Registry explorer

Benchmarks, with the evaluation context attached.

Search the scientific scope, filter access and task type, then inspect every work and run behind an entry. Filters persist in the URL.

109 records · Download all benchmarks CSV

Benchmark	Kind / release	Domain	Scientific task	Access	Runs
AB-Bind Antibody-focused mutational binding data with accompanying structures for computational affinity prediction.	dataset 2015-11-06	Protein-protein bindingAntibody-antigen	Unclassified	Fully open	0
AbBiBench A framework using antibody–antigen complexes to evaluate affinity prediction and antibody redesign.	suite 2025-05-23	Life scienceProtein scienceProtein design+2	Unclassified	Fully open Provisional · medium	0
Anthropic Computational Biology Eval Private Anthropic computational-biology evaluation direction reported only through a model-trend chart, without public tasks, counts, or protocol details.	track 2026-01-11	Life scienceBioinformatics	Unclassified	Private or internal	1
Anthropic Key Life Sciences Evals An Anthropic private internal suite reported only through an official accuracy chart covering scientific figure interpretation, computational biology, and protein understanding.	suite 2026-01-11	Life scienceBioinformaticsProtein science	Unclassified	Private or internal	0
Anthropic Protein Understanding Eval Private Anthropic protein-understanding evaluation direction reported only through a model-trend chart, without public tasks, counts, or protocol details.	track 2026-01-11	Life scienceProtein science	Unclassified	Private or internal	1
Anthropic Scientific Figure Interpretation Eval Private Anthropic evaluation direction for scientific figure interpretation, reported only through a model-trend chart with no task count or released examples.	track 2026-01-11	Life scienceMolecular and cell biology	Scientific evidence interpretation	Private or internal	1
ATOM3D A living collection of eight curated 3D molecular-learning tasks spanning small molecules, protein interactions and mutations, ligand binding, and protein/RNA structure ranking.	suite 2020-12-07	Protein structureProtein-protein bindingProtein-ligand binding+1	Small-molecule property prediction Protein-protein interface prediction+6	Fully open	1
BEACON A 13-task RNA representation benchmark covering structure, function, processing, modification, translation, degradation, programmable switches, and CRISPR activity.	suite 2024-06-14	TranscriptomicsGenomicsMolecular and cell biology	RNA structure prediction RNA processing and translation prediction+6	Fully open	1
benchmark-dual human CRISPR-Cas9 library A human CRISPR-Cas9 paired-guide library created to compare dual- and single-targeting strategies in loss-of-function screens.	dataset 2025-02-26	GenomicsMolecular and cell biologyAssays and screening	Unclassified	Fully open	0
benchmark human CRISPR-Cas9 library A human CRISPR-Cas9 guide-RNA library assembled to compare single-targeting library performance in loss-of-function screens.	dataset 2025-02-26	GenomicsMolecular and cell biologyAssays and screening	Unclassified	Fully open	0
Biology-Instructions A multi-omics sequence-instruction suite with 21 formal predictive tasks across DNA, RNA, protein, and multi-molecule inputs; the final paper reports task-specific held-out evaluations rather than a single aggregate score.	suite 2024-12-26	GenomicsTranscriptomicsEpigenomics+5	Antibody-antigen interaction RNA processing and translation prediction+16	Partially open	0
Biology-Instructions Antibody-Antigen Neutralization Binary neutralization prediction for an antibody-antigen protein-sequence pair, evaluated with Matthews correlation coefficient.	track 2024-12-26	Protein sequenceProtein-protein bindingAntibody-antigen	Antibody-antigen interaction	Partially open	3
Biology-Instructions APA Isoform Prediction Regression of alternative-polyadenylation isoform usage from an RNA sequence, reported as squared Pearson correlation under the paper's R2 label.	track 2024-12-26	Transcriptomics	RNA processing and translation prediction	Partially open	3
Biology-Instructions Core Promoter Detection Binary detection of a core promoter in a short DNA sequence, evaluated with Matthews correlation coefficient.	track 2024-12-26	Genomics	Promoter detection	Partially open	3
Biology-Instructions CRISPR On-Target Prediction Regression of CRISPR guide on-target activity from an RNA sequence, evaluated with Spearman rank correlation.	track 2024-12-26	GenomicsTranscriptomics	CRISPR guide activity prediction	Partially open	3
Biology-Instructions Enhancer Activity Prediction Two-output regression of housekeeping and developmental enhancer activity from a DNA sequence, evaluated with separate Pearson correlations.	track 2024-12-26	GenomicsEpigenomicsAssays and screening	Enhancer activity prediction	Partially open	3
Biology-Instructions Enzyme Commission Number Prediction Multi-label Enzyme Commission number prediction from a protein sequence, evaluated with the creator's Fmax implementation.	track 2024-12-26	Protein sequenceProteomics	Protein function annotation	Partially open	3
Biology-Instructions Epigenetic Marks Prediction Binary prediction of whether a DNA sequence carries an epigenetic mark, evaluated with Matthews correlation coefficient.	track 2024-12-26	GenomicsEpigenomics	Epigenetic-mark prediction	Partially open	3
Biology-Instructions Enhancer-Promoter Interaction Prediction Binary interaction prediction for enhancer and promoter DNA sequences, evaluated with Matthews correlation coefficient.	track 2024-12-26	GenomicsEpigenomicsMolecular and cell biology	Enhancer-promoter interaction prediction	Partially open	3
Biology-Instructions Protein Fluorescence Prediction Regression of protein fluorescence from an amino-acid sequence, evaluated with Spearman rank correlation.	track 2024-12-26	Protein sequenceAssays and screening	Protein fluorescence prediction	Partially open	3
