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Sep 2

ATOMMIC: An Advanced Toolbox for Multitask Medical Imaging Consistency to facilitate Artificial Intelligence applications from acquisition to analysis in Magnetic Resonance Imaging

AI is revolutionizing MRI along the acquisition and processing chain. Advanced AI frameworks have been developed to apply AI in various successive tasks, such as image reconstruction, quantitative parameter map estimation, and image segmentation. Existing frameworks are often designed to perform tasks independently or are focused on specific models or datasets, limiting generalization. We introduce ATOMMIC, an open-source toolbox that streamlines AI applications for accelerated MRI reconstruction and analysis. ATOMMIC implements several tasks using DL networks and enables MultiTask Learning (MTL) to perform related tasks integrated, targeting generalization in the MRI domain. We first review the current state of AI frameworks for MRI through a comprehensive literature search and by parsing 12,479 GitHub repositories. We benchmark 25 DL models on eight publicly available datasets to present distinct applications of ATOMMIC on accelerated MRI reconstruction, image segmentation, quantitative parameter map estimation, and joint accelerated MRI reconstruction and image segmentation utilizing MTL. Our findings demonstrate that ATOMMIC is the only MTL framework with harmonized complex-valued and real-valued data support. Evaluations on single tasks show that physics-based models, which enforce data consistency by leveraging the physical properties of MRI, outperform other models in reconstructing highly accelerated acquisitions. Physics-based models that produce high reconstruction quality can accurately estimate quantitative parameter maps. When high-performing reconstruction models are combined with robust segmentation networks utilizing MTL, performance is improved in both tasks. ATOMMIC facilitates MRI reconstruction and analysis by standardizing workflows, enhancing data interoperability, integrating unique features like MTL, and effectively benchmarking DL models.

Scaling Multimodal Pre-Training via Cross-Modality Gradient Harmonization

Self-supervised pre-training recently demonstrates success on large-scale multimodal data, and state-of-the-art contrastive learning methods often enforce the feature consistency from cross-modality inputs, such as video/audio or video/text pairs. Despite its convenience to formulate and leverage in practice, such cross-modality alignment (CMA) is only a weak and noisy supervision, since two modalities can be semantically misaligned even they are temporally aligned. For example, even in the commonly adopted instructional videos, a speaker can sometimes refer to something that is not visually present in the current frame; and the semantic misalignment would only be more unpredictable for the raw videos from the internet. We conjecture that might cause conflicts and biases among modalities, and may hence prohibit CMA from scaling up to training with larger and more heterogeneous data. This paper first verifies our conjecture by observing that, even in the latest VATT pre-training using only instructional videos, there exist strong gradient conflicts between different CMA losses within the same video, audio, text triplet, indicating them as the noisy source of supervision. We then propose to harmonize such gradients, via two techniques: (i) cross-modality gradient realignment: modifying different CMA loss gradients for each sample triplet, so that their gradient directions are more aligned; and (ii) gradient-based curriculum learning: leveraging the gradient conflict information on an indicator of sample noisiness, to develop a curriculum learning strategy to prioritize training on less noisy sample triplets. Applying those techniques to pre-training VATT on the HowTo100M dataset, we consistently improve its performance on different downstream tasks. Moreover, we are able to scale VATT pre-training to more complicated non-narrative Youtube8M dataset to further improve the state-of-the-arts.

Relightful Harmonization: Lighting-aware Portrait Background Replacement

Portrait harmonization aims to composite a subject into a new background, adjusting its lighting and color to ensure harmony with the background scene. Existing harmonization techniques often only focus on adjusting the global color and brightness of the foreground and ignore crucial illumination cues from the background such as apparent lighting direction, leading to unrealistic compositions. We introduce Relightful Harmonization, a lighting-aware diffusion model designed to seamlessly harmonize sophisticated lighting effect for the foreground portrait using any background image. Our approach unfolds in three stages. First, we introduce a lighting representation module that allows our diffusion model to encode lighting information from target image background. Second, we introduce an alignment network that aligns lighting features learned from image background with lighting features learned from panorama environment maps, which is a complete representation for scene illumination. Last, to further boost the photorealism of the proposed method, we introduce a novel data simulation pipeline that generates synthetic training pairs from a diverse range of natural images, which are used to refine the model. Our method outperforms existing benchmarks in visual fidelity and lighting coherence, showing superior generalization in real-world testing scenarios, highlighting its versatility and practicality.

BlindHarmony: "Blind" Harmonization for MR Images via Flow model

In MRI, images of the same contrast (e.g., T_1) from the same subject can exhibit noticeable differences when acquired using different hardware, sequences, or scan parameters. These differences in images create a domain gap that needs to be bridged by a step called image harmonization, to process the images successfully using conventional or deep learning-based image analysis (e.g., segmentation). Several methods, including deep learning-based approaches, have been proposed to achieve image harmonization. However, they often require datasets from multiple domains for deep learning training and may still be unsuccessful when applied to images from unseen domains. To address this limitation, we propose a novel concept called `Blind Harmonization', which utilizes only target domain data for training but still has the capability to harmonize images from unseen domains. For the implementation of blind harmonization, we developed BlindHarmony using an unconditional flow model trained on target domain data. The harmonized image is optimized to have a correlation with the input source domain image while ensuring that the latent vector of the flow model is close to the center of the Gaussian distribution. BlindHarmony was evaluated on both simulated and real datasets and compared to conventional methods. BlindHarmony demonstrated noticeable performance on both datasets, highlighting its potential for future use in clinical settings. The source code is available at: https://github.com/SNU-LIST/BlindHarmony

Harmonizing the object recognition strategies of deep neural networks with humans

The many successes of deep neural networks (DNNs) over the past decade have largely been driven by computational scale rather than insights from biological intelligence. Here, we explore if these trends have also carried concomitant improvements in explaining the visual strategies humans rely on for object recognition. We do this by comparing two related but distinct properties of visual strategies in humans and DNNs: where they believe important visual features are in images and how they use those features to categorize objects. Across 84 different DNNs trained on ImageNet and three independent datasets measuring the where and the how of human visual strategies for object recognition on those images, we find a systematic trade-off between DNN categorization accuracy and alignment with human visual strategies for object recognition. State-of-the-art DNNs are progressively becoming less aligned with humans as their accuracy improves. We rectify this growing issue with our neural harmonizer: a general-purpose training routine that both aligns DNN and human visual strategies and improves categorization accuracy. Our work represents the first demonstration that the scaling laws that are guiding the design of DNNs today have also produced worse models of human vision. We release our code and data at https://serre-lab.github.io/Harmonization to help the field build more human-like DNNs.

ClinLinker: Medical Entity Linking of Clinical Concept Mentions in Spanish

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

tasksource: Structured Dataset Preprocessing Annotations for Frictionless Extreme Multi-Task Learning and Evaluation

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

DTT: An Example-Driven Tabular Transformer for Joinability by Leveraging Large Language Models

Many organizations rely on data from government and third-party sources, and those sources rarely follow the same data formatting. This introduces challenges in integrating data from multiple sources or aligning external sources with internal databases. Commercial database systems do not offer adequate support for integrating data from heterogeneous sources, and manual integration is both time-consuming and inefficient. State-of-the-art data integration approaches that rely on similarity functions and textual transformations often fail to handle challenging cases where multiple mappings are required, or the mappings go beyond simple textual transformations. In this paper, we study the potentials of deep neural models for transforming tables for joinability. In particular, we cast the problem as a prediction task and develop a framework that leverages large deep-learning language models to transform tabular data from a source formatting to a desired target representation. Our framework can efficiently learn the patterns for mapping a source formatting into an expected target using just a few examples, which can then be used for tasks such as table joining, filling in missing values, and error detection. Compared to state-of-the-art mapping and joining approaches, our framework delivers noticeably more accurate and scalable performance on both real-world and synthetic datasets. Our experimental evaluation also shows that the performance of the proposed framework using our fine-tuned model is at par or better than large language models such as GPT-3, despite the significant difference in size, and that using large language models within our framework improves their performance.

