Daily Papers

Large language models (LLMs) have transformed various sectors, including education, finance, and medicine, by enhancing content generation and decision-making processes. However, their integration into the medical field is cautious due to hallucinations, instances where generated content deviates from factual accuracy, potentially leading to adverse outcomes. To address this, we introduce Hyper-RAG, a hypergraph-driven Retrieval-Augmented Generation method that comprehensively captures both pairwise and beyond-pairwise correlations in domain-specific knowledge, thereby mitigating hallucinations. Experiments on the NeurologyCrop dataset with six prominent LLMs demonstrated that Hyper-RAG improves accuracy by an average of 12.3% over direct LLM use and outperforms Graph RAG and Light RAG by 6.3% and 6.0%, respectively. Additionally, Hyper-RAG maintained stable performance with increasing query complexity, unlike existing methods which declined. Further validation across nine diverse datasets showed a 35.5% performance improvement over Light RAG using a selection-based assessment. The lightweight variant, Hyper-RAG-Lite, achieved twice the retrieval speed and a 3.3% performance boost compared with Light RAG. These results confirm Hyper-RAG's effectiveness in enhancing LLM reliability and reducing hallucinations, making it a robust solution for high-stakes applications like medical diagnostics.

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.

We present FOMO60K, a large-scale, heterogeneous dataset of 60,529 brain Magnetic Resonance Imaging (MRI) scans from 13,900 sessions and 11,187 subjects, aggregated from 16 publicly available sources. The dataset includes both clinical- and research-grade images, multiple MRI sequences, and a wide range of anatomical and pathological variability, including scans with large brain anomalies. Minimal preprocessing was applied to preserve the original image characteristics while reducing barriers to entry for new users. Accompanying code for self-supervised pretraining and finetuning is provided. FOMO60K is intended to support the development and benchmarking of self-supervised learning methods in medical imaging at scale.

This paper presents an annotated dataset of brain MRI images designed to advance the field of brain symmetry study. Magnetic resonance imaging (MRI) has gained interest in analyzing brain symmetry in neonatal infants, and challenges remain due to the vast size differences between fetal and adult brains. Classification methods for brain structural MRI use scales and visual cues to assess hemisphere symmetry, which can help diagnose neonatal patients by comparing hemispheres and anatomical regions of interest in the brain. Using the Developing Human Connectome Project dataset, this work presents a dataset comprising cerebral images extracted as slices across selected portions of interest for clinical evaluation . All the extracted images are annotated with the brain's midline. All the extracted images are annotated with the brain's midline. From the assumption that a decrease in symmetry is directly related to possible clinical pathologies, the dataset can contribute to a more precise diagnosis because it can be used to train deep learning model application in neonatal cerebral MRI anomaly detection from postnatal infant scans thanks to computer vision. Such models learn to identify and classify anomalies by identifying potential asymmetrical patterns in medical MRI images. Furthermore, this dataset can contribute to the research and development of methods using the relative symmetry of the two brain hemispheres for crucial diagnosis and treatment planning.

Deep Learning has revolutionized various fields, including Computer Vision, Natural Language Processing, as well as Biomedical research. Within the field of neuroscience, specifically in electrophysiological neuroimaging, researchers are starting to explore leveraging deep learning to make predictions on their data without extensive feature engineering. The availability of large-scale datasets is a crucial aspect of allowing the experimentation of Deep Learning models. We are publishing the first large-scale clinical EEG dataset that simplifies data access and management for Deep Learning. This dataset contains eyes-closed EEG data prepared from a collection of 1,574 juvenile participants from the Healthy Brain Network. We demonstrate a use case integrating this framework, and discuss why providing such neuroinformatics infrastructure to the community is critical for future scientific discoveries.

There is renewed interest in modeling and understanding the nervous system of the nematode Caenorhabditis elegans (C. elegans), as this small model system provides a path to bridge the gap between nervous system structure (connectivity) and function (physiology). However, existing physiology datasets, whether involving passive recording or stimulation, are in distinct formats, and connectome datasets require preprocessing before analysis can commence. Here we compile and homogenize datasets of neural activity and connectivity. Our neural activity dataset is derived from 11 C. elegans neuroimaging experiments, while our connectivity dataset is compiled from 9 connectome annotations based on 3 primary electron microscopy studies and 1 signal propagation study. Physiology datasets, collected under varying protocols, measure calcium fluorescence in labeled subsets of the worm's 300 neurons. Our preprocessing pipeline standardizes these datasets by consistently ordering labeled neurons and resampling traces to a common sampling rate, yielding recordings from approximately 900 worms and 250 uniquely labeled neurons. The connectome datasets, collected from electron microscopy reconstructions, represent the entire nervous system as a graph of connections. Our collection is accessible on HuggingFace, facilitating analysis of the structure-function relationship in biology using modern neural network architectures and enabling cross-lab and cross-animal comparisons.

Dream2Image is the world's first dataset combining EEG signals, dream transcriptions, and AI-generated images. Based on 38 participants and more than 31 hours of dream EEG recordings, it contains 129 samples offering: the final seconds of brain activity preceding awakening (T-15, T-30, T-60, T-120), raw reports of dream experiences, and an approximate visual reconstruction of the dream. This dataset provides a novel resource for dream research, a unique resource to study the neural correlates of dreaming, to develop models for decoding dreams from brain activity, and to explore new approaches in neuroscience, psychology, and artificial intelligence. Available in open access on Hugging Face and GitHub, Dream2Image provides a multimodal resource designed to support research at the interface of artificial intelligence and neuroscience. It was designed to inspire researchers and extend the current approaches to brain activity decoding. Limitations include the relatively small sample size and the variability of dream recall, which may affect generalizability.

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.

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

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.

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.

Availability of large and diverse medical datasets is often challenged by privacy and data sharing restrictions. For successful application of machine learning techniques for disease diagnosis, prognosis, and precision medicine, large amounts of data are necessary for model building and optimization. To help overcome such limitations in the context of brain MRI, we present NeuroSynth: a collection of generative models of normative regional volumetric features derived from structural brain imaging. NeuroSynth models are trained on real brain imaging regional volumetric measures from the iSTAGING consortium, which encompasses over 40,000 MRI scans across 13 studies, incorporating covariates such as age, sex, and race. Leveraging NeuroSynth, we produce and offer 18,000 synthetic samples spanning the adult lifespan (ages 22-90 years), alongside the model's capability to generate unlimited data. Experimental results indicate that samples generated from NeuroSynth agree with the distributions obtained from real data. Most importantly, the generated normative data significantly enhance the accuracy of downstream machine learning models on tasks such as disease classification. Data and models are available at: https://huggingface.co/spaces/rongguangw/neuro-synth.

Leading vision-language models (VLMs) are trained on general Internet content, overlooking scientific journals' rich, domain-specific knowledge. Training on specialty-specific literature could yield high-performance, task-specific tools, enabling generative AI to match generalist models in specialty publishing, educational, and clinical tasks. We created NeuroPubs, a multimodal dataset of 23,000 Neurosurgery Publications articles (134M words, 78K image-caption pairs). Using NeuroPubs, VLMs generated publication-ready graphical abstracts (70% of 100 abstracts) and board-style questions indistinguishable from human-written ones (54% of 89,587 questions). We used these questions to train CNS-Obsidian, a 34B-parameter VLM. In a blinded, randomized controlled trial, our model demonstrated non-inferiority to then state-of-the-art GPT-4o in neurosurgical differential diagnosis (clinical utility, 40.62% upvotes vs. 57.89%, p=0.1150; accuracy, 59.38% vs. 65.79%, p=0.3797). Our pilot study demonstrates how training generative AI models on specialty-specific journal content - without large-scale internet data - results in high-performance academic and clinical tools, enabling domain-tailored AI across diverse fields.

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.

Medical benchmark datasets significantly contribute to developing Large Language Models (LLMs) for medical knowledge extraction, diagnosis, summarization, and other uses. Yet, current benchmarks are mainly derived from exam questions given to medical students or cases described in the medical literature, lacking the complexity of real-world patient cases that deviate from classic textbook abstractions. These include rare diseases, uncommon presentations of common diseases, and unexpected treatment responses. Here, we construct Clinically Uncommon Patient Cases and Diagnosis Dataset (CUPCase) based on 3,562 real-world case reports from BMC, including diagnoses in open-ended textual format and as multiple-choice options with distractors. Using this dataset, we evaluate the ability of state-of-the-art LLMs, including both general-purpose and Clinical LLMs, to identify and correctly diagnose a patient case, and test models' performance when only partial information about cases is available. Our findings show that general-purpose GPT-4o attains the best performance in both the multiple-choice task (average accuracy of 87.9%) and the open-ended task (BERTScore F1 of 0.764), outperforming several LLMs with a focus on the medical domain such as Meditron-70B and MedLM-Large. Moreover, GPT-4o was able to maintain 87% and 88% of its performance with only the first 20% of tokens of the case presentation in multiple-choice and free text, respectively, highlighting the potential of LLMs to aid in early diagnosis in real-world cases. CUPCase expands our ability to evaluate LLMs for clinical decision support in an open and reproducible manner.

Pathology diagnosis based on EEG signals and decoding brain activity holds immense importance in understanding neurological disorders. With the advancement of artificial intelligence methods and machine learning techniques, the potential for accurate data-driven diagnoses and effective treatments has grown significantly. However, applying machine learning algorithms to real-world datasets presents diverse challenges at multiple levels. The scarcity of labelled data, especially in low regime scenarios with limited availability of real patient cohorts due to high costs of recruitment, underscores the vital deployment of scaling and transfer learning techniques. In this study, we explore a real-world pathology classification task to highlight the effectiveness of data and model scaling and cross-dataset knowledge transfer. As such, we observe varying performance improvements through data scaling, indicating the need for careful evaluation and labelling. Additionally, we identify the challenges of possible negative transfer and emphasize the significance of some key components to overcome distribution shifts and potential spurious correlations and achieve positive transfer. We see improvement in the performance of the target model on the target (NMT) datasets by using the knowledge from the source dataset (TUAB) when a low amount of labelled data was available. Our findings indicate a small and generic model (e.g. ShallowNet) performs well on a single dataset, however, a larger model (e.g. TCN) performs better on transfer and learning from a larger and diverse dataset.

We present NDAI-NeuroMAP, the first neuroscience-domain-specific dense vector embedding model engineered for high-precision information retrieval tasks. Our methodology encompasses the curation of an extensive domain-specific training corpus comprising 500,000 carefully constructed triplets (query-positive-negative configurations), augmented with 250,000 neuroscience-specific definitional entries and 250,000 structured knowledge-graph triplets derived from authoritative neurological ontologies. We employ a sophisticated fine-tuning approach utilizing the FremyCompany/BioLORD-2023 foundation model, implementing a multi-objective optimization framework combining contrastive learning with triplet-based metric learning paradigms. Comprehensive evaluation on a held-out test dataset comprising approximately 24,000 neuroscience-specific queries demonstrates substantial performance improvements over state-of-the-art general-purpose and biomedical embedding models. These empirical findings underscore the critical importance of domain-specific embedding architectures for neuroscience-oriented RAG systems and related clinical natural language processing applications.