Biology-Instructions RNA Modification Prediction Multi-label prediction of RNA chemical modifications, evaluated with macro area under the ROC curve.	track 2024-12-26	TranscriptomicsEpigenomics	RNA modification prediction	Partially open	3
Biology-Instructions Mean Ribosome Loading Prediction Regression of mean ribosome loading from an RNA sequence, reported as squared Pearson correlation under the paper's R2 label.	track 2024-12-26	Transcriptomics	RNA processing and translation prediction	Partially open	3
Biology-Instructions Non-coding RNA Function Classification Thirteen-class functional classification of a non-coding RNA sequence, evaluated with exact extracted-label accuracy.	track 2024-12-26	Transcriptomics	RNA function classification	Partially open	3
Biology-Instructions Promoter Detection 300 Binary promoter detection in a 300-base-pair DNA context, evaluated with Matthews correlation coefficient.	track 2024-12-26	Genomics	Promoter detection	Partially open	3
Biology-Instructions Programmable RNA Switches Three-output regression of ON, OFF, and ON/OFF programmable RNA-switch values, aggregated as their mean squared Pearson correlation.	track 2024-12-26	TranscriptomicsMolecular and cell biology	RNA design	Partially open	3
Biology-Instructions RNA-Protein Interaction Prediction Binary interaction prediction for an RNA and protein sequence pair, evaluated with Matthews correlation coefficient.	track 2024-12-26	TranscriptomicsProtein sequenceRNA-protein binding+1	RNA-protein interaction prediction	Partially open	3
Biology-Instructions siRNA Efficiency Prediction Regression of siRNA efficiency from paired sequence context, evaluated with the SAIS-inspired mixed score.	track 2024-12-26	TranscriptomicsMulti-omics	siRNA efficacy prediction	Partially open	3
Biology-Instructions Protein Solubility Prediction Binary protein-solubility prediction from an amino-acid sequence, evaluated with accuracy.	track 2024-12-26	Protein sequence	Protein solubility prediction	Partially open	3
Biology-Instructions Protein Stability Prediction Regression of protein stability from an amino-acid sequence, evaluated with Spearman rank correlation.	track 2024-12-26	Protein sequence	Protein stability prediction	Partially open	3
Biology-Instructions Human Transcription Binding Sites Detection Binary detection of transcription-factor binding sites in human DNA sequences, evaluated with Matthews correlation coefficient.	track 2024-12-26	Genomics	Transcription-factor binding-site prediction	Partially open	3
Biology-Instructions Mouse Transcription Binding Sites Detection Binary detection of transcription-factor binding sites in mouse DNA sequences, evaluated with Matthews correlation coefficient.	track 2024-12-26	Genomics	Transcription-factor binding-site prediction	Partially open	3
Biology-Instructions Protein Thermostability Prediction Regression of protein thermostability from an amino-acid sequence, evaluated with Spearman rank correlation.	track 2024-12-26	Protein sequence	Protein stability prediction	Partially open	3
BioMysteryBench An agentic bioinformatics benchmark of objective, expert-authored mysteries over anonymized real-world biological data, scored on final answers rather than prescribed analysis paths.	agentic-eval 2026-04-29	Protein structureGenomicsTranscriptomics+7	End-to-end computational analysis Omics and cellular analysis	Partially open	3
BioSecBench-Surveillance Agentic evaluation of pathogen genomic-surveillance workflow selection and analysis from raw or near-raw sequencing data.	agentic-eval 2026-07-21	GenomicsBioinformatics	Unclassified	Partially open	3
BixBench A containerized benchmark of long-horizon bioinformatics analysis over real published notebooks and associated data, with open-answer and multiple-choice evaluation modes.	agentic-eval 2025-02-28	BioinformaticsGenomicsTranscriptomics+4	End-to-end computational analysis Omics and cellular analysis	Fully open	11
BLADE A cross-domain suite for discerning defensible analysis decisions and generating executable end-to-end analyses for open-ended scientific research questions; four of its twelve source questions are explicitly biological or ecological.	suite 2024-08-19	Life science	End-to-end computational analysis	Fully open	0
BLADE End-to-End Analysis Generation The BLADE track requiring a conceptual-variable specification, executable data-transformation function, and statistical-model function for each open-ended research question and dataset.	track 2024-08-19	Life science	End-to-end computational analysis	Fully open	2
BLADE Decision-Discrimination MCQ The BLADE track for selecting the most or least justifiable conceptual-variable and data-transformation decisions for a research question and dataset.	track 2024-08-19	Life science	Scientific evidence interpretation	Fully open	1
CaM benchmark A multistate protein sequence-design benchmark spanning CaM conformations and binding modes.	dataset 2024-07-11	Life scienceProtein scienceProtein sequence+3	Protein sequence design	Fully open	0
CAMEO Weekly, automated, independent, blind evaluation of registered macromolecular structure-prediction servers on complete PDB entries whose experimental structures are withheld during prediction.	competition 2012-01-01	Protein structureProtein-protein bindingProtein-ligand binding+1	Protein complex structure prediction Protein model quality assessment+1	Partially open	3
CASP Biennial blind community experiments that assess macromolecular structure, complex, ligand, and model-accuracy prediction against experimental structures withheld during prediction.	competition 1994-01-01	Protein structureProtein-protein bindingProtein-ligand binding+1	Protein monomer structure prediction Protein complex structure prediction+3	Partially open	0
