{"id":"W4408007273","doi":"10.1101/2025.02.21.639356","title":"Generative and integrative modeling for transcriptomics with formalin fixed paraffin embedded material","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Molecular Biology Techniques and Applications","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Sunnybrook Health Science Centre; Western University","funders":"","keywords":"Generative grammar; Computer science; Artificial intelligence","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":[0.003890653,0.001071831,0.0009493116,0.001167649,0.0007046782,0.001570376,0.002174325,0.001650539,0.002768886],"category_scores_gemma":[0.006788875,0.001025124,0.002860929,0.001201034,0.001649404,0.0009292499,0.001527798,0.002204925,0.0008029002],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.002171951,"about_ca_system_score_gemma":0.001174901,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.01446436,"about_ca_topic_score_gemma":0.02291698,"domain_scores_codex":[0.999136,0.0003609113,0.00003284648,0.0002745558,0.0001251649,0.00007051607],"domain_scores_gemma":[0.9964485,0.002726782,0.0002529775,0.0002535395,0.0001915615,0.0001265606],"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":[0.00006253286,0.00003382599,0.002127837,0.00006349514,0.0001366516,0.000125909,0.0001338473,0.9469768,0.002585152,0.0354917,0.001365342,0.01089682],"study_design_scores_gemma":[0.000004216378,0.00000518009,0.0002937433,0.0000051789,0.000008795368,0.00001647116,0.00000797579,0.9775588,0.0003102207,0.02114064,0.0006413157,0.000007552845],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.01591323,0.0002619858,0.9815843,0.0003379254,0.00004047629,0.00004351235,0.0006451878,0.0006162355,0.0005571483],"genre_scores_gemma":[0.5361825,0.00121339,0.4423275,0.0008590683,0.0003559009,0.0008777334,0.007478785,0.001320014,0.009385125],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.01446436,"threshold_uncertainty_score":0.02876031,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01008743094832873,"score_gpt":0.2382483208777783,"score_spread":0.2281608899294496,"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."}}