasets demonstrate the effectiveness of our approach in capturing the relevance, diversity, and structural disparities of seller data for buyers, particularly in graph-based data valuation scenarios.

Neural Locality Sensitive Hashing for Entity Blocking

Locality-sensitive hashing (LSH) is a fundamental algorithmic technique widely employed in large-scale data processing applications, such as nearest-neighbor search, entity resolution, and clustering. However, its applicability in some real-world scenarios is limited due to the need for careful design of hashing functions that align with specific metrics. Existing LSH-based Entity Blocking solutions primarily rely on generic similarity metrics such as Jaccard similarity, whereas practical use cases often demand complex and customized similarity rules surpassing the capabilities of generic similarity metrics. Consequently, designing LSH functions for these customized similarity rules presents considerable challenges. In this research, we propose a neuralization approach to enhance locality-sensitive hashing by training deep neural networks to serve as hashing functions for complex metrics. We assess the effectiveness of this approach within the context of the entity resolution problem, which frequently involves the use of task-specific metrics in real-world applications. Specifically, we introduce NLSHBlock (Neural-LSH Block), a novel blocking methodology that leverages pre-trained language models, fine-tuned with a novel LSH-based loss function. Through extensive evaluations conducted on a diverse range of real-world datasets, we demonstrate the superiority of NLSHBlock over existing methods, exhibiting significant performance improvements. Furthermore, we showcase the efficacy of NLSHBlock in enhancing the performance of the entity matching phase, particularly within the semi-supervised setting.

Leveraging Invariant Principle for Heterophilic Graph Structure Distribution Shifts

Heterophilic Graph Neural Networks (HGNNs) have shown promising results for semi-supervised learning tasks on graphs. Notably, most real-world heterophilic graphs are composed of a mixture of nodes with different neighbor patterns, exhibiting local node-level homophilic and heterophilic structures. However, existing works are only devoted to designing better HGNN backbones or architectures for node classification tasks on heterophilic and homophilic graph benchmarks simultaneously, and their analyses of HGNN performance with respect to nodes are only based on the determined data distribution without exploring the effect caused by this structural difference between training and testing nodes. How to learn invariant node representations on heterophilic graphs to handle this structure difference or distribution shifts remains unexplored. In this paper, we first discuss the limitations of previous graph-based invariant learning methods from the perspective of data augmentation. Then, we propose HEI, a framework capable of generating invariant node representations through incorporating heterophily information to infer latent environments without augmentation, which are then used for invariant prediction, under heterophilic graph structure distribution shifts. We theoretically show that our proposed method can achieve guaranteed performance under heterophilic graph structure distribution shifts. Extensive experiments on various benchmarks and backbones can also demonstrate the effectiveness of our method compared with existing state-of-the-art baselines.

DisWOT: Student Architecture Search for Distillation WithOut Training

Knowledge distillation (KD) is an effective training strategy to improve the lightweight student models under the guidance of cumbersome teachers. However, the large architecture difference across the teacher-student pairs limits the distillation gains. In contrast to previous adaptive distillation methods to reduce the teacher-student gap, we explore a novel training-free framework to search for the best student architectures for a given teacher. Our work first empirically show that the optimal model under vanilla training cannot be the winner in distillation. Secondly, we find that the similarity of feature semantics and sample relations between random-initialized teacher-student networks have good correlations with final distillation performances. Thus, we efficiently measure similarity matrixs conditioned on the semantic activation maps to select the optimal student via an evolutionary algorithm without any training. In this way, our student architecture search for Distillation WithOut Training (DisWOT) significantly improves the performance of the model in the distillation stage with at least 180times training acceleration. Additionally, we extend similarity metrics in DisWOT as new distillers and KD-based zero-proxies. Our experiments on CIFAR, ImageNet and NAS-Bench-201 demonstrate that our technique achieves state-of-the-art results on different search spaces. Our project and code are available at https://lilujunai.github.io/DisWOT-CVPR2023/.

