Daily Papers

Background: Health datasets from clinical sources do not reflect the breadth and diversity of disease in the real world, impacting research, medical education, and artificial intelligence (AI) tool development. Dermatology is a suitable area to develop and test a new and scalable method to create representative health datasets. Methods: We used Google Search advertisements to invite contributions to an open access dataset of images of dermatology conditions, demographic and symptom information. With informed contributor consent, we describe and release this dataset containing 10,408 images from 5,033 contributions from internet users in the United States over 8 months starting March 2023. The dataset includes dermatologist condition labels as well as estimated Fitzpatrick Skin Type (eFST) and Monk Skin Tone (eMST) labels for the images. Results: We received a median of 22 submissions/day (IQR 14-30). Female (66.72%) and younger (52% < age 40) contributors had a higher representation in the dataset compared to the US population, and 32.6% of contributors reported a non-White racial or ethnic identity. Over 97.5% of contributions were genuine images of skin conditions. Dermatologist confidence in assigning a differential diagnosis increased with the number of available variables, and showed a weaker correlation with image sharpness (Spearman's P values <0.001 and 0.01 respectively). Most contributions were short-duration (54% with onset < 7 days ago ) and 89% were allergic, infectious, or inflammatory conditions. eFST and eMST distributions reflected the geographical origin of the dataset. The dataset is available at github.com/google-research-datasets/scin . Conclusion: Search ads are effective at crowdsourcing images of health conditions. The SCIN dataset bridges important gaps in the availability of representative images of common skin conditions.

The rapid advancement of Large Language Models (LLMs) and Large Multimodal Models (LMMs) has heightened the demand for AI-based scientific assistants capable of understanding scientific articles and figures. Despite progress, there remains a significant gap in evaluating models' comprehension of professional, graduate-level, and even PhD-level scientific content. Current datasets and benchmarks primarily focus on relatively simple scientific tasks and figures, lacking comprehensive assessments across diverse advanced scientific disciplines. To bridge this gap, we collected a multimodal, multidisciplinary dataset from open-access scientific articles published in Nature Communications journals. This dataset spans 72 scientific disciplines, ensuring both diversity and quality. We created benchmarks with various tasks and settings to comprehensively evaluate LMMs' capabilities in understanding scientific figures and content. Our evaluation revealed that these tasks are highly challenging: many open-source models struggled significantly, and even GPT-4V and GPT-4o faced difficulties. We also explored using our dataset as training resources by constructing visual instruction-following data, enabling the 7B LLaVA model to achieve performance comparable to GPT-4V/o on our benchmark. Additionally, we investigated the use of our interleaved article texts and figure images for pre-training LMMs, resulting in improvements on the material generation task. The source dataset, including articles, figures, constructed benchmarks, and visual instruction-following data, is open-sourced.

The Copernicus Regional Reanalysis for Europe, CERRA, is a high-resolution regional reanalysis dataset for the European domain. In recent years it has shown significant utility across various climate-related tasks, ranging from forecasting and climate change research to renewable energy prediction, resource management, air quality risk assessment, and the forecasting of rare events, among others. Unfortunately, the availability of CERRA is lagging two years behind the current date, due to constraints in acquiring the requisite external data and the intensive computational demands inherent in its generation. As a solution, this paper introduces a novel method using diffusion models to approximate CERRA downscaling in a data-driven manner, without additional informations. By leveraging the lower resolution ERA5 dataset, which provides boundary conditions for CERRA, we approach this as a super-resolution task. Focusing on wind speed around Italy, our model, trained on existing CERRA data, shows promising results, closely mirroring original CERRA data. Validation with in-situ observations further confirms the model's accuracy in approximating ground measurements.

This paper introduces the Pandemic PACT Advanced Categorisation Engine (PPACE) along with its associated dataset. PPACE is a fine-tuned model developed to automatically classify research abstracts from funded biomedical projects according to WHO-aligned research priorities. This task is crucial for monitoring research trends and identifying gaps in global health preparedness and response. Our approach builds on human-annotated projects, which are allocated one or more categories from a predefined list. A large language model is then used to generate `rationales' explaining the reasoning behind these annotations. This augmented data, comprising expert annotations and rationales, is subsequently used to fine-tune a smaller, more efficient model. Developed as part of the Pandemic PACT project, which aims to track and analyse research funding and clinical evidence for a wide range of diseases with outbreak potential, PPACE supports informed decision-making by research funders, policymakers, and independent researchers. We introduce and release both the trained model and the instruction-based dataset used for its training. Our evaluation shows that PPACE significantly outperforms its baselines. The release of PPACE and its associated dataset offers valuable resources for researchers in multilabel biomedical document classification and supports advancements in aligning biomedical research with key global health priorities.

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.

We present CovidQA, the beginnings of a question answering dataset specifically designed for COVID-19, built by hand from knowledge gathered from Kaggle's COVID-19 Open Research Dataset Challenge. To our knowledge, this is the first publicly available resource of its type, and intended as a stopgap measure for guiding research until more substantial evaluation resources become available. While this dataset, comprising 124 question-article pairs as of the present version 0.1 release, does not have sufficient examples for supervised machine learning, we believe that it can be helpful for evaluating the zero-shot or transfer capabilities of existing models on topics specifically related to COVID-19. This paper describes our methodology for constructing the dataset and presents the effectiveness of a number of baselines, including term-based techniques and various transformer-based models. The dataset is available at http://covidqa.ai/

This paper embarks on an exploration into the Large Language Model (LLM) datasets, which play a crucial role in the remarkable advancements of LLMs. The datasets serve as the foundational infrastructure analogous to a root system that sustains and nurtures the development of LLMs. Consequently, examination of these datasets emerges as a critical topic in research. In order to address the current lack of a comprehensive overview and thorough analysis of LLM datasets, and to gain insights into their current status and future trends, this survey consolidates and categorizes the fundamental aspects of LLM datasets from five perspectives: (1) Pre-training Corpora; (2) Instruction Fine-tuning Datasets; (3) Preference Datasets; (4) Evaluation Datasets; (5) Traditional Natural Language Processing (NLP) Datasets. The survey sheds light on the prevailing challenges and points out potential avenues for future investigation. Additionally, a comprehensive review of the existing available dataset resources is also provided, including statistics from 444 datasets, covering 8 language categories and spanning 32 domains. Information from 20 dimensions is incorporated into the dataset statistics. The total data size surveyed surpasses 774.5 TB for pre-training corpora and 700M instances for other datasets. We aim to present the entire landscape of LLM text datasets, serving as a comprehensive reference for researchers in this field and contributing to future studies. Related resources are available at: https://github.com/lmmlzn/Awesome-LLMs-Datasets.

Large Language Models (LLMs), particularly those similar to ChatGPT, have significantly influenced the field of Natural Language Processing (NLP). While these models excel in general language tasks, their performance in domain-specific downstream tasks such as biomedical and clinical Named Entity Recognition (NER), Relation Extraction (RE), and Medical Natural Language Inference (NLI) is still evolving. In this context, our study investigates the potential of instruction tuning for biomedical language processing, applying this technique to two general LLMs of substantial scale. We present a comprehensive, instruction-based model trained on a dataset that consists of approximately 200,000 instruction-focused samples. This dataset represents a carefully curated compilation of existing data, meticulously adapted and reformatted to align with the specific requirements of our instruction-based tasks. This initiative represents an important step in utilising such models to achieve results on par with specialised encoder-only models like BioBERT and BioClinicalBERT for various classical biomedical NLP tasks. Our work includes an analysis of the dataset's composition and its impact on model performance, providing insights into the intricacies of instruction tuning. By sharing our codes, models, and the distinctively assembled instruction-based dataset, we seek to encourage ongoing research and development in this area.

We present a new challenging dataset, CPPE - 5 (Medical Personal Protective Equipment), with the goal to allow the study of subordinate categorization of medical personal protective equipments, which is not possible with other popular data sets that focus on broad-level categories (such as PASCAL VOC, ImageNet, Microsoft COCO, OpenImages, etc). To make it easy for models trained on this dataset to be used in practical scenarios in complex scenes, our dataset mainly contains images that show complex scenes with several objects in each scene in their natural context. The image collection for this dataset focuses on: obtaining as many non-iconic images as possible and making sure all the images are real-life images, unlike other existing datasets in this area. Our dataset includes 5 object categories (coveralls, face shields, gloves, masks, and goggles), and each image is annotated with a set of bounding boxes and positive labels. We present a detailed analysis of the dataset in comparison to other popular broad category datasets as well as datasets focusing on personal protective equipments, we also find that at present there exist no such publicly available datasets. Finally, we also analyze performance and compare model complexities on baseline and state-of-the-art models for bounding box results. Our code, data, and trained models are available at https://git.io/cppe5-dataset.

Systematic literature reviews (SLRs) play an essential role in summarising, synthesising and validating scientific evidence. In recent years, there has been a growing interest in using machine learning techniques to automate the identification of relevant studies for SLRs. However, the lack of standardised evaluation datasets makes comparing the performance of such automated literature screening systems difficult. In this paper, we analyse the citation screening evaluation datasets, revealing that many of the available datasets are either too small, suffer from data leakage or have limited applicability to systems treating automated literature screening as a classification task, as opposed to, for example, a retrieval or question-answering task. To address these challenges, we introduce CSMeD, a meta-dataset consolidating nine publicly released collections, providing unified access to 325 SLRs from the fields of medicine and computer science. CSMeD serves as a comprehensive resource for training and evaluating the performance of automated citation screening models. Additionally, we introduce CSMeD-FT, a new dataset designed explicitly for evaluating the full text publication screening task. To demonstrate the utility of CSMeD, we conduct experiments and establish baselines on new datasets.

Generative machine learning offers new opportunities to better understand complex Earth system dynamics. Recent diffusion-based methods address spectral biases and improve ensemble calibration in weather forecasting compared to deterministic methods, yet have so far proven difficult to scale stably at high resolutions. We introduce AERIS, a 1.3 to 80B parameter pixel-level Swin diffusion transformer to address this gap, and SWiPe, a generalizable technique that composes window parallelism with sequence and pipeline parallelism to shard window-based transformers without added communication cost or increased global batch size. On Aurora (10,080 nodes), AERIS sustains 10.21 ExaFLOPS (mixed precision) and a peak performance of 11.21 ExaFLOPS with 1 times 1 patch size on the 0.25{\deg} ERA5 dataset, achieving 95.5% weak scaling efficiency, and 81.6% strong scaling efficiency. AERIS outperforms the IFS ENS and remains stable on seasonal scales to 90 days, highlighting the potential of billion-parameter diffusion models for weather and climate prediction.

Over the past few years, due to the rapid development of machine learning (ML) models for weather forecasting, state-of-the-art ML models have shown superior performance compared to the European Centre for Medium-Range Weather Forecasts (ECMWF)'s high-resolution forecast (HRES) in 10-day forecasts at a spatial resolution of 0.25 degree. However, the challenge remains to perform comparably to the ECMWF ensemble mean (EM) in 15-day forecasts. Previous studies have demonstrated the importance of mitigating the accumulation of forecast errors for effective long-term forecasts. Despite numerous efforts to reduce accumulation errors, including autoregressive multi-time step loss, using a single model is found to be insufficient to achieve optimal performance in both short and long lead times. Therefore, we present FuXi, a cascaded ML weather forecasting system that provides 15-day global forecasts with a temporal resolution of 6 hours and a spatial resolution of 0.25 degree. FuXi is developed using 39 years of the ECMWF ERA5 reanalysis dataset. The performance evaluation, based on latitude-weighted root mean square error (RMSE) and anomaly correlation coefficient (ACC), demonstrates that FuXi has comparable forecast performance to ECMWF EM in 15-day forecasts, making FuXi the first ML-based weather forecasting system to accomplish this achievement.

Respiratory viral infections pose a global health burden, yet the cellular immune responses driving protection or pathology remain unclear. Natural infection cohorts often lack pre-exposure baseline data and structured temporal sampling. In contrast, inoculation and vaccination trials generate insightful longitudinal transcriptomic data. However, the scattering of these datasets across platforms, along with inconsistent metadata and preprocessing procedure, hinders AI-driven discovery. To address these challenges, we developed the Human Respiratory Viral Immunization LongitudinAl Gene Expression (HR-VILAGE-3K3M) repository: an AI-ready, rigorously curated dataset that integrates 14,136 RNA-seq profiles from 3,178 subjects across 66 studies encompassing over 2.56 million cells. Spanning vaccination, inoculation, and mixed exposures, the dataset includes microarray, bulk RNA-seq, and single-cell RNA-seq from whole blood, PBMCs, and nasal swabs, sourced from GEO, ImmPort, and ArrayExpress. We harmonized subject-level metadata, standardized outcome measures, applied unified preprocessing pipelines with rigorous quality control, and aligned all data to official gene symbols. To demonstrate the utility of HR-VILAGE-3K3M, we performed predictive modeling of vaccine responders and evaluated batch-effect correction methods. Beyond these initial demonstrations, it supports diverse systems immunology applications and benchmarking of feature selection and transfer learning algorithms. Its scale and heterogeneity also make it ideal for pretraining foundation models of the human immune response and for advancing multimodal learning frameworks. As the largest longitudinal transcriptomic resource for human respiratory viral immunization, it provides an accessible platform for reproducible AI-driven research, accelerating systems immunology and vaccine development against emerging viral threats.

We introduce Arboretum, the largest publicly accessible dataset designed to advance AI for biodiversity applications. This dataset, curated from the iNaturalist community science platform and vetted by domain experts to ensure accuracy, includes 134.6 million images, surpassing existing datasets in scale by an order of magnitude. The dataset encompasses image-language paired data for a diverse set of species from birds (Aves), spiders/ticks/mites (Arachnida), insects (Insecta), plants (Plantae), fungus/mushrooms (Fungi), snails (Mollusca), and snakes/lizards (Reptilia), making it a valuable resource for multimodal vision-language AI models for biodiversity assessment and agriculture research. Each image is annotated with scientific names, taxonomic details, and common names, enhancing the robustness of AI model training. We showcase the value of Arboretum by releasing a suite of CLIP models trained using a subset of 40 million captioned images. We introduce several new benchmarks for rigorous assessment, report accuracy for zero-shot learning, and evaluations across life stages, rare species, confounding species, and various levels of the taxonomic hierarchy. We anticipate that Arboretum will spur the development of AI models that can enable a variety of digital tools ranging from pest control strategies, crop monitoring, and worldwide biodiversity assessment and environmental conservation. These advancements are critical for ensuring food security, preserving ecosystems, and mitigating the impacts of climate change. Arboretum is publicly available, easily accessible, and ready for immediate use. Please see the https://baskargroup.github.io/Arboretum/{project website} for links to our data, models, and code.