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

Accurate segmentation and classification of brain tumors from Magnetic Resonance Imaging (MRI) remain key challenges in medical image analysis, primarily due to the lack of high-quality, balanced, and diverse datasets with expert annotations. In this work, we address this gap by introducing BRISC, a dataset designed for brain tumor segmentation and classification tasks, featuring high-resolution segmentation masks. The dataset comprises 6,000 contrast-enhanced T1-weighted MRI scans, which were collated from multiple public datasets that lacked segmentation labels. Our primary contribution is the subsequent expert annotation of these images, performed by certified radiologists and physicians. It includes three major tumor types, namely glioma, meningioma, and pituitary, as well as non-tumorous cases. Each sample includes high-resolution labels and is categorized across axial, sagittal, and coronal imaging planes to facilitate robust model development and cross-view generalization. To demonstrate the utility of the dataset, we provide benchmark results for both tasks using standard deep learning models. The BRISC dataset is made publicly available. datasetlink: Kaggle (https://www.kaggle.com/datasets/briscdataset/brisc2025/), Figshare (https://doi.org/10.6084/m9.figshare.30533120), Zenodo (https://doi.org/10.5281/zenodo.17524350)

Neural networks are fundamental in artificial intelligence, driving progress in computer vision and natural language processing. High-quality datasets are crucial for their development, and there is growing interest in datasets composed of neural networks themselves to support benchmarking, automated machine learning (AutoML), and model analysis. We introduce LEMUR, an open source dataset of neural network models with well-structured code for diverse architectures across tasks such as object detection, image classification, segmentation, and natural language processing. LEMUR is primarily designed to provide a rich source of structured model representations and associated performance data, enabling the fine-tuning of large language models for AutoML applications. Leveraging Python and PyTorch, LEMUR enables seamless extension to new datasets and models while maintaining consistency. It integrates an Optuna-powered framework for evaluation, hyperparameter optimization, statistical analysis, and graphical insights. LEMUR VR extension enables the seamless deployment of models in virtual reality, optimizing their performance on resource-constrained devices. Providing tools for model evaluation, preprocessing, and database management, LEMUR supports researchers and practitioners in developing, testing, and analyzing neural networks. It offers an API that delivers comprehensive information about neural network models and their complete performance statistics with a single request, which can be used in experiments with code-generating large language models. The LEMUR and its plugins are accessible as open source projects under the MIT license at https://github.com/ABrain-One/nn-dataset, https://github.com/ABrain-One/nn-plots and https://github.com/ABrain-One/nn-vr.

Recent accelerations in multi-modal applications have been made possible with the plethora of image and text data available online. However, the scarcity of analogous data in the medical field, specifically in histopathology, has halted comparable progress. To enable similar representation learning for histopathology, we turn to YouTube, an untapped resource of videos, offering 1,087 hours of valuable educational histopathology videos from expert clinicians. From YouTube, we curate Quilt: a large-scale vision-language dataset consisting of 768,826 image and text pairs. Quilt was automatically curated using a mixture of models, including large language models, handcrafted algorithms, human knowledge databases, and automatic speech recognition. In comparison, the most comprehensive datasets curated for histopathology amass only around 200K samples. We combine Quilt with datasets from other sources, including Twitter, research papers, and the internet in general, to create an even larger dataset: Quilt-1M, with 1M paired image-text samples, marking it as the largest vision-language histopathology dataset to date. We demonstrate the value of Quilt-1M by fine-tuning a pre-trained CLIP model. Our model outperforms state-of-the-art models on both zero-shot and linear probing tasks for classifying new histopathology images across 13 diverse patch-level datasets of 8 different sub-pathologies and cross-modal retrieval tasks.

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.

Contrastive pretraining on parallel image-text data has attained great success in vision-language processing (VLP), as exemplified by CLIP and related methods. However, prior explorations tend to focus on general domains in the web. Biomedical images and text are rather different, but publicly available datasets are small and skew toward chest X-ray, thus severely limiting progress. In this paper, we conducted by far the largest study on biomedical VLP, using 15 million figure-caption pairs extracted from biomedical research articles in PubMed Central. Our dataset (PMC-15M) is two orders of magnitude larger than existing biomedical image-text datasets such as MIMIC-CXR, and spans a diverse range of biomedical images. The standard CLIP method is suboptimal for the biomedical domain. We propose BiomedCLIP with domain-specific adaptations tailored to biomedical VLP. We conducted extensive experiments and ablation studies on standard biomedical imaging tasks from retrieval to classification to visual question-answering (VQA). BiomedCLIP established new state of the art in a wide range of standard datasets, substantially outperformed prior VLP approaches. Surprisingly, BiomedCLIP even outperformed radiology-specific state-of-the-art models such as BioViL on radiology-specific tasks such as RSNA pneumonia detection, thus highlighting the utility in large-scale pretraining across all biomedical image types. We will release our models at https://aka.ms/biomedclip to facilitate future research in biomedical VLP.

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/.

Solving open-ended science questions remains challenging for large language models, particularly due to inherently unreliable supervision and evaluation. The bottleneck lies in the data construction and reward design for scientific post-training. We develop a large-scale, systematic data processing pipeline that transforms heterogeneous open-source science data into Dr. SCI dataset, which comprises of 1M questions across eight STEM subjects, with explicit verifiable/open-ended splits, scalable difficulty annotation, and fine-grained rubrics that operationalize evaluation for open-ended answers. Building on this dataset, we propose the Dr. SCI post-training pipeline, which redesigns the standard SFT -> RL workflow through three components: (i) Exploration-Expanding SFT, which broadens the model's reasoning pattern coverage prior to RL; (ii) Dynamic Difficulty Curriculum, which adapts training data to the model's evolving scientific capability; and (iii) SciRubric-Guided RL, which enables stable reinforcement learning on open-ended scientific questions via rubric-based evaluation with explicit answer correctness. Qwen3-4B-Base trained using Dr. SCI pipeline achieves 63.2 on GPQA-diamond and 32.4 on GPQA-general, consistently improves over strong post-trained baselines such as o1-mini and GPT-4o, demonstrating substantial gains in scientific reasoning, especially in open-ended settings.

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.

Large multimodal datasets have been instrumental in recent breakthroughs such as CLIP, Stable Diffusion, and GPT-4. At the same time, datasets rarely receive the same research attention as model architectures or training algorithms. To address this shortcoming in the machine learning ecosystem, we introduce DataComp, a benchmark where the training code is fixed and researchers innovate by proposing new training sets. We provide a testbed for dataset experiments centered around a new candidate pool of 12.8B image-text pairs from Common Crawl. Participants in our benchmark design new filtering techniques or curate new data sources and then evaluate their new dataset by running our standardized CLIP training code and testing on 38 downstream test sets. Our benchmark consists of multiple scales, with four candidate pool sizes and associated compute budgets ranging from 12.8M to 12.8B samples seen during training. This multi-scale design facilitates the study of scaling trends and makes the benchmark accessible to researchers with varying resources. Our baseline experiments show that the DataComp workflow is a promising way of improving multimodal datasets. We introduce DataComp-1B, a dataset created by applying a simple filtering algorithm to the 12.8B candidate pool. The resulting 1.4B subset enables training a CLIP ViT-L/14 from scratch to 79.2% zero-shot accuracy on ImageNet. Our new ViT-L/14 model outperforms a larger ViT-g/14 trained on LAION-2B by 0.7 percentage points while requiring 9x less training compute. We also outperform OpenAI's CLIP ViT-L/14 by 3.7 percentage points, which is trained with the same compute budget as our model. These gains highlight the potential for improving model performance by carefully curating training sets. We view DataComp-1B as only the first step and hope that DataComp paves the way toward the next generation of multimodal datasets.

Scarcity of large publicly available retinal fundus image datasets for automated glaucoma detection has been the bottleneck for successful application of artificial intelligence towards practical Computer-Aided Diagnosis (CAD). A few small datasets that are available for research community usually suffer from impractical image capturing conditions and stringent inclusion criteria. These shortcomings in already limited choice of existing datasets make it challenging to mature a CAD system so that it can perform in real-world environment. In this paper we present a large publicly available retinal fundus image dataset for glaucoma classification called G1020. The dataset is curated by conforming to standard practices in routine ophthalmology and it is expected to serve as standard benchmark dataset for glaucoma detection. This database consists of 1020 high resolution colour fundus images and provides ground truth annotations for glaucoma diagnosis, optic disc and optic cup segmentation, vertical cup-to-disc ratio, size of neuroretinal rim in inferior, superior, nasal and temporal quadrants, and bounding box location for optic disc. We also report baseline results by conducting extensive experiments for automated glaucoma diagnosis and segmentation of optic disc and optic cup.

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.

Computational microscopy, in which hardware and algorithms of an imaging system are jointly designed, shows promise for making imaging systems that cost less, perform more robustly, and collect new types of information. Often, the performance of computational imaging systems, especially those that incorporate machine learning, is sample-dependent. Thus, standardized datasets are an essential tool for comparing the performance of different approaches. Here, we introduce the Berkeley Single Cell Computational Microscopy (BSCCM) dataset, which contains over ~12,000,000 images of 400,000 of individual white blood cells. The dataset contains images captured with multiple illumination patterns on an LED array microscope and fluorescent measurements of the abundance of surface proteins that mark different cell types. We hope this dataset will provide a valuable resource for the development and testing of new algorithms in computational microscopy and computer vision with practical biomedical applications.

The data article describes the Road Damage Dataset, RDD2022, which comprises 47,420 road images from six countries, Japan, India, the Czech Republic, Norway, the United States, and China. The images have been annotated with more than 55,000 instances of road damage. Four types of road damage, namely longitudinal cracks, transverse cracks, alligator cracks, and potholes, are captured in the dataset. The annotated dataset is envisioned for developing deep learning-based methods to detect and classify road damage automatically. The dataset has been released as a part of the Crowd sensing-based Road Damage Detection Challenge (CRDDC2022). The challenge CRDDC2022 invites researchers from across the globe to propose solutions for automatic road damage detection in multiple countries. The municipalities and road agencies may utilize the RDD2022 dataset, and the models trained using RDD2022 for low-cost automatic monitoring of road conditions. Further, computer vision and machine learning researchers may use the dataset to benchmark the performance of different algorithms for other image-based applications of the same type (classification, object detection, etc.).

Cognitive neuroscience is enjoying rapid increase in extensive public brain-imaging datasets. It opens the door to large-scale statistical models. Finding a unified perspective for all available data calls for scalable and automated solutions to an old challenge: how to aggregate heterogeneous information on brain function into a universal cognitive system that relates mental operations/cognitive processes/psychological tasks to brain networks? We cast this challenge in a machine-learning approach to predict conditions from statistical brain maps across different studies. For this, we leverage multi-task learning and multi-scale dimension reduction to learn low-dimensional representations of brain images that carry cognitive information and can be robustly associated with psychological stimuli. Our multi-dataset classification model achieves the best prediction performance on several large reference datasets, compared to models without cognitive-aware low-dimension representations, it brings a substantial performance boost to the analysis of small datasets, and can be introspected to identify universal template cognitive concepts.