CASP17 Immune Complexes Dedicated CASP17 category for blind prediction of antibody-antigen, nanobody-antigen, and T-cell receptor complex structures.	track 2026-04-28	Protein structureProtein-protein bindingAntibody-antigen	Antibody-antigen interaction	Partially open	0
CASP Protein-Ligand Prediction Formal CASP track for blind prediction of protein-ligand binding poses, binding affinity or rank, binding pockets, and pose confidence.	track 2024-05-01	Protein structureProtein-ligand bindingMedicinal chemistry	Protein-ligand pose prediction Protein-ligand binding affinity	Partially open	3
CASP Protein Monomers Formal CASP track assessing blind predictions of single-protein structures and post hoc protein evaluation units against withheld experimental coordinates.	track 1994-01-01	Protein structure	Protein monomer structure prediction	Partially open	1
CASP Protein Multimers Formal CASP track assessing blind protein-complex predictions, including overall folds, interfaces, stoichiometry-free phases, and model-selection phases.	track 2024-05-01	Protein structureProtein-protein bindingAntibody-antigen	Protein complex structure prediction Protein model quality assessment	Partially open	1
CompBioBench A 100-task agent benchmark of objectively gradable computational-biology problems requiring multi-step reasoning, bespoke code, tools, and real-world external resources.	agentic-eval 2026-04-06	Protein structureGenomicsTranscriptomics+5	End-to-end computational analysis Omics and cellular analysis	Partially open	9
Comprehensive benchmark of differential transcript usage analysis for bulk and single-cell RNA sequencing A reusable benchmark for comparing differential transcript usage detection tools across simulated and real transcriptomics data.	suite Provisional · medium 2025-09-11	TranscriptomicsSingle-cell	Unclassified	Fully open Provisional · medium	0
crafted experiments Real single-cell RNA-seq data augmented with known gene perturbations for comparing feature-selection methods.	suite 2025-01-07	Life scienceTranscriptomicsSingle-cell+1	Unclassified	Fully open	0
FLIP A supervised protein sequence-to-fitness benchmark that turns three experimental landscapes into 15 biologically motivated dataset splits for testing generalization in protein engineering.	suite 2021-10-11	Protein sequenceProtein designProtein-protein binding	Protein fitness prediction Protein mutation-effect prediction	Fully open	0
FLIP AAV Seven supervised splits over sampled and machine-designed AAV2 VP-1 capsid variants, measuring generalization across mutation depth, fitness, and sampled-versus-designed pools.	track 2021-10-11	Protein sequenceProtein design	Protein fitness prediction	Fully open	7
FLIP GB1 Five supervised splits over a downsampled, highly epistatic four-site GB1 immunoglobulin-binding landscape, designed to test mutation-depth and low-to-high-fitness generalization.	track 2021-10-11	Protein sequenceProtein-protein bindingProtein design	Protein fitness prediction	Fully open	5
FLIP Meltome Thermostability Three supervised sequence-to-melting-temperature splits spanning all species, human proteins, and a single human cell line, with sequence-cluster-aware train/test separation.	track 2021-10-11	Protein sequenceProtein designProteomics	Protein stability prediction	Fully open	3
GeneBench-Pro A research-level agent benchmark of 129 synthetic, multistage computational-biology analyses that require iterative QC, statistical modeling, diagnostics, and decision-relevant judgment.	agentic-eval 2026-06-30	GenomicsTranscriptomicsEpigenomics+6	End-to-end computational analysis Omics and cellular analysis	Partially open	13
Genomic Benchmarks A versioned collection of nine DNA sequence-classification datasets covering regulatory elements, promoters, enhancers, open chromatin, species, and coding-context discrimination.	suite 2023-05-01	GenomicsEpigenomics	Enhancer activity prediction Promoter detection+2	Fully open	1
GuacaMol A reproducible benchmark for de novo molecular design with five distribution-learning tests and twenty goal-directed generation problems in the current v2 suite.	suite 2018-11-23	Medicinal chemistry	Small-molecule generation	Fully open	1
LAB-Bench A practical biology-research suite of 2,457 multiple-choice questions across eight broad categories and 31 versioned task files, with public and private contamination-monitoring splits.	suite 2024-07-14	Life scienceMolecular and cell biologyAssays and screening+8	Scientific database retrieval Scientific evidence interpretation+3	Partially open	0
LAB-Bench CloningScenarios Human-hard, multi-step multiple-choice scenarios involving plasmids, DNA fragments, enzymes, and molecular-cloning workflows.	track 2024-07-14	Molecular and cell biologyGenomics	Experiment and protocol planning	Partially open	4
LAB-Bench DbQA Database-retrieval category spanning 10 genomics, clinical, protein, regulatory, vaccine-response, and viral-PPI tasks.	track 2024-07-14	BioinformaticsGenomicsTranscriptomics+5	Scientific database retrieval	Partially open	0
LAB-Bench DbQA — Disease gene associations Identifies genes associated with a phenotype in DisGeNET but not OMIM.	track 2024-07-14	GenomicsClinical and translationalBioinformatics	Scientific database retrieval	Partially open	1
LAB-Bench DbQA — Gene location Retrieves human-gene cytogenetic locations from the stated Ensembl release.	track 2024-07-14	GenomicsBioinformatics	Scientific database retrieval	Partially open	1
LAB-Bench DbQA — miRNA targets Retrieves computationally predicted human miRNA targets from miRDB.	track 2024-07-14	TranscriptomicsGenomicsBioinformatics	Scientific database retrieval	Partially open	1
LAB-Bench DbQA — Mouse tumor gene sets Retrieves genes in Mammalian Phenotype Tumor Ontology gene sets.	track 2024-07-14	GenomicsClinical and translationalBioinformatics	Scientific database retrieval	Partially open	1