OpenDataLab: Empowering General Artificial Intelligence with Open Datasets

The advancement of artificial intelligence (AI) hinges on the quality and accessibility of data, yet the current fragmentation and variability of data sources hinder efficient data utilization. The dispersion of data sources and diversity of data formats often lead to inefficiencies in data retrieval and processing, significantly impeding the progress of AI research and applications. To address these challenges, this paper introduces OpenDataLab, a platform designed to bridge the gap between diverse data sources and the need for unified data processing. OpenDataLab integrates a wide range of open-source AI datasets and enhances data acquisition efficiency through intelligent querying and high-speed downloading services. The platform employs a next-generation AI Data Set Description Language (DSDL), which standardizes the representation of multimodal and multi-format data, improving interoperability and reusability. Additionally, OpenDataLab optimizes data processing through tools that complement DSDL. By integrating data with unified data descriptions and smart data toolchains, OpenDataLab can improve data preparation efficiency by 30\%. We anticipate that OpenDataLab will significantly boost artificial general intelligence (AGI) research and facilitate advancements in related AI fields. For more detailed information, please visit the platform's official website: https://opendatalab.com.

Building Flexible, Scalable, and Machine Learning-ready Multimodal Oncology Datasets

The advancements in data acquisition, storage, and processing techniques have resulted in the rapid growth of heterogeneous medical data. Integrating radiological scans, histopathology images, and molecular information with clinical data is essential for developing a holistic understanding of the disease and optimizing treatment. The need for integrating data from multiple sources is further pronounced in complex diseases such as cancer for enabling precision medicine and personalized treatments. This work proposes Multimodal Integration of Oncology Data System (MINDS) - a flexible, scalable, and cost-effective metadata framework for efficiently fusing disparate data from public sources such as the Cancer Research Data Commons (CRDC) into an interconnected, patient-centric framework. MINDS offers an interface for exploring relationships across data types and building cohorts for developing large-scale multimodal machine learning models. By harmonizing multimodal data, MINDS aims to potentially empower researchers with greater analytical ability to uncover diagnostic and prognostic insights and enable evidence-based personalized care. MINDS tracks granular end-to-end data provenance, ensuring reproducibility and transparency. The cloud-native architecture of MINDS can handle exponential data growth in a secure, cost-optimized manner while ensuring substantial storage optimization, replication avoidance, and dynamic access capabilities. Auto-scaling, access controls, and other mechanisms guarantee pipelines' scalability and security. MINDS overcomes the limitations of existing biomedical data silos via an interoperable metadata-driven approach that represents a pivotal step toward the future of oncology data integration.

Solving Data Quality Problems with Desbordante: a Demo

Data profiling is an essential process in modern data-driven industries. One of its critical components is the discovery and validation of complex statistics, including functional dependencies, data constraints, association rules, and others. However, most existing data profiling systems that focus on complex statistics do not provide proper integration with the tools used by contemporary data scientists. This creates a significant barrier to the adoption of these tools in the industry. Moreover, existing systems were not created with industrial-grade workloads in mind. Finally, they do not aim to provide descriptive explanations, i.e. why a given pattern is not found. It is a significant issue as it is essential to understand the underlying reasons for a specific pattern's absence to make informed decisions based on the data. Because of that, these patterns are effectively rest in thin air: their application scope is rather limited, they are rarely used by the broader public. At the same time, as we are going to demonstrate in this presentation, complex statistics can be efficiently used to solve many classic data quality problems. Desbordante is an open-source data profiler that aims to close this gap. It is built with emphasis on industrial application: it is efficient, scalable, resilient to crashes, and provides explanations. Furthermore, it provides seamless Python integration by offloading various costly operations to the C++ core, not only mining. In this demonstration, we show several scenarios that allow end users to solve different data quality problems. Namely, we showcase typo detection, data deduplication, and data anomaly detection scenarios.

Valentine: Evaluating Matching Techniques for Dataset Discovery

Data scientists today search large data lakes to discover and integrate datasets. In order to bring together disparate data sources, dataset discovery methods rely on some form of schema matching: the process of establishing correspondences between datasets. Traditionally, schema matching has been used to find matching pairs of columns between a source and a target schema. However, the use of schema matching in dataset discovery methods differs from its original use. Nowadays schema matching serves as a building block for indicating and ranking inter-dataset relationships. Surprisingly, although a discovery method's success relies highly on the quality of the underlying matching algorithms, the latest discovery methods employ existing schema matching algorithms in an ad-hoc fashion due to the lack of openly-available datasets with ground truth, reference method implementations, and evaluation metrics. In this paper, we aim to rectify the problem of evaluating the effectiveness and efficiency of schema matching methods for the specific needs of dataset discovery. To this end, we propose Valentine, an extensible open-source experiment suite to execute and organize large-scale automated matching experiments on tabular data. Valentine includes implementations of seminal schema matching methods that we either implemented from scratch (due to absence of open source code) or imported from open repositories. The contributions of Valentine are: i) the definition of four schema matching scenarios as encountered in dataset discovery methods, ii) a principled dataset fabrication process tailored to the scope of dataset discovery methods and iii) the most comprehensive evaluation of schema matching techniques to date, offering insight on the strengths and weaknesses of existing techniques, that can serve as a guide for employing schema matching in future dataset discovery methods.

Deep Learning, Machine Learning, Advancing Big Data Analytics and Management

Advancements in artificial intelligence, machine learning, and deep learning have catalyzed the transformation of big data analytics and management into pivotal domains for research and application. This work explores the theoretical foundations, methodological advancements, and practical implementations of these technologies, emphasizing their role in uncovering actionable insights from massive, high-dimensional datasets. The study presents a systematic overview of data preprocessing techniques, including data cleaning, normalization, integration, and dimensionality reduction, to prepare raw data for analysis. Core analytics methodologies such as classification, clustering, regression, and anomaly detection are examined, with a focus on algorithmic innovation and scalability. Furthermore, the text delves into state-of-the-art frameworks for data mining and predictive modeling, highlighting the role of neural networks, support vector machines, and ensemble methods in tackling complex analytical challenges. Special emphasis is placed on the convergence of big data with distributed computing paradigms, including cloud and edge computing, to address challenges in storage, computation, and real-time analytics. The integration of ethical considerations, including data privacy and compliance with global standards, ensures a holistic perspective on data management. Practical applications across healthcare, finance, marketing, and policy-making illustrate the real-world impact of these technologies. Through comprehensive case studies and Python-based implementations, this work equips researchers, practitioners, and data enthusiasts with the tools to navigate the complexities of modern data analytics. It bridges the gap between theory and practice, fostering the development of innovative solutions for managing and leveraging data in the era of artificial intelligence.

FAIR Jupyter: a knowledge graph approach to semantic sharing and granular exploration of a computational notebook reproducibility dataset

The way in which data are shared can affect their utility and reusability. Here, we demonstrate how data that we had previously shared in bulk can be mobilized further through a knowledge graph that allows for much more granular exploration and interrogation. The original dataset is about the computational reproducibility of GitHub-hosted Jupyter notebooks associated with biomedical publications. It contains rich metadata about the publications, associated GitHub repositories and Jupyter notebooks, and the notebooks' reproducibility. We took this dataset, converted it into semantic triples and loaded these into a triple store to create a knowledge graph, FAIR Jupyter, that we made accessible via a web service. This enables granular data exploration and analysis through queries that can be tailored to specific use cases. Such queries may provide details about any of the variables from the original dataset, highlight relationships between them or combine some of the graph's content with materials from corresponding external resources. We provide a collection of example queries addressing a range of use cases in research and education. We also outline how sets of such queries can be used to profile specific content types, either individually or by class. We conclude by discussing how such a semantically enhanced sharing of complex datasets can both enhance their FAIRness, i.e., their findability, accessibility, interoperability, and reusability, and help identify and communicate best practices, particularly with regards to data quality, standardization, automation and reproducibility.