Obtaining text datasets with semantic annotations is an effortful process, yet crucial for supervised training in natural language processsing (NLP). In general, developing and applying new NLP pipelines in domain-specific contexts for tasks often requires custom designed datasets to address NLP tasks in supervised machine learning fashion. When operating in non-English languages for medical data processing, this exposes several minor and major, interconnected problems such as lack of task-matching datasets as well as task-specific pre-trained models. In our work we suggest to leverage pretrained language models for training data acquisition in order to retrieve sufficiently large datasets for training smaller and more efficient models for use-case specific tasks. To demonstrate the effectiveness of your approach, we create a custom dataset which we use to train a medical NER model for German texts, GPTNERMED, yet our method remains language-independent in principle. Our obtained dataset as well as our pre-trained models are publicly available at: https://github.com/frankkramer-lab/GPTNERMED

In recent years, the application of machine learning to minimally invasive surgery (MIS) has attracted considerable interest. Datasets are critical to the use of such techniques. This paper presents a unique dataset recorded during ex vivo pseudo-cholecystectomy procedures on pig livers using the da Vinci Research Kit (dVRK). Unlike existing datasets, it addresses a critical gap by providing comprehensive kinematic data, recordings of all pedal inputs, and offers a time-stamped record of the endoscope's movements. This expanded version also includes segmentation and keypoint annotations of images, enhancing its utility for computer vision applications. Contributed by seven surgeons with varied backgrounds and experience levels that are provided as a part of this expanded version, the dataset is an important new resource for surgical robotics research. It enables the development of advanced methods for evaluating surgeon skills, tools for providing better context awareness, and automation of surgical tasks. Our work overcomes the limitations of incomplete recordings and imprecise kinematic data found in other datasets. To demonstrate the potential of the dataset for advancing automation in surgical robotics, we introduce two models that predict clutch usage and camera activation, a 3D scene reconstruction example, and the results from our keypoint and segmentation models.

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.

Open-source benchmark datasets have been a critical component for advancing machine learning for robot perception in terrestrial applications. Benchmark datasets enable the widespread development of state-of-the-art machine learning methods, which require large datasets for training, validation, and thorough comparison to competing approaches. Underwater environments impose several operational challenges that hinder efforts to collect large benchmark datasets for marine robot perception. Furthermore, a low abundance of targets of interest relative to the size of the search space leads to increased time and cost required to collect useful datasets for a specific task. As a result, there is limited availability of labeled benchmark datasets for underwater applications. We present the AI4Shipwrecks dataset, which consists of 24 distinct shipwreck sites totaling 286 high-resolution labeled side scan sonar images to advance the state-of-the-art in autonomous sonar image understanding. We leverage the unique abundance of targets in Thunder Bay National Marine Sanctuary in Lake Huron, MI, to collect and compile a sonar imagery benchmark dataset through surveys with an autonomous underwater vehicle (AUV). We consulted with expert marine archaeologists for the labeling of robotically gathered data. We then leverage this dataset to perform benchmark experiments for comparison of state-of-the-art supervised segmentation methods, and we present insights on opportunities and open challenges for the field. The dataset and benchmarking tools will be released as an open-source benchmark dataset to spur innovation in machine learning for Great Lakes and ocean exploration. The dataset and accompanying software are available at https://umfieldrobotics.github.io/ai4shipwrecks/.

Developing and validating artificial intelligence models in medical imaging requires datasets that are large, granular, and diverse. To date, the majority of publicly available breast imaging datasets lack in one or more of these areas. Models trained on these data may therefore underperform on patient populations or pathologies that have not previously been encountered. The EMory BrEast imaging Dataset (EMBED) addresses these gaps by providing 3650,000 2D and DBT screening and diagnostic mammograms for 116,000 women divided equally between White and African American patients. The dataset also contains 40,000 annotated lesions linked to structured imaging descriptors and 61 ground truth pathologic outcomes grouped into six severity classes. Our goal is to share this dataset with research partners to aid in development and validation of breast AI models that will serve all patients fairly and help decrease bias in medical AI.

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.

The scale, variety, and quantity of publicly-available NLP datasets has grown rapidly as researchers propose new tasks, larger models, and novel benchmarks. Datasets is a community library for contemporary NLP designed to support this ecosystem. Datasets aims to standardize end-user interfaces, versioning, and documentation, while providing a lightweight front-end that behaves similarly for small datasets as for internet-scale corpora. The design of the library incorporates a distributed, community-driven approach to adding datasets and documenting usage. After a year of development, the library now includes more than 650 unique datasets, has more than 250 contributors, and has helped support a variety of novel cross-dataset research projects and shared tasks. The library is available at https://github.com/huggingface/datasets.

Magnetic resonance imaging (MRI) is a crucial tool to identify brain abnormalities in a wide range of neurological disorders. In focal epilepsy MRI is used to identify structural cerebral abnormalities. For covert lesions, machine learning and artificial intelligence algorithms may improve lesion detection if abnormalities are not evident on visual inspection. The success of this approach depends on the volume and quality of training data. Herein, we release an open-source dataset of preprocessed MRI scans from 442 individuals with drug-refractory focal epilepsy who had neurosurgical resections, and detailed demographic information. The MRI scan data includes the preoperative 3D T1 and where available 3D FLAIR, as well as a manually inspected complete surface reconstruction and volumetric parcellations. Demographic information includes age, sex, age of onset of epilepsy, location of surgery, histopathology of resected specimen, occurrence and frequency of focal seizures with and without impairment of awareness, focal to bilateral tonic-clonic seizures, number of anti-seizure medications (ASMs) at time of surgery, and a total of 1764 patient years of post-surgical follow up. Crucially, we also include resection masks delineated from post-surgical imaging. To demonstrate the veracity of our data, we successfully replicated previous studies showing long-term outcomes of seizure freedom in the range of around 50%. Our imaging data replicates findings of group level atrophy in patients compared to controls. Resection locations in the cohort were predominantly in the temporal and frontal lobes. We envisage our dataset, shared openly with the community, will catalyse the development and application of computational methods in clinical neurology.

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.

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.

Agentic artificial intelligence systems promise to accelerate scientific workflows, but neuroimaging poses unique challenges: heterogeneous modalities (sMRI, fMRI, dMRI, EEG), long multi-stage pipelines, and persistent reproducibility risks. To address this gap, we present NeuroClaw, a domain-specialized multi-agent research assistant for executable and reproducible neuroimaging research. NeuroClaw operates directly on raw neuroimaging data across formats and modalities, grounding decisions in dataset semantics and BIDS metadata so users need not prepare curated inputs or bespoke model code. The platform combines harness engineering with end-to-end environment management, including pinned Python environments, Docker support, automated installers for common neuroimaging tools, and GPU configuration. In practice, this layer emphasizes checkpointing, post-execution verification, structured audit traces, and controlled runtime setup, making toolchains more transparent while improving reproducibility and auditability. A three-tier skill/agent hierarchy separates user-facing interaction, high-level orchestration, and low-level tool skills to decompose complex workflows into safe, reusable units. Alongside the NeuroClaw framework, we introduce NeuroBench, a system-level benchmark for executability, artifact validity, and reproducibility readiness. Across multiple multimodal LLMs, NeuroClaw-enabled runs yield consistent and substantial score improvements compared with direct agent invocation. Project homepage: https://cuhk-aim-group.github.io/NeuroClaw/index.html

A major barrier to developing vision large language models (LLMs) in dermatology is the lack of large image--text pairs dataset. We introduce DermaSynth, a dataset comprising of 92,020 synthetic image--text pairs curated from 45,205 images (13,568 clinical and 35,561 dermatoscopic) for dermatology-related clinical tasks. Leveraging state-of-the-art LLMs, using Gemini 2.0, we used clinically related prompts and self-instruct method to generate diverse and rich synthetic texts. Metadata of the datasets were incorporated into the input prompts by targeting to reduce potential hallucinations. The resulting dataset builds upon open access dermatological image repositories (DERM12345, BCN20000, PAD-UFES-20, SCIN, and HIBA) that have permissive CC-BY-4.0 licenses. We also fine-tuned a preliminary Llama-3.2-11B-Vision-Instruct model, DermatoLlama 1.0, on 5,000 samples. We anticipate this dataset to support and accelerate AI research in dermatology. Data and code underlying this work are accessible at https://github.com/abdurrahimyilmaz/DermaSynth.

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.

MindBigData 2023 MNIST-8B is the largest, to date (June 1st 2023), brain signals open dataset created for Machine Learning, based on EEG signals from a single subject captured using a custom 128 channels device, replicating the full 70,000 digits from Yaan LeCun et all MNIST dataset. The brain signals were captured while the subject was watching the pixels of the original digits one by one on a screen and listening at the same time to the spoken number 0 to 9 from the real label. The data, collection procedures, hardware and software created are described in detail, background extra information and other related datasets can be found at our previous paper MindBigData 2022: A Large Dataset of Brain Signals.

Spine-related diseases have high morbidity and cause a huge burden of social cost. Spine imaging is an essential tool for noninvasively visualizing and assessing spinal pathology. Segmenting vertebrae in computed tomography (CT) images is the basis of quantitative medical image analysis for clinical diagnosis and surgery planning of spine diseases. Current publicly available annotated datasets on spinal vertebrae are small in size. Due to the lack of a large-scale annotated spine image dataset, the mainstream deep learning-based segmentation methods, which are data-driven, are heavily restricted. In this paper, we introduce a large-scale spine CT dataset, called CTSpine1K, curated from multiple sources for vertebra segmentation, which contains 1,005 CT volumes with over 11,100 labeled vertebrae belonging to different spinal conditions. Based on this dataset, we conduct several spinal vertebrae segmentation experiments to set the first benchmark. We believe that this large-scale dataset will facilitate further research in many spine-related image analysis tasks, including but not limited to vertebrae segmentation, labeling, 3D spine reconstruction from biplanar radiographs, image super-resolution, and enhancement.

Collecting a high-quality dataset is a critical task that demands meticulous attention to detail, as overlooking certain aspects can render the entire dataset unusable. Autonomous driving challenges remain a prominent area of research, requiring further exploration to enhance the perception and planning performance of vehicles. However, existing datasets are often incomplete. For instance, datasets that include perception information generally lack planning data, while planning datasets typically consist of extensive driving sequences where the ego vehicle predominantly drives forward, offering limited behavioral diversity. In addition, many real datasets struggle to evaluate their models, especially for planning tasks, since they lack a proper closed-loop evaluation setup. The CARLA Leaderboard 2.0 challenge, which provides a diverse set of scenarios to address the long-tail problem in autonomous driving, has emerged as a valuable alternative platform for developing perception and planning models in both open-loop and closed-loop evaluation setups. Nevertheless, existing datasets collected on this platform present certain limitations. Some datasets appear to be tailored primarily for limited sensor configuration, with particular sensor configurations. To support end-to-end autonomous driving research, we have collected a new dataset comprising over 2.85 million frames using the CARLA simulation environment for the diverse Leaderboard 2.0 challenge scenarios. Our dataset is designed not only for planning tasks but also supports dynamic object detection, lane divider detection, centerline detection, traffic light recognition, prediction tasks and visual language action models . Furthermore, we demonstrate its versatility by training various models using our dataset. Moreover, we also provide numerical rarity scores to understand how rarely the current state occurs in the dataset.

