{"id":"W4411488407","doi":"10.1101/2025.06.14.659567","title":"Scoring gene importance by interpreting single-cell foundation models","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Single-cell and spatial transcriptomics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"Roche (Canada)","funders":"","keywords":"Foundation (evidence); Attribution; Psychology; Computational biology; Computer science; Biology; Social psychology; Geography","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.003326024,0.0008010815,0.0006658143,0.002527836,0.0004145363,0.002182879,0.001107197,0.0007021219,0.002628624],"category_scores_gemma":[0.009077584,0.0003268244,0.001012358,0.001883617,0.0009523927,0.001013224,0.001657365,0.000951062,0.0007887777],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0008287773,"about_ca_system_score_gemma":0.001007483,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001741663,"about_ca_topic_score_gemma":0.00237037,"domain_scores_codex":[0.9987173,0.000339416,0.00007556563,0.0003115013,0.0004463893,0.0001099124],"domain_scores_gemma":[0.9955819,0.002216052,0.0006103268,0.0008052205,0.0004936755,0.0002927188],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.001102203,0.0001352987,0.09321105,0.0007801788,0.0004250163,0.001138914,0.0004031277,0.5978101,0.110252,0.06567275,0.00918955,0.1198797],"study_design_scores_gemma":[0.00001720012,0.00006224977,0.006448433,0.00002325623,0.00004662741,0.0002314473,0.00008633504,0.9157476,0.01852343,0.05484741,0.003928325,0.00003768211],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.1925986,0.0004459874,0.7930575,0.0002575028,0.0001169412,0.00008605618,0.00463522,0.005719488,0.003082632],"genre_scores_gemma":[0.8222026,0.0003599369,0.1696724,0.0001339667,0.00005755212,0.0001335799,0.005257009,0.0008311398,0.001351934],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.003326024,"threshold_uncertainty_score":0.01758993,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01448750407037082,"score_gpt":0.2113571217096481,"score_spread":0.1968696176392773,"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."}}