{"id":"W4412615070","doi":"10.1186/s13059-025-03682-8","title":"Joint representation and visualization of derailed cell states with Decipher","year":2025,"lang":"en","type":"article","venue":"Genome biology","topic":"Single-cell and spatial transcriptomics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":6,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Montréal; Centre Hospitalier Universitaire Sainte-Justine","funders":"National Cancer Institute; Fonds de Recherche du Québec - Santé; Marie-Josée and Henry R. Kravis Center for Molecular Oncology; Alan and Sandra Gerry Metastasis and Tumor Ecosystems Center; Chan Zuckerberg Initiative; Howard Hughes Medical Institute","keywords":"DECIPHER; Biology; Visualization; Human genetics; Genome Biology; Computational biology; Evolutionary biology; Representation (politics); Joint (building); Genome; Bioinformatics; Genetics; Genomics; Computer science; Artificial intelligence; Engineering; Gene","routes":{"ca_aff":true,"ca_fund":true,"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":[0.0003241622,0.00037664,0.0003233896,0.000442102,0.0001685745,0.000656244,0.0003974798,0.0004465309,0.001514421],"category_scores_gemma":[0.0007720367,0.0002676522,0.0004353097,0.0003172222,0.0004300606,0.00052247,0.0009290534,0.0005818997,0.0002656527],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004825005,"about_ca_system_score_gemma":0.0005185162,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002403934,"about_ca_topic_score_gemma":0.005368141,"domain_scores_codex":[0.9999236,0.00001574213,0.000003512464,0.00003003552,0.00001683076,0.00001033371],"domain_scores_gemma":[0.9998387,0.00007326076,0.00002299352,0.00003638025,0.00001360467,0.00001505574],"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":[0.0003629417,0.00007135679,0.01450938,0.0002015003,0.0001592917,0.0004004441,0.0004582228,0.6222516,0.2274915,0.02700577,0.003848443,0.1032395],"study_design_scores_gemma":[0.000006257262,0.00001757147,0.002230072,0.000007092761,0.00000891432,0.00008380888,0.00003863314,0.9590967,0.0217173,0.01509637,0.001682096,0.00001515631],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.2116821,0.0004047447,0.7777479,0.0005020466,0.00003816534,0.00003052145,0.00253754,0.005570962,0.001486054],"genre_scores_gemma":[0.8442782,0.0004110798,0.1511602,0.0001160587,0.00001445023,0.00006824273,0.002035638,0.000492529,0.001423652],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.002403934,"threshold_uncertainty_score":0.005066276,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01055773315096001,"score_gpt":0.2520563304314073,"score_spread":0.2414985972804473,"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."}}