Stable Vectorization of Multiparameter Persistent Homology using Signed Barcodes as Measures

Persistent homology (PH) provides topological descriptors for geometric data, such as weighted graphs, which are interpretable, stable to perturbations, and invariant under, e.g., relabeling. Most applications of PH focus on the one-parameter case -- where the descriptors summarize the changes in topology of data as it is filtered by a single quantity of interest -- and there is now a wide array of methods enabling the use of one-parameter PH descriptors in data science, which rely on the stable vectorization of these descriptors as elements of a Hilbert space. Although the multiparameter PH (MPH) of data that is filtered by several quantities of interest encodes much richer information than its one-parameter counterpart, the scarceness of stability results for MPH descriptors has so far limited the available options for the stable vectorization of MPH. In this paper, we aim to bring together the best of both worlds by showing how the interpretation of signed barcodes -- a recent family of MPH descriptors -- as signed measures leads to natural extensions of vectorization strategies from one parameter to multiple parameters. The resulting feature vectors are easy to define and to compute, and provably stable. While, as a proof of concept, we focus on simple choices of signed barcodes and vectorizations, we already see notable performance improvements when comparing our feature vectors to state-of-the-art topology-based methods on various types of data.

PatentSBERTa: A Deep NLP based Hybrid Model for Patent Distance and Classification using Augmented SBERT

This study provides an efficient approach for using text data to calculate patent-to-patent (p2p) technological similarity, and presents a hybrid framework for leveraging the resulting p2p similarity for applications such as semantic search and automated patent classification. We create embeddings using Sentence-BERT (SBERT) based on patent claims. We leverage SBERTs efficiency in creating embedding distance measures to map p2p similarity in large sets of patent data. We deploy our framework for classification with a simple Nearest Neighbors (KNN) model that predicts Cooperative Patent Classification (CPC) of a patent based on the class assignment of the K patents with the highest p2p similarity. We thereby validate that the p2p similarity captures their technological features in terms of CPC overlap, and at the same demonstrate the usefulness of this approach for automatic patent classification based on text data. Furthermore, the presented classification framework is simple and the results easy to interpret and evaluate by end-users. In the out-of-sample model validation, we are able to perform a multi-label prediction of all assigned CPC classes on the subclass (663) level on 1,492,294 patents with an accuracy of 54% and F1 score > 66%, which suggests that our model outperforms the current state-of-the-art in text-based multi-label and multi-class patent classification. We furthermore discuss the applicability of the presented framework for semantic IP search, patent landscaping, and technology intelligence. We finally point towards a future research agenda for leveraging multi-source patent embeddings, their appropriateness across applications, as well as to improve and validate patent embeddings by creating domain-expert curated Semantic Textual Similarity (STS) benchmark datasets.

MICDIR: Multi-scale Inverse-consistent Deformable Image Registration using UNetMSS with Self-Constructing Graph Latent

Image registration is the process of bringing different images into a common coordinate system - a technique widely used in various applications of computer vision, such as remote sensing, image retrieval, and, most commonly, medical imaging. Deep learning based techniques have been applied successfully to tackle various complex medical image processing problems, including medical image registration. Over the years, several image registration techniques have been proposed using deep learning. Deformable image registration techniques such as Voxelmorph have been successful in capturing finer changes and providing smoother deformations. However, Voxelmorph, as well as ICNet and FIRE, do not explicitly encode global dependencies (i.e. the overall anatomical view of the supplied image) and, therefore, cannot track large deformations. In order to tackle the aforementioned problems, this paper extends the Voxelmorph approach in three different ways. To improve the performance in case of small as well as large deformations, supervision of the model at different resolutions has been integrated using a multi-scale UNet. To support the network to learn and encode the minute structural co-relations of the given image-pairs, a self-constructing graph network (SCGNet) has been used as the latent of the multi-scale UNet - which can improve the learning process of the model and help the model to generalise better. And finally, to make the deformations inverse-consistent, cycle consistency loss has been employed. On the task of registration of brain MRIs, the proposed method achieved significant improvements over ANTs and VoxelMorph, obtaining a Dice score of 0.8013 \pm 0.0243 for intramodal and 0.6211 \pm 0.0309 for intermodal, while VoxelMorph achieved 0.7747 \pm 0.0260 and 0.6071 \pm 0.0510, respectively

Integrating Knowledge Graph embedding and pretrained Language Models in Hypercomplex Spaces

Knowledge Graphs, such as Wikidata, comprise structural and textual knowledge in order to represent knowledge. For each of the two modalities dedicated approaches for graph embedding and language models learn patterns that allow for predicting novel structural knowledge. Few approaches have integrated learning and inference with both modalities and these existing ones could only partially exploit the interaction of structural and textual knowledge. In our approach, we build on existing strong representations of single modalities and we use hypercomplex algebra to represent both, (i), single-modality embedding as well as, (ii), the interaction between different modalities and their complementary means of knowledge representation. More specifically, we suggest Dihedron and Quaternion representations of 4D hypercomplex numbers to integrate four modalities namely structural knowledge graph embedding, word-level representations (e.g.\ Word2vec, Fasttext), sentence-level representations (Sentence transformer), and document-level representations (sentence transformer, Doc2vec). Our unified vector representation scores the plausibility of labelled edges via Hamilton and Dihedron products, thus modeling pairwise interactions between different modalities. Extensive experimental evaluation on standard benchmark datasets shows the superiority of our two new models using abundant textual information besides sparse structural knowledge to enhance performance in link prediction tasks.