LAB-Bench DbQA — Oncogenic signatures Retrieves membership in MSigDB C6 oncogenic-signature gene sets.	track 2024-07-14	GenomicsClinical and translationalBioinformatics	Scientific database retrieval	Partially open	1
LAB-Bench DbQA — GTRD transcription-factor binding sites Retrieves promoter-region transcription-factor binding-site annotations from GTRD.	track 2024-07-14	GenomicsEpigenomicsBioinformatics	Scientific database retrieval Transcription-factor binding-site prediction	Partially open	1
LAB-Bench DbQA — Protein variant from sequence Uses a protein sequence and ClinVar lookup to identify benign or pathogenic variants.	track 2024-07-14	Protein sequenceClinical and translationalBioinformatics	Scientific database retrieval Protein clinical variant interpretation	Partially open	1
LAB-Bench DbQA — Protein variant with multiple sequences Identifies ClinVar variant pathogenicity while reasoning across multiple protein sequences.	track 2024-07-14	Protein sequenceClinical and translationalBioinformatics	Scientific database retrieval Protein clinical variant interpretation	Partially open	1
LAB-Bench DbQA — Vaccine response gene sets Retrieves membership in MSigDB vaccine-response gene sets.	track 2024-07-14	TranscriptomicsClinical and translationalBioinformatics	Scientific database retrieval	Partially open	1
LAB-Bench DbQA — Viral protein–protein interactions Retrieves predicted human interaction partners of viral proteins from P-HIPSter.	track 2024-07-14	Protein-protein bindingProtein scienceVirology+1	Protein-protein interaction prediction Scientific database retrieval	Partially open	1
LAB-Bench FigQA Multiple-choice interpretation and multi-element reasoning over scientific figures shown without captions or paper context.	track 2024-07-14	Life scienceMolecular and cell biology	Scientific evidence interpretation	Partially open	5
LAB-Bench LitQA2 Literature-retrieval questions whose answers require findings in full research papers rather than titles or abstracts.	track 2024-07-14	Life science	Scientific evidence interpretation	Partially open	1
LAB-Bench ProtocolQA Troubleshoots intentionally modified published biological protocols by selecting steps that would repair the stated outcome.	track 2024-07-14	Assays and screeningMolecular and cell biology	Experiment and protocol planning	Partially open	4
LAB-Bench SeqQA Sequence-comprehension and manipulation category spanning 15 formal tasks involving PCR, restriction digestion, ORFs, translation, GC content, and DNA–protein relationships.	track 2024-07-14	GenomicsTranscriptomicsProtein sequence+1	DNA sequence design RNA processing and translation prediction	Partially open	1
LAB-Bench SeqQA — ORF amino-acid position Finds the amino acid encoded at a specified position in the longest ORF of a DNA sequence.	track 2024-07-14	GenomicsProtein sequence	RNA processing and translation prediction	Partially open	1
LAB-Bench SeqQA — ORF amino-acid sequence Translates the longest ORF in a DNA sequence to its amino-acid sequence.	track 2024-07-14	GenomicsProtein sequence	RNA processing and translation prediction	Partially open	1
LAB-Bench SeqQA — ORF count above length Counts open reading frames encoding proteins above a specified amino-acid length.	track 2024-07-14	GenomicsProtein sequence	RNA processing and translation prediction	Partially open	1
LAB-Bench SeqQA — Translation efficiency Selects an RNA sequence whose ORF context is most likely to yield high translation efficiency.	track 2024-07-14	TranscriptomicsProtein sequence	RNA processing and translation prediction	Partially open	1
LAB-Bench SeqQA — Gene-to-restriction primers Selects restriction-cloning primers from a named gene and enzyme pair.	track 2024-07-14	GenomicsMolecular and cell biology	DNA sequence design	Partially open	1
LAB-Bench SeqQA — Gene-to-Gibson primers (HindIII) Selects primers for Gibson assembly into a HindIII-linearized vector.	track 2024-07-14	GenomicsMolecular and cell biology	DNA sequence design	Partially open	1
LAB-Bench SeqQA — Gene-to-Gibson primers (SmaI) Selects primers for Gibson assembly into a SmaI-linearized vector.	track 2024-07-14	GenomicsMolecular and cell biology	DNA sequence design	Partially open	1
LAB-Bench SeqQA — Primers-to-restriction enzymes Infers restriction enzymes from a gene name and primer pair.	track 2024-07-14	GenomicsMolecular and cell biology	DNA sequence analysis	Partially open	1
LAB-Bench SeqQA — Amplicon length to primers Selects primers that produce a requested amplicon length from a DNA template.	track 2024-07-14	GenomicsMolecular and cell biology	DNA sequence design	Partially open	1
LAB-Bench SeqQA — Primers to amplicon length Calculates expected amplicon length from a primer pair and DNA template.	track 2024-07-14	GenomicsMolecular and cell biology	DNA sequence analysis	Partially open	1
LAB-Bench SeqQA — Sequence-to-restriction primers Selects restriction-cloning primers from an explicit gene sequence and enzyme pair.	track 2024-07-14	GenomicsMolecular and cell biology	DNA sequence design	Partially open	1
LAB-Bench SeqQA — Amplicon sequence to primers Selects primers that produce a requested amplicon sequence from a DNA template.	track 2024-07-14	GenomicsMolecular and cell biology	DNA sequence design	Partially open	1
LAB-Bench SeqQA — GC percentage Calculates the rounded GC percentage of a DNA sequence.	track 2024-07-14	Genomics	DNA sequence analysis	Partially open	1
LAB-Bench SeqQA — Restriction-fragment lengths Calculates fragment lengths after restriction digestion of a DNA sequence.	track 2024-07-14	GenomicsMolecular and cell biology	DNA sequence analysis	Partially open	1
LAB-Bench SeqQA — Restriction-fragment count Calculates the number of fragments after restriction digestion of a DNA sequence.	track 2024-07-14	GenomicsMolecular and cell biology	DNA sequence analysis	Partially open	1
LAB-Bench SuppQA Retrieval and interpretation questions answerable from paper supplementary text or PDF tables.	track 2024-07-14	Life science	Scientific evidence interpretation	Partially open	1
