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68 entries in Medicine

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AlphaFoldDBLiteFoldAlphaFoldDB prediction index — open database of predicted protein 3D structures with confidence scores, providing structural coverage for known protein sequences at scale.Predicted StructuresExplore
B3DBmaomlabBlood-Brain Barrier Database (B3DB) — curated permeability measurements for compounds, supporting CNS drug-discovery ML benchmarks.BBB PermeabilityExplore
BioMysteryBench-fullAnthropicFull BioMysteryBench evaluation set — challenging biology problems used to probe expert-level scientific reasoning in frontier models.Biology BenchmarkExplore
BioMysteryBench-previewAnthropicPreview slice of BioMysteryBench — challenging, expert-curated biology problems for evaluating AI scientific reasoning capability.Biology BenchmarkExplore
camelyon16-featuresowkinPre-extracted features from the CAMELYON16 breast cancer lymph node metastasis detection challenge, enabling efficient benchmarking of MIL methods.Computational PathologyExplore
clinvar-vepHuggingFaceBioClinVar variants annotated with VEP (Variant Effect Predictor) — formatted for benchmarking genomic-LLM pathogenicity classification.Clinical VariantsExplore
CryptoCENmaomlabCryptoCEN — Cryptococcus coexpression network dataset for fungal pathogen biology and drug-target prioritisation.Coexpression NetworkExplore
CT_DeepLesion-MedSAM2wanglabCT volumes from the DeepLesion benchmark with mask annotations restructured for training and evaluating MedSAM2, the universal medical image segmentation foundation model.Medical ImagingExplore
CycPepMPDBLiteFoldCycPeptMPDB — public dataset of experimentally measured membrane permeability for cyclic peptides, the standard resource for peptide-permeability modelling.Peptide PropertiesExplore
DisProtLiteFoldDisProt — manually curated database of intrinsically disordered proteins and regions with experimental evidence and functional annotations.Protein AnnotationExplore
drug-target-activityeve-bioDrug-target interaction measurements for 1,397 FDA-approved small molecule drugs.Drug DiscoveryExplore
DynaCLR-databiohubTraining and evaluation data for DynaCLR — dynamic contrastive learning of cell embeddings from live-cell microscopy time series, including infection-status labels.MicroscopyExplore
EmeraldBaytahoebioEmerald Bay — single-cell perturbation dataset of 1.8M+ transcriptomic profiles spanning 52 cell lines × 91 drug treatments (plus combinations), generated on Tahoe’s MOSAIC high-throughput platform with paired transcriptional and drug-phenotype readouts over a five-day culture.Single-Cell PerturbationExplore
ether0-benchmarkfuturehouseChemistry reasoning benchmark covering SMILES-based tasks including reaction prediction, retrosynthesis, and molecular property estimation for evaluating chemistry LLMs.Chemistry BenchmarkExplore
finemed-frdoctolib-lab21.1M documents and 19.2B words of French medical text curated from FineWeb-2, FinePDFs, and FineWiki — annotated for medical subdomain, educational quality, and medical-term density; the pretraining corpus for DoctoBERT and DoctoModernBERT.Medical Pretraining CorpusExplore
finemed-rephrased-frdoctolib-labLLM-rephrased variant of FineMed-fr (13.6M documents) — synthetically rewritten French medical text used alongside the original corpus to pretrain DoctoBERT and DoctoModernBERT.Medical Pretraining CorpusExplore
FireProtDBLiteFoldFireProtDB — curated thermostability mutation data for proteins, supporting protein-engineering and stability-prediction modelling.Protein StabilityExplore
foundry_moses_v1-1foundry-mlFoundry mirror of MOSES — molecular sets benchmark for evaluating generative chemistry models on drug-like molecule generation.Molecular GenerationExplore
healthbenchopenaiRealistic multi-turn health conversations graded against physician-written rubrics across multiple axes (accuracy, completeness, communication) — an open evaluation benchmark for AI assistants in medicine.Medical BenchmarkExplore
healthbench-professionalopenaiProfessional-graded subset of HealthBench: physician evaluators score model responses to clinically realistic conversations, targeting expert-level health assessment.Medical BenchmarkExplore
her2-challenge-2026owkinHER2 scoring challenge dataset with H&E-stained whole-slide images for evaluating AI-based HER2 status prediction in breast cancer.Computational PathologyExplore
hestMahmoodLabHEST-1k — 1,276 spatial-transcriptomic profiles each linked and aligned to a Whole Slide Image (pixel size <1.15 µm/px), the largest paired histology + spatial-transcriptomics resource on the Hub.Spatial TranscriptomicsExplore
hest-benchMahmoodLabHEST-Bench — companion benchmark to HEST-1k for evaluating spatial-transcriptomics and pathology foundation models on aligned histology / expression tasks.Pathology BenchmarkExplore
HumanProteinAtlasLiteFoldHuman Protein Atlas — gene and protein expression across tissues, cells, organs, pathology, and subcellular locations for human proteins.Protein AnnotationExplore