The sparsity of labelled data is an obstacle to the development of Relation Extraction models and the completion of databases in various biomedical areas. While being of high interest in drug-discovery, the natural-products literature, reporting the identification of potential bioactive compounds from organisms, is a concrete example of such an overlooked topic. To mark the start of this new task, we created the first curated evaluation dataset and extracted literature items from the LOTUS database to build training sets. To this end, we developed a new sampler inspired by diversity metrics in ecology, named Greedy Maximum Entropy sampler, or GME-sampler (https://github.com/idiap/gme-sampler). The strategic optimization of both balance and diversity of the selected items in the evaluation set is important given the resource-intensive nature of manual curation. After quantifying the noise in the training set, in the form of discrepancies between the input abstracts text and the expected output labels, we explored different strategies accordingly. Framing the task as an end-to-end Relation Extraction, we evaluated the performance of standard fine-tuning as a generative task and few-shot learning with open Large Language Models (LLaMA 7B-65B). In addition to their evaluation in few-shot settings, we explore the potential of open Large Language Models (Vicuna-13B) as synthetic data generator and propose a new workflow for this purpose. All evaluated models exhibited substantial improvements when fine-tuned on synthetic abstracts rather than the original noisy data. We provide our best performing (f1-score=59.0) BioGPT-Large model for end-to-end RE of natural-products relationships along with all the generated synthetic data and the evaluation dataset. See more details at https://github.com/idiap/abroad-re.

Reproducibility remains a significant challenge in machine learning (ML) for healthcare. In this field, datasets, model pipelines, and even task/cohort definitions are often private, leading to a significant barrier in sharing, iterating, and understanding ML results on electronic health record (EHR) datasets. In this paper, we address a significant part of this problem by introducing the Automatic Cohort Extraction System for Event-Stream Datasets (ACES). This tool is designed to simultaneously simplify the development of task/cohorts for ML in healthcare and enable the reproduction of these cohorts, both at an exact level for single datasets and at a conceptual level across datasets. To accomplish this, ACES provides (1) a highly intuitive and expressive configuration language for defining both dataset-specific concepts and dataset-agnostic inclusion/exclusion criteria, and (2) a pipeline to automatically extract patient records that meet these defined criteria from real-world data. ACES can be automatically applied to any dataset in either the Medical Event Data Standard (MEDS) or EventStreamGPT (ESGPT) formats, or to *any* dataset for which the necessary task-specific predicates can be extracted in an event-stream form. ACES has the potential to significantly lower the barrier to entry for defining ML tasks, redefine the way researchers interact with EHR datasets, and significantly improve the state of reproducibility for ML studies in this modality. ACES is available at https://github.com/justin13601/aces.

Artificial intelligence has significantly advanced skin cancer diagnosis by enabling rapid and accurate detection of malignant lesions. In this domain, most publicly available image datasets consist of single, isolated skin lesions positioned at the center of the image. While these lesion-centric datasets have been fundamental for developing diagnostic algorithms, they lack the context of the surrounding skin, which is critical for improving lesion detection. The iToBoS dataset was created to address this challenge. It includes 16,954 images of skin regions from 100 participants, captured using 3D total body photography. Each image roughly corresponds to a 7 times 9 cm section of skin with all suspicious lesions annotated using bounding boxes. Additionally, the dataset provides metadata such as anatomical location, age group, and sun damage score for each image. This dataset aims to facilitate training and benchmarking of algorithms, with the goal of enabling early detection of skin cancer and deployment of this technology in non-clinical environments.

Keeping track of all relevant recent publications and experimental results for a research area is a challenging task. Prior work has demonstrated the efficacy of information extraction models in various scientific areas. Recently, several datasets have been released for the yet understudied materials science domain. However, these datasets focus on sub-problems such as parsing synthesis procedures or on sub-domains, e.g., solid oxide fuel cells. In this resource paper, we present MuLMS, a new dataset of 50 open-access articles, spanning seven sub-domains of materials science. The corpus has been annotated by domain experts with several layers ranging from named entities over relations to frame structures. We present competitive neural models for all tasks and demonstrate that multi-task training with existing related resources leads to benefits.

This paper introduces a new IncidentAI dataset for safety prevention. Different from prior corpora that usually contain a single task, our dataset comprises three tasks: named entity recognition, cause-effect extraction, and information retrieval. The dataset is annotated by domain experts who have at least six years of practical experience as high-pressure gas conservation managers. We validate the contribution of the dataset in the scenario of safety prevention. Preliminary results on the three tasks show that NLP techniques are beneficial for analyzing incident reports to prevent future failures. The dataset facilitates future research in NLP and incident management communities. The access to the dataset is also provided (the IncidentAI dataset is available at: https://github.com/Cinnamon/incident-ai-dataset).

Modern machine learning relies on datasets to develop and validate research ideas. Given the growth of publicly available data, finding the right dataset to use is increasingly difficult. Any research question imposes explicit and implicit constraints on how well a given dataset will enable researchers to answer this question, such as dataset size, modality, and domain. We operationalize the task of recommending datasets given a short natural language description of a research idea, to help people find relevant datasets for their needs. Dataset recommendation poses unique challenges as an information retrieval problem; datasets are hard to directly index for search and there are no corpora readily available for this task. To facilitate this task, we build the DataFinder Dataset which consists of a larger automatically-constructed training set (17.5K queries) and a smaller expert-annotated evaluation set (392 queries). Using this data, we compare various information retrieval algorithms on our test set and present a superior bi-encoder retriever for text-based dataset recommendation. This system, trained on the DataFinder Dataset, finds more relevant search results than existing third-party dataset search engines. To encourage progress on dataset recommendation, we release our dataset and models to the public.

Timely and effective response to humanitarian crises requires quick and accurate analysis of large amounts of text data - a process that can highly benefit from expert-assisted NLP systems trained on validated and annotated data in the humanitarian response domain. To enable creation of such NLP systems, we introduce and release HumSet, a novel and rich multilingual dataset of humanitarian response documents annotated by experts in the humanitarian response community. The dataset provides documents in three languages (English, French, Spanish) and covers a variety of humanitarian crises from 2018 to 2021 across the globe. For each document, HUMSET provides selected snippets (entries) as well as assigned classes to each entry annotated using common humanitarian information analysis frameworks. HUMSET also provides novel and challenging entry extraction and multi-label entry classification tasks. In this paper, we take a first step towards approaching these tasks and conduct a set of experiments on Pre-trained Language Models (PLM) to establish strong baselines for future research in this domain. The dataset is available at https://blog.thedeep.io/humset/.

We present two large datasets of labelled plant-images that are suited towards the training of machine learning and computer vision models. The first dataset encompasses as the day of writing over 1.2 million images of indoor-grown crops and weeds common to the Canadian Prairies and many US states. The second dataset consists of over 540,000 images of plants imaged in farmland. All indoor plant images are labelled by species and we provide rich etadata on the level of individual images. This comprehensive database allows to filter the datasets under user-defined specifications such as for example the crop-type or the age of the plant. Furthermore, the indoor dataset contains images of plants taken from a wide variety of angles, including profile shots, top-down shots, and angled perspectives. The images taken from plants in fields are all from a top-down perspective and contain usually multiple plants per image. For these images metadata is also available. In this paper we describe both datasets' characteristics with respect to plant variety, plant age, and number of images. We further introduce an open-access sample of the indoor-dataset that contains 1,000 images of each species covered in our dataset. These, in total 14,000 images, had been selected, such that they form a representative sample with respect to plant age and ndividual plants per species. This sample serves as a quick entry point for new users to the dataset, allowing them to explore the data on a small scale and find the parameters of data most useful for their application without having to deal with hundreds of thousands of individual images.

Modern machine learning research relies on relatively few carefully curated datasets. Even in these datasets, and typically in `untidy' or raw data, practitioners are faced with significant issues of data quality and diversity which can be prohibitively labor intensive to address. Existing methods for dealing with these challenges tend to make strong assumptions about the particular issues at play, and often require a priori knowledge or metadata such as domain labels. Our work is orthogonal to these methods: we instead focus on providing a unified and efficient framework for Metadata Archaeology -- uncovering and inferring metadata of examples in a dataset. We curate different subsets of data that might exist in a dataset (e.g. mislabeled, atypical, or out-of-distribution examples) using simple transformations, and leverage differences in learning dynamics between these probe suites to infer metadata of interest. Our method is on par with far more sophisticated mitigation methods across different tasks: identifying and correcting mislabeled examples, classifying minority-group samples, prioritizing points relevant for training and enabling scalable human auditing of relevant examples.

Recent advances in multi-modal algorithms have driven and been driven by the increasing availability of large image-text datasets, leading to significant strides in various fields, including computational pathology. However, in most existing medical image-text datasets, the text typically provides high-level summaries that may not sufficiently describe sub-tile regions within a large pathology image. For example, an image might cover an extensive tissue area containing cancerous and healthy regions, but the accompanying text might only specify that this image is a cancer slide, lacking the nuanced details needed for in-depth analysis. In this study, we introduce STimage-1K4M, a novel dataset designed to bridge this gap by providing genomic features for sub-tile images. STimage-1K4M contains 1,149 images derived from spatial transcriptomics data, which captures gene expression information at the level of individual spatial spots within a pathology image. Specifically, each image in the dataset is broken down into smaller sub-image tiles, with each tile paired with 15,000-30,000 dimensional gene expressions. With 4,293,195 pairs of sub-tile images and gene expressions, STimage-1K4M offers unprecedented granularity, paving the way for a wide range of advanced research in multi-modal data analysis an innovative applications in computational pathology, and beyond.

Training and evaluating language models increasingly requires the construction of meta-datasets --diverse collections of curated data with clear provenance. Natural language prompting has recently lead to improved zero-shot generalization by transforming existing, supervised datasets into a diversity of novel pretraining tasks, highlighting the benefits of meta-dataset curation. While successful in general-domain text, translating these data-centric approaches to biomedical language modeling remains challenging, as labeled biomedical datasets are significantly underrepresented in popular data hubs. To address this challenge, we introduce BigBIO a community library of 126+ biomedical NLP datasets, currently covering 12 task categories and 10+ languages. BigBIO facilitates reproducible meta-dataset curation via programmatic access to datasets and their metadata, and is compatible with current platforms for prompt engineering and end-to-end few/zero shot language model evaluation. We discuss our process for task schema harmonization, data auditing, contribution guidelines, and outline two illustrative use cases: zero-shot evaluation of biomedical prompts and large-scale, multi-task learning. BigBIO is an ongoing community effort and is available at https://github.com/bigscience-workshop/biomedical

The proliferation of open-source scientific software for science and research presents opportunities and challenges. In this paper, we introduce the SciCat dataset -- a comprehensive collection of Free-Libre Open Source Software (FLOSS) projects, designed to address the need for a curated repository of scientific and research software. This collection is crucial for understanding the creation of scientific software and aiding in its development. To ensure extensive coverage, our approach involves selecting projects from a pool of 131 million deforked repositories from the World of Code data source. Subsequently, we analyze README.md files using OpenAI's advanced language models. Our classification focuses on software designed for scientific purposes, research-related projects, and research support software. The SciCat dataset aims to become an invaluable tool for researching science-related software, shedding light on emerging trends, prevalent practices, and challenges in the field of scientific software development. Furthermore, it includes data that can be linked to the World of Code, GitHub, and other platforms, providing a solid foundation for conducting comparative studies between scientific and non-scientific software.

Large Language Models (LLMs)' search capabilities have garnered significant attention. Existing benchmarks, such as OpenAI's BrowseComp, primarily focus on general search scenarios and fail to adequately address the specific demands of academic search. These demands include deeper literature tracing and organization, professional support for academic databases, the ability to navigate long-tail academic knowledge, and ensuring academic rigor. Here, we proposed ScholarSearch, the first dataset specifically designed to evaluate the complex information retrieval capabilities of Large Language Models (LLMs) in academic research. ScholarSearch possesses the following key characteristics: Academic Practicality, where question content closely mirrors real academic learning and research environments, avoiding deliberately misleading models; High Difficulty, with answers that are challenging for single models (e.g., Grok DeepSearch or Gemini Deep Research) to provide directly, often requiring at least three deep searches to derive; Concise Evaluation, where limiting conditions ensure answers are as unique as possible, accompanied by clear sources and brief solution explanations, greatly facilitating subsequent audit and verification, surpassing the current lack of analyzed search datasets both domestically and internationally; and Broad Coverage, as the dataset spans at least 15 different academic disciplines. Through ScholarSearch, we expect to more precisely measure and promote the performance improvement of LLMs in complex academic information retrieval tasks. The data is available at: https://huggingface.co/datasets/PKU-DS-LAB/ScholarSearch

Clinical diagnosis of the eye is performed over multifarious data modalities including scalar clinical labels, vectorized biomarkers, two-dimensional fundus images, and three-dimensional Optical Coherence Tomography (OCT) scans. Clinical practitioners use all available data modalities for diagnosing and treating eye diseases like Diabetic Retinopathy (DR) or Diabetic Macular Edema (DME). Enabling usage of machine learning algorithms within the ophthalmic medical domain requires research into the relationships and interactions between all relevant data over a treatment period. Existing datasets are limited in that they neither provide data nor consider the explicit relationship modeling between the data modalities. In this paper, we introduce the Ophthalmic Labels for Investigating Visual Eye Semantics (OLIVES) dataset that addresses the above limitation. This is the first OCT and near-IR fundus dataset that includes clinical labels, biomarker labels, disease labels, and time-series patient treatment information from associated clinical trials. The dataset consists of 1268 near-IR fundus images each with at least 49 OCT scans, and 16 biomarkers, along with 4 clinical labels and a disease diagnosis of DR or DME. In total, there are 96 eyes' data averaged over a period of at least two years with each eye treated for an average of 66 weeks and 7 injections. We benchmark the utility of OLIVES dataset for ophthalmic data as well as provide benchmarks and concrete research directions for core and emerging machine learning paradigms within medical image analysis.

In this work, we present a manually annotated corpus for Adverse Event (AE) extraction from discharge summaries of elderly patients, a population often underrepresented in clinical NLP resources. The dataset includes 14 clinically significant AEs-such as falls, delirium, and intracranial haemorrhage, along with contextual attributes like negation, diagnosis type, and in-hospital occurrence. Uniquely, the annotation schema supports both discontinuous and overlapping entities, addressing challenges rarely tackled in prior work. We evaluate multiple models using FlairNLP across three annotation granularities: fine-grained, coarse-grained, and coarse-grained with negation. While transformer-based models (e.g., BERT-cased) achieve strong performance on document-level coarse-grained extraction (F1 = 0.943), performance drops notably for fine-grained entity-level tasks (e.g., F1 = 0.675), particularly for rare events and complex attributes. These results demonstrate that despite high-level scores, significant challenges remain in detecting underrepresented AEs and capturing nuanced clinical language. Developed within a Trusted Research Environment (TRE), the dataset is available upon request via DataLoch and serves as a robust benchmark for evaluating AE extraction methods and supporting future cross-dataset generalisation.

