{"id":"W3189850282","doi":"10.1142/s0219720021400096","title":"Small parsimony for natural genomes in the DCJ-indel model","year":2021,"lang":"en","type":"preprint","venue":"Journal of Bioinformatics and Computational Biology","topic":"Genome Rearrangement Algorithms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Simon Fraser University","funders":"","keywords":"Indel; Genome; Phylogenetic tree; Tree (set theory); Maximum parsimony; Biology; Gene duplication; Computational biology; Gene; Evolutionary biology; Genetics; Computer science; Algorithm; Combinatorics; Mathematics","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":[0.0005518281,0.0001769,0.0002964793,0.0001214154,0.00005126826,0.00007342934,0.0003227994,0.0002276309,0.000001089985],"category_scores_gemma":[0.00005103694,0.0001247715,0.0001822366,0.00004624435,0.00007044049,0.000005498611,0.0002411862,0.0002839761,2.263258e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001880039,"about_ca_system_score_gemma":0.0003071041,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00000176088,"about_ca_topic_score_gemma":0.000009392935,"domain_scores_codex":[0.9988853,0.00005315211,0.0006348498,0.0001347122,0.0001145363,0.0001774968],"domain_scores_gemma":[0.99891,0.00007247556,0.0005146015,0.0001333807,0.0003295559,0.00003998812],"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":[0.0004766244,0.0005045582,0.004409419,0.001146016,0.00164054,0.0000208023,0.005776588,0.854935,0.005897915,0.003038332,0.002696524,0.1194577],"study_design_scores_gemma":[0.001943322,0.0006660376,0.002361337,0.00008867993,0.0001112724,0.0002441242,0.002132467,0.967231,0.0002125377,0.0219357,0.002635761,0.0004377877],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.7937796,0.007963656,0.1962968,0.0009439637,0.0004150991,0.0003984453,0.00009503918,0.000002111627,0.0001053273],"genre_scores_gemma":[0.8458447,0.001152864,0.1511682,0.000810359,0.0002407271,0.00001668261,0.0007323035,0.00001109064,0.00002297339],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1190199,"threshold_uncertainty_score":0.5088034,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02635207495149361,"score_gpt":0.2675109896771377,"score_spread":0.241158914725644,"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."}}