SESA: Supervised Explicit Semantic Analysis

In recent years supervised representation learning has provided state of the art or close to the state of the art results in semantic analysis tasks including ranking and information retrieval. The core idea is to learn how to embed items into a latent space such that they optimize a supervised objective in that latent space. The dimensions of the latent space have no clear semantics, and this reduces the interpretability of the system. For example, in personalization models, it is hard to explain why a particular item is ranked high for a given user profile. We propose a novel model of representation learning called Supervised Explicit Semantic Analysis (SESA) that is trained in a supervised fashion to embed items to a set of dimensions with explicit semantics. The model learns to compare two objects by representing them in this explicit space, where each dimension corresponds to a concept from a knowledge base. This work extends Explicit Semantic Analysis (ESA) with a supervised model for ranking problems. We apply this model to the task of Job-Profile relevance in LinkedIn in which a set of skills defines our explicit dimensions of the space. Every profile and job are encoded to this set of skills their similarity is calculated in this space. We use RNNs to embed text input into this space. In addition to interpretability, our model makes use of the web-scale collaborative skills data that is provided by users for each LinkedIn profile. Our model provides state of the art result while it remains interpretable.

How Expressive are Graph Neural Networks in Recommendation?

Graph Neural Networks (GNNs) have demonstrated superior performance on various graph learning tasks, including recommendation, where they leverage user-item collaborative filtering signals in graphs. However, theoretical formulations of their capability are scarce, despite their empirical effectiveness in state-of-the-art recommender models. Recently, research has explored the expressiveness of GNNs in general, demonstrating that message passing GNNs are at most as powerful as the Weisfeiler-Lehman test, and that GNNs combined with random node initialization are universal. Nevertheless, the concept of "expressiveness" for GNNs remains vaguely defined. Most existing works adopt the graph isomorphism test as the metric of expressiveness, but this graph-level task may not effectively assess a model's ability in recommendation, where the objective is to distinguish nodes of different closeness. In this paper, we provide a comprehensive theoretical analysis of the expressiveness of GNNs in recommendation, considering three levels of expressiveness metrics: graph isomorphism (graph-level), node automorphism (node-level), and topological closeness (link-level). We propose the topological closeness metric to evaluate GNNs' ability to capture the structural distance between nodes, which aligns closely with the objective of recommendation. To validate the effectiveness of this new metric in evaluating recommendation performance, we introduce a learning-less GNN algorithm that is optimal on the new metric and can be optimal on the node-level metric with suitable modification. We conduct extensive experiments comparing the proposed algorithm against various types of state-of-the-art GNN models to explore the explainability of the new metric in the recommendation task. For reproducibility, implementation codes are available at https://github.com/HKUDS/GTE.

Efficiently Computing Similarities to Private Datasets

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.

Conditional Graph Information Bottleneck for Molecular Relational Learning

Molecular relational learning, whose goal is to learn the interaction behavior between molecular pairs, got a surge of interest in molecular sciences due to its wide range of applications. Recently, graph neural networks have recently shown great success in molecular relational learning by modeling a molecule as a graph structure, and considering atom-level interactions between two molecules. Despite their success, existing molecular relational learning methods tend to overlook the nature of chemistry, i.e., a chemical compound is composed of multiple substructures such as functional groups that cause distinctive chemical reactions. In this work, we propose a novel relational learning framework, called CGIB, that predicts the interaction behavior between a pair of graphs by detecting core subgraphs therein. The main idea is, given a pair of graphs, to find a subgraph from a graph that contains the minimal sufficient information regarding the task at hand conditioned on the paired graph based on the principle of conditional graph information bottleneck. We argue that our proposed method mimics the nature of chemical reactions, i.e., the core substructure of a molecule varies depending on which other molecule it interacts with. Extensive experiments on various tasks with real-world datasets demonstrate the superiority of CGIB over state-of-the-art baselines. Our code is available at https://github.com/Namkyeong/CGIB.