LAB-Bench TableQA Lookup, calculation, and reasoning questions over table images extracted from scientific papers.	track 2024-07-14	Life science	Scientific evidence interpretation	Partially open	1
LifeSciBench Expert-authored, artifact-rich free-response tasks that evaluate realistic research judgment across applied life-science workflows.	agentic-eval 2026-06-17	Life scienceProtein scienceProtein sequence+12	Protein design Protein-protein interaction prediction+1	Private or internal	1
MoleculeNet The original molecular-machine-learning benchmark of 17 dataset collections and more than 800 prediction endpoints spanning quantum, physicochemical, biophysical, and physiological properties.	suite 2017-03-02	Medicinal chemistryProtein-ligand bindingAssays and screening+1	Small-molecule property prediction ADMET and toxicity prediction+1	Fully open	1
PapD benchmark A multistate protein sequence-design benchmark targeting the multispecific PapD binding interface.	dataset 2024-07-11	Life scienceProtein scienceProtein sequence+3	Protein sequence design	Fully open	0
PPB-Affinity A reusable protein-protein binding-affinity dataset with complex structures, measured affinities, receptor and ligand chains, and mutation annotations.	dataset 2024-12-03	Protein-protein binding	Unclassified	Fully open	0
ProteinGym Versioned deep-mutational-scanning and clinical-variant benchmarks for protein fitness prediction and design in zero-shot and supervised regimes.	suite 2023-12-08	Protein sequenceProtein designProtein-ligand binding+1	Protein mutation-effect prediction Protein fitness prediction+2	Fully open	0
ProteinGym Clinical Indels ProteinGym track for classifying short human clinical insertion and deletion variants against ClinVar and gnomAD-derived labels.	track 2023-12-08	Protein sequenceClinical and translational	Protein clinical variant interpretation	Fully open	0
ProteinGym Clinical Substitutions ProteinGym track for classifying expert-annotated human clinical substitution variants on a per-protein basis.	track 2023-12-08	Protein sequenceClinical and translational	Protein clinical variant interpretation	Fully open	0
ProteinGym DMS Indels ProteinGym track for predicting experimental fitness measurements of insertion and deletion mutants across deep-mutational-scanning assays.	track 2023-12-08	Protein sequenceProtein design	Protein mutation-effect prediction Protein fitness prediction	Fully open	0
ProteinGym DMS Substitutions ProteinGym track for predicting experimental fitness measurements of substitution mutants across deep-mutational-scanning assays.	track 2023-12-08	Protein sequenceProtein designProtein-ligand binding	Protein mutation-effect prediction Protein fitness prediction	Fully open	1
ProteinLMBench A creator-curated set of 944 protein-science multiple-choice questions with answer explanations, generated from research literature and released for evaluating text LLM protein understanding.	dataset 2024-04-29	Protein scienceProtein sequenceProtein structure+3	Protein structure prediction Protein design+1	Fully open	1
RfaH benchmark A multistate protein sequence-design benchmark using the fold-switching conformations of RfaH.	dataset 2024-07-11	Life scienceProtein scienceProtein sequence+2	Protein sequence design	Fully open	0
scBench Agentic evaluation suite for data-grounded single-cell analysis across diverse sequencing technologies and workflow stages.	agentic-eval 2026-02-09	Life scienceTranscriptomicsSingle-cell+1	Unclassified	Partially open	0
scIB A 13-task benchmark of single-cell data integration across simulated, scRNA-seq, and scATAC-seq settings, evaluated with 14 batch-removal and biological-conservation metrics.	suite 2021-12-23	Single-cellTranscriptomicsEpigenomics	Single-cell data integration	Fully open	1
SCIGYM An agentic systems-biology suite in which language models iteratively perturb simulated SBML systems, analyze time-series observations in Python, and reconstruct hidden biological reactions.	suite 2025-05-16	Life scienceMolecular and cell biologyBioinformatics	Reaction-network reconstruction Simulation-based experiment	Fully open	0
SCIGYM Large The formally released SCIGYM track containing the 213 systems not included in the creator paper's model evaluation, with systems reaching up to 400 reactions.	track 2025-05-16	Life scienceMolecular and cell biologyBioinformatics	Reaction-network reconstruction Simulation-based experiment	Fully open	0
SCIGYM Small The formally released and creator-evaluated SCIGYM track containing biological systems with fewer than ten reactions.	track 2025-05-16	Life scienceMolecular and cell biologyBioinformatics	Reaction-network reconstruction Simulation-based experiment	Fully open	2
Single-cell Omics Arena A benchmark for evaluating LLM cell-type annotation across scRNA-seq and single-cell multiomics data.	suite 2025-11-24	TranscriptomicsSingle-cellMulti-omics+1	Cell-type annotation	Partially open Conflicted · high	2
SpatialBench A benchmark of deterministic, verifiable agentic problems derived from real spatial-transcriptomics workflows, testing whether agents can manipulate data and recover key biological results.	agentic-eval 2025-12-26	Spatial omicsTranscriptomicsSingle-cell+1	Cell-type annotation Cell-state clustering+2	Partially open	7
TAPE A five-task benchmark for protein representation learning spanning secondary structure, residue contacts, remote homology, fluorescence, and stability.	suite 2019-06-19	Protein sequenceProtein structureProtein design	Protein secondary-structure prediction Protein contact-map prediction+3	Fully open	1
VirBench Retrieval benchmark that tests whether scientific agents can answer verified viral-sequence questions by querying NCBI Virus.	agentic-eval 2025-05-20	VirologyGenomicsBioinformatics	Unclassified	Metadata only	1