The Data Provenance Initiative: A Large Scale Audit of Dataset Licensing & Attribution in AI

The race to train language models on vast, diverse, and inconsistently documented datasets has raised pressing concerns about the legal and ethical risks for practitioners. To remedy these practices threatening data transparency and understanding, we convene a multi-disciplinary effort between legal and machine learning experts to systematically audit and trace 1800+ text datasets. We develop tools and standards to trace the lineage of these datasets, from their source, creators, series of license conditions, properties, and subsequent use. Our landscape analysis highlights the sharp divides in composition and focus of commercially open vs closed datasets, with closed datasets monopolizing important categories: lower resource languages, more creative tasks, richer topic variety, newer and more synthetic training data. This points to a deepening divide in the types of data that are made available under different license conditions, and heightened implications for jurisdictional legal interpretations of copyright and fair use. We also observe frequent miscategorization of licenses on widely used dataset hosting sites, with license omission of 72%+ and error rates of 50%+. This points to a crisis in misattribution and informed use of the most popular datasets driving many recent breakthroughs. As a contribution to ongoing improvements in dataset transparency and responsible use, we release our entire audit, with an interactive UI, the Data Provenance Explorer, which allows practitioners to trace and filter on data provenance for the most popular open source finetuning data collections: www.dataprovenance.org.

Data Cards: Purposeful and Transparent Dataset Documentation for Responsible AI

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

BARS: Towards Open Benchmarking for Recommender Systems

The past two decades have witnessed the rapid development of personalized recommendation techniques. Despite significant progress made in both research and practice of recommender systems, to date, there is a lack of a widely-recognized benchmarking standard in this field. Many existing studies perform model evaluations and comparisons in an ad-hoc manner, for example, by employing their own private data splits or using different experimental settings. Such conventions not only increase the difficulty in reproducing existing studies, but also lead to inconsistent experimental results among them. This largely limits the credibility and practical value of research results in this field. To tackle these issues, we present an initiative project (namely BARS) aiming for open benchmarking for recommender systems. In comparison to some earlier attempts towards this goal, we take a further step by setting up a standardized benchmarking pipeline for reproducible research, which integrates all the details about datasets, source code, hyper-parameter settings, running logs, and evaluation results. The benchmark is designed with comprehensiveness and sustainability in mind. It covers both matching and ranking tasks, and also enables researchers to easily follow and contribute to the research in this field. This project will not only reduce the redundant efforts of researchers to re-implement or re-run existing baselines, but also drive more solid and reproducible research on recommender systems. We would like to call upon everyone to use the BARS benchmark for future evaluation, and contribute to the project through the portal at: https://openbenchmark.github.io/BARS.

IndicLLMSuite: A Blueprint for Creating Pre-training and Fine-Tuning Datasets for Indian Languages

Despite the considerable advancements in English LLMs, the progress in building comparable models for other languages has been hindered due to the scarcity of tailored resources. Our work aims to bridge this divide by introducing an expansive suite of resources specifically designed for the development of Indic LLMs, covering 22 languages, containing a total of 251B tokens and 74.8M instruction-response pairs. Recognizing the importance of both data quality and quantity, our approach combines highly curated manually verified data, unverified yet valuable data, and synthetic data. We build a clean, open-source pipeline for curating pre-training data from diverse sources, including websites, PDFs, and videos, incorporating best practices for crawling, cleaning, flagging, and deduplication. For instruction-fine tuning, we amalgamate existing Indic datasets, translate/transliterate English datasets into Indian languages, and utilize LLaMa2 and Mixtral models to create conversations grounded in articles from Indian Wikipedia and Wikihow. Additionally, we address toxicity alignment by generating toxic prompts for multiple scenarios and then generate non-toxic responses by feeding these toxic prompts to an aligned LLaMa2 model. We hope that the datasets, tools, and resources released as a part of this work will not only propel the research and development of Indic LLMs but also establish an open-source blueprint for extending such efforts to other languages. The data and other artifacts created as part of this work are released with permissive licenses.

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.

Challenges and Considerations in Annotating Legal Data: A Comprehensive Overview

The process of annotating data within the legal sector is filled with distinct challenges that differ from other fields, primarily due to the inherent complexities of legal language and documentation. The initial task usually involves selecting an appropriate raw dataset that captures the intricate aspects of legal texts. Following this, extracting text becomes a complicated task, as legal documents often have complex structures, footnotes, references, and unique terminology. The importance of data cleaning is magnified in this context, ensuring that redundant information is eliminated while maintaining crucial legal details and context. Creating comprehensive yet straightforward annotation guidelines is imperative, as these guidelines serve as the road map for maintaining uniformity and addressing the subtle nuances of legal terminology. Another critical aspect is the involvement of legal professionals in the annotation process. Their expertise is valuable in ensuring that the data not only remains contextually accurate but also adheres to prevailing legal standards and interpretations. This paper provides an expanded view of these challenges and aims to offer a foundational understanding and guidance for researchers and professionals engaged in legal data annotation projects. In addition, we provide links to our created and fine-tuned datasets and language models. These resources are outcomes of our discussed projects and solutions to challenges faced while working on them.

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").

Automotive Perception Software Development: An Empirical Investigation into Data, Annotation, and Ecosystem Challenges

Software that contains machine learning algorithms is an integral part of automotive perception, for example, in driving automation systems. The development of such software, specifically the training and validation of the machine learning components, require large annotated datasets. An industry of data and annotation services has emerged to serve the development of such data-intensive automotive software components. Wide-spread difficulties to specify data and annotation needs challenge collaborations between OEMs (Original Equipment Manufacturers) and their suppliers of software components, data, and annotations. This paper investigates the reasons for these difficulties for practitioners in the Swedish automotive industry to arrive at clear specifications for data and annotations. The results from an interview study show that a lack of effective metrics for data quality aspects, ambiguities in the way of working, unclear definitions of annotation quality, and deficits in the business ecosystems are causes for the difficulty in deriving the specifications. We provide a list of recommendations that can mitigate challenges when deriving specifications and we propose future research opportunities to overcome these challenges. Our work contributes towards the on-going research on accountability of machine learning as applied to complex software systems, especially for high-stake applications such as automated driving.

Rankify: A Comprehensive Python Toolkit for Retrieval, Re-Ranking, and Retrieval-Augmented Generation

Retrieval, re-ranking, and retrieval-augmented generation (RAG) are critical components of modern applications in information retrieval, question answering, or knowledge-based text generation. However, existing solutions are often fragmented, lacking a unified framework that easily integrates these essential processes. The absence of a standardized implementation, coupled with the complexity of retrieval and re-ranking workflows, makes it challenging for researchers to compare and evaluate different approaches in a consistent environment. While existing toolkits such as Rerankers and RankLLM provide general-purpose reranking pipelines, they often lack the flexibility required for fine-grained experimentation and benchmarking. In response to these challenges, we introduce Rankify, a powerful and modular open-source toolkit designed to unify retrieval, re-ranking, and RAG within a cohesive framework. Rankify supports a wide range of retrieval techniques, including dense and sparse retrievers, while incorporating state-of-the-art re-ranking models to enhance retrieval quality. Additionally, Rankify includes a collection of pre-retrieved datasets to facilitate benchmarking, available at Huggingface (https://huggingface.co/datasets/abdoelsayed/reranking-datasets-light). To encourage adoption and ease of integration, we provide comprehensive documentation (http://rankify.readthedocs.io/), an open-source implementation on GitHub (https://github.com/DataScienceUIBK/rankify), and a PyPI package for easy installation (https://pypi.org/project/rankify/). As a unified and lightweight framework, Rankify allows researchers and practitioners to advance retrieval and re-ranking methodologies while ensuring consistency, scalability, and ease of use.

Meta-rater: A Multi-dimensional Data Selection Method for Pre-training Language Models

The composition of pre-training datasets for large language models (LLMs) remains largely undisclosed, hindering transparency and efforts to optimize data quality, a critical driver of model performance. Current data selection methods, such as natural language quality assessments, diversity-based filters, and classifier-based approaches, are limited by single-dimensional evaluation or redundancy-focused strategies. To address these gaps, we propose four dimensions to evaluate data quality: professionalism, readability, reasoning, and cleanliness. We further introduce Meta-rater,a multi-dimensional data selection method that integrates these dimensions with existing quality metrics through learned optimal weightings. Meta-rater employs proxy models to train a regression model that predicts validation loss, enabling the identification of optimal combinations of quality scores. Experiments demonstrate that Meta-rater doubles convergence speed for 1.3B parameter models and improves downstream task performance by 3.23, with advantages that scale to models as large as 7.2B parameters. Our work establishes that holistic, multi-dimensional quality integration significantly outperforms conventional single-dimension approaches, offering a scalable paradigm for enhancing pre-training efficiency and model capability. To advance future research, we release scripts, data, and models at https://github.com/opendatalab/Meta-rater.