The Impacts of Data, Ordering, and Intrinsic Dimensionality on Recall in Hierarchical Navigable Small Worlds

Vector search systems, pivotal in AI applications, often rely on the Hierarchical Navigable Small Worlds (HNSW) algorithm. However, the behaviour of HNSW under real-world scenarios using vectors generated with deep learning models remains under-explored. Existing Approximate Nearest Neighbours (ANN) benchmarks and research typically has an over-reliance on simplistic datasets like MNIST or SIFT1M and fail to reflect the complexity of current use-cases. Our investigation focuses on HNSW's efficacy across a spectrum of datasets, including synthetic vectors tailored to mimic specific intrinsic dimensionalities, widely-used retrieval benchmarks with popular embedding models, and proprietary e-commerce image data with CLIP models. We survey the most popular HNSW vector databases and collate their default parameters to provide a realistic fixed parameterisation for the duration of the paper. We discover that the recall of approximate HNSW search, in comparison to exact K Nearest Neighbours (KNN) search, is linked to the vector space's intrinsic dimensionality and significantly influenced by the data insertion sequence. Our methodology highlights how insertion order, informed by measurable properties such as the pointwise Local Intrinsic Dimensionality (LID) or known categories, can shift recall by up to 12 percentage points. We also observe that running popular benchmark datasets with HNSW instead of KNN can shift rankings by up to three positions for some models. This work underscores the need for more nuanced benchmarks and design considerations in developing robust vector search systems using approximate vector search algorithms. This study presents a number of scenarios with varying real world applicability which aim to better increase understanding and future development of ANN algorithms and embedding

Image-based table recognition: data, model, and evaluation

Important information that relates to a specific topic in a document is often organized in tabular format to assist readers with information retrieval and comparison, which may be difficult to provide in natural language. However, tabular data in unstructured digital documents, e.g., Portable Document Format (PDF) and images, are difficult to parse into structured machine-readable format, due to complexity and diversity in their structure and style. To facilitate image-based table recognition with deep learning, we develop the largest publicly available table recognition dataset PubTabNet (https://github.com/ibm-aur-nlp/PubTabNet), containing 568k table images with corresponding structured HTML representation. PubTabNet is automatically generated by matching the XML and PDF representations of the scientific articles in PubMed Central Open Access Subset (PMCOA). We also propose a novel attention-based encoder-dual-decoder (EDD) architecture that converts images of tables into HTML code. The model has a structure decoder which reconstructs the table structure and helps the cell decoder to recognize cell content. In addition, we propose a new Tree-Edit-Distance-based Similarity (TEDS) metric for table recognition, which more appropriately captures multi-hop cell misalignment and OCR errors than the pre-established metric. The experiments demonstrate that the EDD model can accurately recognize complex tables solely relying on the image representation, outperforming the state-of-the-art by 9.7% absolute TEDS score.

Specialized Document Embeddings for Aspect-based Similarity of Research Papers

Document embeddings and similarity measures underpin content-based recommender systems, whereby a document is commonly represented as a single generic embedding. However, similarity computed on single vector representations provides only one perspective on document similarity that ignores which aspects make two documents alike. To address this limitation, aspect-based similarity measures have been developed using document segmentation or pairwise multi-class document classification. While segmentation harms the document coherence, the pairwise classification approach scales poorly to large scale corpora. In this paper, we treat aspect-based similarity as a classical vector similarity problem in aspect-specific embedding spaces. We represent a document not as a single generic embedding but as multiple specialized embeddings. Our approach avoids document segmentation and scales linearly w.r.t.the corpus size. In an empirical study, we use the Papers with Code corpus containing 157,606 research papers and consider the task, method, and dataset of the respective research papers as their aspects. We compare and analyze three generic document embeddings, six specialized document embeddings and a pairwise classification baseline in the context of research paper recommendations. As generic document embeddings, we consider FastText, SciBERT, and SPECTER. To compute the specialized document embeddings, we compare three alternative methods inspired by retrofitting, fine-tuning, and Siamese networks. In our experiments, Siamese SciBERT achieved the highest scores. Additional analyses indicate an implicit bias of the generic document embeddings towards the dataset aspect and against the method aspect of each research paper. Our approach of aspect-based document embeddings mitigates potential risks arising from implicit biases by making them explicit.