Scientific researchers need intensive information about datasets to effectively evaluate and develop theories and methodologies. The information needs regarding datasets are implicitly embedded in particular research tasks, rather than explicitly expressed in search queries. However, existing scientific retrieval and question-answering (QA) datasets typically address straightforward questions, which do not align with the distribution of real-world research inquiries. To bridge this gap, we developed ScIRGen, a dataset generation framework for scientific QA \& retrieval that more accurately reflects the information needs of professional science researchers, and uses it to create a large-scale scientific retrieval-augmented generation (RAG) dataset with realistic queries, datasets and papers. Technically, we designed a dataset-oriented information extraction method that leverages academic papers to augment the dataset representation. We then proposed a question generation framework by employing cognitive taxonomy to ensure the quality of synthesized questions. We also design a method to automatically filter synthetic answers based on the perplexity shift of LLMs, which is highly aligned with human judgment of answers' validity. Collectively, these methodologies culminated in the creation of the 61k QA dataset, ScIRGen-Geo. We benchmarked representative methods on the ScIRGen-Geo dataset for their question-answering and retrieval capabilities, finding out that current methods still suffer from reasoning from complex questions. This work advances the development of more sophisticated tools to support the intricate information needs of the scientific community.

Large Language Models (LLMs) are at the forefront of NLP achievements but fall short in dealing with shortcut learning, factual inconsistency, and vulnerability to adversarial inputs.These shortcomings are especially critical in medical contexts, where they can misrepresent actual model capabilities. Addressing this, we present SemEval-2024 Task 2: Safe Biomedical Natural Language Inference for ClinicalTrials. Our contributions include the refined NLI4CT-P dataset (i.e., Natural Language Inference for Clinical Trials - Perturbed), designed to challenge LLMs with interventional and causal reasoning tasks, along with a comprehensive evaluation of methods and results for participant submissions. A total of 106 participants registered for the task contributing to over 1200 individual submissions and 25 system overview papers. This initiative aims to advance the robustness and applicability of NLI models in healthcare, ensuring safer and more dependable AI assistance in clinical decision-making. We anticipate that the dataset, models, and outcomes of this task can support future research in the field of biomedical NLI. The dataset, competition leaderboard, and website are publicly available.

Anthropogenic ecological crisis constitutes a significant challenge that all within the academy must urgently face, including the Natural Language Processing (NLP) community. While recent years have seen increasing work revolving around climate-centric discourse, crucial environmental and ecological topics outside of climate change remain largely unaddressed, despite their prominent importance. Mainstream NLP tasks, such as sentiment analysis, dominate the scene, but there remains an untouched space in the literature involving the analysis of environmental impacts of certain events and practices. To address this gap, this paper presents EcoVerse, an annotated English Twitter dataset of 3,023 tweets spanning a wide spectrum of environmental topics. We propose a three-level annotation scheme designed for Eco-Relevance Classification, Stance Detection, and introducing an original approach for Environmental Impact Analysis. We detail the data collection, filtering, and labeling process that led to the creation of the dataset. Remarkable Inter-Annotator Agreement indicates that the annotation scheme produces consistent annotations of high quality. Subsequent classification experiments using BERT-based models, including ClimateBERT, are presented. These yield encouraging results, while also indicating room for a model specifically tailored for environmental texts. The dataset is made freely available to stimulate further research.

Audio-language models (ALMs) process sounds to provide a linguistic description of sound-producing events and scenes. Recent advances in computing power and dataset creation have led to significant progress in this domain. This paper surveys existing datasets used for training audio-language models, emphasizing the recent trend towards using large, diverse datasets to enhance model performance. Key sources of these datasets include the Freesound platform and AudioSet that have contributed to the field's rapid growth. Although prior surveys primarily address techniques and training details, this survey categorizes and evaluates a wide array of datasets, addressing their origins, characteristics, and use cases. It also performs a data leak analysis to ensure dataset integrity and mitigate bias between datasets. This survey was conducted by analyzing research papers up to and including December 2023, and does not contain any papers after that period.

This paper presents a Patherea, a framework for point-based cell detection and classification that provides a complete solution for developing and evaluating state-of-the-art approaches. We introduce a large-scale dataset collected to directly replicate a clinical workflow for Ki-67 proliferation index estimation and use it to develop an efficient point-based approach that directly predicts point-based predictions, without the need for intermediate representations. The proposed approach effectively utilizes point proposal candidates with the hybrid Hungarian matching strategy and a flexible architecture that enables the usage of various backbones and (pre)training strategies. We report state-of-the-art results on existing public datasets - Lizard, BRCA-M2C, BCData, and the newly proposed Patherea dataset. We show that the performance on existing public datasets is saturated and that the newly proposed Patherea dataset represents a significantly harder challenge for the recently proposed approaches. We also demonstrate the effectiveness of recently proposed pathology foundational models that our proposed approach can natively utilize and benefit from. We also revisit the evaluation protocol that is used in the broader field of cell detection and classification and identify the erroneous calculation of performance metrics. Patherea provides a benchmarking utility that addresses the identified issues and enables a fair comparison of different approaches. The dataset and the code will be publicly released upon acceptance.

Extracting key information from scientific papers has the potential to help researchers work more efficiently and accelerate the pace of scientific progress. Over the last few years, research on Scientific Information Extraction (SciIE) witnessed the release of several new systems and benchmarks. However, existing paper-focused datasets mostly focus only on specific parts of a manuscript (e.g., abstracts) and are single-modality (i.e., text- or table-only), due to complex processing and expensive annotations. Moreover, core information can be present in either text or tables or across both. To close this gap in data availability and enable cross-modality IE, while alleviating labeling costs, we propose a semi-supervised pipeline for annotating entities in text, as well as entities and relations in tables, in an iterative procedure. Based on this pipeline, we release novel resources for the scientific community, including a high-quality benchmark, a large-scale corpus, and a semi-supervised annotation pipeline. We further report the performance of state-of-the-art IE models on the proposed benchmark dataset, as a baseline. Lastly, we explore the potential capability of large language models such as ChatGPT for the current task. Our new dataset, results, and analysis validate the effectiveness and efficiency of our semi-supervised pipeline, and we discuss its remaining limitations.

The rapid rollout of AI in heterogeneous public and societal sectors has subsequently escalated the need for compliance with regulatory standards and frameworks. The EU AI Act has emerged as a landmark in the regulatory landscape. The development of solutions that elicit the level of AI systems' compliance with such standards is often limited by the lack of resources, hindering the semi-automated or automated evaluation of their performance. This generates the need for manual work, which is often error-prone, resource-limited or limited to cases not clearly described by the regulation. This paper presents an open, transparent, and reproducible method of creating a resource that facilitates the evaluation of NLP models with a strong focus on RAG systems. We have developed a dataset that contain the tasks of risk-level classification, article retrieval, obligation generation, and question-answering for the EU AI Act. The dataset files are in a machine-to-machine appropriate format. To generate the files, we utilise domain knowledge as an exegetical basis, combining with the processing and reasoning power of large language models to generate scenarios along with the respective tasks. Our methodology demonstrates a way to harness language models for grounded generation with high document relevancy. Besides, we overcome limitations such as navigating the decision boundaries of risk-levels that are not explicitly defined within the EU AI Act, such as limited and minimal cases. Finally, we demonstrate our dataset's effectiveness by evaluating a RAG-based solution that reaches 0.87 and 0.85 F1-score for prohibited and high-risk scenarios.

The difficulty of monitoring biodiversity at fine scales and over large areas limits ecological knowledge and conservation efforts. To fill this gap, Species Distribution Models (SDMs) predict species across space from spatially explicit features. Yet, they face the challenge of integrating the rich but heterogeneous data made available over the past decade, notably millions of opportunistic species observations and standardized surveys, as well as multi-modal remote sensing data. In light of that, we have designed and developed a new European-scale dataset for SDMs at high spatial resolution (10-50 m), including more than 10k species (i.e., most of the European flora). The dataset comprises 5M heterogeneous Presence-Only records and 90k exhaustive Presence-Absence survey records, all accompanied by diverse environmental rasters (e.g., elevation, human footprint, and soil) that are traditionally used in SDMs. In addition, it provides Sentinel-2 RGB and NIR satellite images with 10 m resolution, a 20-year time-series of climatic variables, and satellite time-series from the Landsat program. In addition to the data, we provide an openly accessible SDM benchmark (hosted on Kaggle), which has already attracted an active community and a set of strong baselines for single predictor/modality and multimodal approaches. All resources, e.g., the dataset, pre-trained models, and baseline methods (in the form of notebooks), are available on Kaggle, allowing one to start with our dataset literally with two mouse clicks.

Recent advancements in Digital Pathology (DP), particularly through artificial intelligence and Foundation Models, have underscored the importance of large-scale, diverse, and richly annotated datasets. Despite their critical role, publicly available Whole Slide Image (WSI) datasets often lack sufficient scale, tissue diversity, and comprehensive clinical metadata, limiting the robustness and generalizability of AI models. In response, we introduce the HISTAI dataset, a large, multimodal, open-access WSI collection comprising over 60,000 slides from various tissue types. Each case in the HISTAI dataset is accompanied by extensive clinical metadata, including diagnosis, demographic information, detailed pathological annotations, and standardized diagnostic coding. The dataset aims to fill gaps identified in existing resources, promoting innovation, reproducibility, and the development of clinically relevant computational pathology solutions. The dataset can be accessed at https://github.com/HistAI/HISTAI.

This paper introduces ClimateGPT, a model family of domain-specific large language models that synthesize interdisciplinary research on climate change. We trained two 7B models from scratch on a science-oriented dataset of 300B tokens. For the first model, the 4.2B domain-specific tokens were included during pre-training and the second was adapted to the climate domain after pre-training. Additionally, ClimateGPT-7B, 13B and 70B are continuously pre-trained from Llama~2 on a domain-specific dataset of 4.2B tokens. Each model is instruction fine-tuned on a high-quality and human-generated domain-specific dataset that has been created in close cooperation with climate scientists. To reduce the number of hallucinations, we optimize the model for retrieval augmentation and propose a hierarchical retrieval strategy. To increase the accessibility of our model to non-English speakers, we propose to make use of cascaded machine translation and show that this approach can perform comparably to natively multilingual models while being easier to scale to a large number of languages. Further, to address the intrinsic interdisciplinary aspect of climate change we consider different research perspectives. Therefore, the model can produce in-depth answers focusing on different perspectives in addition to an overall answer. We propose a suite of automatic climate-specific benchmarks to evaluate LLMs. On these benchmarks, ClimateGPT-7B performs on par with the ten times larger Llama-2-70B Chat model while not degrading results on general domain benchmarks. Our human evaluation confirms the trends we saw in our benchmarks. All models were trained and evaluated using renewable energy and are released publicly.

Objective digital data is scarce yet needed in many domains to enable research that can transform the standard of healthcare. While data from consumer-grade wearables and smartphones is more accessible, there is critical need for similar data from clinical-grade devices used by patients with a diagnosed condition. The prevalence of wearable medical devices in the diabetes domain sets the stage for unique research and development within this field and beyond. However, the scarcity of open-source datasets presents a major barrier to progress. To facilitate broader research on diabetes-relevant problems and accelerate development of robust computational solutions, we provide the DiaTrend dataset. The DiaTrend dataset is composed of intensive longitudinal data from wearable medical devices, including a total of 27,561 days of continuous glucose monitor data and 8,220 days of insulin pump data from 54 patients with diabetes. This dataset is useful for developing novel analytic solutions that can reduce the disease burden for people living with diabetes and increase knowledge on chronic condition management in outpatient settings.

The development of vision-language models (VLMs) is driven by large-scale and diverse multimodal datasets. However, progress toward generalist biomedical VLMs is limited by the lack of annotated, publicly accessible datasets across biology and medicine. Existing efforts are restricted to narrow domains, missing the full diversity of biomedical knowledge encoded in scientific literature. To address this gap, we introduce BIOMEDICA, a scalable, open-source framework to extract, annotate, and serialize the entirety of the PubMed Central Open Access subset into an easy-to-use, publicly accessible dataset.Our framework produces a comprehensive archive with over 24 million unique image-text pairs from over 6 million articles. Metadata and expert-guided annotations are also provided. We demonstrate the utility and accessibility of our resource by releasing BMCA-CLIP, a suite of CLIP-style models continuously pre-trained on the BIOMEDICA dataset via streaming, eliminating the need to download 27 TB of data locally.On average, our models achieve state-of-the-art performance across 40 tasks - spanning pathology, radiology, ophthalmology, dermatology, surgery, molecular biology, parasitology, and cell biology - excelling in zero-shot classification with a 6.56% average improvement (as high as 29.8% and 17.5% in dermatology and ophthalmology, respectively), and stronger image-text retrieval, all while using 10x less compute. To foster reproducibility and collaboration, we release our codebase and dataset for the broader research community.

Biodiversity research requires complete and detailed information to study ecosystem dynamics at different scales. Employing data-driven methods like Machine Learning is getting traction in ecology and more specific biodiversity, offering alternative modelling pathways. For these methods to deliver accurate results there is the need for large, curated and multimodal datasets that offer granular spatial and temporal resolutions. In this work, we introduce BioCube, a multimodal, fine-grained global dataset for ecology and biodiversity research. BioCube incorporates species observations through images, audio recordings and descriptions, environmental DNA, vegetation indices, agricultural, forest, land indicators, and high-resolution climate variables. All observations are geospatially aligned under the WGS84 geodetic system, spanning from 2000 to 2020. The dataset will become available at https://huggingface.co/datasets/BioDT/BioCube while the acquisition and processing code base at https://github.com/BioDT/bfm-data.

Motivation: The gut microbiota has recently emerged as a key factor that underpins certain connections between diet and human health. A tremendous amount of knowledge has been amassed from experimental studies on diet, human metabolism and microbiome. However, this evidence remains mostly buried in scientific publications, and biomedical literature mining in this domain remains scarce. We developed DiMB-RE, a comprehensive corpus annotated with 15 entity types (e.g., Nutrient, Microorganism) and 13 relation types (e.g., increases, improves) capturing diet-microbiome associations. We also trained and evaluated state-of-the-art natural language processing (NLP) models for named entity, trigger, and relation extraction as well as factuality detection using DiMB-RE. Results: DiMB-RE consists of 14,450 entities and 4,206 relationships from 165 articles. While NLP models performed reasonably well for named entity recognition (0.760 F_{1}), end-to-end relation extraction performance was modest (0.356 F_{1}), partly due to missed entities and triggers as well as cross-sentence relations. Conclusions: To our knowledge, DiMB-RE is largest and most diverse dataset focusing on diet-microbiome interactions. It can serve as a benchmark corpus for biomedical literature mining. Availability: DiMB-RE and the NLP models are available at https://github.com/ScienceNLP-Lab/DiMB-RE.