Polyps in the colon are widely known cancer precursors identified by colonoscopy. Whilst most polyps are benign, the polyp's number, size and surface structure are linked to the risk of colon cancer. Several methods have been developed to automate polyp detection and segmentation. However, the main issue is that they are not tested rigorously on a large multicentre purpose-built dataset, one reason being the lack of a comprehensive public dataset. As a result, the developed methods may not generalise to different population datasets. To this extent, we have curated a dataset from six unique centres incorporating more than 300 patients. The dataset includes both single frame and sequence data with 3762 annotated polyp labels with precise delineation of polyp boundaries verified by six senior gastroenterologists. To our knowledge, this is the most comprehensive detection and pixel-level segmentation dataset (referred to as PolypGen) curated by a team of computational scientists and expert gastroenterologists. The paper provides insight into data construction and annotation strategies, quality assurance, and technical validation. Our dataset can be downloaded from https://doi.org/10.7303/syn26376615.

Foundation models have demonstrated remarkable success across diverse domains and tasks, primarily due to the thrive of large-scale, diverse, and high-quality datasets. However, in the field of medical imaging, the curation and assembling of such medical datasets are highly challenging due to the reliance on clinical expertise and strict ethical and privacy constraints, resulting in a scarcity of large-scale unified medical datasets and hindering the development of powerful medical foundation models. In this work, we present the largest survey to date of medical image datasets, covering over 1,000 open-access datasets with a systematic catalog of their modalities, tasks, anatomies, annotations, limitations, and potential for integration. Our analysis exposes a landscape that is modest in scale, fragmented across narrowly scoped tasks, and unevenly distributed across organs and modalities, which in turn limits the utility of existing medical image datasets for developing versatile and robust medical foundation models. To turn fragmentation into scale, we propose a metadata-driven fusion paradigm (MDFP) that integrates public datasets with shared modalities or tasks, thereby transforming multiple small data silos into larger, more coherent resources. Building on MDFP, we release an interactive discovery portal that enables end-to-end, automated medical image dataset integration, and compile all surveyed datasets into a unified, structured table that clearly summarizes their key characteristics and provides reference links, offering the community an accessible and comprehensive repository. By charting the current terrain and offering a principled path to dataset consolidation, our survey provides a practical roadmap for scaling medical imaging corpora, supporting faster data discovery, more principled dataset creation, and more capable medical foundation models.

One of the critical biotic stress factors paddy farmers face is diseases caused by bacteria, fungi, and other organisms. These diseases affect plants' health severely and lead to significant crop loss. Most of these diseases can be identified by regularly observing the leaves and stems under expert supervision. In a country with vast agricultural regions and limited crop protection experts, manual identification of paddy diseases is challenging. Thus, to add a solution to this problem, it is necessary to automate the disease identification process and provide easily accessible decision support tools to enable effective crop protection measures. However, the lack of availability of public datasets with detailed disease information limits the practical implementation of accurate disease detection systems. This paper presents Paddy Doctor, a visual image dataset for identifying paddy diseases. Our dataset contains 16,225 annotated paddy leaf images across 13 classes (12 diseases and normal leaf). We benchmarked the Paddy Doctor dataset using a Convolutional Neural Network (CNN) and four transfer learning based models (VGG16, MobileNet, Xception, and ResNet34). The experimental results showed that ResNet34 achieved the highest F1-score of 97.50%. We release our dataset and reproducible code in the open source for community use.

We introduce a new challenge to test the STEM skills of neural models. The problems in the real world often require solutions, combining knowledge from STEM (science, technology, engineering, and math). Unlike existing datasets, our dataset requires the understanding of multimodal vision-language information of STEM. Our dataset features one of the largest and most comprehensive datasets for the challenge. It includes 448 skills and 1,073,146 questions spanning all STEM subjects. Compared to existing datasets that often focus on examining expert-level ability, our dataset includes fundamental skills and questions designed based on the K-12 curriculum. We also add state-of-the-art foundation models such as CLIP and GPT-3.5-Turbo to our benchmark. Results show that the recent model advances only help master a very limited number of lower grade-level skills (2.5% in the third grade) in our dataset. In fact, these models are still well below (averaging 54.7%) the performance of elementary students, not to mention near expert-level performance. To understand and increase the performance on our dataset, we teach the models on a training split of our dataset. Even though we observe improved performance, the model performance remains relatively low compared to average elementary students. To solve STEM problems, we will need novel algorithmic innovations from the community.

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

With the rapid development of artificial intelligence (AI) in medical image processing, deep learning in color fundus photography (CFP) analysis is also evolving. Although there are some open-source, labeled datasets of CFPs in the ophthalmology community, large-scale datasets for screening only have labels of disease categories, and datasets with annotations of fundus structures are usually small in size. In addition, labeling standards are not uniform across datasets, and there is no clear information on the acquisition device. Here we release a multi-annotation, multi-quality, and multi-device color fundus image dataset for glaucoma analysis on an original challenge -- Retinal Fundus Glaucoma Challenge 2nd Edition (REFUGE2). The REFUGE2 dataset contains 2000 color fundus images with annotations of glaucoma classification, optic disc/cup segmentation, as well as fovea localization. Meanwhile, the REFUGE2 challenge sets three sub-tasks of automatic glaucoma diagnosis and fundus structure analysis and provides an online evaluation framework. Based on the characteristics of multi-device and multi-quality data, some methods with strong generalizations are provided in the challenge to make the predictions more robust. This shows that REFUGE2 brings attention to the characteristics of real-world multi-domain data, bridging the gap between scientific research and clinical application.

The evaluation of object detection models is usually performed by optimizing a single metric, e.g. mAP, on a fixed set of datasets, e.g. Microsoft COCO and Pascal VOC. Due to image retrieval and annotation costs, these datasets consist largely of images found on the web and do not represent many real-life domains that are being modelled in practice, e.g. satellite, microscopic and gaming, making it difficult to assert the degree of generalization learned by the model. We introduce the Roboflow-100 (RF100) consisting of 100 datasets, 7 imagery domains, 224,714 images, and 805 class labels with over 11,170 labelling hours. We derived RF100 from over 90,000 public datasets, 60 million public images that are actively being assembled and labelled by computer vision practitioners in the open on the web application Roboflow Universe. By releasing RF100, we aim to provide a semantically diverse, multi-domain benchmark of datasets to help researchers test their model's generalizability with real-life data. RF100 download and benchmark replication are available on GitHub.

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.

The recent 'Mpox' outbreak, formerly known as 'Monkeypox', has become a significant public health concern and has spread to over 110 countries globally. The challenge of clinically diagnosing mpox early on is due, in part, to its similarity to other types of rashes. Computer-aided screening tools have been proven valuable in cases where Polymerase Chain Reaction (PCR) based diagnosis is not immediately available. Deep learning methods are powerful in learning complex data representations, but their efficacy largely depends on adequate training data. To address this challenge, we present the "Mpox Skin Lesion Dataset Version 2.0 (MSLD v2.0)" as a follow-up to the previously released openly accessible dataset, one of the first datasets containing mpox lesion images. This dataset contains images of patients with mpox and five other non-mpox classes (chickenpox, measles, hand-foot-mouth disease, cowpox, and healthy). We benchmark the performance of several state-of-the-art deep learning models, including VGG16, ResNet50, DenseNet121, MobileNetV2, EfficientNetB3, InceptionV3, and Xception, to classify mpox and other infectious skin diseases. In order to reduce the impact of racial bias, we utilize a color space data augmentation method to increase skin color variability during training. Additionally, by leveraging transfer learning implemented with pre-trained weights generated from the HAM10000 dataset, an extensive collection of pigmented skin lesion images, we achieved the best overall accuracy of 83.59pm2.11%. Finally, the developed models are incorporated within a prototype web application to analyze uploaded skin images by a user and determine whether a subject is a suspected mpox patient.

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 increasing interest in developing Artificial Intelligence applications in the medical domain, suffers from the lack of high-quality dataset, mainly due to privacy-related issues. Moreover, the recent rising of Multimodal Large Language Models (MLLM) leads to a need for multimodal medical datasets, where clinical reports and findings are attached to the corresponding CT or MR scans. This paper illustrates the entire workflow for building the data set MedPix 2.0. Starting from the well-known multimodal dataset MedPix\textregistered, mainly used by physicians, nurses and healthcare students for Continuing Medical Education purposes, a semi-automatic pipeline was developed to extract visual and textual data followed by a manual curing procedure where noisy samples were removed, thus creating a MongoDB database. Along with the dataset, we developed a GUI aimed at navigating efficiently the MongoDB instance, and obtaining the raw data that can be easily used for training and/or fine-tuning MLLMs. To enforce this point, we also propose a CLIP-based model trained on MedPix 2.0 for scan classification tasks.

We introduce DAHL, a benchmark dataset and automated evaluation system designed to assess hallucination in long-form text generation, specifically within the biomedical domain. Our benchmark dataset, meticulously curated from biomedical research papers, consists of 8,573 questions across 29 categories. DAHL evaluates fact-conflicting hallucinations in Large Language Models (LLMs) by deconstructing responses into atomic units, each representing a single piece of information. The accuracy of these responses is averaged to produce the DAHL Score, offering a more in-depth evaluation of hallucinations compared to previous methods that rely on multiple-choice tasks. We conduct experiments with 8 different models, finding that larger models tend to hallucinate less; however, beyond a model size of 7 to 8 billion parameters, further scaling does not significantly improve factual accuracy. The DAHL Score holds potential as an efficient alternative to human-annotated preference labels, being able to be expanded to other specialized domains. We release the dataset and code in public.

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.

Scientific reasoning is critical for developing AI scientists and supporting human researchers in advancing the frontiers of natural science discovery. However, the open-source community has primarily focused on mathematics and coding while neglecting the scientific domain, largely due to the absence of open, large-scale, high-quality, verifiable scientific reasoning datasets. To bridge this gap, we first present TextbookReasoning, an open dataset featuring truthful reference answers extracted from 12k university-level scientific textbooks, comprising 650k reasoning questions spanning 7 scientific disciplines. We further introduce MegaScience, a large-scale mixture of high-quality open-source datasets totaling 1.25 million instances, developed through systematic ablation studies that evaluate various data selection methodologies to identify the optimal subset for each publicly available scientific dataset. Meanwhile, we build a comprehensive evaluation system covering diverse subjects and question types across 15 benchmarks, incorporating comprehensive answer extraction strategies to ensure accurate evaluation metrics. Our experiments demonstrate that our datasets achieve superior performance and training efficiency with more concise response lengths compared to existing open-source scientific datasets. Furthermore, we train Llama3.1, Qwen2.5, and Qwen3 series base models on MegaScience, which significantly outperform the corresponding official instruct models in average performance. In addition, MegaScience exhibits greater effectiveness for larger and stronger models, suggesting a scaling benefit for scientific tuning. We release our data curation pipeline, evaluation system, datasets, and seven trained models to the community to advance scientific reasoning research.