Source Code Data Augmentation for Deep Learning: A Survey

The increasingly popular adoption of deep learning models in many critical source code tasks motivates the development of data augmentation (DA) techniques to enhance training data and improve various capabilities (e.g., robustness and generalizability) of these models. Although a series of DA methods have been proposed and tailored for source code models, there lacks a comprehensive survey and examination to understand their effectiveness and implications. This paper fills this gap by conducting a comprehensive and integrative survey of data augmentation for source code, wherein we systematically compile and encapsulate existing literature to provide a comprehensive overview of the field. We start with an introduction of data augmentation in source code and then provide a discussion on major representative approaches. Next, we highlight the general strategies and techniques to optimize the DA quality. Subsequently, we underscore techniques useful in real-world source code scenarios and downstream tasks. Finally, we outline the prevailing challenges and potential opportunities for future research. In essence, we aim to demystify the corpus of existing literature on source code DA for deep learning, and foster further exploration in this sphere. Complementing this, we present a continually updated GitHub repository that hosts a list of update-to-date papers on DA for source code modeling, accessible at https://github.com/terryyz/DataAug4Code.

Datasheets Aren't Enough: DataRubrics for Automated Quality Metrics and Accountability

High-quality datasets are fundamental to training and evaluating machine learning models, yet their creation-especially with accurate human annotations-remains a significant challenge. Many dataset paper submissions lack originality, diversity, or rigorous quality control, and these shortcomings are often overlooked during peer review. Submissions also frequently omit essential details about dataset construction and properties. While existing tools such as datasheets aim to promote transparency, they are largely descriptive and do not provide standardized, measurable methods for evaluating data quality. Similarly, metadata requirements at conferences promote accountability but are inconsistently enforced. To address these limitations, this position paper advocates for the integration of systematic, rubric-based evaluation metrics into the dataset review process-particularly as submission volumes continue to grow. We also explore scalable, cost-effective methods for synthetic data generation, including dedicated tools and LLM-as-a-judge approaches, to support more efficient evaluation. As a call to action, we introduce DataRubrics, a structured framework for assessing the quality of both human- and model-generated datasets. Leveraging recent advances in LLM-based evaluation, DataRubrics offers a reproducible, scalable, and actionable solution for dataset quality assessment, enabling both authors and reviewers to uphold higher standards in data-centric research. We also release code to support reproducibility of LLM-based evaluations at https://github.com/datarubrics/datarubrics.

EHRCon: Dataset for Checking Consistency between Unstructured Notes and Structured Tables in Electronic Health Records

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

Enforcing public data archiving policies in academic publishing: A study of ecology journals

To improve the quality and efficiency of research, groups within the scientific community seek to exploit the value of data sharing. Funders, institutions, and specialist organizations are developing and implementing strategies to encourage or mandate data sharing within and across disciplines, with varying degrees of success. Academic journals in ecology and evolution have adopted several types of public data archiving policies requiring authors to make data underlying scholarly manuscripts freely available. Yet anecdotes from the community and studies evaluating data availability suggest that these policies have not obtained the desired effects, both in terms of quantity and quality of available datasets. We conducted a qualitative, interview-based study with journal editorial staff and other stakeholders in the academic publishing process to examine how journals enforce data archiving policies. We specifically sought to establish who editors and other stakeholders perceive as responsible for ensuring data completeness and quality in the peer review process. Our analysis revealed little consensus with regard to how data archiving policies should be enforced and who should hold authors accountable for dataset submissions. Themes in interviewee responses included hopefulness that reviewers would take the initiative to review datasets and trust in authors to ensure the completeness and quality of their datasets. We highlight problematic aspects of these thematic responses and offer potential starting points for improvement of the public data archiving process.

Toxicity of the Commons: Curating Open-Source Pre-Training Data

Open-source large language models are becoming increasingly available and popular among researchers and practitioners. While significant progress has been made on open-weight models, open training data is a practice yet to be adopted by the leading open-weight models creators. At the same time, there researchers are working to make language models safer. We propose a data curation pipeline to reduce harmful outputs by models trained on public domain data. There are unique challenges to working with public domain data, as these sources differ from web text in both form and content. Many sources are historical documents and are the result of Optical Character Recognition (OCR). Consequently, current state-of-the-art approaches to toxicity filtering are often infeasible or inappropriate for open data models. In this paper, we introduce a new fully open-source pipeline for open-data toxicity filtering. Our contributions are threefold. We create a custom training dataset, ToxicCommons, which is composed of texts which have been classified across five different dimensions (racial/origin-based, gender/sex-based, religious, ability-based discrimination, and violence). We use this dataset to train a custom classifier, Celadon, that can be used to detect toxic content in open data more efficiently at a larger scale. Finally, we describe the balanced approach to content filtration that optimizes safety filtering with respect to the filtered data available for training.

SustainBench: Benchmarks for Monitoring the Sustainable Development Goals with Machine Learning

Progress toward the United Nations Sustainable Development Goals (SDGs) has been hindered by a lack of data on key environmental and socioeconomic indicators, which historically have come from ground surveys with sparse temporal and spatial coverage. Recent advances in machine learning have made it possible to utilize abundant, frequently-updated, and globally available data, such as from satellites or social media, to provide insights into progress toward SDGs. Despite promising early results, approaches to using such data for SDG measurement thus far have largely evaluated on different datasets or used inconsistent evaluation metrics, making it hard to understand whether performance is improving and where additional research would be most fruitful. Furthermore, processing satellite and ground survey data requires domain knowledge that many in the machine learning community lack. In this paper, we introduce SustainBench, a collection of 15 benchmark tasks across 7 SDGs, including tasks related to economic development, agriculture, health, education, water and sanitation, climate action, and life on land. Datasets for 11 of the 15 tasks are released publicly for the first time. Our goals for SustainBench are to (1) lower the barriers to entry for the machine learning community to contribute to measuring and achieving the SDGs; (2) provide standard benchmarks for evaluating machine learning models on tasks across a variety of SDGs; and (3) encourage the development of novel machine learning methods where improved model performance facilitates progress towards the SDGs.

Quality Not Quantity: On the Interaction between Dataset Design and Robustness of CLIP

Web-crawled datasets have enabled remarkable generalization capabilities in recent image-text models such as CLIP (Contrastive Language-Image pre-training) or Flamingo, but little is known about the dataset creation processes. In this work, we introduce a testbed of six publicly available data sources - YFCC, LAION, Conceptual Captions, WIT, RedCaps, Shutterstock - to investigate how pre-training distributions induce robustness in CLIP. We find that the performance of the pre-training data varies substantially across distribution shifts, with no single data source dominating. Moreover, we systematically study the interactions between these data sources and find that combining multiple sources does not necessarily yield better models, but rather dilutes the robustness of the best individual data source. We complement our empirical findings with theoretical insights from a simple setting, where combining the training data also results in diluted robustness. In addition, our theoretical model provides a candidate explanation for the success of the CLIP-based data filtering technique recently employed in the LAION dataset. Overall our results demonstrate that simply gathering a large amount of data from the web is not the most effective way to build a pre-training dataset for robust generalization, necessitating further study into dataset design. Code is available at https://github.com/mlfoundations/clip_quality_not_quantity.

Fidelity and Privacy of Synthetic Medical Data

The digitization of medical records ushered in a new era of big data to clinical science, and with it the possibility that data could be shared, to multiply insights beyond what investigators could abstract from paper records. The need to share individual-level medical data to accelerate innovation in precision medicine continues to grow, and has never been more urgent, as scientists grapple with the COVID-19 pandemic. However, enthusiasm for the use of big data has been tempered by a fully appropriate concern for patient autonomy and privacy. That is, the ability to extract private or confidential information about an individual, in practice, renders it difficult to share data, since significant infrastructure and data governance must be established before data can be shared. Although HIPAA provided de-identification as an approved mechanism for data sharing, linkage attacks were identified as a major vulnerability. A variety of mechanisms have been established to avoid leaking private information, such as field suppression or abstraction, strictly limiting the amount of information that can be shared, or employing mathematical techniques such as differential privacy. Another approach, which we focus on here, is creating synthetic data that mimics the underlying data. For synthetic data to be a useful mechanism in support of medical innovation and a proxy for real-world evidence, one must demonstrate two properties of the synthetic dataset: (1) any analysis on the real data must be matched by analysis of the synthetic data (statistical fidelity) and (2) the synthetic data must preserve privacy, with minimal risk of re-identification (privacy guarantee). In this paper we propose a framework for quantifying the statistical fidelity and privacy preservation properties of synthetic datasets and demonstrate these metrics for synthetic data generated by Syntegra technology.

