{"id":"W4412143524","doi":"10.1101/2025.07.05.663295","title":"PromptBio: A Multi-Agent AI Platform for Bioinformatics Data Analysis","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Gene expression and cancer classification","field":"Biochemistry, Genetics and Molecular Biology","cited_by":8,"is_retracted":false,"has_abstract":true,"ca_institutions":"Prompt (Canada)","funders":"","keywords":"Computer science; Computational biology; Bioinformatics; Biology","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.000513555,0.0004594007,0.0004818337,0.0003656262,0.0001662771,0.0001843867,0.001327381,0.0006659123,0.00001422348],"category_scores_gemma":[0.0002206829,0.0004643681,0.0002771507,0.0005561903,0.00006972361,0.0000175083,0.001415099,0.000302189,0.000009145628],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00009218319,"about_ca_system_score_gemma":0.0009241919,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001811283,"about_ca_topic_score_gemma":0.00001318896,"domain_scores_codex":[0.9974992,0.00004238177,0.0006322768,0.001164166,0.0002452697,0.0004166825],"domain_scores_gemma":[0.9954081,0.00001494653,0.0004626244,0.003424615,0.0005003161,0.0001893637],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.0001502032,0.0003790522,0.004365488,0.00122908,0.002836431,0.000002031479,0.0000176846,0.0008127947,0.9680387,0.0002000415,0.0219202,0.00004825752],"study_design_scores_gemma":[0.001671925,0.000110018,0.01696167,0.0002757027,0.002015674,6.931234e-9,0.00001835047,0.06504647,0.6376455,0.000001949272,0.2748231,0.001429706],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.1010549,0.002705711,0.8818851,0.000623757,0.001988336,0.003107136,0.008363429,0.0002435237,0.00002810169],"genre_scores_gemma":[0.9061375,0.0008097407,0.09019625,0.001000343,0.0005108324,0.0009036254,0.0001892561,0.00008340937,0.0001691001],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.8050825,"threshold_uncertainty_score":0.9997808,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03950044942999849,"score_gpt":0.2929468059211738,"score_spread":0.2534463564911754,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}