{"id":"W4385985668","doi":"10.1186/s13059-023-03034-4","title":"GTM-decon: guided-topic modeling of single-cell transcriptomes enables sub-cell-type and disease-subtype deconvolution of bulk transcriptomes","year":2023,"lang":"en","type":"article","venue":"Genome biology","topic":"Single-cell and spatial transcriptomics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":14,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University","funders":"Canada First Research Excellence Fund; Natural Sciences and Engineering Research Council of Canada; Canada Research Chairs","keywords":"Transcriptome; Deconvolution; Computational biology; Cell type; Biology; Phenotype; Cell; Gene; Type (biology); Gene expression; Computer science; Genetics; Algorithm","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":[0.001826814,0.001281207,0.001131515,0.0007283703,0.0005036125,0.001138565,0.001146955,0.001266461,0.00144826],"category_scores_gemma":[0.004004451,0.0005843945,0.002515125,0.000704413,0.0007204661,0.0009035467,0.001366226,0.001885521,0.001031057],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0007074448,"about_ca_system_score_gemma":0.001259157,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.005609105,"about_ca_topic_score_gemma":0.01173729,"domain_scores_codex":[0.9995141,0.0001461984,0.0000222162,0.000196701,0.00007036592,0.00005037522],"domain_scores_gemma":[0.9988925,0.0006858016,0.0000711097,0.0001658717,0.0001227595,0.00006201595],"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":[0.0009202185,0.0002156748,0.01770623,0.0005910459,0.0008403559,0.000491086,0.0009026256,0.5821177,0.1496012,0.02066568,0.0120155,0.2139327],"study_design_scores_gemma":[0.00002037409,0.00004275729,0.001673168,0.00001513443,0.00004611619,0.00008727396,0.00005490778,0.9694672,0.01224036,0.01341797,0.002900241,0.00003439366],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.03131478,0.0004223036,0.9637029,0.0001551201,0.00004551783,0.00004418022,0.0009306304,0.002915503,0.0004690295],"genre_scores_gemma":[0.4657464,0.000756501,0.515454,0.0005748728,0.000143397,0.0005728232,0.009007315,0.003027296,0.004717437],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.005609105,"threshold_uncertainty_score":0.01115286,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03242862360646157,"score_gpt":0.2400454751686547,"score_spread":0.2076168515621931,"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."}}