IEDBLiteFoldIEDB assay export — experimentally characterised B-cell, T-cell, and MHC-binding epitopes across infectious, allergic, autoimmune, and transplant settings.ImmunologyExplore
MedDialogOpenMedDoctor-patient medical dialogue dataset for training and evaluating clinical conversation models — covers triage, symptom checking, and diagnostic reasoning.Medical DialogueExplore
medical-o1-reasoning-SFTFreedomIntelligenceMedical chain-of-thought reasoning dataset (o1-style) for supervised fine-tuning of medical LLMs — one of the most-liked medical training corpora on Hugging Face (1000+ likes).Medical Reasoning CorpusExplore
medical-o1-verifiable-problemFreedomIntelligenceVerifiable medical reasoning problems with checker functions — supports RL/reward-model training for medical-LLM alignment beyond static SFT.Medical RL Reward DataExplore
Medical-Reasoning-SFT-MegaOpenMedLarge supervised fine-tuning corpus for clinical reasoning — multi-step medical question-answer chains with rationales for training instruction-following medical LLMs.SFT Reasoning CorpusExplore
MedSynthAhmad0067Realistic synthetic medical dialogue–SOAP note pairs generated to support training and evaluation of clinical documentation models without exposing real patient data.Clinical NLPExplore
MegaScale-Tsuboyama2023LiteFoldMegaScale (Tsuboyama et al., 2023) — large-scale experimental measurements of protein stability across hundreds of thousands of mutations for stability prediction modelling.Protein StabilityExplore
miriad-4.4Mmiriad4.4M-example medical reasoning subset of MIRIAD — earlier release used for benchmarking medical instruction-tuning workflows.Medical Reasoning CorpusExplore
miriad-5.8Mmiriad5.8M-example medical instruction-tuning and reasoning corpus curated from clinical literature for training healthcare LLMs at scale.Medical Reasoning CorpusExplore
nct-crc-heowkinColorectal cancer tissue classification dataset with H&E-stained patches across 9 tissue classes, widely used for benchmarking pathology models.Computational PathologyExplore
OASopigObserved Antibody Space: a curated database of over one billion antibody sequences from immune repertoire sequencing studies, the standard resource for antibody ML.Antibody SequencesExplore
Octant_CYP_inhibition_reactivity_blog_releaseopenadmetOctant CYP inhibition and chemical reactivity dataset measuring cytochrome P450 activity across a diverse compound library for ADMET modelling.Drug DiscoveryExplore
openadmet-expansionrx-challenge-dataopenadmetFull ExpansionRx challenge dataset of RNA-targeted small-molecule compounds with measured ADMET properties for open pharmacokinetics benchmarking.Drug DiscoveryExplore
openadmet-expansionrx-challenge-train-dataopenadmetTraining data for the OpenADMET ExpansionRx ADMET prediction challenge.Drug DiscoveryExplore
opengenome2arcinstituteCurated collection of prokaryotic and eukaryotic genomic sequences for training and benchmarking large-scale biological foundation models.GenomicsExplore
OpenTMEAignosticsPre-analyzed H&E whole-slide images from TCGA across breast, bladder, colorectal, liver, and lung cancers — cell-level annotations and tumour-microenvironment spatial features generated by Atlas H&E-TME.Digital PathologyExplore
parse-de-rhaistertahoebioDifferential-expression summary statistics for the Parse PBMC cytokine screen (12 donors × 18 immune cell types × 90 cytokines), derived from the Arc Institute ST-HVG-Parse dataset — per-gene fold changes, significance, and pseudobulk deltas used to train Rhaister.Cytokine Differential ExpressionExplore
Patho-BenchMahmoodLabPatho-Bench — benchmark designed to evaluate patch and slide encoder foundation models for whole-slide images across cancer subtyping, biomarker prediction, and survival tasks.Pathology BenchmarkExplore
PATHOS-PLM-EMBEDDINGSDSIMBPATHOS protein language-model embeddings — precomputed feature representations supporting pathogenicity prediction and downstream macromolecular ML on protein sequences.Protein EmbeddingsExplore
PDBLiteFoldHub-packaged index over the Protein Data Bank mmCIF entries — the global archive of experimentally-determined 3D structures of biological macromolecules.Protein StructureExplore
Perturb-SapiensarcinstituteLarge-scale human single-cell perturbation dataset used in the STACK foundation-model lineage — paired baseline and perturbed expression profiles for genetic perturbation screens.Single-Cell PerturbationExplore
plism-dataset-tilesowkinLarge-scale histopathology tile dataset for benchmarking robustness of pathology foundation models across staining and scanner variability.Computational PathologyExplore
replogle-nadig-de-rhaistertahoebioDifferential-expression summary statistics for the Replogle-Nadig genome-scale CRISPR screen (4 cell lines × ~2,000 gene knockdowns: HepG2, Jurkat, K562, RPE1) — per-gene fold changes, significance, and pseudobulk deltas used to train Rhaister.CRISPR Differential ExpressionExplore
Replogle-Nadig-PreprintarcinstituteReplogle-Nadig single-cell perturbation dataset (preprint release) — Perturb-seq screens used in the STATE single-cell embedding work for perturbation-response modelling.Single-Cell PerturbationExplore

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