{"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":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0002413196,0.000287509,0.0004549581,0.0001992946,0.0000838253,0.0000114098,0.0002736516,0.0003100174,0.00002789824],"category_scores_gemma":[0.00005724489,0.0002829639,0.0001744131,0.0003097253,0.000259829,0.00001018899,0.00005263627,0.00009755751,0.000007403551],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001717039,"about_ca_system_score_gemma":0.0001669821,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00006257514,"about_ca_topic_score_gemma":0.00001919791,"domain_scores_codex":[0.9982054,0.0001026355,0.0005885178,0.000552705,0.0001049798,0.0004457452],"domain_scores_gemma":[0.9990442,0.0000293296,0.0001479441,0.0003795295,0.000216348,0.0001826623],"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":[0.0002577998,0.0001495188,0.01000545,0.0003032209,0.00006835374,0.000002715208,0.0001875036,0.001011553,0.98731,0.00006463011,0.0000968105,0.0005424252],"study_design_scores_gemma":[0.003641067,0.00176016,0.005695743,0.00006167781,0.0002917447,0.00001550984,0.0003440664,0.004672109,0.9726673,0.002199764,0.007675378,0.0009754974],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9839767,0.01201779,0.002595376,0.0001009421,0.0004753705,0.000244834,0.0001329713,0.00004047341,0.0004155676],"genre_scores_gemma":[0.9947739,0.003728576,0.0003473911,0.0000929116,0.0001473716,0.00001171857,0.0005107527,0.00004362721,0.0003438066],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01464273,"threshold_uncertainty_score":0.9999623,"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."}}