AB-Bind

Antibody-focused mutational binding data with accompanying structures for computational affinity prediction.

dataset2015-11-06Fully open

Evaluation runs0

Latest versioninitial-release

AbBiBench

A framework using antibody–antigen complexes to evaluate affinity prediction and antibody redesign.

suite2025-05-23Fully open Provisional · medium

Evaluation runs0

Latest versioninitial-release

Anthropic Computational Biology Eval

Private Anthropic computational-biology evaluation direction reported only through a model-trend chart, without public tasks, counts, or protocol details.

track2026-01-11Private or internal

Evaluation runs1

Latest versionreported-2026-01-11

Anthropic Key Life Sciences Evals

An Anthropic private internal suite reported only through an official accuracy chart covering scientific figure interpretation, computational biology, and protein understanding.

suite2026-01-11Private or internal

Evaluation runs0

Latest versionreported-2026-01-11

Anthropic Protein Understanding Eval

Private Anthropic protein-understanding evaluation direction reported only through a model-trend chart, without public tasks, counts, or protocol details.

track2026-01-11Private or internal

Evaluation runs1

Latest versionreported-2026-01-11

Anthropic Scientific Figure Interpretation Eval

Private Anthropic evaluation direction for scientific figure interpretation, reported only through a model-trend chart with no task count or released examples.

track2026-01-11Private or internal

Evaluation runs1

Latest versionreported-2026-01-11

ATOM3D

A living collection of eight curated 3D molecular-learning tasks spanning small molecules, protein interactions and mutations, ligand binding, and protein/RNA structure ranking.

suite2020-12-07Fully open

Evaluation runs1

Latest versionv0.2.6

BEACON

A 13-task RNA representation benchmark covering structure, function, processing, modification, translation, degradation, programmable switches, and CRISPR activity.

suite2024-06-14Fully open

Evaluation runs1

Latest versionneurips-2024

benchmark-dual human CRISPR-Cas9 library

A human CRISPR-Cas9 paired-guide library created to compare dual- and single-targeting strategies in loss-of-function screens.

dataset2025-02-26Fully open

Evaluation runs0

Latest versioninitial-release

benchmark human CRISPR-Cas9 library

A human CRISPR-Cas9 guide-RNA library assembled to compare single-targeting library performance in loss-of-function screens.

dataset2025-02-26Fully open

Evaluation runs0

Latest versioninitial-release

A multi-omics sequence-instruction suite with 21 formal predictive tasks across DNA, RNA, protein, and multi-molecule inputs; the final paper reports task-specific held-out evaluations rather than a single aggregate score.

suite2024-12-26Partially open

Evaluation runs0

Latest versionemnlp-2025

Biology-Instructions Antibody-Antigen Neutralization

Binary neutralization prediction for an antibody-antigen protein-sequence pair, evaluated with Matthews correlation coefficient.

track2024-12-26Partially open

Evaluation runs3

Latest versionemnlp-2025

Biology-Instructions APA Isoform Prediction

Regression of alternative-polyadenylation isoform usage from an RNA sequence, reported as squared Pearson correlation under the paper's R2 label.