Analysis of Linear Mode Connectivity via Permutation-Based Weight Matching

Recently, Ainsworth et al. showed that using weight matching (WM) to minimize the L_2 distance in a permutation search of model parameters effectively identifies permutations that satisfy linear mode connectivity (LMC), in which the loss along a linear path between two independently trained models with different seeds remains nearly constant. This paper provides a theoretical analysis of LMC using WM, which is crucial for understanding stochastic gradient descent's effectiveness and its application in areas like model merging. We first experimentally and theoretically show that permutations found by WM do not significantly reduce the L_2 distance between two models and the occurrence of LMC is not merely due to distance reduction by WM in itself. We then provide theoretical insights showing that permutations can change the directions of the singular vectors, but not the singular values, of the weight matrices in each layer. This finding shows that permutations found by WM mainly align the directions of singular vectors associated with large singular values across models. This alignment brings the singular vectors with large singular values, which determine the model functionality, closer between pre-merged and post-merged models, so that the post-merged model retains functionality similar to the pre-merged models, making it easy to satisfy LMC. Finally, we analyze the difference between WM and straight-through estimator (STE), a dataset-dependent permutation search method, and show that WM outperforms STE, especially when merging three or more models.

Unsupervised Matching of Data and Text

Entity resolution is a widely studied problem with several proposals to match records across relations. Matching textual content is a widespread task in many applications, such as question answering and search. While recent methods achieve promising results for these two tasks, there is no clear solution for the more general problem of matching textual content and structured data. We introduce a framework that supports this new task in an unsupervised setting for any pair of corpora, being relational tables or text documents. Our method builds a fine-grained graph over the content of the corpora and derives word embeddings to represent the objects to match in a low dimensional space. The learned representation enables effective and efficient matching at different granularity, from relational tuples to text sentences and paragraphs. Our flexible framework can exploit pre-trained resources, but it does not depends on their existence and achieves better quality performance in matching content when the vocabulary is domain specific. We also introduce optimizations in the graph creation process with an "expand and compress" approach that first identifies new valid relationships across elements, to improve matching, and then prunes nodes and edges, to reduce the graph size. Experiments on real use cases and public datasets show that our framework produces embeddings that outperform word embeddings and fine-tuned language models both in results' quality and in execution times.

Automated SSIM Regression for Detection and Quantification of Motion Artefacts in Brain MR Images

Motion artefacts in magnetic resonance brain images can have a strong impact on diagnostic confidence. The assessment of MR image quality is fundamental before proceeding with the clinical diagnosis. Motion artefacts can alter the delineation of structures such as the brain, lesions or tumours and may require a repeat scan. Otherwise, an inaccurate (e.g. correct pathology but wrong severity) or incorrect diagnosis (e.g. wrong pathology) may occur. "Image quality assessment" as a fast, automated step right after scanning can assist in deciding if the acquired images are diagnostically sufficient. An automated image quality assessment based on the structural similarity index (SSIM) regression through a residual neural network is proposed in this work. Additionally, a classification into different groups - by subdividing with SSIM ranges - is evaluated. Importantly, this method predicts SSIM values of an input image in the absence of a reference ground truth image. The networks were able to detect motion artefacts, and the best performance for the regression and classification task has always been achieved with ResNet-18 with contrast augmentation. The mean and standard deviation of residuals' distribution were mu=-0.0009 and sigma=0.0139, respectively. Whilst for the classification task in 3, 5 and 10 classes, the best accuracies were 97, 95 and 89\%, respectively. The results show that the proposed method could be a tool for supporting neuro-radiologists and radiographers in evaluating image quality quickly.

Cross-Modal Implicit Relation Reasoning and Aligning for Text-to-Image Person Retrieval

Text-to-image person retrieval aims to identify the target person based on a given textual description query. The primary challenge is to learn the mapping of visual and textual modalities into a common latent space. Prior works have attempted to address this challenge by leveraging separately pre-trained unimodal models to extract visual and textual features. However, these approaches lack the necessary underlying alignment capabilities required to match multimodal data effectively. Besides, these works use prior information to explore explicit part alignments, which may lead to the distortion of intra-modality information. To alleviate these issues, we present IRRA: a cross-modal Implicit Relation Reasoning and Aligning framework that learns relations between local visual-textual tokens and enhances global image-text matching without requiring additional prior supervision. Specifically, we first design an Implicit Relation Reasoning module in a masked language modeling paradigm. This achieves cross-modal interaction by integrating the visual cues into the textual tokens with a cross-modal multimodal interaction encoder. Secondly, to globally align the visual and textual embeddings, Similarity Distribution Matching is proposed to minimize the KL divergence between image-text similarity distributions and the normalized label matching distributions. The proposed method achieves new state-of-the-art results on all three public datasets, with a notable margin of about 3%-9% for Rank-1 accuracy compared to prior methods.