Biological neural networks define the brain function and intelligence of humans and other mammals, and form ultra-large, spatial, structured graphs. Their neuronal organization is closely interconnected with the spatial organization of the brain's microvasculature, which supplies oxygen to the neurons and builds a complementary spatial graph. This vasculature (or the vessel structure) plays an important role in neuroscience; for example, the organization of (and changes to) vessel structure can represent early signs of various pathologies, e.g. Alzheimer's disease or stroke. Recently, advances in tissue clearing have enabled whole brain imaging and segmentation of the entirety of the mouse brain's vasculature. Building on these advances in imaging, we are presenting an extendable dataset of whole-brain vessel graphs based on specific imaging protocols. Specifically, we extract vascular graphs using a refined graph extraction scheme leveraging the volume rendering engine Voreen and provide them in an accessible and adaptable form through the OGB and PyTorch Geometric dataloaders. Moreover, we benchmark numerous state-of-the-art graph learning algorithms on the biologically relevant tasks of vessel prediction and vessel classification using the introduced vessel graph dataset. Our work paves a path towards advancing graph learning research into the field of neuroscience. Complementarily, the presented dataset raises challenging graph learning research questions for the machine learning community, in terms of incorporating biological priors into learning algorithms, or in scaling these algorithms to handle sparse,spatial graphs with millions of nodes and edges. All datasets and code are available for download at https://github.com/jocpae/VesselGraph .

The Annotated Germs for Automated Recognition (AGAR) dataset is an image database of microbial colonies cultured on agar plates. It contains 18000 photos of five different microorganisms as single or mixed cultures, taken under diverse lighting conditions with two different cameras. All the images are classified into "countable", "uncountable", and "empty", with the "countable" class labeled by microbiologists with colony location and species identification (336442 colonies in total). This study describes the dataset itself and the process of its development. In the second part, the performance of selected deep neural network architectures for object detection, namely Faster R-CNN and Cascade R-CNN, was evaluated on the AGAR dataset. The results confirmed the great potential of deep learning methods to automate the process of microbe localization and classification based on Petri dish photos. Moreover, AGAR is the first publicly available dataset of this kind and size and will facilitate the future development of machine learning models. The data used in these studies can be found at https://agar.neurosys.com/.

The field of Machine Learning, a subset of Artificial Intelligence, has led to remarkable advancements in many areas, including medicine. Machine Learning algorithms require large datasets to train computer models successfully. Although there are medical image datasets available, more image datasets are needed from a variety of medical entities, especially cancer pathology. Even more scarce are ML-ready image datasets. To address this need, we created an image dataset (LC25000) with 25,000 color images in 5 classes. Each class contains 5,000 images of the following histologic entities: colon adenocarcinoma, benign colonic tissue, lung adenocarcinoma, lung squamous cell carcinoma, and benign lung tissue. All images are de-identified, HIPAA compliant, validated, and freely available for download to AI researchers.

Background and Objective: Colorectal cancer prevention relies on early detection of polyps during colonoscopy. Existing public datasets, such as CVC-ClinicDB and Kvasir-SEG, provide valuable benchmarks but are limited by small sample sizes, curated image selection, or lack of real-world artifacts. There remains a need for datasets that capture the complexity of clinical practice, particularly in resource-constrained settings. Methods: We introduce a dataset, BUET Polyp Dataset (BPD), of colonoscopy images collected using Olympus 170 and Pentax i-Scan series endoscopes under routine clinical conditions. The dataset contains images with corresponding expert-annotated binary masks, reflecting diverse challenges such as motion blur, specular highlights, stool artifacts, blood, and low-light frames. Annotations were manually reviewed by clinical experts to ensure quality. To demonstrate baseline performance, we provide benchmark results for classification using VGG16, ResNet50, and InceptionV3, and for segmentation using UNet variants with VGG16, ResNet34, and InceptionV4 backbones. Results: The dataset comprises 1,288 images with polyps from 164 patients with corresponding ground-truth masks and 1,657 polyp-free images from 31 patients. Benchmarking experiments achieved up to 90.8% accuracy for binary classification (VGG16) and a maximum Dice score of 0.64 with InceptionV4-UNet for segmentation. Performance was lower compared to curated datasets, reflecting the real-world difficulty of images with artifacts and variable quality.

In computational pathology, automatic nuclei instance segmentation plays an essential role in whole slide image analysis. While many computerized approaches have been proposed for this task, supervised deep learning (DL) methods have shown superior segmentation performances compared to classical machine learning and image processing techniques. However, these models need fully annotated datasets for training which is challenging to acquire, especially in the medical domain. In this work, we release one of the biggest fully manually annotated datasets of nuclei in Hematoxylin and Eosin (H&E)-stained histological images, called NuInsSeg. This dataset contains 665 image patches with more than 30,000 manually segmented nuclei from 31 human and mouse organs. Moreover, for the first time, we provide additional ambiguous area masks for the entire dataset. These vague areas represent the parts of the images where precise and deterministic manual annotations are impossible, even for human experts. The dataset and detailed step-by-step instructions to generate related segmentation masks are publicly available at https://www.kaggle.com/datasets/ipateam/nuinsseg and https://github.com/masih4/NuInsSeg, respectively.

Mangroves are dynamic coastal ecosystems that are crucial to environmental health, economic stability, and climate resilience. The monitoring and preservation of mangroves are of global importance, with remote sensing technologies playing a pivotal role in these efforts. The integration of cutting-edge artificial intelligence with satellite data opens new avenues for ecological monitoring, potentially revolutionizing conservation strategies at a time when the protection of natural resources is more crucial than ever. The objective of this work is to provide a comprehensive evaluation of recent deep-learning models on the task of mangrove segmentation. We first introduce and make available a novel open-source dataset, MagSet-2, incorporating mangrove annotations from the Global Mangrove Watch and satellite images from Sentinel-2, from mangrove positions all over the world. We then benchmark three architectural groups, namely convolutional, transformer, and mamba models, using the created dataset. The experimental outcomes further validate the deep learning community's interest in the Mamba model, which surpasses other architectures in all metrics.

Semantic segmentation of medical images aims to associate a pixel with a label in a medical image without human initialization. The success of semantic segmentation algorithms is contingent on the availability of high-quality imaging data with corresponding labels provided by experts. We sought to create a large collection of annotated medical image datasets of various clinically relevant anatomies available under open source license to facilitate the development of semantic segmentation algorithms. Such a resource would allow: 1) objective assessment of general-purpose segmentation methods through comprehensive benchmarking and 2) open and free access to medical image data for any researcher interested in the problem domain. Through a multi-institutional effort, we generated a large, curated dataset representative of several highly variable segmentation tasks that was used in a crowd-sourced challenge - the Medical Segmentation Decathlon held during the 2018 Medical Image Computing and Computer Aided Interventions Conference in Granada, Spain. Here, we describe these ten labeled image datasets so that these data may be effectively reused by the research community.

Magnetic resonance imaging (MRI) is a central modality for stroke imaging. It is used upon patient admission to make treatment decisions such as selecting patients for intravenous thrombolysis or endovascular therapy. MRI is later used in the duration of hospital stay to predict outcome by visualizing infarct core size and location. Furthermore, it may be used to characterize stroke etiology, e.g. differentiation between (cardio)-embolic and non-embolic stroke. Computer based automated medical image processing is increasingly finding its way into clinical routine. Previous iterations of the Ischemic Stroke Lesion Segmentation (ISLES) challenge have aided in the generation of identifying benchmark methods for acute and sub-acute ischemic stroke lesion segmentation. Here we introduce an expert-annotated, multicenter MRI dataset for segmentation of acute to subacute stroke lesions. This dataset comprises 400 multi-vendor MRI cases with high variability in stroke lesion size, quantity and location. It is split into a training dataset of n=250 and a test dataset of n=150. All training data will be made publicly available. The test dataset will be used for model validation only and will not be released to the public. This dataset serves as the foundation of the ISLES 2022 challenge with the goal of finding algorithmic methods to enable the development and benchmarking of robust and accurate segmentation algorithms for ischemic stroke.

This paper provides a detailed analysis of the NeuroPiano dataset, which comprise 104 audio recordings of student piano performances accompanied with 2255 textual feedback and ratings given by professional pianists. We offer a statistical overview of the dataset, focusing on the standardization of annotations and inter-annotator agreement across 12 evaluative questions concerning performance quality. We also explore the predictive relationship between audio features and teacher ratings via machine learning, as well as annotations provided for text analysis of the responses.

Resection and whole brain radiotherapy (WBRT) are the standards of care for the treatment of patients with brain metastases (BM) but are often associated with cognitive side effects. Stereotactic radiosurgery (SRS) involves a more targeted treatment approach and has been shown to avoid the side effects associated with WBRT. However, SRS requires precise identification and delineation of BM. While many AI algorithms have been developed for this purpose, their clinical adoption has been limited due to poor model performance in the clinical setting. Major reasons for non-generalizable algorithms are the limitations in the datasets used for training the AI network. The purpose of this study was to create a large, heterogenous, annotated BM dataset for training and validation of AI models to improve generalizability. We present a BM dataset of 200 patients with pretreatment T1, T1 post-contrast, T2, and FLAIR MR images. The dataset includes contrast-enhancing and necrotic 3D segmentations on T1 post-contrast and whole tumor (including peritumoral edema) 3D segmentations on FLAIR. Our dataset contains 975 contrast-enhancing lesions, many of which are sub centimeter, along with clinical and imaging feature information. We used a streamlined approach to database-building leveraging a PACS-integrated segmentation workflow.

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.

Medical image editing has emerged as a pivotal technology with broad applications in data augmentation, model interpretability, medical education, and treatment simulation. However, the lack of large-scale, high-quality, and openly accessible datasets tailored for medical contexts with strict anatomical and clinical constraints has significantly hindered progress in this domain. To bridge this gap, we introduce Med-Banana-50K, a comprehensive dataset of over 50k medically curated image edits spanning chest X-ray, brain MRI, and fundus photography across 23 diseases. Each sample supports bidirectional lesion editing (addition and removal) and is constructed using Gemini-2.5-Flash-Image based on real clinical images. A key differentiator of our dataset is the medically grounded quality control protocol: we employ an LLM-as-Judge evaluation framework with criteria such as instruction compliance, structural plausibility, image realism, and fidelity preservation, alongside iterative refinement over up to five rounds. Additionally, Med-Banana-50K includes around 37,000 failed editing attempts with full evaluation logs to support preference learning and alignment research. By offering a large-scale, medically rigorous, and fully documented resource, Med-Banana-50K establishes a critical foundation for developing and evaluating reliable medical image editing systems. Our dataset and code are publicly available. [https://github.com/richardChenzhihui/med-banana-50k].

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.

Medical language models (MLMs) have become pivotal in advancing medical natural language processing. However, prior models that rely on pre-training or supervised fine-tuning often exhibit low data efficiency and limited practicality in real-world clinical applications. While OpenAIs O1 highlights test-time scaling in mathematics, attempts to replicate this approach in medicine typically distill responses from GPT-series models to open-source models, focusing primarily on multiple-choice tasks. This strategy, though straightforward, neglects critical concerns like data privacy and realistic deployment in clinical settings. In this work, we present a deployable, small-scale medical language model, \mone, designed for long-chain reasoning in clinical tasks using a self-evolution paradigm. Starting with a seed dataset of around 8,000 instances spanning five domains and 16 datasets, we prompt a base policy model to perform Monte Carlo Tree Search (MCTS) to construct verifiable reasoning chains. Each reasoning step is assigned an evolution rollout value, allowing verified trajectories to train the policy model and the reward model. During inference, the policy model generates multiple responses, and the reward model selects the one with the highest reward score. Experiments on eleven evaluation datasets demonstrate that \mone outperforms prior open-source models by 2 points, with the addition of the reward model further boosting performance (sim13 points), surpassing GPT-4o-mini. Code and data are available at https://github.com/pixas/MedSSS.