track2024-12-26Partially open

Evaluation runs3

Latest versionemnlp-2025

Biology-Instructions Core Promoter Detection

Binary detection of a core promoter in a short DNA sequence, evaluated with Matthews correlation coefficient.

track2024-12-26Partially open

Evaluation runs3

Latest versionemnlp-2025

Biology-Instructions CRISPR On-Target Prediction

Regression of CRISPR guide on-target activity from an RNA sequence, evaluated with Spearman rank correlation.

track2024-12-26Partially open

Evaluation runs3

Latest versionemnlp-2025

Biology-Instructions Enhancer Activity Prediction

Two-output regression of housekeeping and developmental enhancer activity from a DNA sequence, evaluated with separate Pearson correlations.

track2024-12-26Partially open

Evaluation runs3

Latest versionemnlp-2025

Biology-Instructions Enzyme Commission Number Prediction

Multi-label Enzyme Commission number prediction from a protein sequence, evaluated with the creator's Fmax implementation.

track2024-12-26Partially open

Evaluation runs3

Latest versionemnlp-2025

Biology-Instructions Epigenetic Marks Prediction

Binary prediction of whether a DNA sequence carries an epigenetic mark, evaluated with Matthews correlation coefficient.

track2024-12-26Partially open

Evaluation runs3

Latest versionemnlp-2025

Biology-Instructions Enhancer-Promoter Interaction Prediction

Binary interaction prediction for enhancer and promoter DNA sequences, evaluated with Matthews correlation coefficient.

track2024-12-26Partially open

Evaluation runs3

Latest versionemnlp-2025

Biology-Instructions Protein Fluorescence Prediction

Regression of protein fluorescence from an amino-acid sequence, evaluated with Spearman rank correlation.

track2024-12-26Partially open

Evaluation runs3

Latest versionemnlp-2025

Biology-Instructions RNA Modification Prediction

Multi-label prediction of RNA chemical modifications, evaluated with macro area under the ROC curve.

track2024-12-26Partially open

Evaluation runs3

Latest versionemnlp-2025

Biology-Instructions Mean Ribosome Loading Prediction

Regression of mean ribosome loading from an RNA sequence, reported as squared Pearson correlation under the paper's R2 label.

track2024-12-26Partially open

Evaluation runs3

Latest versionemnlp-2025

Biology-Instructions Non-coding RNA Function Classification

Thirteen-class functional classification of a non-coding RNA sequence, evaluated with exact extracted-label accuracy.

track2024-12-26Partially open

Evaluation runs3

Latest versionemnlp-2025

Biology-Instructions Promoter Detection 300

Binary promoter detection in a 300-base-pair DNA context, evaluated with Matthews correlation coefficient.

track2024-12-26Partially open

Evaluation runs3

Latest versionemnlp-2025

Biology-Instructions Programmable RNA Switches

Three-output regression of ON, OFF, and ON/OFF programmable RNA-switch values, aggregated as their mean squared Pearson correlation.

track2024-12-26Partially open

Evaluation runs3

Latest versionemnlp-2025

Biology-Instructions RNA-Protein Interaction Prediction

Binary interaction prediction for an RNA and protein sequence pair, evaluated with Matthews correlation coefficient.

track2024-12-26Partially open

Evaluation runs3

Latest versionemnlp-2025

Biology-Instructions siRNA Efficiency Prediction

Regression of siRNA efficiency from paired sequence context, evaluated with the SAIS-inspired mixed score.

track2024-12-26Partially open

Evaluation runs3

Latest versionemnlp-2025

Biology-Instructions Protein Solubility Prediction

Binary protein-solubility prediction from an amino-acid sequence, evaluated with accuracy.

track2024-12-26Partially open

Evaluation runs3

Latest versionemnlp-2025

Biology-Instructions Protein Stability Prediction

Regression of protein stability from an amino-acid sequence, evaluated with Spearman rank correlation.

track2024-12-26Partially open

Evaluation runs3

Latest versionemnlp-2025

Biology-Instructions Human Transcription Binding Sites Detection

Binary detection of transcription-factor binding sites in human DNA sequences, evaluated with Matthews correlation coefficient.

track2024-12-26Partially open

Evaluation runs3

Latest versionemnlp-2025

Biology-Instructions Mouse Transcription Binding Sites Detection

Binary detection of transcription-factor binding sites in mouse DNA sequences, evaluated with Matthews correlation coefficient.

track2024-12-26Partially open

Evaluation runs3

Latest versionemnlp-2025

Biology-Instructions Protein Thermostability Prediction

Regression of protein thermostability from an amino-acid sequence, evaluated with Spearman rank correlation.

track2024-12-26Partially open

Evaluation runs3

Latest versionemnlp-2025

BioMysteryBench

An agentic bioinformatics benchmark of objective, expert-authored mysteries over anonymized real-world biological data, scored on final answers rather than prescribed analysis paths.

agentic-eval2026-04-29Partially open

Evaluation runs3

Latest versionv11

BioSecBench-Surveillance

Agentic evaluation of pathogen genomic-surveillance workflow selection and analysis from raw or near-raw sequencing data.

agentic-eval2026-07-21Partially open

Evaluation runs3

Latest versioninitial-release

BixBench

A containerized benchmark of long-horizon bioinformatics analysis over real published notebooks and associated data, with open-answer and multiple-choice evaluation modes.