In this paper, we introduce GUIDE, a novel dataset tailored for the advancement of Multimodal Large Language Model (MLLM) applications, particularly focusing on Robotic Process Automation (RPA) use cases. Our dataset encompasses diverse data from various websites including Apollo(62.67\%), Gmail(3.43\%), Calendar(10.98\%) and Canva(22.92\%). Each data entry includes an image, a task description, the last action taken, CoT and the next action to be performed along with grounding information of where the action needs to be executed. The data is collected using our in-house advanced annotation tool NEXTAG (Next Action Grounding and Annotation Tool). The data is adapted for multiple OS, browsers and display types. It is collected by multiple annotators to capture the variation of design and the way person uses a website. Through this dataset, we aim to facilitate research and development in the realm of LLMs for graphical user interfaces, particularly in tasks related to RPA. The dataset's multi-platform nature and coverage of diverse websites enable the exploration of cross-interface capabilities in automation tasks. We believe that our dataset will serve as a valuable resource for advancing the capabilities of multi-platform LLMs in practical applications, fostering innovation in the field of automation and natural language understanding. Using GUIDE, we build V-Zen, the first RPA model to automate multiple websites using our in-House Automation tool AUTONODE

SciLaD is a novel, large-scale dataset of scientific language constructed entirely using open-source frameworks and publicly available data sources. It comprises a curated English split containing over 10 million scientific publications and a multilingual, unfiltered TEI XML split including more than 35 million publications. We also publish the extensible pipeline for generating SciLaD. The dataset construction and processing workflow demonstrates how open-source tools can enable large-scale, scientific data curation while maintaining high data quality. Finally, we pre-train a RoBERTa model on our dataset and evaluate it across a comprehensive set of benchmarks, achieving performance comparable to other scientific language models of similar size, validating the quality and utility of SciLaD. We publish the dataset and evaluation pipeline to promote reproducibility, transparency, and further research in natural scientific language processing and understanding including scholarly document processing.

In this paper, we release a largest ever medical Question Answering (QA) dataset with 26 million QA pairs. We benchmark many existing approaches in our dataset in terms of both retrieval and generation. Experimental results show that the existing models perform far lower than expected and the released dataset is still challenging in the pre-trained language model era. Moreover, we also experimentally show the benefit of the proposed dataset in many aspects: (i) trained models for other QA datasets in a zero-shot fashion; and (ii) as external knowledge for retrieval-augmented generation (RAG); and (iii) improving existing pre-trained language models by using the QA pairs as a pre-training corpus in continued training manner. We believe that this dataset will not only contribute to medical research but also facilitate both the patients and clinical doctors. See https://github.com/FreedomIntelligence/Huatuo-26M.

The advent of data-driven weather forecasting models, which learn from hundreds of terabytes (TB) of reanalysis data, has significantly advanced forecasting capabilities. However, the substantial costs associated with data storage and transmission present a major challenge for data providers and users, affecting resource-constrained researchers and limiting their accessibility to participate in AI-based meteorological research. To mitigate this issue, we introduce an efficient neural codec, the Variational Autoencoder Transformer (VAEformer), for extreme compression of climate data to significantly reduce data storage cost, making AI-based meteorological research portable to researchers. Our approach diverges from recent complex neural codecs by utilizing a low-complexity Auto-Encoder transformer. This encoder produces a quantized latent representation through variance inference, which reparameterizes the latent space as a Gaussian distribution. This method improves the estimation of distributions for cross-entropy coding. Extensive experiments demonstrate that our VAEformer outperforms existing state-of-the-art compression methods in the context of climate data. By applying our VAEformer, we compressed the most popular ERA5 climate dataset (226 TB) into a new dataset, CRA5 (0.7 TB). This translates to a compression ratio of over 300 while retaining the dataset's utility for accurate scientific analysis. Further, downstream experiments show that global weather forecasting models trained on the compact CRA5 dataset achieve forecasting accuracy comparable to the model trained on the original dataset. Code, the CRA5 dataset, and the pre-trained model are available at https://github.com/taohan10200/CRA5.

Large-scale data sets on scholarly publications are the basis for a variety of bibliometric analyses and natural language processing (NLP) applications. Especially data sets derived from publication's full-text have recently gained attention. While several such data sets already exist, we see key shortcomings in terms of their domain and time coverage, citation network completeness, and representation of full-text content. To address these points, we propose a new version of the data set unarXive. We base our data processing pipeline and output format on two existing data sets, and improve on each of them. Our resulting data set comprises 1.9 M publications spanning multiple disciplines and 32 years. It furthermore has a more complete citation network than its predecessors and retains a richer representation of document structure as well as non-textual publication content such as mathematical notation. In addition to the data set, we provide ready-to-use training/test data for citation recommendation and IMRaD classification. All data and source code is publicly available at https://github.com/IllDepence/unarXive.

Large language models (LLMs) trained on general domain corpora showed remarkable results on natural language processing (NLP) tasks. However, previous research demonstrated LLMs trained using domain-focused corpora perform better on specialized tasks. Inspired by this pivotal insight, we developed INDUS, a comprehensive suite of LLMs tailored for the Earth science, biology, physics, heliophysics, planetary sciences and astrophysics domains and trained using curated scientific corpora drawn from diverse data sources. The suite of models include: (1) an encoder model trained using domain-specific vocabulary and corpora to address natural language understanding tasks, (2) a contrastive-learning-based general text embedding model trained using a diverse set of datasets drawn from multiple sources to address information retrieval tasks and (3) smaller versions of these models created using knowledge distillation techniques to address applications which have latency or resource constraints. We also created three new scientific benchmark datasets namely, CLIMATE-CHANGE-NER (entity-recognition), NASA-QA (extractive QA) and NASA-IR (IR) to accelerate research in these multi-disciplinary fields. Finally, we show that our models outperform both general-purpose encoders (RoBERTa) and existing domain-specific encoders (SciBERT) on these new tasks as well as existing benchmark tasks in the domains of interest.

Skin lesion datasets provide essential information for understanding various skin conditions and developing effective diagnostic tools. They aid the artificial intelligence-based early detection of skin cancer, facilitate treatment planning, and contribute to medical education and research. Published large datasets have partially coverage the subclassifications of the skin lesions. This limitation highlights the need for more expansive and varied datasets to reduce false predictions and help improve the failure analysis for skin lesions. This study presents a diverse dataset comprising 12,345 dermatoscopic images with 38 subclasses of skin lesions collected in Turkiye which comprises different skin types in the transition zone between Europe and Asia. Each subgroup contains high-resolution photos and expert annotations, providing a strong and reliable basis for future research. The detailed analysis of each subgroup provided in this study facilitates targeted research endeavors and enhances the depth of understanding regarding the skin lesions. This dataset distinguishes itself through a diverse structure with 5 super classes, 15 main classes, 38 subclasses and its 12,345 high-resolution dermatoscopic images.

The San Andreas Fault system, known for its frequent seismic activity, provides an extensive dataset for earthquake studies. The region's well-instrumented seismic networks have been crucial in advancing research on earthquake statistics, physics, and subsurface Earth structures. In recent years, earthquake data from California has become increasingly valuable for deep learning applications, such as Generalized Phase Detection (GPD) for phase detection and polarity determination, and PhaseNet for phase arrival-time picking. The continuous accumulation of data, particularly those manually labeled by human analysts, serves as an essential resource for advancing both regional and global deep learning models. To support the continued development of machine learning and data mining studies, we have compiled a unified California Earthquake Event Dataset (CEED) that integrates seismic records from the Northern California Earthquake Data Center (NCEDC) and the Southern California Earthquake Data Center (SCEDC). The dataset includes both automatically and manually determined parameters such as earthquake origin time, source location, P/S phase arrivals, first-motion polarities, and ground motion intensity measurements. The dataset is organized in an event-based format organized by year spanning from 2000 to 2024, facilitating cross-referencing with event catalogs and enabling continuous updates in future years. This comprehensive open-access dataset is designed to support diverse applications including developing deep learning models, creating enhanced catalog products, and research into earthquake processes, fault zone structures, and seismic risks.

Seeking answers to questions within long scientific research articles is a crucial area of study that aids readers in quickly addressing their inquiries. However, existing question-answering (QA) datasets based on scientific papers are limited in scale and focus solely on textual content. To address this limitation, we introduce SPIQA (Scientific Paper Image Question Answering), the first large-scale QA dataset specifically designed to interpret complex figures and tables within the context of scientific research articles across various domains of computer science. Leveraging the breadth of expertise and ability of multimodal large language models (MLLMs) to understand figures, we employ automatic and manual curation to create the dataset. We craft an information-seeking task involving multiple images that cover a wide variety of plots, charts, tables, schematic diagrams, and result visualizations. SPIQA comprises 270K questions divided into training, validation, and three different evaluation splits. Through extensive experiments with 12 prominent foundational models, we evaluate the ability of current multimodal systems to comprehend the nuanced aspects of research articles. Additionally, we propose a Chain-of-Thought (CoT) evaluation strategy with in-context retrieval that allows fine-grained, step-by-step assessment and improves model performance. We further explore the upper bounds of performance enhancement with additional textual information, highlighting its promising potential for future research and the dataset's impact on revolutionizing how we interact with scientific literature.

Climate models have been key for assessing the impact of climate change and simulating future climate scenarios. The machine learning (ML) community has taken an increased interest in supporting climate scientists' efforts on various tasks such as climate model emulation, downscaling, and prediction tasks. Many of those tasks have been addressed on datasets created with single climate models. However, both the climate science and ML communities have suggested that to address those tasks at scale, we need large, consistent, and ML-ready climate model datasets. Here, we introduce ClimateSet, a dataset containing the inputs and outputs of 36 climate models from the Input4MIPs and CMIP6 archives. In addition, we provide a modular dataset pipeline for retrieving and preprocessing additional climate models and scenarios. We showcase the potential of our dataset by using it as a benchmark for ML-based climate model emulation. We gain new insights about the performance and generalization capabilities of the different ML models by analyzing their performance across different climate models. Furthermore, the dataset can be used to train an ML emulator on several climate models instead of just one. Such a "super emulator" can quickly project new climate change scenarios, complementing existing scenarios already provided to policymakers. We believe ClimateSet will create the basis needed for the ML community to tackle climate-related tasks at scale.

The World Health Organization added Disease X to their shortlist of blueprint priority diseases to represent a hypothetical, unknown pathogen that could cause a future epidemic. During different virus outbreaks of the past, such as COVID-19, Influenza, Lyme Disease, and Zika virus, researchers from various disciplines utilized Google Trends to mine multimodal components of web behavior to study, investigate, and analyze the global awareness, preparedness, and response associated with these respective virus outbreaks. As the world prepares for Disease X, a dataset on web behavior related to Disease X would be crucial to contribute towards the timely advancement of research in this field. Furthermore, none of the prior works in this field have focused on the development of a dataset to compile relevant web behavior data, which would help to prepare for Disease X. To address these research challenges, this work presents a dataset of web behavior related to Disease X, which emerged from different geographic regions of the world, between February 2018 and August 2023. Specifically, this dataset presents the search interests related to Disease X from 94 geographic regions. The dataset was developed by collecting data using Google Trends. The relevant search interests for all these regions for each month in this time range are available in this dataset. This paper also discusses the compliance of this dataset with the FAIR principles of scientific data management. Finally, an analysis of this dataset is presented to uphold the applicability, relevance, and usefulness of this dataset for the investigation of different research questions in the interrelated fields of Big Data, Data Mining, Healthcare, Epidemiology, and Data Analysis with a specific focus on Disease X.

Datasets play a critical role in medical imaging research, yet issues such as label quality, shortcuts, and metadata are often overlooked. This lack of attention may harm the generalizability of algorithms and, consequently, negatively impact patient outcomes. While existing medical imaging literature reviews mostly focus on machine learning (ML) methods, with only a few focusing on datasets for specific applications, these reviews remain static -- they are published once and not updated thereafter. This fails to account for emerging evidence, such as biases, shortcuts, and additional annotations that other researchers may contribute after the dataset is published. We refer to these newly discovered findings of datasets as research artifacts. To address this gap, we propose a living review that continuously tracks public datasets and their associated research artifacts across multiple medical imaging applications. Our approach includes a framework for the living review to monitor data documentation artifacts, and an SQL database to visualize the citation relationships between research artifact and dataset. Lastly, we discuss key considerations for creating medical imaging datasets, review best practices for data annotation, discuss the significance of shortcuts and demographic diversity, and emphasize the importance of managing datasets throughout their entire lifecycle. Our demo is publicly available at http://inthepicture.itu.dk/.

The rapid advancement of large language models (LLMs) has revolutionized text generation, making it increasingly difficult to distinguish between human- and AI-generated content. This poses a significant challenge to academic integrity, particularly in scientific publishing and multilingual contexts where detection resources are often limited. To address this critical gap, we introduce the AINL-Eval 2025 Shared Task, specifically focused on the detection of AI-generated scientific abstracts in Russian. We present a novel, large-scale dataset comprising 52,305 samples, including human-written abstracts across 12 diverse scientific domains and AI-generated counterparts from five state-of-the-art LLMs (GPT-4-Turbo, Gemma2-27B, Llama3.3-70B, Deepseek-V3, and GigaChat-Lite). A core objective of the task is to challenge participants to develop robust solutions capable of generalizing to both (i) previously unseen scientific domains and (ii) models not included in the training data. The task was organized in two phases, attracting 10 teams and 159 submissions, with top systems demonstrating strong performance in identifying AI-generated content. We also establish a continuous shared task platform to foster ongoing research and long-term progress in this important area. The dataset and platform are publicly available at https://github.com/iis-research-team/AINL-Eval-2025.

Surficial geologic mapping is essential for understanding Earth surface processes, addressing modern challenges such as climate change and national security, and supporting common applications in engineering and resource management. However, traditional mapping methods are labor-intensive, limiting spatial coverage and introducing potential biases. To address these limitations, we introduce EarthScape, a novel, AI-ready multimodal dataset specifically designed for surficial geologic mapping and Earth surface analysis. EarthScape integrates high-resolution aerial RGB and near-infrared (NIR) imagery, digital elevation models (DEM), multi-scale DEM-derived terrain features, and hydrologic and infrastructure vector data. The dataset provides detailed annotations for seven distinct surficial geologic classes encompassing various geological processes. We present a comprehensive data processing pipeline using open-sourced raw data and establish baseline benchmarks using different spatial modalities to demonstrate the utility of EarthScape. As a living dataset with a vision for expansion, EarthScape bridges the gap between computer vision and Earth sciences, offering a valuable resource for advancing research in multimodal learning, geospatial analysis, and geological mapping. Our code is available at https://github.com/masseygeo/earthscape.

In this report, we introduce SciFive, a domain-specific T5 model that has been pre-trained on large biomedical corpora. Our model outperforms the current SOTA methods (i.e. BERT, BioBERT, Base T5) on tasks in named entity relation, relation extraction, natural language inference, and question-answering. We show that text-generation methods have significant potential in a broad array of biomedical NLP tasks, particularly those requiring longer, more complex outputs. Our results support the exploration of more difficult text generation tasks and the development of new methods in this area

Identifying patient cohorts is fundamental to numerous healthcare tasks, including clinical trial recruitment and retrospective studies. Current cohort retrieval methods in healthcare organizations rely on automated queries of structured data combined with manual curation, which are time-consuming, labor-intensive, and often yield low-quality results. Recent advancements in large language models (LLMs) and information retrieval (IR) offer promising avenues to revolutionize these systems. Major challenges include managing extensive eligibility criteria and handling the longitudinal nature of unstructured Electronic Medical Records (EMRs) while ensuring that the solution remains cost-effective for real-world application. This paper introduces a new task, Automatic Cohort Retrieval (ACR), and evaluates the performance of LLMs and commercial, domain-specific neuro-symbolic approaches. We provide a benchmark task, a query dataset, an EMR dataset, and an evaluation framework. Our findings underscore the necessity for efficient, high-quality ACR systems capable of longitudinal reasoning across extensive patient databases.

