{"id":"W2081112743","doi":"10.1089/106652703322756195","title":"A Transition Probability Model for Amino Acid Substitutions from Blocks","year":2003,"lang":"en","type":"article","venue":"Journal of Computational Biology","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":140,"is_retracted":false,"has_abstract":true,"ca_institutions":"University Health Network; Ontario Institute for Cancer Research","funders":"","keywords":"Substitution (logic); Sequence (biology); Distance matrices in phylogeny; Sequence alignment; Function (biology); Stochastic matrix; Matrix (chemical analysis); Protein sequencing; Computer science; Protein evolution; Algorithm; Evolutionary algorithm; Mathematics; Peptide sequence; Combinatorics; Biology; Genetics; Artificial intelligence; Machine learning; Chemistry","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":[0.00198656,0.0007196104,0.001650901,0.001635786,0.0009961966,0.002139557,0.003391224,0.002479219,0.01327432],"category_scores_gemma":[0.007580881,0.0008248806,0.001533668,0.001746336,0.001829613,0.004434119,0.001416353,0.002951708,0.004466276],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001119636,"about_ca_system_score_gemma":0.001052711,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.005342313,"about_ca_topic_score_gemma":0.003502453,"domain_scores_codex":[0.9988821,0.0002789804,0.00005255702,0.0003469677,0.0002370713,0.0002023215],"domain_scores_gemma":[0.9958792,0.002697455,0.000356773,0.000411104,0.0004173948,0.0002380647],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"theoretical_or_conceptual","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0002127001,0.0001370371,0.002974316,0.0001970848,0.00009746139,0.0005716429,0.0005075969,0.2487376,0.005437119,0.7030964,0.008254901,0.02977609],"study_design_scores_gemma":[0.0000564241,0.00005642551,0.0005474046,0.00002511994,0.00003932506,0.0002828557,0.00002670237,0.8095279,0.0004817348,0.1839977,0.004915052,0.00004320842],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.04508565,0.0006720875,0.9391358,0.001092354,0.0002283363,0.0001559273,0.001254678,0.0007855513,0.0115896],"genre_scores_gemma":[0.7536561,0.002066079,0.1635603,0.0006916936,0.0004958037,0.001230494,0.002358297,0.0005728132,0.07536843],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.01327432,"threshold_uncertainty_score":0.04440701,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02387444716844759,"score_gpt":0.2631178745095681,"score_spread":0.2392434273411206,"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."}}