Exploring the Potential of AI-Generated Synthetic Datasets: A Case Study on Telematics Data with ChatGPT

This research delves into the construction and utilization of synthetic datasets, specifically within the telematics sphere, leveraging OpenAI's powerful language model, ChatGPT. Synthetic datasets present an effective solution to challenges pertaining to data privacy, scarcity, and control over variables - characteristics that make them particularly valuable for research pursuits. The utility of these datasets, however, largely depends on their quality, measured through the lenses of diversity, relevance, and coherence. To illustrate this data creation process, a hands-on case study is conducted, focusing on the generation of a synthetic telematics dataset. The experiment involved an iterative guidance of ChatGPT, progressively refining prompts and culminating in the creation of a comprehensive dataset for a hypothetical urban planning scenario in Columbus, Ohio. Upon generation, the synthetic dataset was subjected to an evaluation, focusing on the previously identified quality parameters and employing descriptive statistics and visualization techniques for a thorough analysis. Despite synthetic datasets not serving as perfect replacements for actual world data, their potential in specific use-cases, when executed with precision, is significant. This research underscores the potential of AI models like ChatGPT in enhancing data availability for complex sectors like telematics, thus paving the way for a myriad of new research opportunities.

EUR-Lex-Sum: A Multi- and Cross-lingual Dataset for Long-form Summarization in the Legal Domain

Existing summarization datasets come with two main drawbacks: (1) They tend to focus on overly exposed domains, such as news articles or wiki-like texts, and (2) are primarily monolingual, with few multilingual datasets. In this work, we propose a novel dataset, called EUR-Lex-Sum, based on manually curated document summaries of legal acts from the European Union law platform (EUR-Lex). Documents and their respective summaries exist as cross-lingual paragraph-aligned data in several of the 24 official European languages, enabling access to various cross-lingual and lower-resourced summarization setups. We obtain up to 1,500 document/summary pairs per language, including a subset of 375 cross-lingually aligned legal acts with texts available in all 24 languages. In this work, the data acquisition process is detailed and key characteristics of the resource are compared to existing summarization resources. In particular, we illustrate challenging sub-problems and open questions on the dataset that could help the facilitation of future research in the direction of domain-specific cross-lingual summarization. Limited by the extreme length and language diversity of samples, we further conduct experiments with suitable extractive monolingual and cross-lingual baselines for future work. Code for the extraction as well as access to our data and baselines is available online at: https://github.com/achouhan93/eur-lex-sum.

Author Once, Publish Everywhere: Portable Metadata Authoring with the CEDAR Embeddable Editor

High-quality, "rich" metadata are essential for making research data findable, interoperable, and reusable. The Center for Expanded Data Annotation and Retrieval (CEDAR) has long addressed this need by providing tools to design machine-actionable metadata templates that encode community standards in a computable form. To make these capabilities more accessible within real-world research workflows, we have developed the CEDAR Embeddable Editor (CEE)-a lightweight, interoperable Web Component that brings structured, standards-based metadata authoring directly into third-party platforms. The CEE dynamically renders metadata forms from machine-actionable templates and produces semantically rich metadata in JSON-LD format. It supports ontology-based value selection via the BioPortal ontology repository, and it includes external authority resolution for persistent identifiers such as ORCIDs for individuals and RORs for research organizations. Crucially, the CEE requires no custom user-interface development, allowing deployment across diverse platforms. The CEE has been successfully integrated into generalist scientific data repositories such as Dryad and the Open Science Framework, demonstrating its ability to support discipline-specific metadata creation. By supporting the embedding of metadata authoring within existing research environments, the CEE can facilitate the adoption of community standards and help improve metadata quality across scientific disciplines.

QuaDMix: Quality-Diversity Balanced Data Selection for Efficient LLM Pretraining

Quality and diversity are two critical metrics for the training data of large language models (LLMs), positively impacting performance. Existing studies often optimize these metrics separately, typically by first applying quality filtering and then adjusting data proportions. However, these approaches overlook the inherent trade-off between quality and diversity, necessitating their joint consideration. Given a fixed training quota, it is essential to evaluate both the quality of each data point and its complementary effect on the overall dataset. In this paper, we introduce a unified data selection framework called QuaDMix, which automatically optimizes the data distribution for LLM pretraining while balancing both quality and diversity. Specifically, we first propose multiple criteria to measure data quality and employ domain classification to distinguish data points, thereby measuring overall diversity. QuaDMix then employs a unified parameterized data sampling function that determines the sampling probability of each data point based on these quality and diversity related labels. To accelerate the search for the optimal parameters involved in the QuaDMix framework, we conduct simulated experiments on smaller models and use LightGBM for parameters searching, inspired by the RegMix method. Our experiments across diverse models and datasets demonstrate that QuaDMix achieves an average performance improvement of 7.2% across multiple benchmarks. These results outperform the independent strategies for quality and diversity, highlighting the necessity and ability to balance data quality and diversity.

Matchmaker: Self-Improving Large Language Model Programs for Schema Matching

Schema matching -- the task of finding matches between attributes across disparate data sources with different tables and hierarchies -- is critical for creating interoperable machine learning (ML)-ready data. Addressing this fundamental data-centric problem has wide implications, especially in domains like healthcare, finance and e-commerce -- but also has the potential to benefit ML models more generally, by increasing the data available for ML model training. However, schema matching is a challenging ML task due to structural/hierarchical and semantic heterogeneity between different schemas. Previous ML approaches to automate schema matching have either required significant labeled data for model training, which is often unrealistic or suffer from poor zero-shot performance. To this end, we propose Matchmaker - a compositional language model program for schema matching, comprised of candidate generation, refinement and confidence scoring. Matchmaker also self-improves in a zero-shot manner without the need for labeled demonstrations via a novel optimization approach, which constructs synthetic in-context demonstrations to guide the language model's reasoning process. Empirically, we demonstrate on real-world medical schema matching benchmarks that Matchmaker outperforms previous ML-based approaches, highlighting its potential to accelerate data integration and interoperability of ML-ready data.

On the State of German (Abstractive) Text Summarization

With recent advancements in the area of Natural Language Processing, the focus is slowly shifting from a purely English-centric view towards more language-specific solutions, including German. Especially practical for businesses to analyze their growing amount of textual data are text summarization systems, which transform long input documents into compressed and more digestible summary texts. In this work, we assess the particular landscape of German abstractive text summarization and investigate the reasons why practically useful solutions for abstractive text summarization are still absent in industry. Our focus is two-fold, analyzing a) training resources, and b) publicly available summarization systems. We are able to show that popular existing datasets exhibit crucial flaws in their assumptions about the original sources, which frequently leads to detrimental effects on system generalization and evaluation biases. We confirm that for the most popular training dataset, MLSUM, over 50% of the training set is unsuitable for abstractive summarization purposes. Furthermore, available systems frequently fail to compare to simple baselines, and ignore more effective and efficient extractive summarization approaches. We attribute poor evaluation quality to a variety of different factors, which are investigated in more detail in this work: A lack of qualitative (and diverse) gold data considered for training, understudied (and untreated) positional biases in some of the existing datasets, and the lack of easily accessible and streamlined pre-processing strategies or analysis tools. We provide a comprehensive assessment of available models on the cleaned datasets, and find that this can lead to a reduction of more than 20 ROUGE-1 points during evaluation. The code for dataset filtering and reproducing results can be found online at https://github.com/dennlinger/summaries

CCI4.0: A Bilingual Pretraining Dataset for Enhancing Reasoning in Large Language Models