Natural disasters, such as floods, tornadoes, or wildfires, are increasingly pervasive as the Earth undergoes global warming. It is difficult to predict when and where an incident will occur, so timely emergency response is critical to saving the lives of those endangered by destructive events. Fortunately, technology can play a role in these situations. Social media posts can be used as a low-latency data source to understand the progression and aftermath of a disaster, yet parsing this data is tedious without automated methods. Prior work has mostly focused on text-based filtering, yet image and video-based filtering remains largely unexplored. In this work, we present the Incidents1M Dataset, a large-scale multi-label dataset which contains 977,088 images, with 43 incident and 49 place categories. We provide details of the dataset construction, statistics and potential biases; introduce and train a model for incident detection; and perform image-filtering experiments on millions of images on Flickr and Twitter. We also present some applications on incident analysis to encourage and enable future work in computer vision for humanitarian aid. Code, data, and models are available at http://incidentsdataset.csail.mit.edu.

Accurate pain assessment in patients with limited ability to communicate, such as older adults with dementia, represents a critical healthcare challenge. Robust automated systems of pain detection may facilitate such assessments. Existing pain detection datasets, however, suffer from limited ethnic/racial diversity, privacy constraints, and underrepresentation of older adults who are the primary target population for clinical deployment. We present SynPAIN, a large-scale synthetic dataset containing 10,710 facial expression images (5,355 neutral/expressive pairs) across five ethnicities/races, two age groups (young: 20-35, old: 75+), and two genders. Using commercial generative AI tools, we created demographically balanced synthetic identities with clinically meaningful pain expressions. Our validation demonstrates that synthetic pain expressions exhibit expected pain patterns, scoring significantly higher than neutral and non-pain expressions using clinically validated pain assessment tools based on facial action unit analysis. We experimentally demonstrate SynPAIN's utility in identifying algorithmic bias in existing pain detection models. Through comprehensive bias evaluation, we reveal substantial performance disparities across demographic characteristics. These performance disparities were previously undetectable with smaller, less diverse datasets. Furthermore, we demonstrate that age-matched synthetic data augmentation improves pain detection performance on real clinical data, achieving a 7.0% improvement in average precision. SynPAIN addresses critical gaps in pain assessment research by providing the first publicly available, demographically diverse synthetic dataset specifically designed for older adult pain detection, while establishing a framework for measuring and mitigating algorithmic bias. The dataset is available at https://doi.org/10.5683/SP3/WCXMAP

To assess the effectiveness of any medical intervention, researchers must conduct a time-intensive and highly manual literature review. NLP systems can help to automate or assist in parts of this expensive process. In support of this goal, we release MS^2 (Multi-Document Summarization of Medical Studies), a dataset of over 470k documents and 20k summaries derived from the scientific literature. This dataset facilitates the development of systems that can assess and aggregate contradictory evidence across multiple studies, and is the first large-scale, publicly available multi-document summarization dataset in the biomedical domain. We experiment with a summarization system based on BART, with promising early results. We formulate our summarization inputs and targets in both free text and structured forms and modify a recently proposed metric to assess the quality of our system's generated summaries. Data and models are available at https://github.com/allenai/ms2

We introduce the French Land cover from Aerospace ImageRy (FLAIR), an extensive dataset from the French National Institute of Geographical and Forest Information (IGN) that provides a unique and rich resource for large-scale geospatial analysis. FLAIR contains high-resolution aerial imagery with a ground sample distance of 20 cm and over 20 billion individually labeled pixels for precise land-cover classification. The dataset also integrates temporal and spectral data from optical satellite time series. FLAIR thus combines data with varying spatial, spectral, and temporal resolutions across over 817 km2 of acquisitions representing the full landscape diversity of France. This diversity makes FLAIR a valuable resource for the development and evaluation of novel methods for large-scale land-cover semantic segmentation and raises significant challenges in terms of computer vision, data fusion, and geospatial analysis. We also provide powerful uni- and multi-sensor baseline models that can be employed to assess algorithm's performance and for downstream applications. Through its extent and the quality of its annotation, FLAIR aims to spur improvements in monitoring and understanding key anthropogenic development indicators such as urban growth, deforestation, and soil artificialization. Dataset and codes can be accessed at https://ignf.github.io/FLAIR/

The effective application of foundation models to translational research in immune-mediated diseases requires multimodal patient-level representations that can capture complex phenotypes emerging from multicellular interactions. Yet most current biological foundation models focus only on single-cell resolution and are evaluated on technical metrics often disconnected from actual drug development tasks and challenges. Here, we introduce EVA, the first cross-species, multimodal foundation model of immunology and inflammation, a therapeutic area where shared pathogenic mechanisms create unique opportunities for transfer learning. EVA harmonizes transcriptomics data across species, platforms, and resolutions, and integrates histology data to produce rich, unified patient representations. We establish clear scaling laws, demonstrating that increasing model size and compute translates to improvements in both pretraining and downstream tasks performance. We introduce a comprehensive evaluation suite of 39 tasks spanning the drug development pipeline: zero-shot target efficacy and gene function prediction for discovery, cross-species or cross-diseases molecular perturbations for preclinical development, and patient stratification with treatment response prediction or disease activity prediction for clinical trials applications. We benchmark EVA against several state-of-the-art biological foundation models and baselines on these tasks, and demonstrate state-of-the-art results on each task category. Using mechanistic interpretability, we further identify biological meaningful features, revealing intertwined representations across species and technologies. We release an open version of EVA for transcriptomics to accelerate research on immune-mediated diseases.

We introduce Biomed-Enriched, a biomedical text dataset constructed from PubMed via a two-stage annotation process. In the first stage, a large language model annotates 400K paragraphs from PubMed scientific articles, assigning scores for their type (review, study, clinical case, other), domain (clinical, biomedical, other), and educational quality. The educational quality score (rated 1 to 5) estimates how useful a paragraph is for college-level learning. These annotations are then used to fine-tune a small language model, which propagates the labels across the full PMC-OA corpus. The resulting metadata allows us to extract refined subsets, including 2M clinical case paragraphs with over 450K high-quality ones from articles with commercial-use licenses, and to construct several variants via quality filtering and domain upsampling. Clinical text is typically difficult to access due to privacy constraints, as hospital records cannot be publicly shared. Hence, our dataset provides an alternative large-scale, openly available collection of clinical cases from PubMed, making it a valuable resource for biomedical and clinical NLP. Preliminary continual-pretraining experiments with OLMo2 suggest these curated subsets enable targeted improvements, with clinical upsampling boosting performance by ~5% on MMLU ProfMed and educational quality filtering improving MedQA and MedMCQA by ~1%. Combinations of these techniques led to faster convergence, reaching same performance with a third of training tokens, indicating potential for more efficient and effective biomedical pretraining strategies.

Retrieval models are often evaluated on partially-annotated datasets. Each query is mapped to a few relevant texts and the remaining corpus is assumed to be irrelevant. As a result, models that successfully retrieve false negatives are punished in evaluation. Unfortunately, completely annotating all texts for every query is not resource efficient. In this work, we show that using partially-annotated datasets in evaluation can paint a distorted picture. We curate D-MERIT, a passage retrieval evaluation set from Wikipedia, aspiring to contain all relevant passages for each query. Queries describe a group (e.g., ``journals about linguistics'') and relevant passages are evidence that entities belong to the group (e.g., a passage indicating that Language is a journal about linguistics). We show that evaluating on a dataset containing annotations for only a subset of the relevant passages might result in misleading ranking of the retrieval systems and that as more relevant texts are included in the evaluation set, the rankings converge. We propose our dataset as a resource for evaluation and our study as a recommendation for balance between resource-efficiency and reliable evaluation when annotating evaluation sets for text retrieval.

Stroke remains a leading cause of global morbidity and mortality, placing a heavy socioeconomic burden. Over the past decade, advances in endovascular reperfusion therapy and the use of CT and MRI imaging for treatment guidance have significantly improved patient outcomes and are now standard in clinical practice. To develop machine learning algorithms that can extract meaningful and reproducible models of brain function for both clinical and research purposes from stroke images - particularly for lesion identification, brain health quantification, and prognosis - large, diverse, and well-annotated public datasets are essential. While only a few datasets with (sub-)acute stroke data were previously available, several large, high-quality datasets have recently been made publicly accessible. However, these existing datasets include only MRI data. In contrast, our dataset is the first to offer comprehensive longitudinal stroke data, including acute CT imaging with angiography and perfusion, follow-up MRI at 2-9 days, as well as acute and longitudinal clinical data up to a three-month outcome. The dataset includes a training dataset of n = 150 and a test dataset of n = 100 scans. Training data is publicly available, while test data will be used exclusively for model validation. We are making this dataset available as part of the 2024 edition of the Ischemic Stroke Lesion Segmentation (ISLES) challenge (https://www.isles-challenge.org/), which continuously aims to establish benchmark methods for acute and sub-acute ischemic stroke lesion segmentation, aiding in creating open stroke imaging datasets and evaluating cutting-edge image processing algorithms.

PROTACs are a promising therapeutic modality that harnesses the cell's built-in degradation machinery to degrade specific proteins. Despite their potential, developing new PROTACs is challenging and requires significant domain expertise, time, and cost. Meanwhile, machine learning has transformed drug design and development. In this work, we present a strategy for curating open-source PROTAC data and an open-source deep learning tool for predicting the degradation activity of novel PROTAC molecules. The curated dataset incorporates important information such as pDC_{50}, D_{max}, E3 ligase type, POI amino acid sequence, and experimental cell type. Our model architecture leverages learned embeddings from pretrained machine learning models, in particular for encoding protein sequences and cell type information. We assessed the quality of the curated data and the generalization ability of our model architecture against new PROTACs and targets via three tailored studies, which we recommend other researchers to use in evaluating their degradation activity models. In each study, three models predict protein degradation in a majority vote setting, reaching a top test accuracy of 82.6% and 0.848 ROC AUC, and a test accuracy of 61% and 0.615 ROC AUC when generalizing to novel protein targets. Our results are not only comparable to state-of-the-art models for protein degradation prediction, but also part of an open-source implementation which is easily reproducible and less computationally complex than existing approaches.

We present both the Lucie Training Dataset and the Lucie-7B foundation model. The Lucie Training Dataset is a multilingual collection of textual corpora centered around French and designed to offset anglo-centric biases found in many datasets for large language model pretraining. Its French data is pulled not only from traditional web sources, but also from French cultural heritage documents, filling an important gap in modern datasets. Beyond French, which makes up the largest share of the data, we added documents to support several other European languages, including English, Spanish, German, and Italian. Apart from its value as a resource for French language and culture, an important feature of this dataset is that it prioritizes data rights by minimizing copyrighted material. In addition, building on the philosophy of past open projects, it is redistributed in the form used for training and its processing is described on Hugging Face and GitHub. The Lucie-7B foundation model is trained on equal amounts of data in French and English -- roughly 33% each -- in an effort to better represent cultural aspects of French-speaking communities. We also describe two instruction fine-tuned models, Lucie-7B-Instruct-v1.1 and Lucie-7B-Instruct-human-data, which we release as demonstrations of Lucie-7B in use. These models achieve promising results compared to state-of-the-art models, demonstrating that an open approach prioritizing data rights can still deliver strong performance. We see these models as an initial step toward developing more performant, aligned models in the near future. Model weights for Lucie-7B and the Lucie instruct models, along with intermediate checkpoints for the former, are published on Hugging Face, while model training and data preparation code is available on GitHub. This makes Lucie-7B one of the first OSI compliant language models according to the new OSI definition.

We present PeerQA, a real-world, scientific, document-level Question Answering (QA) dataset. PeerQA questions have been sourced from peer reviews, which contain questions that reviewers raised while thoroughly examining the scientific article. Answers have been annotated by the original authors of each paper. The dataset contains 579 QA pairs from 208 academic articles, with a majority from ML and NLP, as well as a subset of other scientific communities like Geoscience and Public Health. PeerQA supports three critical tasks for developing practical QA systems: Evidence retrieval, unanswerable question classification, and answer generation. We provide a detailed analysis of the collected dataset and conduct experiments establishing baseline systems for all three tasks. Our experiments and analyses reveal the need for decontextualization in document-level retrieval, where we find that even simple decontextualization approaches consistently improve retrieval performance across architectures. On answer generation, PeerQA serves as a challenging benchmark for long-context modeling, as the papers have an average size of 12k tokens. Our code and data is available at https://github.com/UKPLab/peerqa.

Advancing AI in computational pathology requires large, high-quality, and diverse datasets, yet existing public datasets are often limited in organ diversity, class coverage, or annotation quality. To bridge this gap, we introduce SPIDER (Supervised Pathology Image-DEscription Repository), the largest publicly available patch-level dataset covering multiple organ types, including Skin, Colorectal, and Thorax, with comprehensive class coverage for each organ. SPIDER provides high-quality annotations verified by expert pathologists and includes surrounding context patches, which enhance classification performance by providing spatial context. Alongside the dataset, we present baseline models trained on SPIDER using the Hibou-L foundation model as a feature extractor combined with an attention-based classification head. The models achieve state-of-the-art performance across multiple tissue categories and serve as strong benchmarks for future digital pathology research. Beyond patch classification, the model enables rapid identification of significant areas, quantitative tissue metrics, and establishes a foundation for multimodal approaches. Both the dataset and trained models are publicly available to advance research, reproducibility, and AI-driven pathology development. Access them at: https://github.com/HistAI/SPIDER

With the exacerbation of the biodiversity and climate crises, macroecological pursuits such as global biodiversity mapping become more urgent. Remote sensing offers a wealth of Earth observation data for ecological studies, but the scarcity of labeled datasets remains a major challenge. Recently, self-supervised learning has enabled learning representations from unlabeled data, triggering the development of pretrained geospatial models with generalizable features. However, these models are often trained on datasets biased toward areas of high human activity, leaving entire ecological regions underrepresented. Additionally, while some datasets attempt to address seasonality through multi-date imagery, they typically follow calendar seasons rather than local phenological cycles. To better capture vegetation seasonality at a global scale, we propose a simple phenology-informed sampling strategy and introduce corresponding SSL4Eco, a multi-date Sentinel-2 dataset, on which we train an existing model with a season-contrastive objective. We compare representations learned from SSL4Eco against other datasets on diverse ecological downstream tasks and demonstrate that our straightforward sampling method consistently improves representation quality, highlighting the importance of dataset construction. The model pretrained on SSL4Eco reaches state of the art performance on 7 out of 8 downstream tasks spanning (multi-label) classification and regression. We release our code, data, and model weights to support macroecological and computer vision research at https://github.com/PlekhanovaElena/ssl4eco.