Electron microscopy (EM) enables the reconstruction of neural circuits at the level of individual synapses, which has been transformative for scientific discoveries. However, due to the complex morphology, an accurate reconstruction of cortical axons has become a major challenge. Worse still, there is no publicly available large-scale EM dataset from the cortex that provides dense ground truth segmentation for axons, making it difficult to develop and evaluate large-scale axon reconstruction methods. To address this, we introduce the AxonEM dataset, which consists of two 30x30x30 um^3 EM image volumes from the human and mouse cortex, respectively. We thoroughly proofread over 18,000 axon instances to provide dense 3D axon instance segmentation, enabling large-scale evaluation of axon reconstruction methods. In addition, we densely annotate nine ground truth subvolumes for training, per each data volume. With this, we reproduce two published state-of-the-art methods and provide their evaluation results as a baseline. We publicly release our code and data at https://connectomics-bazaar.github.io/proj/AxonEM/index.html to foster the development of advanced methods.

Brain tumors, particularly gliomas, pose significant chall-enges due to their complex growth patterns, infiltrative nature, and the variability in brain structure across individuals, which makes accurate diagnosis and monitoring difficult. Deep learning models have been developed to accurately delineate these tumors. However, most of these models were trained on relatively homogenous high-resource datasets, limiting their robustness when deployed in underserved regions. In this study, we performed segmentation-aware offline data augmentation on the BraTS-Africa dataset to increase the data sample size and diversity to enhance generalization. We further constructed an ensemble of three distinct architectures, MedNeXt, SegMamba, and Residual-Encoder U-Net, to leverage their complementary strengths. Our best-performing model, MedNeXt, was trained on 1000 epochs and achieved the highest average lesion-wise dice and normalized surface distance scores of 0.86 and 0.81 respectively. However, the ensemble model trained for 500 epochs produced the most balanced segmentation performance across the tumour subregions. This work demonstrates that a combination of advanced augmentation and model ensembling can improve segmentation accuracy and robustness on diverse and underrepresented datasets. Code available at: https://github.com/SPARK-Academy-2025/SPARK-2025/tree/main/SPARK2025_BraTs_MODELS/SPARK_NeuroAshanti

Is it possible to develop an "AI Pathologist" to pass the board-certified examination of the American Board of Pathology? To achieve this goal, the first step is to create a visual question answering (VQA) dataset where the AI agent is presented with a pathology image together with a question and is asked to give the correct answer. Our work makes the first attempt to build such a dataset. Different from creating general-domain VQA datasets where the images are widely accessible and there are many crowdsourcing workers available and capable of generating question-answer pairs, developing a medical VQA dataset is much more challenging. First, due to privacy concerns, pathology images are usually not publicly available. Second, only well-trained pathologists can understand pathology images, but they barely have time to help create datasets for AI research. To address these challenges, we resort to pathology textbooks and online digital libraries. We develop a semi-automated pipeline to extract pathology images and captions from textbooks and generate question-answer pairs from captions using natural language processing. We collect 32,799 open-ended questions from 4,998 pathology images where each question is manually checked to ensure correctness. To our best knowledge, this is the first dataset for pathology VQA. Our dataset will be released publicly to promote research in medical VQA.

We describe a Magnetic Resonance Imaging (MRI) dataset from individuals from the African nation of Nigeria. The dataset contains pseudonymized structural MRI (T1w, T2w, FLAIR) data of clinical quality. The dataset contains data from 36 images from healthy control subjects, 32 images from individuals diagnosed with age-related dementia and 20 from individuals with Parkinson's disease. There is currently a paucity of data from the African continent. Given the potential for Africa to contribute to the global neuroscience community, this first MRI dataset represents both an opportunity and benchmark for future studies to share data from the African continent.

Training of neural networks for automated diagnosis of pigmented skin lesions is hampered by the small size and lack of diversity of available datasets of dermatoscopic images. We tackle this problem by releasing the HAM10000 ("Human Against Machine with 10000 training images") dataset. We collected dermatoscopic images from different populations acquired and stored by different modalities. Given this diversity we had to apply different acquisition and cleaning methods and developed semi-automatic workflows utilizing specifically trained neural networks. The final dataset consists of 10015 dermatoscopic images which are released as a training set for academic machine learning purposes and are publicly available through the ISIC archive. This benchmark dataset can be used for machine learning and for comparisons with human experts. Cases include a representative collection of all important diagnostic categories in the realm of pigmented lesions. More than 50% of lesions have been confirmed by pathology, while the ground truth for the rest of the cases was either follow-up, expert consensus, or confirmation by in-vivo confocal microscopy.

We introduce EuroCropsML, an analysis-ready remote sensing machine learning dataset for time series crop type classification of agricultural parcels in Europe. It is the first dataset designed to benchmark transnational few-shot crop type classification algorithms that supports advancements in algorithmic development and research comparability. It comprises 706 683 multi-class labeled data points across 176 classes, featuring annual time series of per-parcel median pixel values from Sentinel-2 L1C data for 2021, along with crop type labels and spatial coordinates. Based on the open-source EuroCrops collection, EuroCropsML is publicly available on Zenodo.

Vision-language models hold considerable promise for ophthalmology, but their development depends on large-scale, high-quality image-text datasets that remain scarce. We present PubMed-Ophtha, a hierarchical dataset of 102,023 ophthalmological image-caption pairs extracted from 15,842 open-access articles in PubMed Central. Unlike existing datasets, figures are extracted directly from article PDFs at full resolution and decomposed into their constituent panels, panel identifiers, and individual images. Each image is annotated with its imaging modality -- color fundus photography, optical coherence tomography, retinal imaging, or other -- and a mark status indicating the presence of annotation marks such as arrows. Figure captions are split into panel-level subcaptions using a two-step LLM approach, achieving a mean average sentence BLEU score of 0.913 on human-annotated data. Panel and image detection models reach a mAP@0.50 of 0.909 and 0.892, respectively, and figure extraction achieves a median IoU of 0.997. To support reproducibility, we additionally release the human-annotated ground-truth data, all trained models, and the full dataset generation pipeline.

Before deployment in the real-world deep neural networks require thorough evaluation of how they handle both knowns, inputs represented in the training data, and unknowns (anomalies). This is especially important for scene understanding tasks with safety critical applications, such as in autonomous driving. Existing datasets allow evaluation of only knowns or unknowns - but not both, which is required to establish "in the wild" suitability of deep neural network models. To bridge this gap, we propose a novel anomaly segmentation dataset, ISSU, that features a diverse set of anomaly inputs from cluttered real-world environments. The dataset is twice larger than existing anomaly segmentation datasets, and provides a training, validation and test set for controlled in-domain evaluation. The test set consists of a static and temporal part, with the latter comprised of videos. The dataset provides annotations for both closed-set (knowns) and anomalies, enabling closed-set and open-set evaluation. The dataset covers diverse conditions, such as domain and cross-sensor shift, illumination variation and allows ablation of anomaly detection methods with respect to these variations. Evaluation results of current state-of-the-art methods confirm the need for improvements especially in domain-generalization, small and large object segmentation.

Curating a large scale medical imaging dataset for machine learning applications is both time consuming and expensive. Balancing the workload between model development, data collection and annotations is difficult for machine learning practitioners, especially under time constraints. Causal analysis is often used in medicine and economics to gain insights about the effects of actions and policies. In this paper we explore the effect of dataset interventions on the output of image classification models. Through a causal approach we investigate the effects of the quantity and type of data we need to incorporate in a dataset to achieve better performance for specific subtasks. The main goal of this paper is to highlight the potential of causal analysis as a tool for resource optimization for developing medical imaging ML applications. We explore this concept with a synthetic dataset and an exemplary use-case for Diabetic Retinopathy image analysis.

Remote sensing image scene classification plays an important role in a wide range of applications and hence has been receiving remarkable attention. During the past years, significant efforts have been made to develop various datasets or present a variety of approaches for scene classification from remote sensing images. However, a systematic review of the literature concerning datasets and methods for scene classification is still lacking. In addition, almost all existing datasets have a number of limitations, including the small scale of scene classes and the image numbers, the lack of image variations and diversity, and the saturation of accuracy. These limitations severely limit the development of new approaches especially deep learning-based methods. This paper first provides a comprehensive review of the recent progress. Then, we propose a large-scale dataset, termed "NWPU-RESISC45", which is a publicly available benchmark for REmote Sensing Image Scene Classification (RESISC), created by Northwestern Polytechnical University (NWPU). This dataset contains 31,500 images, covering 45 scene classes with 700 images in each class. The proposed NWPU-RESISC45 (i) is large-scale on the scene classes and the total image number, (ii) holds big variations in translation, spatial resolution, viewpoint, object pose, illumination, background, and occlusion, and (iii) has high within-class diversity and between-class similarity. The creation of this dataset will enable the community to develop and evaluate various data-driven algorithms. Finally, several representative methods are evaluated using the proposed dataset and the results are reported as a useful baseline for future research.

CPU performance prediction, which involves forecasting the performance scores of a CPU based on its hardware characteristics during its operation, is a critical technology for computational system design and resource management in the big data era. However, this research field currently faces two significant challenges. First, collecting real-world data is challenging due to the wide variety of CPU products on the market and the highly specialized nature of relevant hardware characteristics. In the research process, this field lacks a standard dataset with unified hardware characteristics, wide data coverage, and comprehensive benchmarks. Second, existing methods based on hardware simulation models or machine learning exhibit notable shortcomings, such as lengthy simulation test cycles and low prediction accuracy. To bridge these gaps, we first collect, preprocess, and standardize historical data from the 4th Generation Intel Xeon Scalable Processors across multiple benchmark suites to create a new dataset, named PerfCastDB. Subsequently, we design a deep learning based model called Nova CPU Performance Predictor (NCPP) as the baseline for this new dataset. The NCPP network is designed based on group attention mechanism. It effectively quantifies the implicit relationships between hardware characteristics within and across groups and comprehensively models the impact of various hardware characteristics on CPU performance prediction. We conduct comparative experiments using the proposed PerfCastDB dataset. Compared to existing approaches, NCPP achieves superior evaluation results, demonstrating its effectiveness. Furthermore, we have open-sourced part of the dataset and the NCPP network code to facilitate subsequent research. The resources can be accessed at https://github.com/xiaoman-liu/NCPP.

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

We present PubMed 200k RCT, a new dataset based on PubMed for sequential sentence classification. The dataset consists of approximately 200,000 abstracts of randomized controlled trials, totaling 2.3 million sentences. Each sentence of each abstract is labeled with their role in the abstract using one of the following classes: background, objective, method, result, or conclusion. The purpose of releasing this dataset is twofold. First, the majority of datasets for sequential short-text classification (i.e., classification of short texts that appear in sequences) are small: we hope that releasing a new large dataset will help develop more accurate algorithms for this task. Second, from an application perspective, researchers need better tools to efficiently skim through the literature. Automatically classifying each sentence in an abstract would help researchers read abstracts more efficiently, especially in fields where abstracts may be long, such as the medical field.