We introduce CCI4.0, a large-scale bilingual pre-training dataset engineered for superior data quality and diverse human-like reasoning trajectory. CCI4.0 occupies roughly 35 TB of disk space and comprises two sub-datasets: CCI4.0-M2-Base and CCI4.0-M2-CoT. CCI4.0-M2-Base combines a 5.2 TB carefully curated Chinese web corpus, a 22.5 TB English subset from Nemotron-CC, and diverse sources from math, wiki, arxiv, and code. Although these data are mostly sourced from well-processed datasets, the quality standards of various domains are dynamic and require extensive expert experience and labor to process. So, we propose a novel pipeline justifying data quality mainly based on models through two-stage deduplication, multiclassifier quality scoring, and domain-aware fluency filtering. We extract 4.5 billion pieces of CoT(Chain-of-Thought) templates, named CCI4.0-M2-CoT. Differing from the distillation of CoT from larger models, our proposed staged CoT extraction exemplifies diverse reasoning patterns and significantly decreases the possibility of hallucination. Empirical evaluations demonstrate that LLMs pre-trained in CCI4.0 benefit from cleaner, more reliable training signals, yielding consistent improvements in downstream tasks, especially in math and code reflection tasks. Our results underscore the critical role of rigorous data curation and human thinking templates in advancing LLM performance, shedding some light on automatically processing pretraining corpora.

Revisiting Table Detection Datasets for Visually Rich Documents

Table Detection has become a fundamental task for visually rich document understanding with the surging number of electronic documents. However, popular public datasets widely used in related studies have inherent limitations, including noisy and inconsistent samples, limited training samples, and limited data sources. These limitations make these datasets unreliable to evaluate the model performance and cannot reflect the actual capacity of models. Therefore, this study revisits some open datasets with high-quality annotations, identifies and cleans the noise, and aligns the annotation definitions of these datasets to merge a larger dataset, termed Open-Tables. Moreover, to enrich the data sources, we propose a new ICT-TD dataset using the PDF files of Information and Communication Technologies (ICT) commodities, a different domain containing unique samples that hardly appear in open datasets. To ensure the label quality of the dataset, we annotated the dataset manually following the guidance of a domain expert. The proposed dataset is challenging and can be a sample of actual cases in the business context. We built strong baselines using various state-of-the-art object detection models. Our experimental results show that the domain differences among existing open datasets are minor despite having different data sources. Our proposed Open-Tables and ICT-TD can provide a more reliable evaluation for models because of their high quality and consistent annotations. Besides, they are more suitable for cross-domain settings. Our experimental results show that in the cross-domain setting, benchmark models trained with cleaned Open-Tables dataset can achieve 0.6\%-2.6\% higher weighted average F1 than the corresponding ones trained with the noisy version of Open-Tables, demonstrating the reliability of the proposed datasets. The datasets are public available.

Parsed Categoric Encodings with Automunge

The Automunge open source python library platform for tabular data pre-processing automates feature engineering data transformations of numerical encoding and missing data infill to received tidy data on bases fit to properties of columns in a designated train set for consistent and efficient application to subsequent data pipelines such as for inference, where transformations may be applied to distinct columns in "family tree" sets with generations and branches of derivations. Included in the library of transformations are methods to extract structure from bounded categorical string sets by way of automated string parsing, in which comparisons between entries in the set of unique values are parsed to identify character subset overlaps which may be encoded by appended columns of boolean overlap detection activations or by replacing string entries with identified overlap partitions. Further string parsing options, which may also be applied to unbounded categoric sets, include extraction of numeric substring partitions from entries or search functions to identify presence of specified substring partitions. The aggregation of these methods into "family tree" sets of transformations are demonstrated for use to automatically extract structure from categoric string compositions in relation to the set of entries in a column, such as may be applied to prepare categoric string set encodings for machine learning without human intervention.

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.

FedSyn: Synthetic Data Generation using Federated Learning

As Deep Learning algorithms continue to evolve and become more sophisticated, they require massive datasets for model training and efficacy of models. Some of those data requirements can be met with the help of existing datasets within the organizations. Current Machine Learning practices can be leveraged to generate synthetic data from an existing dataset. Further, it is well established that diversity in generated synthetic data relies on (and is perhaps limited by) statistical properties of available dataset within a single organization or entity. The more diverse an existing dataset is, the more expressive and generic synthetic data can be. However, given the scarcity of underlying data, it is challenging to collate big data in one organization. The diverse, non-overlapping dataset across distinct organizations provides an opportunity for them to contribute their limited distinct data to a larger pool that can be leveraged to further synthesize. Unfortunately, this raises data privacy concerns that some institutions may not be comfortable with. This paper proposes a novel approach to generate synthetic data - FedSyn. FedSyn is a collaborative, privacy preserving approach to generate synthetic data among multiple participants in a federated and collaborative network. FedSyn creates a synthetic data generation model, which can generate synthetic data consisting of statistical distribution of almost all the participants in the network. FedSyn does not require access to the data of an individual participant, hence protecting the privacy of participant's data. The proposed technique in this paper leverages federated machine learning and generative adversarial network (GAN) as neural network architecture for synthetic data generation. The proposed method can be extended to many machine learning problem classes in finance, health, governance, technology and many more.

PRISM: Patient Records Interpretation for Semantic Clinical Trial Matching using Large Language Models

Clinical trial matching is the task of identifying trials for which patients may be potentially eligible. Typically, this task is labor-intensive and requires detailed verification of patient electronic health records (EHRs) against the stringent inclusion and exclusion criteria of clinical trials. This process is manual, time-intensive, and challenging to scale up, resulting in many patients missing out on potential therapeutic options. Recent advancements in Large Language Models (LLMs) have made automating patient-trial matching possible, as shown in multiple concurrent research studies. However, the current approaches are confined to constrained, often synthetic datasets that do not adequately mirror the complexities encountered in real-world medical data. In this study, we present the first, end-to-end large-scale empirical evaluation of clinical trial matching using real-world EHRs. Our study showcases the capability of LLMs to accurately match patients with appropriate clinical trials. We perform experiments with proprietary LLMs, including GPT-4 and GPT-3.5, as well as our custom fine-tuned model called OncoLLM and show that OncoLLM, despite its significantly smaller size, not only outperforms GPT-3.5 but also matches the performance of qualified medical doctors. All experiments were carried out on real-world EHRs that include clinical notes and available clinical trials from a single cancer center in the United States.

M3LEO: A Multi-Modal, Multi-Label Earth Observation Dataset Integrating Interferometric SAR and Multispectral Data

Satellite-based remote sensing has revolutionised the way we address global challenges. Huge quantities of Earth Observation (EO) data are generated by satellite sensors daily, but processing these large datasets for use in ML pipelines is technically and computationally challenging. While some preprocessed Earth observation datasets exist, their content is often limited to optical or near-optical wavelength data, which is ineffective at night or in adverse weather conditions. Synthetic Aperture Radar (SAR), an active sensing technique based on microwave length radiation, offers a viable alternative. However, the application of machine learning to SAR has been limited due to a lack of ML-ready data and pipelines, particularly for the full diversity of SAR data, including polarimetry, coherence and interferometry. In this work, we introduce M3LEO, a multi-modal, multi-label Earth observation dataset that includes polarimetric, interferometric, and coherence SAR data derived from Sentinel-1, alongside multispectral Sentinel-2 imagery and auxiliary data describing terrain properties such as land use. M3LEO spans approximately 17M 4x4 km data chips from six diverse geographic regions. The dataset is complemented by a flexible PyTorch Lightning framework configured using Hydra to accommodate its use across diverse ML applications in Earth observation. We provide tools to process any dataset available on popular platforms such as Google Earth Engine for seamless integration with our framework. We show that the distribution shift in self-supervised embeddings is substantial across geographic regions, even when controlling for terrain properties. Data: huggingface.co/M3LEO, Code: github.com/spaceml-org/M3LEO.