Research in question answering datasets and models has gained a lot of attention in the research community. Many of them release their own question answering datasets as well as the models. There is tremendous progress that we have seen in this area of research. The aim of this survey is to recognize, summarize and analyze the existing datasets that have been released by many researchers, especially in non-English datasets as well as resources such as research code, and evaluation metrics. In this paper, we review question answering datasets that are available in common languages other than English such as French, German, Japanese, Chinese, Arabic, Russian, as well as the multilingual and cross-lingual question-answering datasets.

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

Metadata extraction is essential for cataloging and preserving datasets, enabling effective research discovery and reproducibility, especially given the current exponential growth in scientific research. While Masader (Alyafeai et al.,2021) laid the groundwork for extracting a wide range of metadata attributes from Arabic NLP datasets' scholarly articles, it relies heavily on manual annotation. In this paper, we present MOLE, a framework that leverages Large Language Models (LLMs) to automatically extract metadata attributes from scientific papers covering datasets of languages other than Arabic. Our schema-driven methodology processes entire documents across multiple input formats and incorporates robust validation mechanisms for consistent output. Additionally, we introduce a new benchmark to evaluate the research progress on this task. Through systematic analysis of context length, few-shot learning, and web browsing integration, we demonstrate that modern LLMs show promising results in automating this task, highlighting the need for further future work improvements to ensure consistent and reliable performance. We release the code: https://github.com/IVUL-KAUST/MOLE and dataset: https://huggingface.co/datasets/IVUL-KAUST/MOLE for the research community.

Scientific information extraction (SciIE) is critical for converting unstructured knowledge from scholarly articles into structured data (entities and relations). Several datasets have been proposed for training and validating SciIE models. However, due to the high complexity and cost of annotating scientific texts, those datasets restrict their annotations to specific parts of paper, such as abstracts, resulting in the loss of diverse entity mentions and relations in context. In this paper, we release a new entity and relation extraction dataset for entities related to datasets, methods, and tasks in scientific articles. Our dataset contains 106 manually annotated full-text scientific publications with over 24k entities and 12k relations. To capture the intricate use and interactions among entities in full texts, our dataset contains a fine-grained tag set for relations. Additionally, we provide an out-of-distribution test set to offer a more realistic evaluation. We conduct comprehensive experiments, including state-of-the-art supervised models and our proposed LLM-based baselines, and highlight the challenges presented by our dataset, encouraging the development of innovative models to further the field of SciIE.

Keeping track of scientific challenges, advances and emerging directions is a fundamental part of research. However, researchers face a flood of papers that hinders discovery of important knowledge. In biomedicine, this directly impacts human lives. To address this problem, we present a novel task of extraction and search of scientific challenges and directions, to facilitate rapid knowledge discovery. We construct and release an expert-annotated corpus of texts sampled from full-length papers, labeled with novel semantic categories that generalize across many types of challenges and directions. We focus on a large corpus of interdisciplinary work relating to the COVID-19 pandemic, ranging from biomedicine to areas such as AI and economics. We apply a model trained on our data to identify challenges and directions across the corpus and build a dedicated search engine. In experiments with 19 researchers and clinicians using our system, we outperform a popular scientific search engine in assisting knowledge discovery. Finally, we show that models trained on our resource generalize to the wider biomedical domain and to AI papers, highlighting its broad utility. We make our data, model and search engine publicly available. https://challenges.apps.allenai.org/

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.

This paper introduces the Emirates Multi-Task (EMT) dataset - the first publicly available dataset for autonomous driving collected in the Arab Gulf region. The EMT dataset captures the unique road topology, high traffic congestion, and distinctive characteristics of the Gulf region, including variations in pedestrian clothing and weather conditions. It contains over 30,000 frames from a dash-camera perspective, along with 570,000 annotated bounding boxes, covering approximately 150 kilometers of driving routes. The EMT dataset supports three primary tasks: tracking, trajectory forecasting and intention prediction. Each benchmark dataset is complemented with corresponding evaluations: (1) multi-agent tracking experiments, focusing on multi-class scenarios and occlusion handling; (2) trajectory forecasting evaluation using deep sequential and interaction-aware models; and (3) intention benchmark experiments conducted for predicting agents intentions from observed trajectories. The dataset is publicly available at avlab.io/emt-dataset, and pre-processing scripts along with evaluation models can be accessed at github.com/AV-Lab/emt-dataset.

We present the PanAf20K dataset, the largest and most diverse open-access annotated video dataset of great apes in their natural environment. It comprises more than 7 million frames across ~20,000 camera trap videos of chimpanzees and gorillas collected at 18 field sites in tropical Africa as part of the Pan African Programme: The Cultured Chimpanzee. The footage is accompanied by a rich set of annotations and benchmarks making it suitable for training and testing a variety of challenging and ecologically important computer vision tasks including ape detection and behaviour recognition. Furthering AI analysis of camera trap information is critical given the International Union for Conservation of Nature now lists all species in the great ape family as either Endangered or Critically Endangered. We hope the dataset can form a solid basis for engagement of the AI community to improve performance, efficiency, and result interpretation in order to support assessments of great ape presence, abundance, distribution, and behaviour and thereby aid conservation efforts.

In this paper we present AnswerCarefully, a dataset for promoting the safety and appropriateness of Japanese LLM outputs. The dataset consists of 1,800 pairs of questions and reference answers, where the questions require special attention in answering. It covers a wide range of risk categories established in prior English-language datasets, but the data samples are original in that they are manually created to reflect the socio-cultural context of LLM usage in Japan. We show that using this dataset for instruction to fine-tune a Japanese LLM led to improved output safety without compromising the utility of general responses. We also report the results of a safety evaluation of 12 Japanese LLMs using this dataset as a benchmark. Finally, we describe the latest update on the dataset which provides English translations and annotations of the questions, aimed at facilitating the derivation of similar datasets in different languages and regions.

Introduction: The scientific publishing landscape is expanding rapidly, creating challenges for researchers to stay up-to-date with the evolution of the literature. Natural Language Processing (NLP) has emerged as a potent approach to automating knowledge extraction from this vast amount of publications and preprints. Tasks such as Named-Entity Recognition (NER) and Named-Entity Linking (NEL), in conjunction with context-dependent semantic interpretation, offer promising and complementary approaches to extracting structured information and revealing key concepts. Results: We present the SourceData-NLP dataset produced through the routine curation of papers during the publication process. A unique feature of this dataset is its emphasis on the annotation of bioentities in figure legends. We annotate eight classes of biomedical entities (small molecules, gene products, subcellular components, cell lines, cell types, tissues, organisms, and diseases), their role in the experimental design, and the nature of the experimental method as an additional class. SourceData-NLP contains more than 620,000 annotated biomedical entities, curated from 18,689 figures in 3,223 papers in molecular and cell biology. We illustrate the dataset's usefulness by assessing BioLinkBERT and PubmedBERT, two transformers-based models, fine-tuned on the SourceData-NLP dataset for NER. We also introduce a novel context-dependent semantic task that infers whether an entity is the target of a controlled intervention or the object of measurement. Conclusions: SourceData-NLP's scale highlights the value of integrating curation into publishing. Models trained with SourceData-NLP will furthermore enable the development of tools able to extract causal hypotheses from the literature and assemble them into knowledge graphs.

Multimodal summarization with multimodal output (MSMO) has emerged as a promising research direction. Nonetheless, numerous limitations exist within existing public MSMO datasets, including insufficient upkeep, data inaccessibility, limited size, and the absence of proper categorization, which pose significant challenges to effective research. To address these challenges and provide a comprehensive dataset for this new direction, we have meticulously curated the MultiSum dataset. Our new dataset features (1) Human-validated summaries for both video and textual content, providing superior human instruction and labels for multimodal learning. (2) Comprehensively and meticulously arranged categorization, spanning 17 principal categories and 170 subcategories to encapsulate a diverse array of real-world scenarios. (3) Benchmark tests performed on the proposed dataset to assess varied tasks and methods, including video temporal segmentation, video summarization, text summarization, and multimodal summarization. To champion accessibility and collaboration, we release the MultiSum dataset and the data collection tool as fully open-source resources, fostering transparency and accelerating future developments. Our project website can be found at https://multisum-dataset.github.io/.

The absence of explicitly tailored, accessible annotated datasets for educational purposes presents a notable obstacle for NLP tasks in languages with limited resources.This study initially explores the feasibility of using machine translation (MT) to convert an existing dataset into a Tigrinya dataset in SQuAD format. As a result, we present TIGQA, an expert annotated educational dataset consisting of 2.68K question-answer pairs covering 122 diverse topics such as climate, water, and traffic. These pairs are from 537 context paragraphs in publicly accessible Tigrinya and Biology books. Through comprehensive analyses, we demonstrate that the TIGQA dataset requires skills beyond simple word matching, requiring both single-sentence and multiple-sentence inference abilities. We conduct experiments using state-of-the art MRC methods, marking the first exploration of such models on TIGQA. Additionally, we estimate human performance on the dataset and juxtapose it with the results obtained from pretrained models.The notable disparities between human performance and best model performance underscore the potential for further enhancements to TIGQA through continued research. Our dataset is freely accessible via the provided link to encourage the research community to address the challenges in the Tigrinya MRC.

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

The vast majority of existing datasets for Named Entity Recognition (NER) are built primarily on news, research papers and Wikipedia with a few exceptions, created from historical and literary texts. What is more, English is the main source for data for further labelling. This paper aims to fill in multiple gaps by creating a novel dataset "Razmecheno", gathered from the diary texts of the project "Prozhito" in Russian. Our dataset is of interest for multiple research lines: literary studies of diary texts, transfer learning from other domains, low-resource or cross-lingual named entity recognition. Razmecheno comprises 1331 sentences and 14119 tokens, sampled from diaries, written during the Perestroika. The annotation schema consists of five commonly used entity tags: person, characteristics, location, organisation, and facility. The labelling is carried out on the crowdsourcing platfrom Yandex.Toloka in two stages. First, workers selected sentences, which contain an entity of particular type. Second, they marked up entity spans. As a result 1113 entities were obtained. Empirical evaluation of Razmecheno is carried out with off-the-shelf NER tools and by fine-tuning pre-trained contextualized encoders. We release the annotated dataset for open access.

We introduce SynGP500, a clinician-curated collection of 500 synthetic Australian general practice medical notes. The dataset integrates curriculum-based clinical breadth (RACGP 2022 Curriculum), epidemiologically-calibrated prevalence (BEACH study), and diverse consultation contexts. This approach systematically includes both common presentations and less-common curriculum-specified conditions that GPs must recognize but appear infrequently in single practice populations, potentially supporting more generalizable model training than datasets constrained by naturally occurring case distributions. SynGP500 is messy by design, reflecting the authentic complexity of healthcare delivery: telegraphic documentation, typos, patient non-adherence, socioeconomic barriers, and clinician-patient disagreements, unlike sanitized synthetic datasets that obscure clinical realities. Multi-faceted validation demonstrates dataset quality through epidemiological alignment with real Australian GP consultation patterns (BEACH study), stylometric analysis confirming high linguistic variation, semantic diversity analysis demonstrating broad coverage, and exploratory downstream evaluation using self-supervised medical concept extraction, showing F1 improvements. SynGP500 addresses a critical national gap, providing researchers and educators with a resource for developing and evaluating clinical NLP methods for Australian general practice while inherently protecting patient privacy.

In the general domain, large multimodal models (LMMs) have achieved significant advancements, yet challenges persist in applying them to specific fields, especially agriculture. As the backbone of the global economy, agriculture confronts numerous challenges, with pests and diseases being particularly concerning due to their complexity, variability, rapid spread, and high resistance. This paper specifically addresses these issues. We construct the first multimodal instruction-following dataset in the agricultural domain, covering over 221 types of pests and diseases with approximately 400,000 data entries. This dataset aims to explore and address the unique challenges in pest and disease control. Based on this dataset, we propose a knowledge-infused training method to develop Agri-LLaVA, an agricultural multimodal conversation system. To accelerate progress in this field and inspire more researchers to engage, we design a diverse and challenging evaluation benchmark for agricultural pests and diseases. Experimental results demonstrate that Agri-LLaVA excels in agricultural multimodal conversation and visual understanding, providing new insights and approaches to address agricultural pests and diseases. By open-sourcing our dataset and model, we aim to promote research and development in LMMs within the agricultural domain and make significant contributions to tackle the challenges of agricultural pests and diseases. All resources can be found at https://github.com/Kki2Eve/Agri-LLaVA.

The rapid advancement in artificial intelligence and natural language processing has led to the development of large-scale datasets aimed at benchmarking the performance of machine learning models. Herein, we introduce 'RetChemQA,' a comprehensive benchmark dataset designed to evaluate the capabilities of such models in the domain of reticular chemistry. This dataset includes both single-hop and multi-hop question-answer pairs, encompassing approximately 45,000 Q&As for each type. The questions have been extracted from an extensive corpus of literature containing about 2,530 research papers from publishers including NAS, ACS, RSC, Elsevier, and Nature Publishing Group, among others. The dataset has been generated using OpenAI's GPT-4 Turbo, a cutting-edge model known for its exceptional language understanding and generation capabilities. In addition to the Q&A dataset, we also release a dataset of synthesis conditions extracted from the corpus of literature used in this study. The aim of RetChemQA is to provide a robust platform for the development and evaluation of advanced machine learning algorithms, particularly for the reticular chemistry community. The dataset is structured to reflect the complexities and nuances of real-world scientific discourse, thereby enabling nuanced performance assessments across a variety of tasks. The dataset is available at the following link: https://github.com/nakulrampal/RetChemQA

The rapid advancement of large language models has fundamentally shifted the bottleneck in AI development from computational power to data availability-with countless valuable datasets remaining hidden across specialized repositories, research appendices, and domain platforms. As reasoning capabilities and deep research methodologies continue to evolve, a critical question emerges: can AI agents transcend conventional search to systematically discover any dataset that meets specific user requirements, enabling truly autonomous demand-driven data curation? We introduce DatasetResearch, the first comprehensive benchmark evaluating AI agents' ability to discover and synthesize datasets from 208 real-world demands across knowledge-intensive and reasoning-intensive tasks. Our tri-dimensional evaluation framework reveals a stark reality: even advanced deep research systems achieve only 22% score on our challenging DatasetResearch-pro subset, exposing the vast gap between current capabilities and perfect dataset discovery. Our analysis uncovers a fundamental dichotomy-search agents excel at knowledge tasks through retrieval breadth, while synthesis agents dominate reasoning challenges via structured generation-yet both catastrophically fail on "corner cases" outside existing distributions. These findings establish the first rigorous baseline for dataset discovery agents and illuminate the path toward AI systems capable of finding any dataset in the digital universe. Our benchmark and comprehensive analysis provide the foundation for the next generation of self-improving AI systems and are publicly available at https://github.com/GAIR-NLP/DatasetResearch.

