BioMysteryBench-full

BioMysteryBench (full set) 90 mystery-bioinformatics problems. Each problem provides anonymized biological data files and asks a question that requires real analysis (alignment, expression, variant calling, motif discovery, structure, etc.) to answer — the source dataset cannot be looked up. v11 (2026-07): 9 problems removed and 24 problems edited after an answer-key audit — see CHANGELOG.md. Contents problems.csv / problems.parquet — one row per problem: id — problem identifier question — the task prompt shown to the model answer_rubric — the grading criterion (contains the expected answer) allowed_domains — network domains the solving environment may reach human_solvable — yes if at least one human benchmarker solved it, no if none did data/ .zip — each problem's data files; extract into the working directory before solving Rules Looking up GEO/SRA/ENA/BioProject accession IDs to identify the original dataset, source publication, or study metadata is not allowed. Standard bioinformatics database use (gene ID lookup, sequence annotation, reference genome download, BLAST) is allowed. License and terms of use Problem statements, rubrics, and task formulation are released under CC BY 4.0. Access is conditioned on agreeing not to use these benchmark materials to train, fine-tune, or distill machine-learning models. The data/ archives are anonymized derivatives of public-archive submissions and remain subject to their original repositories' data-use policies. See LICENSE. Problems in this set id human_solvable question hb001 yes Which organ is this cell type single-cell RNA-seq dataset derived from?… hb002 yes What bacteria is found in this sequenced dataset? Provide the bacteria's scientific name as the answ… hb003 yes Name one gene that was knocked out in the experimental sample compared to the control samples. Provi… hb008 yes What mouse reference genome were the RNA-seq reads aligned to? Provide the genome assembly name (e.g… hb009 yes What genetic disease does Samp