{"id":"W4284894578","doi":"10.1186/s13059-022-02716-9","title":"scSTEM: clustering pseudotime ordered single-cell data","year":2022,"lang":"en","type":"article","venue":"Genome biology","topic":"Single-cell and spatial transcriptomics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":9,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University","funders":"National Cancer Institute; National Institutes of Health","keywords":"Biology; Human genetics; Cluster analysis; Computational biology; Genome Biology; Evolutionary biology; Computational genomics; Genetics; Genomics; Computer science; Artificial intelligence; Genome; Gene","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002739317,0.0001978455,0.0002110531,0.00006168675,0.000265677,0.00002075253,0.0009843077,0.0001332797,0.0003140913],"category_scores_gemma":[0.00002260243,0.0002102637,0.000069036,0.0001187,0.00009151317,0.000003823954,0.001273232,0.0001720365,0.00003319902],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003432241,"about_ca_system_score_gemma":0.00008395221,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00006267949,"about_ca_topic_score_gemma":0.00005809599,"domain_scores_codex":[0.9983516,0.0001671491,0.0002756703,0.0007043766,0.00008465205,0.0004165905],"domain_scores_gemma":[0.9987888,0.00001411531,0.0000951043,0.0009836924,0.00003384338,0.00008441571],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0001170303,0.0001570005,0.001256461,0.00001571203,0.0000395646,0.00000545743,0.00004399508,0.0002599336,0.9957513,0.00001615704,0.0007179976,0.001619437],"study_design_scores_gemma":[0.00148936,0.001433935,0.0004120221,0.00000235092,0.00003947158,0.000106295,0.0001614672,0.0008271757,0.0311242,0.00005749144,0.9637644,0.0005818049],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9792434,0.003773158,0.00937986,0.0003853221,0.001344598,0.0003599106,0.000750577,0.00006450652,0.004698648],"genre_scores_gemma":[0.9917972,0.0000847905,0.001542076,0.0006775003,0.0003899927,0.00002601823,0.003649265,0.00004408238,0.001789077],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.964627,"threshold_uncertainty_score":0.8574305,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04464286254573301,"score_gpt":0.2457821154735761,"score_spread":0.2011392529278431,"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."}}