Reducing traffic accidents is an important public safety challenge. However, the majority of studies on traffic accident analysis and prediction have used small-scale datasets with limited coverage, which limits their impact and applicability; and existing large-scale datasets are either private, old, or do not include important contextual information such as environmental stimuli (weather, points-of-interest, etc.). In order to help the research community address these shortcomings we have - through a comprehensive process of data collection, integration, and augmentation - created a large-scale publicly available database of accident information named US-Accidents. US-Accidents currently contains data about 2.25 million instances of traffic accidents that took place within the contiguous United States, and over the last three years. Each accident record consists of a variety of intrinsic and contextual attributes such as location, time, natural language description, weather, period-of-day, and points-of-interest. We present this dataset in this paper, along with a wide range of insights gleaned from this dataset with respect to the spatiotemporal characteristics of accidents. The dataset is publicly available at https://smoosavi.org/datasets/us_accidents.

In this paper, we introduce fastHDMI, a Python package designed for efficient variable screening in high-dimensional datasets, particularly neuroimaging data. This work pioneers the application of three mutual information estimation methods for neuroimaging variable selection, a novel approach implemented via fastHDMI. These advancements enhance our ability to analyze the complex structures of neuroimaging datasets, providing improved tools for variable selection in high-dimensional spaces. Using the preprocessed ABIDE dataset, we evaluate the performance of these methods through extensive simulations. The tests cover a range of conditions, including linear and nonlinear associations, as well as continuous and binary outcomes. Our results highlight the superiority of the FFTKDE-based mutual information estimation for feature screening in continuous nonlinear outcomes, while binning-based methods outperform others for binary outcomes with nonlinear probability preimages. For linear simulations, both Pearson correlation and FFTKDE-based methods show comparable performance for continuous outcomes, while Pearson excels in binary outcomes with linear probability preimages. A comprehensive case study using the ABIDE dataset further demonstrates fastHDMI's practical utility, showcasing the predictive power of models built from variables selected using our screening techniques. This research affirms the computational efficiency and methodological strength of fastHDMI, significantly enriching the toolkit available for neuroimaging analysis.

LibriBrain represents the largest single-subject MEG dataset to date for speech decoding, with over 50 hours of recordings -- 5times larger than the next comparable dataset and 50times larger than most. This unprecedented `depth' of within-subject data enables exploration of neural representations at a scale previously unavailable with non-invasive methods. LibriBrain comprises high-quality MEG recordings together with detailed annotations from a single participant listening to naturalistic spoken English, covering nearly the full Sherlock Holmes canon. Designed to support advances in neural decoding, LibriBrain comes with a Python library for streamlined integration with deep learning frameworks, standard data splits for reproducibility, and baseline results for three foundational decoding tasks: speech detection, phoneme classification, and word classification. Baseline experiments demonstrate that increasing training data yields substantial improvements in decoding performance, highlighting the value of scaling up deep, within-subject datasets. By releasing this dataset, we aim to empower the research community to advance speech decoding methodologies and accelerate the development of safe, effective clinical brain-computer interfaces.

Large Language Model (LLM)-based systems increasingly rely on function calling to enable structured and controllable interaction with external data sources, yet existing datasets do not address mental health-oriented access to wearable sensor data. This paper presents a synthetic function-calling dataset designed for mental health assistance grounded in wearable health signals such as sleep, physical activity, cardiovascular measures, stress indicators, and metabolic data. The dataset maps diverse natural language queries to standardized API calls derived from a widely adopted health data schema. Each sample includes a user query, a query category, an explicit reasoning step, a normalized temporal parameter, and a target function. The dataset covers explicit, implicit, behavioral, symptom-based, and metaphorical expressions, which reflect realistic mental health-related user interactions. This resource supports research on intent grounding, temporal reasoning, and reliable function invocation in LLM-based mental health agents and is publicly released to promote reproducibility and future work.

Large language models (LLMs) have shown great potential for healthcare applications. However, existing evaluation benchmarks provide minimal coverage of Alzheimer's Disease and Related Dementias (ADRD). To address this gap, we introduce ADRD-Bench, the first ADRD-specific benchmark dataset designed for rigorous evaluation of LLMs. ADRD-Bench has two components: 1) ADRD Unified QA, a synthesis of 1,352 questions consolidated from seven established medical benchmarks, providing a unified assessment of clinical knowledge; and 2) ADRD Caregiving QA, a novel set of 149 questions derived from the Aging Brain Care (ABC) program, a widely used, evidence-based brain health management program. Guided by a program with national expertise in comprehensive ADRD care, this new set was designed to mitigate the lack of practical caregiving context in existing benchmarks. We evaluated 33 state-of-the-art LLMs on the proposed ADRD-Bench. Results showed that the accuracy of open-weight general models ranged from 0.63 to 0.93 (mean: 0.78; std: 0.09). The accuracy of open-weight medical models ranged from 0.48 to 0.93 (mean: 0.82; std: 0.13). The accuracy of closed-source general models ranged from 0.83 to 0.91 (mean: 0.89; std: 0.03). While top-tier models achieved high accuracies (>0.9), case studies revealed that inconsistent reasoning quality and stability limit their reliability, highlighting a critical need for domain-specific improvement to enhance LLMs' knowledge and reasoning grounded in daily caregiving data. The entire dataset is available at https://github.com/IIRL-ND/ADRD-Bench.

PanTS is a large-scale, multi-institutional dataset curated to advance research in pancreatic CT analysis. It contains 36,390 CT scans from 145 medical centers, with expert-validated, voxel-wise annotations of over 993,000 anatomical structures, covering pancreatic tumors, pancreas head, body, and tail, and 24 surrounding anatomical structures such as vascular/skeletal structures and abdominal/thoracic organs. Each scan includes metadata such as patient age, sex, diagnosis, contrast phase, in-plane spacing, slice thickness, etc. AI models trained on PanTS achieve significantly better performance in pancreatic tumor detection, localization, and segmentation compared to those trained on existing public datasets. Our analysis indicates that these gains are directly attributable to the 16x larger-scale tumor annotations and indirectly supported by the 24 additional surrounding anatomical structures. As the largest and most comprehensive resource of its kind, PanTS offers a new benchmark for developing and evaluating AI models in pancreatic CT analysis.

In this paper, we present DendroMap, a novel approach to interactively exploring large-scale image datasets for machine learning (ML). ML practitioners often explore image datasets by generating a grid of images or projecting high-dimensional representations of images into 2-D using dimensionality reduction techniques (e.g., t-SNE). However, neither approach effectively scales to large datasets because images are ineffectively organized and interactions are insufficiently supported. To address these challenges, we develop DendroMap by adapting Treemaps, a well-known visualization technique. DendroMap effectively organizes images by extracting hierarchical cluster structures from high-dimensional representations of images. It enables users to make sense of the overall distributions of datasets and interactively zoom into specific areas of interests at multiple levels of abstraction. Our case studies with widely-used image datasets for deep learning demonstrate that users can discover insights about datasets and trained models by examining the diversity of images, identifying underperforming subgroups, and analyzing classification errors. We conducted a user study that evaluates the effectiveness of DendroMap in grouping and searching tasks by comparing it with a gridified version of t-SNE and found that participants preferred DendroMap. DendroMap is available at https://div-lab.github.io/dendromap/.

Instance segmentation of neurons in volumetric light microscopy images of nervous systems enables groundbreaking research in neuroscience by facilitating joint functional and morphological analyses of neural circuits at cellular resolution. Yet said multi-neuron light microscopy data exhibits extremely challenging properties for the task of instance segmentation: Individual neurons have long-ranging, thin filamentous and widely branching morphologies, multiple neurons are tightly inter-weaved, and partial volume effects, uneven illumination and noise inherent to light microscopy severely impede local disentangling as well as long-range tracing of individual neurons. These properties reflect a current key challenge in machine learning research, namely to effectively capture long-range dependencies in the data. While respective methodological research is buzzing, to date methods are typically benchmarked on synthetic datasets. To address this gap, we release the FlyLight Instance Segmentation Benchmark (FISBe) dataset, the first publicly available multi-neuron light microscopy dataset with pixel-wise annotations. In addition, we define a set of instance segmentation metrics for benchmarking that we designed to be meaningful with regard to downstream analyses. Lastly, we provide three baselines to kick off a competition that we envision to both advance the field of machine learning regarding methodology for capturing long-range data dependencies, and facilitate scientific discovery in basic neuroscience.

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.

Recent English Common Crawl datasets like FineWeb-Edu and DCLM achieved significant benchmark gains via aggressive model-based filtering, but at the cost of removing 90% of data. This limits their suitability for long token horizon training, such as 15T tokens for Llama 3.1. In this paper, we show how to achieve better trade-offs between accuracy and data quantity by a combination of classifier ensembling, synthetic data rephrasing, and reduced reliance on heuristic filters. When training 8B parameter models for 1T tokens, using a high-quality subset of our data improves MMLU by 5.6 over DCLM, demonstrating the efficacy of our methods for boosting accuracies over a relatively short token horizon. Furthermore, our full 6.3T token dataset matches DCLM on MMLU, but contains four times more unique real tokens than DCLM. This unlocks state-of-the-art training over a long token horizon: an 8B parameter model trained for 15T tokens, of which 7.2T came from our dataset, is better than the Llama 3.1 8B model: +5 on MMLU, +3.1 on ARC-Challenge, and +0.5 on average across ten diverse tasks. The dataset is available at https://data.commoncrawl.org/contrib/Nemotron/Nemotron-CC/index.html

A database of images of approximately 960 unique plants belonging to 12 species at several growth stages is made publicly available. It comprises annotated RGB images with a physical resolution of roughly 10 pixels per mm. To standardise the evaluation of classification results obtained with the database, a benchmark based on f_{1} scores is proposed. The dataset is available at https://vision.eng.au.dk/plant-seedlings-dataset

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.

This paper presents a large publicly available multi-center lumbar spine magnetic resonance imaging (MRI) dataset with reference segmentations of vertebrae, intervertebral discs (IVDs), and spinal canal. The dataset includes 447 sagittal T1 and T2 MRI series from 218 patients with a history of low back pain. It was collected from four different hospitals and was divided into a training (179 patients) and validation (39 patients) set. An iterative data annotation approach was used by training a segmentation algorithm on a small part of the dataset, enabling semi-automatic segmentation of the remaining images. The algorithm provided an initial segmentation, which was subsequently reviewed, manually corrected, and added to the training data. We provide reference performance values for this baseline algorithm and nnU-Net, which performed comparably. We set up a continuous segmentation challenge to allow for a fair comparison of different segmentation algorithms. This study may encourage wider collaboration in the field of spine segmentation, and improve the diagnostic value of lumbar spine MRI.

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.