Balance Act: Mitigating Hubness in Cross-Modal Retrieval with Query and Gallery Banks

In this work, we present a post-processing solution to address the hubness problem in cross-modal retrieval, a phenomenon where a small number of gallery data points are frequently retrieved, resulting in a decline in retrieval performance. We first theoretically demonstrate the necessity of incorporating both the gallery and query data for addressing hubness as hubs always exhibit high similarity with gallery and query data. Second, building on our theoretical results, we propose a novel framework, Dual Bank Normalization (DBNorm). While previous work has attempted to alleviate hubness by only utilizing the query samples, DBNorm leverages two banks constructed from the query and gallery samples to reduce the occurrence of hubs during inference. Next, to complement DBNorm, we introduce two novel methods, dual inverted softmax and dual dynamic inverted softmax, for normalizing similarity based on the two banks. Specifically, our proposed methods reduce the similarity between hubs and queries while improving the similarity between non-hubs and queries. Finally, we present extensive experimental results on diverse language-grounded benchmarks, including text-image, text-video, and text-audio, demonstrating the superior performance of our approaches compared to previous methods in addressing hubness and boosting retrieval performance. Our code is available at https://github.com/yimuwangcs/Better_Cross_Modal_Retrieval.

G-SimCLR : Self-Supervised Contrastive Learning with Guided Projection via Pseudo Labelling

In the realms of computer vision, it is evident that deep neural networks perform better in a supervised setting with a large amount of labeled data. The representations learned with supervision are not only of high quality but also helps the model in enhancing its accuracy. However, the collection and annotation of a large dataset are costly and time-consuming. To avoid the same, there has been a lot of research going on in the field of unsupervised visual representation learning especially in a self-supervised setting. Amongst the recent advancements in self-supervised methods for visual recognition, in SimCLR Chen et al. shows that good quality representations can indeed be learned without explicit supervision. In SimCLR, the authors maximize the similarity of augmentations of the same image and minimize the similarity of augmentations of different images. A linear classifier trained with the representations learned using this approach yields 76.5% top-1 accuracy on the ImageNet ILSVRC-2012 dataset. In this work, we propose that, with the normalized temperature-scaled cross-entropy (NT-Xent) loss function (as used in SimCLR), it is beneficial to not have images of the same category in the same batch. In an unsupervised setting, the information of images pertaining to the same category is missing. We use the latent space representation of a denoising autoencoder trained on the unlabeled dataset and cluster them with k-means to obtain pseudo labels. With this apriori information we batch images, where no two images from the same category are to be found. We report comparable performance enhancements on the CIFAR10 dataset and a subset of the ImageNet dataset. We refer to our method as G-SimCLR.

Contrastive Latent Space Reconstruction Learning for Audio-Text Retrieval

Cross-modal retrieval (CMR) has been extensively applied in various domains, such as multimedia search engines and recommendation systems. Most existing CMR methods focus on image-to-text retrieval, whereas audio-to-text retrieval, a less explored domain, has posed a great challenge due to the difficulty to uncover discriminative features from audio clips and texts. Existing studies are restricted in the following two ways: 1) Most researchers utilize contrastive learning to construct a common subspace where similarities among data can be measured. However, they considers only cross-modal transformation, neglecting the intra-modal separability. Besides, the temperature parameter is not adaptively adjusted along with semantic guidance, which degrades the performance. 2) These methods do not take latent representation reconstruction into account, which is essential for semantic alignment. This paper introduces a novel audio-text oriented CMR approach, termed Contrastive Latent Space Reconstruction Learning (CLSR). CLSR improves contrastive representation learning by taking intra-modal separability into account and adopting an adaptive temperature control strategy. Moreover, the latent representation reconstruction modules are embedded into the CMR framework, which improves modal interaction. Experiments in comparison with some state-of-the-art methods on two audio-text datasets have validated the superiority of CLSR.

Differentiability and Optimization of Multiparameter Persistent Homology

Real-valued functions on geometric data -- such as node attributes on a graph -- can be optimized using descriptors from persistent homology, allowing the user to incorporate topological terms in the loss function. When optimizing a single real-valued function (the one-parameter setting), there is a canonical choice of descriptor for persistent homology: the barcode. The operation mapping a real-valued function to its barcode is differentiable almost everywhere, and the convergence of gradient descent for losses using barcodes is relatively well understood. When optimizing a vector-valued function (the multiparameter setting), there is no unique choice of descriptor for multiparameter persistent homology, and many distinct descriptors have been proposed. This calls for the development of a general framework for differentiability and optimization that applies to a wide range of multiparameter homological descriptors. In this article, we develop such a framework and show that it encompasses well-known descriptors of different flavors, such as signed barcodes and the multiparameter persistence landscape. We complement the theory with numerical experiments supporting the idea that optimizing multiparameter homological descriptors can lead to improved performances compared to optimizing one-parameter descriptors, even when using the simplest and most efficiently computable multiparameter descriptors.