agentic-eval2025-02-28Fully open

Evaluation runs11

Latest versionv1.5

BLADE

A cross-domain suite for discerning defensible analysis decisions and generating executable end-to-end analyses for open-ended scientific research questions; four of its twelve source questions are explicitly biological or ecological.

suite2024-08-19Fully open

Evaluation runs0

Latest versionarXiv v3

BLADE End-to-End Analysis Generation

The BLADE track requiring a conceptual-variable specification, executable data-transformation function, and statistical-model function for each open-ended research question and dataset.

track2024-08-19Fully open

Evaluation runs2

Latest versionarXiv v3

BLADE Decision-Discrimination MCQ

The BLADE track for selecting the most or least justifiable conceptual-variable and data-transformation decisions for a research question and dataset.

track2024-08-19Fully open

Evaluation runs1

Latest versionarXiv v3

CaM benchmark

A multistate protein sequence-design benchmark spanning CaM conformations and binding modes.

dataset2024-07-11Fully open

Evaluation runs0

Latest versioninitial-release

CAMEO

Weekly, automated, independent, blind evaluation of registered macromolecular structure-prediction servers on complete PDB entries whose experimental structures are withheld during prediction.

competition2012-01-01Partially open

Evaluation runs3

Latest versioncurrent-complex-3d

CASP

Biennial blind community experiments that assess macromolecular structure, complex, ligand, and model-accuracy prediction against experimental structures withheld during prediction.

competition1994-01-01Partially open

Evaluation runs0

Latest versionCASP17

CASP17 Immune Complexes

Dedicated CASP17 category for blind prediction of antibody-antigen, nanobody-antigen, and T-cell receptor complex structures.

track2026-04-28Partially open

Evaluation runs0

Latest versionCASP17

CASP Protein-Ligand Prediction

Formal CASP track for blind prediction of protein-ligand binding poses, binding affinity or rank, binding pockets, and pose confidence.

track2024-05-01Partially open

Evaluation runs3

Latest versionCASP17

CASP Protein Monomers

Formal CASP track assessing blind predictions of single-protein structures and post hoc protein evaluation units against withheld experimental coordinates.

track1994-01-01Partially open

Evaluation runs1

Latest versionCASP17

CASP Protein Multimers

Formal CASP track assessing blind protein-complex predictions, including overall folds, interfaces, stoichiometry-free phases, and model-selection phases.

track2024-05-01Partially open

Evaluation runs1

Latest versionCASP17

CompBioBench

A 100-task agent benchmark of objectively gradable computational-biology problems requiring multi-step reasoning, bespoke code, tools, and real-world external resources.

agentic-eval2026-04-06Partially open

Evaluation runs9

Latest versionv1

Comprehensive benchmark of differential transcript usage analysis for bulk and single-cell RNA sequencing

A reusable benchmark for comparing differential transcript usage detection tools across simulated and real transcriptomics data.

suite Provisional · medium2025-09-11Fully open Provisional · medium

Evaluation runs0

Latest versioninitial-release

crafted experiments

Real single-cell RNA-seq data augmented with known gene perturbations for comparing feature-selection methods.

suite2025-01-07Fully open

Evaluation runs0

Latest versioninitial-release

FLIP

A supervised protein sequence-to-fitness benchmark that turns three experimental landscapes into 15 biologically motivated dataset splits for testing generalization in protein engineering.

suite2021-10-11Fully open

Evaluation runs0

Latest versionoriginal-2021

FLIP AAV

Seven supervised splits over sampled and machine-designed AAV2 VP-1 capsid variants, measuring generalization across mutation depth, fitness, and sampled-versus-designed pools.

track2021-10-11Fully open

Evaluation runs7

Latest versionoriginal-2021

FLIP GB1

Five supervised splits over a downsampled, highly epistatic four-site GB1 immunoglobulin-binding landscape, designed to test mutation-depth and low-to-high-fitness generalization.

track2021-10-11Fully open

Evaluation runs5

Latest versionoriginal-2021

FLIP Meltome Thermostability

Three supervised sequence-to-melting-temperature splits spanning all species, human proteins, and a single human cell line, with sequence-cluster-aware train/test separation.

track2021-10-11Fully open

Evaluation runs3

Latest versionoriginal-2021

GeneBench-Pro

A research-level agent benchmark of 129 synthetic, multistage computational-biology analyses that require iterative QC, statistical modeling, diagnostics, and decision-relevant judgment.

agentic-eval2026-06-30Partially open

Evaluation runs13

Latest versionpaper-v1

Genomic Benchmarks

A versioned collection of nine DNA sequence-classification datasets covering regulatory elements, promoters, enhancers, open chromatin, species, and coding-context discrimination.

suite2023-05-01Fully open

Evaluation runs1

Latest versionpackage-1.0.0-snapshot

GuacaMol

A reproducible benchmark for de novo molecular design with five distribution-learning tests and twenty goal-directed generation problems in the current v2 suite.

suite2018-11-23Fully open

Evaluation runs1

Latest versionsuite-v2

LAB-Bench

A practical biology-research suite of 2,457 multiple-choice questions across eight broad categories and 31 versioned task files, with public and private contamination-monitoring splits.

suite2024-07-14Partially open

Evaluation runs0