Scaling Laws for Data Filtering -- Data Curation cannot be Compute Agnostic

Vision-language models (VLMs) are trained for thousands of GPU hours on carefully curated web datasets. In recent times, data curation has gained prominence with several works developing strategies to retain 'high-quality' subsets of 'raw' scraped data. For instance, the LAION public dataset retained only 10% of the total crawled data. However, these strategies are typically developed agnostic of the available compute for training. In this paper, we first demonstrate that making filtering decisions independent of training compute is often suboptimal: the limited high-quality data rapidly loses its utility when repeated, eventually requiring the inclusion of 'unseen' but 'lower-quality' data. To address this quality-quantity tradeoff (QQT), we introduce neural scaling laws that account for the non-homogeneous nature of web data, an angle ignored in existing literature. Our scaling laws (i) characterize the differing 'utility' of various quality subsets of web data; (ii) account for how utility diminishes for a data point at its 'nth' repetition; and (iii) formulate the mutual interaction of various data pools when combined, enabling the estimation of model performance on a combination of multiple data pools without ever jointly training on them. Our key message is that data curation cannot be agnostic of the total compute that a model will be trained for. Our scaling laws allow us to curate the best possible pool for achieving top performance on Datacomp at various compute budgets, carving out a pareto-frontier for data curation. Code is available at https://github.com/locuslab/scaling_laws_data_filtering.

EHRSHOT: An EHR Benchmark for Few-Shot Evaluation of Foundation Models

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

A Vulnerability Code Intent Summary Dataset

In the era of Large Language Models (LLMs), the code summarization technique boosts a lot, along with the emergence of many new significant works. However, the potential of code summarization in the Computer Security Area still remains explored. Can we generate a code summary of a code snippet for its security intention? Thus, this work proposes an innovative large-scale multi-perspective Code Intent Summary Dataset named BADS , aiming to increase the understanding of a given code snippet and reduce the risk in the code developing process. The procedure of establishing a dataset can be divided into four steps: First, we collect samples of codes with known vulnerabilities as well as code generated by AI from multiple sources. Second, we do the data clean and format unification, then do the data combination. Third, we utilize the LLM to automatically Annotate the code snippet. Last, We do the human evaluation to double-check. The dataset contains X code examples which cover Y categories of vulnerability. Our data are from Z open-source projects and CVE entries, and compared to existing work, our dataset not only contains original code but also code function summary and security intent summary, providing context information for research in code security analysis. All information is in CSV format. The contributions of this paper are four-fold: the establishment of a high-quality, multi-perspective Code Intent Summary Dataset; an innovative method in data collection and processing; A new multi-perspective code analysis framework that promotes cross-disciplinary research in the fields of software engineering and cybersecurity; improving the practicality and scalability of the research outcomes by considering the code length limitations in real-world applications. Our dataset and related tools have been publicly released on GitHub.

RedPajama: an Open Dataset for Training Large Language Models

Large language models are increasingly becoming a cornerstone technology in artificial intelligence, the sciences, and society as a whole, yet the optimal strategies for dataset composition and filtering remain largely elusive. Many of the top-performing models lack transparency in their dataset curation and model development processes, posing an obstacle to the development of fully open language models. In this paper, we identify three core data-related challenges that must be addressed to advance open-source language models. These include (1) transparency in model development, including the data curation process, (2) access to large quantities of high-quality data, and (3) availability of artifacts and metadata for dataset curation and analysis. To address these challenges, we release RedPajama-V1, an open reproduction of the LLaMA training dataset. In addition, we release RedPajama-V2, a massive web-only dataset consisting of raw, unfiltered text data together with quality signals and metadata. Together, the RedPajama datasets comprise over 100 trillion tokens spanning multiple domains and with their quality signals facilitate the filtering of data, aiming to inspire the development of numerous new datasets. To date, these datasets have already been used in the training of strong language models used in production, such as Snowflake Arctic, Salesforce's XGen and AI2's OLMo. To provide insight into the quality of RedPajama, we present a series of analyses and ablation studies with decoder-only language models with up to 1.6B parameters. Our findings demonstrate how quality signals for web data can be effectively leveraged to curate high-quality subsets of the dataset, underscoring the potential of RedPajama to advance the development of transparent and high-performing language models at scale.

Automatic Data Augmentation via Invariance-Constrained Learning

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

Knowledge Augmented Machine Learning with Applications in Autonomous Driving: A Survey

The availability of representative datasets is an essential prerequisite for many successful artificial intelligence and machine learning models. However, in real life applications these models often encounter scenarios that are inadequately represented in the data used for training. There are various reasons for the absence of sufficient data, ranging from time and cost constraints to ethical considerations. As a consequence, the reliable usage of these models, especially in safety-critical applications, is still a tremendous challenge. Leveraging additional, already existing sources of knowledge is key to overcome the limitations of purely data-driven approaches. Knowledge augmented machine learning approaches offer the possibility of compensating for deficiencies, errors, or ambiguities in the data, thus increasing the generalization capability of the applied models. Even more, predictions that conform with knowledge are crucial for making trustworthy and safe decisions even in underrepresented scenarios. This work provides an overview of existing techniques and methods in the literature that combine data-driven models with existing knowledge. The identified approaches are structured according to the categories knowledge integration, extraction and conformity. In particular, we address the application of the presented methods in the field of autonomous driving.

LAMBDA: A Large Model Based Data Agent

We introduce ``LAMBDA," a novel open-source, code-free multi-agent data analysis system that that harnesses the power of large models. LAMBDA is designed to address data analysis challenges in complex data-driven applications through the use of innovatively designed data agents that operate iteratively and generatively using natural language. At the core of LAMBDA are two key agent roles: the programmer and the inspector, which are engineered to work together seamlessly. Specifically, the programmer generates code based on the user's instructions and domain-specific knowledge, enhanced by advanced models. Meanwhile, the inspector debugs the code when necessary. To ensure robustness and handle adverse scenarios, LAMBDA features a user interface that allows direct user intervention in the operational loop. Additionally, LAMBDA can flexibly integrate external models and algorithms through our knowledge integration mechanism, catering to the needs of customized data analysis. LAMBDA has demonstrated strong performance on various machine learning datasets. It has the potential to enhance data science practice and analysis paradigm by seamlessly integrating human and artificial intelligence, making it more accessible, effective, and efficient for individuals from diverse backgrounds. The strong performance of LAMBDA in solving data science problems is demonstrated in several case studies, which are presented at https://www.polyu.edu.hk/ama/cmfai/lambda.html.

Docs2KG: Unified Knowledge Graph Construction from Heterogeneous Documents Assisted by Large Language Models

Even for a conservative estimate, 80% of enterprise data reside in unstructured files, stored in data lakes that accommodate heterogeneous formats. Classical search engines can no longer meet information seeking needs, especially when the task is to browse and explore for insight formulation. In other words, there are no obvious search keywords to use. Knowledge graphs, due to their natural visual appeals that reduce the human cognitive load, become the winning candidate for heterogeneous data integration and knowledge representation. In this paper, we introduce Docs2KG, a novel framework designed to extract multimodal information from diverse and heterogeneous unstructured documents, including emails, web pages, PDF files, and Excel files. Dynamically generates a unified knowledge graph that represents the extracted key information, Docs2KG enables efficient querying and exploration of document data lakes. Unlike existing approaches that focus on domain-specific data sources or pre-designed schemas, Docs2KG offers a flexible and extensible solution that can adapt to various document structures and content types. The proposed framework unifies data processing supporting a multitude of downstream tasks with improved domain interpretability. Docs2KG is publicly accessible at https://docs2kg.ai4wa.com, and a demonstration video is available at https://docs2kg.ai4wa.com/Video.

The Dataset Nutrition Label: A Framework To Drive Higher Data Quality Standards

Artificial intelligence (AI) systems built on incomplete or biased data will often exhibit problematic outcomes. Current methods of data analysis, particularly before model development, are costly and not standardized. The Dataset Nutrition Label (the Label) is a diagnostic framework that lowers the barrier to standardized data analysis by providing a distilled yet comprehensive overview of dataset "ingredients" before AI model development. Building a Label that can be applied across domains and data types requires that the framework itself be flexible and adaptable; as such, the Label is comprised of diverse qualitative and quantitative modules generated through multiple statistical and probabilistic modelling backends, but displayed in a standardized format. To demonstrate and advance this concept, we generated and published an open source prototype with seven sample modules on the ProPublica Dollars for Docs dataset. The benefits of the Label are manyfold. For data specialists, the Label will drive more robust data analysis practices, provide an efficient way to select the best dataset for their purposes, and increase the overall quality of AI models as a result of more robust training datasets and the ability to check for issues at the time of model development. For those building and publishing datasets, the Label creates an expectation of explanation, which will drive better data collection practices. We also explore the limitations of the Label, including the challenges of generalizing across diverse datasets, and the risk of using "ground truth" data as a comparison dataset. We discuss ways to move forward given the limitations identified. Lastly, we lay out future directions for the Dataset Nutrition Label project, including research and public policy agendas to further advance consideration of the concept.