Learning to Match Jobs with Resumes from Sparse Interaction Data using Multi-View Co-Teaching Network

With the ever-increasing growth of online recruitment data, job-resume matching has become an important task to automatically match jobs with suitable resumes. This task is typically casted as a supervised text matching problem. Supervised learning is powerful when the labeled data is sufficient. However, on online recruitment platforms, job-resume interaction data is sparse and noisy, which affects the performance of job-resume match algorithms. To alleviate these problems, in this paper, we propose a novel multi-view co-teaching network from sparse interaction data for job-resume matching. Our network consists of two major components, namely text-based matching model and relation-based matching model. The two parts capture semantic compatibility in two different views, and complement each other. In order to address the challenges from sparse and noisy data, we design two specific strategies to combine the two components. First, two components share the learned parameters or representations, so that the original representations of each component can be enhanced. More importantly, we adopt a co-teaching mechanism to reduce the influence of noise in training data. The core idea is to let the two components help each other by selecting more reliable training instances. The two strategies focus on representation enhancement and data enhancement, respectively. Compared with pure text-based matching models, the proposed approach is able to learn better data representations from limited or even sparse interaction data, which is more resistible to noise in training data. Experiment results have demonstrated that our model is able to outperform state-of-the-art methods for job-resume matching.

Causal de Finetti: On the Identification of Invariant Causal Structure in Exchangeable Data

Learning causal structure from observational data often assumes that we observe independent and identically distributed (i.\,i.\,d) data. The traditional approach aims to find a graphical representation that encodes the same set of conditional independence relationships as those present in the observed distribution. It is known that under i.\,i.\,d assumption, even with infinite data, there is a limit to how fine-grained a causal structure we can identify. To overcome this limitation, recent work has explored using data originating from different, related environments to learn richer causal structure. These approaches implicitly rely on the independent causal mechanisms (ICM) principle, which postulates that the mechanism giving rise to an effect given its causes and the mechanism which generates the causes do not inform or influence each other. Thus, components of the causal model can independently change from environment to environment. Despite its wide application in machine learning and causal inference, there is a lack of statistical formalization of the ICM principle and how it enables identification of richer causal structures from grouped data. Here we present new causal de Finetti theorems which offer a first statistical formalization of ICM principle and show how causal structure identification is possible from exchangeable data. Our work provides theoretical justification for a broad range of techniques leveraging multi-environment data to learn causal structure.

Improving Long Document Topic Segmentation Models With Enhanced Coherence Modeling

Topic segmentation is critical for obtaining structured documents and improving downstream tasks such as information retrieval. Due to its ability of automatically exploring clues of topic shift from abundant labeled data, recent supervised neural models have greatly promoted the development of long document topic segmentation, but leaving the deeper relationship between coherence and topic segmentation underexplored. Therefore, this paper enhances the ability of supervised models to capture coherence from both logical structure and semantic similarity perspectives to further improve the topic segmentation performance, proposing Topic-aware Sentence Structure Prediction (TSSP) and Contrastive Semantic Similarity Learning (CSSL). Specifically, the TSSP task is proposed to force the model to comprehend structural information by learning the original relations between adjacent sentences in a disarrayed document, which is constructed by jointly disrupting the original document at topic and sentence levels. Moreover, we utilize inter- and intra-topic information to construct contrastive samples and design the CSSL objective to ensure that the sentences representations in the same topic have higher similarity, while those in different topics are less similar. Extensive experiments show that the Longformer with our approach significantly outperforms old state-of-the-art (SOTA) methods. Our approach improve F_1 of old SOTA by 3.42 (73.74 -> 77.16) and reduces P_k by 1.11 points (15.0 -> 13.89) on WIKI-727K and achieves an average relative reduction of 4.3% on P_k on WikiSection. The average relative P_k drop of 8.38% on two out-of-domain datasets also demonstrates the robustness of our approach.