This study investigates the feasibility of automating clinical coding in Russian, a language with limited biomedical resources. We present a new dataset for ICD coding, which includes diagnosis fields from electronic health records (EHRs) annotated with over 10,000 entities and more than 1,500 unique ICD codes. This dataset serves as a benchmark for several state-of-the-art models, including BERT, LLaMA with LoRA, and RAG, with additional experiments examining transfer learning across domains (from PubMed abstracts to medical diagnosis) and terminologies (from UMLS concepts to ICD codes). We then apply the best-performing model to label an in-house EHR dataset containing patient histories from 2017 to 2021. Our experiments, conducted on a carefully curated test set, demonstrate that training with the automated predicted codes leads to a significant improvement in accuracy compared to manually annotated data from physicians. We believe our findings offer valuable insights into the potential for automating clinical coding in resource-limited languages like Russian, which could enhance clinical efficiency and data accuracy in these contexts.

Medical research generates a large number of publications with the PubMed database already containing >35 million research articles. Integration of the knowledge scattered across this large body of literature could provide key insights into physiological mechanisms and disease processes leading to novel medical interventions. However, it is a great challenge for researchers to utilize this information in full since the scale and complexity of the data greatly surpasses human processing abilities. This becomes especially problematic in cases of extreme urgency like the COVID-19 pandemic. Automated text mining can help extract and connect information from the large body of medical research articles. The first step in text mining is typically the identification of specific classes of keywords (e.g., all protein or disease names), so called Named Entity Recognition (NER). Here we present an end-to-end pipeline for NER of typical entities found in medical research articles, including diseases, cells, chemicals, genes/proteins, and species. The pipeline can access and process large medical research article collections (PubMed, CORD-19) or raw text and incorporates a series of deep learning models fine-tuned on the HUNER corpora collection. In addition, the pipeline can perform dictionary-based NER related to COVID-19 and other medical topics. Users can also load their own NER models and dictionaries to include additional entities. The output consists of publication-ready ranked lists and graphs of detected entities and files containing the annotated texts. An associated script allows rapid inspection of the results for specific entities of interest. As model use cases, the pipeline was deployed on two collections of autophagy-related abstracts from PubMed and on the CORD19 dataset, a collection of 764 398 research article abstracts related to COVID-19.

Teachers and students are increasingly relying on online learning resources to supplement the ones provided in school. This increase in the breadth and depth of available resources is a great thing for students, but only provided they are able to find answers to their queries. Question-answering and information retrieval systems have benefited from public datasets to train and evaluate their algorithms, but most of these datasets have been in English text written by and for adults. We introduce a new public French question-answering dataset collected from Alloprof, a Quebec-based primary and high-school help website, containing 29 349 questions and their explanations in a variety of school subjects from 10 368 students, with more than half of the explanations containing links to other questions or some of the 2 596 reference pages on the website. We also present a case study of this dataset in an information retrieval task. This dataset was collected on the Alloprof public forum, with all questions verified for their appropriateness and the explanations verified both for their appropriateness and their relevance to the question. To predict relevant documents, architectures using pre-trained BERT models were fine-tuned and evaluated. This dataset will allow researchers to develop question-answering, information retrieval and other algorithms specifically for the French speaking education context. Furthermore, the range of language proficiency, images, mathematical symbols and spelling mistakes will necessitate algorithms based on a multimodal comprehension. The case study we present as a baseline shows an approach that relies on recent techniques provides an acceptable performance level, but more work is necessary before it can reliably be used and trusted in a production setting.

The COVID-19 Open Research Dataset (CORD-19) is a growing resource of scientific papers on COVID-19 and related historical coronavirus research. CORD-19 is designed to facilitate the development of text mining and information retrieval systems over its rich collection of metadata and structured full text papers. Since its release, CORD-19 has been downloaded over 200K times and has served as the basis of many COVID-19 text mining and discovery systems. In this article, we describe the mechanics of dataset construction, highlighting challenges and key design decisions, provide an overview of how CORD-19 has been used, and describe several shared tasks built around the dataset. We hope this resource will continue to bring together the computing community, biomedical experts, and policy makers in the search for effective treatments and management policies for COVID-19.

In this paper, we present a multimodal dataset obtained from a honey bee colony in Montr\'eal, Quebec, Canada, spanning the years of 2021 to 2022. This apiary comprised 10 beehives, with microphones recording more than 2000 hours of high quality raw audio, and also sensors capturing temperature, and humidity. Periodic hive inspections involved monitoring colony honey bee population changes, assessing queen-related conditions, and documenting overall hive health. Additionally, health metrics, such as Varroa mite infestation rates and winter mortality assessments were recorded, offering valuable insights into factors affecting hive health status and resilience. In this study, we first outline the data collection process, sensor data description, and dataset structure. Furthermore, we demonstrate a practical application of this dataset by extracting various features from the raw audio to predict colony population using the number of frames of bees as a proxy.

AI-driven discovery can greatly reduce design time and enhance new therapeutics' effectiveness. Models using simulators explore broad design spaces but risk violating implicit constraints due to a lack of experimental priors. For example, in a new analysis we performed on a diverse set of models on the GuacaMol benchmark using supervised classifiers, over 60\% of molecules proposed had high probability of being mutagenic. In this work, we introduce \ourdataset, a dataset of priors for design problems extracted from literature describing compounds used in lab settings. It is constructed with LLM pipelines for discovering therapeutic entities in relevant paragraphs and summarizing information in concise fair-use facts. \ourdataset~ consists of 32.3 million pairs of natural language facts, and appropriate entity representations (i.e. SMILES or refseq IDs). To demonstrate the potential of the data, we train LLM, CLIP, and LLava architectures to reason jointly about text and design targets and evaluate on tasks from the Therapeutic Data Commons (TDC). \ourdataset~is highly effective for creating models with strong priors: in supervised prediction problems that use our data as pretraining, our best models with 15M learnable parameters outperform larger 2B TxGemma on both regression and classification TDC tasks, and perform comparably to 9B models on average. Models built with \ourdataset~can be used as constraints while optimizing for novel molecules in GuacaMol, resulting in proposals that are safer and nearly as effective. We release our dataset at https://huggingface.co/datasets/medexanon/Medex{huggingface.co/datasets/medexanon/Medex}, and will provide expanded versions as available literature grows.

Data Assimilation (DA) plays a critical role in atmospheric science by reconstructing spatially continous estimates of the system state, which serves as initial conditions for scientific analysis. While recent advances in diffusion models have shown great potential for DA tasks, most existing approaches remain purely data-driven and often overlook the physical laws that govern complex atmospheric dynamics. As a result, they may yield physically inconsistent reconstructions that impair downstream applications. To overcome this limitation, we propose PhyDA, a physics-guided diffusion framework designed to ensure physical coherence in atmospheric data assimilation. PhyDA introduces two key components: (1) a Physically Regularized Diffusion Objective that integrates physical constraints into the training process by penalizing deviations from known physical laws expressed as partial differential equations, and (2) a Virtual Reconstruction Encoder that bridges observational sparsity for structured latent representations, further enhancing the model's ability to infer complete and physically coherent states. Experiments on the ERA5 reanalysis dataset demonstrate that PhyDA achieves superior accuracy and better physical plausibility compared to state-of-the-art baselines. Our results emphasize the importance of combining generative modeling with domain-specific physical knowledge and show that PhyDA offers a promising direction for improving real-world data assimilation systems.

Improving the quality of search results can significantly enhance users experience and engagement with search engines. In spite of several recent advancements in the fields of machine learning and data mining, correctly classifying items for a particular user search query has been a long-standing challenge, which still has a large room for improvement. This paper introduces the "Shopping Queries Dataset", a large dataset of difficult Amazon search queries and results, publicly released with the aim of fostering research in improving the quality of search results. The dataset contains around 130 thousand unique queries and 2.6 million manually labeled (query,product) relevance judgements. The dataset is multilingual with queries in English, Japanese, and Spanish. The Shopping Queries Dataset is being used in one of the KDDCup'22 challenges. In this paper, we describe the dataset and present three evaluation tasks along with baseline results: (i) ranking the results list, (ii) classifying product results into relevance categories, and (iii) identifying substitute products for a given query. We anticipate that this data will become the gold standard for future research in the topic of product search.

High-throughput screening techniques are commonly used to obtain large quantities of data in many fields of biology. It is well known that artifacts arising from variability in the technical execution of different experimental batches within such screens confound these observations and can lead to invalid biological conclusions. It is therefore necessary to account for these batch effects when analyzing outcomes. In this paper we describe RxRx1, a biological dataset designed specifically for the systematic study of batch effect correction methods. The dataset consists of 125,510 high-resolution fluorescence microscopy images of human cells under 1,138 genetic perturbations in 51 experimental batches across 4 cell types. Visual inspection of the images alone clearly demonstrates significant batch effects. We propose a classification task designed to evaluate the effectiveness of experimental batch correction methods on these images and examine the performance of a number of correction methods on this task. Our goal in releasing RxRx1 is to encourage the development of effective experimental batch correction methods that generalize well to unseen experimental batches. The dataset can be downloaded at https://rxrx.ai.

Datasets are foundational to many breakthroughs in modern artificial intelligence. Many recent achievements in the space of natural language processing (NLP) can be attributed to the finetuning of pre-trained models on a diverse set of tasks that enables a large language model (LLM) to respond to instructions. Instruction fine-tuning (IFT) requires specifically constructed and annotated datasets. However, existing datasets are almost all in the English language. In this work, our primary goal is to bridge the language gap by building a human-curated instruction-following dataset spanning 65 languages. We worked with fluent speakers of languages from around the world to collect natural instances of instructions and completions. Furthermore, we create the most extensive multilingual collection to date, comprising 513 million instances through templating and translating existing datasets across 114 languages. In total, we contribute four key resources: we develop and open-source the Aya Annotation Platform, the Aya Dataset, the Aya Collection, and the Aya Evaluation Suite. The Aya initiative also serves as a valuable case study in participatory research, involving collaborators from 119 countries. We see this as a valuable framework for future research collaborations that aim to bridge gaps in resources.

Large Language Models (LLMs) are pre-trained on large amounts of data from different sources and domains. These data most often contain trillions of tokens with large portions of copyrighted or proprietary content, which hinders the usage of such models under AI legislation. This raises the need for truly open pre-training data that is compliant with the data security regulations. In this paper, we introduce Common Corpus, the largest open dataset for language model pre-training. The data assembled in Common Corpus are either uncopyrighted or under permissible licenses and amount to about two trillion tokens. The dataset contains a wide variety of languages, ranging from the main European languages to low-resource ones rarely present in pre-training datasets; in addition, it includes a large portion of code data. The diversity of data sources in terms of covered domains and time periods opens up the paths for both research and entrepreneurial needs in diverse areas of knowledge. In this technical report, we present the detailed provenance of data assembling and the details of dataset filtering and curation. Being already used by such industry leaders as Anthropic and multiple LLM training projects, we believe that Common Corpus will become a critical infrastructure for open science research in LLMs.

Score-based diffusion modeling is a generative machine learning algorithm that can be used to sample from complex distributions. They achieve this by learning a score function, i.e., the gradient of the log-probability density of the data, and reversing a noising process using the same. Once trained, score-based diffusion models not only generate new samples but also enable zero-shot conditioning of the generated samples on observed data. This promises a novel paradigm for data and model fusion, wherein the implicitly learned distributions of pretrained score-based diffusion models can be updated given the availability of online data in a Bayesian formulation. In this article, we apply such a concept to the super-resolution of a high-dimensional dynamical system, given the real-time availability of low-resolution and experimentally observed sparse sensor measurements from multimodal data. Additional analysis on how score-based sampling can be used for uncertainty estimates is also provided. Our experiments are performed for a super-resolution task that generates the ERA5 atmospheric dataset given sparse observations from a coarse-grained representation of the same and/or from unstructured experimental observations of the IGRA radiosonde dataset. We demonstrate accurate recovery of the high dimensional state given multiple sources of low-fidelity measurements. We also discover that the generative model can balance the influence of multiple dataset modalities during spatiotemporal reconstructions.

Multimodal learning has revolutionized general domain tasks, yet its application in scientific discovery is hindered by the profound semantic gap between complex scientific imagery and sparse textual descriptions. We present S1-MMAlign, a large-scale, multi-disciplinary multimodal dataset comprising over 15.5 million high-quality image-text pairs derived from 2.5 million open-access scientific papers. Spanning disciplines from physics and biology to engineering, the dataset captures diverse visual modalities including experimental setups, heatmaps, and microscopic imagery. To address the pervasive issue of weak alignment in raw scientific captions, we introduce an AI-ready semantic enhancement pipeline that utilizes the Qwen-VL multimodal large model series to recaption images by synthesizing context from paper abstracts and citation contexts. Technical validation demonstrates that this enhancement significantly improves data quality: SciBERT-based pseudo-perplexity metrics show reduced semantic ambiguity, while CLIP scores indicate an 18.21% improvement in image-text alignment. S1-MMAlign provides a foundational resource for advancing scientific reasoning and cross-modal understanding in the era of AI for Science. The dataset is publicly available at https://huggingface.co/datasets/ScienceOne-AI/S1-MMAlign.

Simulating and controlling physical systems described by partial differential equations (PDEs) are crucial tasks across science and engineering. Recently, diffusion generative models have emerged as a competitive class of methods for these tasks due to their ability to capture long-term dependencies and model high-dimensional states. However, diffusion models typically struggle with handling system states with abrupt changes and generalizing to higher resolutions. In this work, we propose Wavelet Diffusion Neural Operator (WDNO), a novel PDE simulation and control framework that enhances the handling of these complexities. WDNO comprises two key innovations. Firstly, WDNO performs diffusion-based generative modeling in the wavelet domain for the entire trajectory to handle abrupt changes and long-term dependencies effectively. Secondly, to address the issue of poor generalization across different resolutions, which is one of the fundamental tasks in modeling physical systems, we introduce multi-resolution training. We validate WDNO on five physical systems, including 1D advection equation, three challenging physical systems with abrupt changes (1D Burgers' equation, 1D compressible Navier-Stokes equation and 2D incompressible fluid), and a real-world dataset ERA5, which demonstrates superior performance on both simulation and control tasks over state-of-the-art methods, with significant improvements in long-term and detail prediction accuracy. Remarkably, in the challenging context of the 2D high-dimensional and indirect control task aimed at reducing smoke leakage, WDNO reduces the leakage by 33.2% compared to the second-best baseline. The code can be found at https://github.com/AI4Science-WestlakeU/wdno.git.

We introduce MedMNIST v2, a large-scale MNIST-like dataset collection of standardized biomedical images, including 12 datasets for 2D and 6 datasets for 3D. All images are pre-processed into a small size of 28x28 (2D) or 28x28x28 (3D) with the corresponding classification labels so that no background knowledge is required for users. Covering primary data modalities in biomedical images, MedMNIST v2 is designed to perform classification on lightweight 2D and 3D images with various dataset scales (from 100 to 100,000) and diverse tasks (binary/multi-class, ordinal regression, and multi-label). The resulting dataset, consisting of 708,069 2D images and 10,214 3D images in total, could support numerous research / educational purposes in biomedical image analysis, computer vision, and machine learning. We benchmark several baseline methods on MedMNIST v2, including 2D / 3D neural networks and open-source / commercial AutoML tools. The data and code are publicly available at https://medmnist.com/.