Named Clinical Entity Recognition Benchmark

This technical report introduces a Named Clinical Entity Recognition Benchmark for evaluating language models in healthcare, addressing the crucial natural language processing (NLP) task of extracting structured information from clinical narratives to support applications like automated coding, clinical trial cohort identification, and clinical decision support. The leaderboard provides a standardized platform for assessing diverse language models, including encoder and decoder architectures, on their ability to identify and classify clinical entities across multiple medical domains. A curated collection of openly available clinical datasets is utilized, encompassing entities such as diseases, symptoms, medications, procedures, and laboratory measurements. Importantly, these entities are standardized according to the Observational Medical Outcomes Partnership (OMOP) Common Data Model, ensuring consistency and interoperability across different healthcare systems and datasets, and a comprehensive evaluation of model performance. Performance of models is primarily assessed using the F1-score, and it is complemented by various assessment modes to provide comprehensive insights into model performance. The report also includes a brief analysis of models evaluated to date, highlighting observed trends and limitations. By establishing this benchmarking framework, the leaderboard aims to promote transparency, facilitate comparative analyses, and drive innovation in clinical entity recognition tasks, addressing the need for robust evaluation methods in healthcare NLP.

Navigating Dataset Documentations in AI: A Large-Scale Analysis of Dataset Cards on Hugging Face

Advances in machine learning are closely tied to the creation of datasets. While data documentation is widely recognized as essential to the reliability, reproducibility, and transparency of ML, we lack a systematic empirical understanding of current dataset documentation practices. To shed light on this question, here we take Hugging Face -- one of the largest platforms for sharing and collaborating on ML models and datasets -- as a prominent case study. By analyzing all 7,433 dataset documentation on Hugging Face, our investigation provides an overview of the Hugging Face dataset ecosystem and insights into dataset documentation practices, yielding 5 main findings: (1) The dataset card completion rate shows marked heterogeneity correlated with dataset popularity. (2) A granular examination of each section within the dataset card reveals that the practitioners seem to prioritize Dataset Description and Dataset Structure sections, while the Considerations for Using the Data section receives the lowest proportion of content. (3) By analyzing the subsections within each section and utilizing topic modeling to identify key topics, we uncover what is discussed in each section, and underscore significant themes encompassing both technical and social impacts, as well as limitations within the Considerations for Using the Data section. (4) Our findings also highlight the need for improved accessibility and reproducibility of datasets in the Usage sections. (5) In addition, our human annotation evaluation emphasizes the pivotal role of comprehensive dataset content in shaping individuals' perceptions of a dataset card's overall quality. Overall, our study offers a unique perspective on analyzing dataset documentation through large-scale data science analysis and underlines the need for more thorough dataset documentation in machine learning research.

The Responsible Foundation Model Development Cheatsheet: A Review of Tools & Resources

Foundation model development attracts a rapidly expanding body of contributors, scientists, and applications. To help shape responsible development practices, we introduce the Foundation Model Development Cheatsheet: a growing collection of 250+ tools and resources spanning text, vision, and speech modalities. We draw on a large body of prior work to survey resources (e.g. software, documentation, frameworks, guides, and practical tools) that support informed data selection, processing, and understanding, precise and limitation-aware artifact documentation, efficient model training, advance awareness of the environmental impact from training, careful model evaluation of capabilities, risks, and claims, as well as responsible model release, licensing and deployment practices. We hope this curated collection of resources helps guide more responsible development. The process of curating this list, enabled us to review the AI development ecosystem, revealing what tools are critically missing, misused, or over-used in existing practices. We find that (i) tools for data sourcing, model evaluation, and monitoring are critically under-serving ethical and real-world needs, (ii) evaluations for model safety, capabilities, and environmental impact all lack reproducibility and transparency, (iii) text and particularly English-centric analyses continue to dominate over multilingual and multi-modal analyses, and (iv) evaluation of systems, rather than just models, is needed so that capabilities and impact are assessed in context.

ICON: Improving Inter-Report Consistency of Radiology Report Generation via Lesion-aware Mix-up Augmentation

Previous research on radiology report generation has made significant progress in terms of increasing the clinical accuracy of generated reports. In this paper, we emphasize another crucial quality that it should possess, i.e., inter-report consistency, which refers to the capability of generating consistent reports for semantically equivalent radiographs. This quality is even of greater significance than the overall report accuracy in terms of ensuring the system's credibility, as a system prone to providing conflicting results would severely erode users' trust. Regrettably, existing approaches struggle to maintain inter-report consistency, exhibiting biases towards common patterns and susceptibility to lesion variants. To address this issue, we propose ICON, which improves the inter-report consistency of radiology report generation. Aiming at enhancing the system's ability to capture the similarities in semantically equivalent lesions, our approach involves first extracting lesions from input images and examining their characteristics. Then, we introduce a lesion-aware mix-up augmentation technique to ensure that the representations of the semantically equivalent lesions align with the same attributes, by linearly interpolating them during the training phase. Extensive experiments on three publicly available chest X-ray datasets verify the effectiveness of our approach, both in terms of improving the consistency and accuracy of the generated reports.

BigDocs: An Open and Permissively-Licensed Dataset for Training Multimodal Models on Document and Code Tasks

Multimodal AI has the potential to significantly enhance document-understanding tasks, such as processing receipts, understanding workflows, extracting data from documents, and summarizing reports. Code generation tasks that require long-structured outputs can also be enhanced by multimodality. Despite this, their use in commercial applications is often limited due to limited access to training data and restrictive licensing, which hinders open access. To address these limitations, we introduce BigDocs-7.5M, a high-quality, open-access dataset comprising 7.5 million multimodal documents across 30 tasks. We use an efficient data curation process to ensure our data is high-quality and license-permissive. Our process emphasizes accountability, responsibility, and transparency through filtering rules, traceable metadata, and careful content analysis. Additionally, we introduce BigDocs-Bench, a benchmark suite with 10 novel tasks where we create datasets that reflect real-world use cases involving reasoning over Graphical User Interfaces (GUI) and code generation from images. Our experiments show that training with BigDocs-Bench improves average performance up to 25.8% over closed-source GPT-4o in document reasoning and structured output tasks such as Screenshot2HTML or Image2Latex generation. Finally, human evaluations showed a preference for outputs from models trained on BigDocs over GPT-4o. This suggests that BigDocs can help both academics and the open-source community utilize and improve AI tools to enhance multimodal capabilities and document reasoning. The project is hosted at https://bigdocs.github.io .

A Survey on Data Selection for Language Models

A major factor in the recent success of large language models is the use of enormous and ever-growing text datasets for unsupervised pre-training. However, naively training a model on all available data may not be optimal (or feasible), as the quality of available text data can vary. Filtering out data can also decrease the carbon footprint and financial costs of training models by reducing the amount of training required. Data selection methods aim to determine which candidate data points to include in the training dataset and how to appropriately sample from the selected data points. The promise of improved data selection methods has caused the volume of research in the area to rapidly expand. However, because deep learning is mostly driven by empirical evidence and experimentation on large-scale data is expensive, few organizations have the resources for extensive data selection research. Consequently, knowledge of effective data selection practices has become concentrated within a few organizations, many of which do not openly share their findings and methodologies. To narrow this gap in knowledge, we present a comprehensive review of existing literature on data selection methods and related research areas, providing a taxonomy of existing approaches. By describing the current landscape of research, this work aims to accelerate progress in data selection by establishing an entry point for new and established researchers. Additionally, throughout this review we draw attention to noticeable holes in the literature and conclude the paper by proposing promising avenues for future research.