Despite the growing scale of medical Vision-Language datasets, the impact of dataset quality on model performance remains under-explored. We introduce Open-PMC, a high-quality medical dataset from PubMed Central, containing 2.2 million image-text pairs, enriched with image modality annotations, subfigures, and summarized in-text references. Notably, the in-text references provide richer medical context, extending beyond the abstract information typically found in captions. Through extensive experiments, we benchmark Open-PMC against larger datasets across retrieval and zero-shot classification tasks. Our results show that dataset quality-not just size-drives significant performance gains. We complement our benchmark with an in-depth analysis of feature representation. Our findings highlight the crucial role of data curation quality in advancing multimodal medical AI. We release Open-PMC, along with the trained models and our codebase.

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.

Preference datasets are essential for training general-domain, instruction-following language models with Reinforcement Learning from Human Feedback (RLHF). Each subsequent data release raises expectations for future data collection, meaning there is a constant need to advance the quality and diversity of openly available preference data. To address this need, we introduce HelpSteer3-Preference, a permissively licensed (CC-BY-4.0), high-quality, human-annotated preference dataset comprising of over 40,000 samples. These samples span diverse real-world applications of large language models (LLMs), including tasks relating to STEM, coding and multilingual scenarios. Using HelpSteer3-Preference, we train Reward Models (RMs) that achieve top performance on RM-Bench (82.4%) and JudgeBench (73.7%). This represents a substantial improvement (~10% absolute) over the previously best-reported results from existing RMs. We demonstrate HelpSteer3-Preference can also be applied to train Generative RMs and how policy models can be aligned with RLHF using our RMs. Dataset (CC-BY-4.0): https://huggingface.co/datasets/nvidia/HelpSteer3#preference

Autonomous driving is among the largest domains in which deep learning has been fundamental for progress within the last years. The rise of datasets went hand in hand with this development. All the more striking is the fact that researchers do not have a tool available that provides a quick, comprehensive and up-to-date overview of data sets and their features in the domain of autonomous driving. In this paper, we present ad-datasets, an online tool that provides such an overview for more than 150 data sets. The tool enables users to sort and filter the data sets according to currently 16 different categories. ad-datasets is an open-source project with community contributions. It is in constant development, ensuring that the content stays up-to-date.

Medical Imaging (MI) datasets are fundamental to artificial intelligence in healthcare. The accuracy, robustness, and fairness of diagnostic algorithms depend on the data (and its quality) used to train and evaluate the models. MI datasets used to be proprietary, but have become increasingly available to the public, including on community-contributed platforms (CCPs) like Kaggle or HuggingFace. While open data is important to enhance the redistribution of data's public value, we find that the current CCP governance model fails to uphold the quality needed and recommended practices for sharing, documenting, and evaluating datasets. In this paper, we conduct an analysis of publicly available machine learning datasets on CCPs, discussing datasets' context, and identifying limitations and gaps in the current CCP landscape. We highlight differences between MI and computer vision datasets, particularly in the potentially harmful downstream effects from poor adoption of recommended dataset management practices. We compare the analyzed datasets across several dimensions, including data sharing, data documentation, and maintenance. We find vague licenses, lack of persistent identifiers and storage, duplicates, and missing metadata, with differences between the platforms. Our research contributes to efforts in responsible data curation and AI algorithms for healthcare.

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.

How do we most effectively treat a disease or condition? Ideally, we could consult a database of evidence gleaned from clinical trials to answer such questions. Unfortunately, no such database exists; clinical trial results are instead disseminated primarily via lengthy natural language articles. Perusing all such articles would be prohibitively time-consuming for healthcare practitioners; they instead tend to depend on manually compiled systematic reviews of medical literature to inform care. NLP may speed this process up, and eventually facilitate immediate consult of published evidence. The Evidence Inference dataset was recently released to facilitate research toward this end. This task entails inferring the comparative performance of two treatments, with respect to a given outcome, from a particular article (describing a clinical trial) and identifying supporting evidence. For instance: Does this article report that chemotherapy performed better than surgery for five-year survival rates of operable cancers? In this paper, we collect additional annotations to expand the Evidence Inference dataset by 25\%, provide stronger baseline models, systematically inspect the errors that these make, and probe dataset quality. We also release an abstract only (as opposed to full-texts) version of the task for rapid model prototyping. The updated corpus, documentation, and code for new baselines and evaluations are available at http://evidence-inference.ebm-nlp.com/.

Large-scale datasets are essential to modern day deep learning. Advocates argue that understanding these methods requires dataset transparency (e.g. "dataset curation, motivation, composition, collection process, etc..."). However, almost no one has suggested the release of the detailed definitions and visual category examples provided to annotators - information critical to understanding the structure of the annotations present in each dataset. These labels are at the heart of public datasets, yet few datasets include the instructions that were used to generate them. We introduce a new task, Labeling Instruction Generation, to address missing publicly available labeling instructions. In Labeling Instruction Generation, we take a reasonably annotated dataset and: 1) generate a set of examples that are visually representative of each category in the dataset; 2) provide a text label that corresponds to each of the examples. We introduce a framework that requires no model training to solve this task and includes a newly created rapid retrieval system that leverages a large, pre-trained vision and language model. This framework acts as a proxy to human annotators that can help to both generate a final labeling instruction set and evaluate its quality. Our framework generates multiple diverse visual and text representations of dataset categories. The optimized instruction set outperforms our strongest baseline across 5 folds by 7.06 mAP for NuImages and 12.9 mAP for COCO.

Data science plays a critical role in clinical research, but it requires professionals with expertise in coding and medical data analysis. Large language models (LLMs) have shown great potential in supporting medical tasks and performing well in general coding tests. However, these tests do not assess LLMs' ability to handle data science tasks in medicine, nor do they explore their practical utility in clinical research. To address this, we developed a dataset consisting of 293 real-world data science coding tasks, based on 39 published clinical studies, covering 128 tasks in Python and 165 tasks in R. This dataset simulates realistic clinical research scenarios using patient data. Our findings reveal that cutting-edge LLMs struggle to generate perfect solutions, frequently failing to follow input instructions, understand target data, and adhere to standard analysis practices. Consequently, LLMs are not yet ready to fully automate data science tasks. We benchmarked advanced adaptation methods and found two to be particularly effective: chain-of-thought prompting, which provides a step-by-step plan for data analysis, which led to a 60% improvement in code accuracy; and self-reflection, enabling LLMs to iteratively refine their code, yielding a 38% accuracy improvement. Building on these insights, we developed a platform that integrates LLMs into the data science workflow for medical professionals. In a user study with five medical doctors, we found that while LLMs cannot fully automate coding tasks, they significantly streamline the programming process. We found that 80% of their submitted code solutions were incorporated from LLM-generated code, with up to 96% reuse in some cases. Our analysis highlights the potential of LLMs, when integrated into expert workflows, to enhance data science efficiency in clinical research.

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.

The sciences of biological and artificial intelligence are ever more intertwined. Neural computational principles inspire new intelligent machines, which are in turn used to advance theoretical understanding of the brain. To promote further exchange of ideas and collaboration between biological and artificial intelligence researchers, we introduce the 2023 installment of the Algonauts Project challenge: How the Human Brain Makes Sense of Natural Scenes (http://algonauts.csail.mit.edu). This installment prompts the fields of artificial and biological intelligence to come together towards building computational models of the visual brain using the largest and richest dataset of fMRI responses to visual scenes, the Natural Scenes Dataset (NSD). NSD provides high-quality fMRI responses to ~73,000 different naturalistic colored scenes, making it the ideal candidate for data-driven model building approaches promoted by the 2023 challenge. The challenge is open to all and makes results directly comparable and transparent through a public leaderboard automatically updated after each submission, thus allowing for rapid model development. We believe that the 2023 installment will spark symbiotic collaborations between biological and artificial intelligence scientists, leading to a deeper understanding of the brain through cutting-edge computational models and to novel ways of engineering artificial intelligent agents through inductive biases from biological systems.

The emerging area of computational pathology (CPath) is ripe ground for the application of deep learning (DL) methods to healthcare due to the sheer volume of raw pixel data in whole-slide images (WSIs) of cancerous tissue slides. However, it is imperative for the DL algorithms relying on nuclei-level details to be able to cope with data from `the clinical wild', which tends to be quite challenging. We study, and extend recently released PanNuke dataset consisting of ~200,000 nuclei categorized into 5 clinically important classes for the challenging tasks of segmenting and classifying nuclei in WSIs. Previous pan-cancer datasets consisted of only up to 9 different tissues and up to 21,000 unlabeled nuclei and just over 24,000 labeled nuclei with segmentation masks. PanNuke consists of 19 different tissue types that have been semi-automatically annotated and quality controlled by clinical pathologists, leading to a dataset with statistics similar to the clinical wild and with minimal selection bias. We study the performance of segmentation and classification models when applied to the proposed dataset and demonstrate the application of models trained on PanNuke to whole-slide images. We provide comprehensive statistics about the dataset and outline recommendations and research directions to address the limitations of existing DL tools when applied to real-world CPath applications.

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.

Recent research in medical image analysis with deep learning almost exclusively focuses on grid- or voxel-based data representations. We challenge this common choice by introducing MedFuncta, a modality-agnostic continuous data representation based on neural fields. We demonstrate how to scale neural fields from single instances to large datasets by exploiting redundancy in medical signals and by applying an efficient meta-learning approach with a context reduction scheme. We further address the spectral bias in commonly used SIREN activations, by introducing an omega_0-schedule, improving reconstruction quality and convergence speed. We validate our proposed approach on a large variety of medical signals of different dimensions and modalities (1D: ECG; 2D: Chest X-ray, Retinal OCT, Fundus Camera, Dermatoscope, Colon Histopathology, Cell Microscopy; 3D: Brain MRI, Lung CT) and successfully demonstrate that we can solve relevant downstream tasks on these representations. We additionally release a large-scale dataset of > 550k annotated neural fields to promote research in this direction.

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 SciClaimEval, a new scientific dataset for the claim verification task. Unlike existing resources, SciClaimEval features authentic claims, including refuted ones, directly extracted from published papers. To create refuted claims, we introduce a novel approach that modifies the supporting evidence (figures and tables), rather than altering the claims or relying on large language models (LLMs) to fabricate contradictions. The dataset provides cross-modal evidence with diverse representations: figures are available as images, while tables are provided in multiple formats, including images, LaTeX source, HTML, and JSON. SciClaimEval contains 1,664 annotated samples from 180 papers across three domains, machine learning, natural language processing, and medicine, validated through expert annotation. We benchmark 11 multimodal foundation models, both open-source and proprietary, across the dataset. Results show that figure-based verification remains particularly challenging for all models, as a substantial performance gap remains between the best system and human baseline.

The Open Images Dataset contains approximately 9 million images and is a widely accepted dataset for computer vision research. As is common practice for large datasets, the annotations are not exhaustive, with bounding boxes and attribute labels for only a subset of the classes in each image. In this paper, we present a new set of annotations on a subset of the Open Images dataset called the MIAP (More Inclusive Annotations for People) subset, containing bounding boxes and attributes for all of the people visible in those images. The attributes and labeling methodology for the MIAP subset were designed to enable research into model fairness. In addition, we analyze the original annotation methodology for the person class and its subclasses, discussing the resulting patterns in order to inform future annotation efforts. By considering both the original and exhaustive annotation sets, researchers can also now study how systematic patterns in training annotations affect modeling.