Fast, Expressive SE(n) Equivariant Networks through Weight-Sharing in Position-Orientation Space

Based on the theory of homogeneous spaces we derive geometrically optimal edge attributes to be used within the flexible message-passing framework. We formalize the notion of weight sharing in convolutional networks as the sharing of message functions over point-pairs that should be treated equally. We define equivalence classes of point-pairs that are identical up to a transformation in the group and derive attributes that uniquely identify these classes. Weight sharing is then obtained by conditioning message functions on these attributes. As an application of the theory, we develop an efficient equivariant group convolutional network for processing 3D point clouds. The theory of homogeneous spaces tells us how to do group convolutions with feature maps over the homogeneous space of positions R^3, position and orientations R^3 {times} S^2, and the group SE(3) itself. Among these, R^3 {times} S^2 is an optimal choice due to the ability to represent directional information, which R^3 methods cannot, and it significantly enhances computational efficiency compared to indexing features on the full SE(3) group. We support this claim with state-of-the-art results -- in accuracy and speed -- on five different benchmarks in 2D and 3D, including interatomic potential energy prediction, trajectory forecasting in N-body systems, and generating molecules via equivariant diffusion models.

A Novel Evaluation Framework for Image2Text Generation

Evaluating the quality of automatically generated image descriptions is challenging, requiring metrics that capture various aspects such as grammaticality, coverage, correctness, and truthfulness. While human evaluation offers valuable insights, its cost and time-consuming nature pose limitations. Existing automated metrics like BLEU, ROUGE, METEOR, and CIDEr aim to bridge this gap but often show weak correlations with human judgment. We address this challenge by introducing a novel evaluation framework rooted in a modern large language model (LLM), such as GPT-4 or Gemini, capable of image generation. In our proposed framework, we begin by feeding an input image into a designated image captioning model, chosen for evaluation, to generate a textual description. Using this description, an LLM then creates a new image. By extracting features from both the original and LLM-created images, we measure their similarity using a designated similarity metric. A high similarity score suggests that the image captioning model has accurately generated textual descriptions, while a low similarity score indicates discrepancies, revealing potential shortcomings in the model's performance. Human-annotated reference captions are not required in our proposed evaluation framework, which serves as a valuable tool for evaluating the effectiveness of image captioning models. Its efficacy is confirmed through human evaluation.

Using Sequences of Life-events to Predict Human Lives

Over the past decade, machine learning has revolutionized computers' ability to analyze text through flexible computational models. Due to their structural similarity to written language, transformer-based architectures have also shown promise as tools to make sense of a range of multi-variate sequences from protein-structures, music, electronic health records to weather-forecasts. We can also represent human lives in a way that shares this structural similarity to language. From one perspective, lives are simply sequences of events: People are born, visit the pediatrician, start school, move to a new location, get married, and so on. Here, we exploit this similarity to adapt innovations from natural language processing to examine the evolution and predictability of human lives based on detailed event sequences. We do this by drawing on arguably the most comprehensive registry data in existence, available for an entire nation of more than six million individuals across decades. Our data include information about life-events related to health, education, occupation, income, address, and working hours, recorded with day-to-day resolution. We create embeddings of life-events in a single vector space showing that this embedding space is robust and highly structured. Our models allow us to predict diverse outcomes ranging from early mortality to personality nuances, outperforming state-of-the-art models by a wide margin. Using methods for interpreting deep learning models, we probe the algorithm to understand the factors that enable our predictions. Our framework allows researchers to identify new potential mechanisms that impact life outcomes and associated possibilities for personalized interventions.

OmniMatch: Effective Self-Supervised Any-Join Discovery in Tabular Data Repositories

How can we discover join relationships among columns of tabular data in a data repository? Can this be done effectively when metadata is missing? Traditional column matching works mainly rely on similarity measures based on exact value overlaps, hence missing important semantics or failing to handle noise in the data. At the same time, recent dataset discovery methods focusing on deep table representation learning techniques, do not take into consideration the rich set of column similarity signals found in prior matching and discovery methods. Finally, existing methods heavily depend on user-provided similarity thresholds, hindering their deployability in real-world settings. In this paper, we propose OmniMatch, a novel join discovery technique that detects equi-joins and fuzzy-joins betwen columns by combining column-pair similarity measures with Graph Neural Networks (GNNs). OmniMatch's GNN can capture column relatedness leveraging graph transitivity, significantly improving the recall of join discovery tasks. At the same time, OmniMatch also increases the precision by augmenting its training data with negative column join examples through an automated negative example generation process. Most importantly, compared to the state-of-the-art matching and discovery methods, OmniMatch exhibits up to 14% higher effectiveness in F1 score and AUC without relying on metadata or user-provided thresholds for each similarity metric.