In this work, we study how URL extraction results depend on input format. We compiled a pilot dataset by extracting URLs from 10 arXiv papers and used the same heuristic method to extract URLs from four formats derived from the PDF files or the source LaTeX files. We found that accurate and complete URL extraction from any single format or a combination of multiple formats is challenging, with the best F1-score of 0.71. Using the pilot dataset, we evaluate extraction performance across formats and show that structured formats like HTML and XML produce more accurate results than PDFs or Text. Combining multiple formats improves coverage, especially when targeting research-critical resources. We further apply URL extraction on two tasks, namely classifying URLs into open-access datasets and software and the others, and analyzing the trend of URLs usage in arXiv papers from 1992 to 2024. These results suggest that using a combination of multiple formats achieves better performance on URL extraction than a single format, and the number of URLs in arXiv papers has been steadily increasing since 1992 to 2014 and has been drastically increasing from 2014 to 2024. The dataset and the Jupyter notebooks used for the preliminary analysis are publicly available at https://github.com/lamps-lab/arxiv-urls

The rapid advancement of large language models (LLMs) has led to increasingly human-like AI-generated text, raising concerns about content authenticity, misinformation, and trustworthiness. Addressing the challenge of reliably detecting AI-generated text and attributing it to specific models requires large-scale, diverse, and well-annotated datasets. In this work, we present a comprehensive dataset comprising over 73,193 text samples that combine authentic New York Times articles with synthetic versions generated by multiple state-of-the-art LLMs including Gemma-2-9b, Mistral-7B, Qwen-2-72B, LLaMA-8B, Yi-Large, and GPT-4-o. The dataset provides original article abstracts as prompts, full human-authored narratives. We establish baseline results for two key tasks: distinguishing human-written from AI-generated text, achieving an accuracy of 58.35\%, and attributing AI texts to their generating models with an accuracy of 8.92\%. By bridging real-world journalistic content with modern generative models, the dataset aims to catalyze the development of robust detection and attribution methods, fostering trust and transparency in the era of generative AI. Our dataset is available at: https://huggingface.co/datasets/Rajarshi-Roy-research/Defactify_Text_Dataset

Pathological diagnosis remains the definitive standard for identifying tumors. The rise of multimodal large models has simplified the process of integrating image analysis with textual descriptions. Despite this advancement, the substantial costs associated with training and deploying these complex multimodal models, together with a scarcity of high-quality training datasets, create a significant divide between cutting-edge technology and its application in the clinical setting. We had meticulously compiled a dataset of approximately 45,000 cases, covering over 6 different tasks, including the classification of organ tissues, generating pathology report descriptions, and addressing pathology-related questions and answers. We have fine-tuned multimodal large models, specifically LLaVA, Qwen-VL, InternLM, with this dataset to enhance instruction-based performance. We conducted a qualitative assessment of the capabilities of the base model and the fine-tuned model in performing image captioning and classification tasks on the specific dataset. The evaluation results demonstrate that the fine-tuned model exhibits proficiency in addressing typical pathological questions. We hope that by making both our models and datasets publicly available, they can be valuable to the medical and research communities.

The face is a rich source of information that can be utilized to infer a person's biological age, sex, phenotype, genetic defects, and health status. All of these factors are relevant for predicting an individual's remaining lifespan. In this study, we collected a dataset of over 24,000 images (from Wikidata/Wikipedia) of individuals who died of natural causes, along with the number of years between when the image was taken and when the person passed away. We made this dataset publicly available. We fine-tuned multiple Convolutional Neural Network (CNN) models on this data, at best achieving a mean absolute error of 8.3 years in the validation data using VGGFace. However, the model's performance diminishes when the person was younger at the time of the image. To demonstrate the potential applications of our remaining lifespan model, we present examples of using it to estimate the average loss of life (in years) due to the COVID-19 pandemic and to predict the increase in life expectancy that might result from a health intervention such as weight loss. Additionally, we discuss the ethical considerations associated with such models.

Progress in AI is driven largely by the scale and quality of training data. Despite this, there is a deficit of empirical analysis examining the attributes of well-established datasets beyond text. In this work we conduct the largest and first-of-its-kind longitudinal audit across modalities--popular text, speech, and video datasets--from their detailed sourcing trends and use restrictions to their geographical and linguistic representation. Our manual analysis covers nearly 4000 public datasets between 1990-2024, spanning 608 languages, 798 sources, 659 organizations, and 67 countries. We find that multimodal machine learning applications have overwhelmingly turned to web-crawled, synthetic, and social media platforms, such as YouTube, for their training sets, eclipsing all other sources since 2019. Secondly, tracing the chain of dataset derivations we find that while less than 33% of datasets are restrictively licensed, over 80% of the source content in widely-used text, speech, and video datasets, carry non-commercial restrictions. Finally, counter to the rising number of languages and geographies represented in public AI training datasets, our audit demonstrates measures of relative geographical and multilingual representation have failed to significantly improve their coverage since 2013. We believe the breadth of our audit enables us to empirically examine trends in data sourcing, restrictions, and Western-centricity at an ecosystem-level, and that visibility into these questions are essential to progress in responsible AI. As a contribution to ongoing improvements in dataset transparency and responsible use, we release our entire multimodal audit, allowing practitioners to trace data provenance across text, speech, and video.

The emergence of vision-language models has transformed medical AI, enabling unprecedented advances in diagnostic capability and clinical applications. However, progress in dermatology has lagged behind other medical domains due to the lack of standard image-text pairs. Existing dermatological datasets are limited in both scale and depth, offering only single-label annotations across a narrow range of diseases instead of rich textual descriptions, and lacking the crucial clinical context needed for real-world applications. To address these limitations, we present Derm1M, the first large-scale vision-language dataset for dermatology, comprising 1,029,761 image-text pairs. Built from diverse educational resources and structured around a standard ontology collaboratively developed by experts, Derm1M provides comprehensive coverage for over 390 skin conditions across four hierarchical levels and 130 clinical concepts with rich contextual information such as medical history, symptoms, and skin tone. To demonstrate Derm1M potential in advancing both AI research and clinical application, we pretrained a series of CLIP-like models, collectively called DermLIP, on this dataset. The DermLIP family significantly outperforms state-of-the-art foundation models on eight diverse datasets across multiple tasks, including zero-shot skin disease classification, clinical and artifacts concept identification, few-shot/full-shot learning, and cross-modal retrieval. Our dataset and code will be public.

Machine learning has emerged as a powerful tool for scientific discovery, enabling researchers to extract meaningful insights from complex datasets. For instance, it has facilitated the identification of disease-predictive genes from gene expression data, significantly advancing healthcare. However, the traditional process for analyzing such datasets demands substantial human effort and expertise for the data selection, processing, and analysis. To address this challenge, we introduce a novel framework, a Team of AI-made Scientists (TAIS), designed to streamline the scientific discovery pipeline. TAIS comprises simulated roles, including a project manager, data engineer, and domain expert, each represented by a Large Language Model (LLM). These roles collaborate to replicate the tasks typically performed by data scientists, with a specific focus on identifying disease-predictive genes. Furthermore, we have curated a benchmark dataset to assess TAIS's effectiveness in gene identification, demonstrating our system's potential to significantly enhance the efficiency and scope of scientific exploration. Our findings represent a solid step towards automating scientific discovery through large language models.

Tracking how data is mentioned and used in research papers provides critical insights for improving data discoverability, quality, and production. However, manually identifying and classifying dataset mentions across vast academic literature is resource-intensive and not scalable. This paper presents a machine learning framework that automates dataset mention detection across research domains by leveraging large language models (LLMs), synthetic data, and a two-stage fine-tuning process. We employ zero-shot extraction from research papers, an LLM-as-a-Judge for quality assessment, and a reasoning agent for refinement to generate a weakly supervised synthetic dataset. The Phi-3.5-mini instruct model is pre-fine-tuned on this dataset, followed by fine-tuning on a manually annotated subset. At inference, a ModernBERT-based classifier efficiently filters dataset mentions, reducing computational overhead while maintaining high recall. Evaluated on a held-out manually annotated sample, our fine-tuned model outperforms NuExtract-v1.5 and GLiNER-large-v2.1 in dataset extraction accuracy. Our results highlight how LLM-generated synthetic data can effectively address training data scarcity, improving generalization in low-resource settings. This framework offers a pathway toward scalable monitoring of dataset usage, enhancing transparency, and supporting researchers, funders, and policymakers in identifying data gaps and strengthening data accessibility for informed decision-making.

Acronym extraction is the task of identifying acronyms and their expanded forms in texts that is necessary for various NLP applications. Despite major progress for this task in recent years, one limitation of existing AE research is that they are limited to the English language and certain domains (i.e., scientific and biomedical). As such, challenges of AE in other languages and domains is mainly unexplored. Lacking annotated datasets in multiple languages and domains has been a major issue to hinder research in this area. To address this limitation, we propose a new dataset for multilingual multi-domain AE. Specifically, 27,200 sentences in 6 typologically different languages and 2 domains, i.e., Legal and Scientific, is manually annotated for AE. Our extensive experiments on the proposed dataset show that AE in different languages and different learning settings has unique challenges, emphasizing the necessity of further research on multilingual and multi-domain AE.

With the advent of artificial intelligence (AI), many researchers are attempting to extract structured information from document-level biomedical literature by fine-tuning large language models (LLMs). However, they face significant challenges such as the need for expensive hardware, like high-performance GPUs and the high labor costs associated with annotating training datasets, especially in biomedical realm. Recent research on LLMs, such as GPT-4 and Llama3, has shown promising performance in zero-shot settings, inspiring us to explore a novel approach to achieve the same results from unannotated full documents using general LLMs with lower hardware and labor costs. Our approach combines two major stages: named entity recognition (NER) and relation extraction (RE). NER identifies chemical, disease and gene entities from the document with synonym and hypernym extraction using an LLM with a crafted prompt. RE extracts relations between entities based on predefined relation schemas and prompts. To enhance the effectiveness of prompt, we propose a five-part template structure and a scenario-based prompt design principles, along with evaluation method to systematically assess the prompts. Finally, we evaluated our approach against fine-tuning and pre-trained models on two biomedical datasets: ChemDisGene and CDR. The experimental results indicate that our proposed method can achieve comparable accuracy levels to fine-tuning and pre-trained models but with reduced human and hardware expenses.

With the rapid development of large language models in recent years, there has been an increasing demand for domain-specific Agents that can cater to the unique needs of enterprises and organizations. Unlike general models, which strive for broad coverage, these specialized Agents rely on focused datasets tailored to their intended applications. This research proposes a pipeline that leverages the power of LLMs and the Retrieval-Augmented Generation related framework to construct high-quality instruction datasets for fine-tuning on specific domains using custom document collections. By ingesting domain-specific documents, the pipeline generates relevant and contextually appropriate instructions, thus effectively creating a comprehensive dataset for fine-tuning LLMs on the target domain. This approach overcomes the limitations of traditional dataset creation methods, which often rely on manual curation or web-scraping techniques that may introduce noise and irrelevant data. Notably, our pipeline offers a dynamic solution that can quickly adapt to updates or modifications in the domain-specific document collection, eliminating the need for complete retraining. Additionally, it addresses the challenge of data scarcity by enabling the generation of instruction datasets from a limited set of initial documents, rendering it suitable for unpopular or specialized domains where comprehensive datasets are scarce. As a case study, we apply this approach to the domain of psychiatry, a field requiring specialized knowledge and sensitive handling of patient information. The resulting fine-tuned LLM demonstrates showcases the viability of the proposed approach and underscores its potential for widespread adoption across various industries and domains where tailored, accurate, and contextually relevant language models are indispensable.

Automated medical image analysis systems often require large amounts of training data with high quality labels, which are difficult and time consuming to generate. This paper introduces Radiology Object in COntext version 2 (ROCOv2), a multimodal dataset consisting of radiological images and associated medical concepts and captions extracted from the PMC Open Access subset. It is an updated version of the ROCO dataset published in 2018, and adds 35,705 new images added to PMC since 2018. It further provides manually curated concepts for imaging modalities with additional anatomical and directional concepts for X-rays. The dataset consists of 79,789 images and has been used, with minor modifications, in the concept detection and caption prediction tasks of ImageCLEFmedical Caption 2023. The dataset is suitable for training image annotation models based on image-caption pairs, or for multi-label image classification using Unified Medical Language System (UMLS) concepts provided with each image. In addition, it can serve for pre-training of medical domain models, and evaluation of deep learning models for multi-task learning.

This paper describes the results of SemEval 2023 task 7 -- Multi-Evidence Natural Language Inference for Clinical Trial Data (NLI4CT) -- consisting of 2 tasks, a Natural Language Inference (NLI) task, and an evidence selection task on clinical trial data. The proposed challenges require multi-hop biomedical and numerical reasoning, which are of significant importance to the development of systems capable of large-scale interpretation and retrieval of medical evidence, to provide personalized evidence-based care. Task 1, the entailment task, received 643 submissions from 40 participants, and Task 2, the evidence selection task, received 364 submissions from 23 participants. The tasks are challenging, with the majority of submitted systems failing to significantly outperform the majority class baseline on the entailment task, and we observe significantly better performance on the evidence selection task than on the entailment task. Increasing the number of model parameters leads to a direct increase in performance, far more significant than the effect of biomedical pre-training. Future works could explore the limitations of large models for generalization and numerical inference, and investigate methods to augment clinical datasets to allow for more rigorous testing and to facilitate fine-tuning. We envisage that the dataset, models, and results of this task will be useful to the biomedical NLI and evidence retrieval communities. The dataset, competition leaderboard, and website are publicly available.

As the global food security landscape continues to evolve, the need for accurate and reliable crop disease diagnosis has never been more pressing. To address global food security concerns, we extend the widely used PlantVillage dataset with additional apple leaf disease classes, enhancing diversity and complexity. Experimental evaluations on both original and extended datasets reveal that existing models struggle with the new additions, highlighting the need for more robust and generalizable computer vision models. Test F1 scores of 99.63% and 97.87% were obtained on the original and extended datasets, respectively. Our study provides a more challenging and diverse benchmark, paving the way for the development of accurate and reliable models for identifying apple leaf diseases under varying imaging conditions. The expanded dataset is available at https://www.kaggle.com/datasets/akinyemijoseph/apple-leaf-disease-dataset-6-classes-v2 enabling future research to build upon our findings.

Traditional Chinese medicine (TCM) tongue diagnosis, while clinically valuable, faces standardization challenges due to subjective interpretation and inconsistent imaging protocols, compounded by the lack of large-scale, annotated datasets for AI development. To address this gap, we present the first specialized dataset for AI-driven TCM tongue diagnosis, comprising 6,719 high-quality images captured under standardized conditions and annotated with 20 pathological symptom categories (averaging 2.54 clinically validated labels per image, all verified by licensed TCM practitioners). The dataset supports multiple annotation formats (COCO, TXT, XML) for broad usability and has been benchmarked using nine deep learning models (YOLOv5/v7/v8 variants, SSD, and MobileNetV2) to demonstrate its utility for AI development. This resource provides a critical foundation for advancing reliable computational tools in TCM, bridging the data shortage that has hindered progress in the field, and facilitating the integration of AI into both research and clinical practice through standardized, high-quality diagnostic data.