{"id":"W2922452497","doi":"10.1093/molbev/msz058","title":"Transmission Trees on a Known Pathogen Phylogeny: Enumeration and Sampling","year":2019,"lang":"en","type":"article","venue":"Molecular Biology and Evolution","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":58,"is_retracted":false,"has_abstract":true,"ca_institutions":"Simon Fraser University","funders":"H2020 European Research Council; Engineering and Physical Sciences Research Council","keywords":"Biology; Phylogenetic tree; Phylogenetics; Bottleneck; Lineage (genetic); Host (biology); Transmission (telecommunications); Tree (set theory); Evolutionary biology; Sampling (signal processing); Computer science; Genetics; Mathematics; Combinatorics; 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":[0.0001152425,0.0001383212,0.0001243722,0.00004107125,0.0001064455,0.0000102003,0.00004580002,0.0001776725,0.000003685408],"category_scores_gemma":[0.00001467403,0.0001230288,0.0000410524,0.00003569647,0.00006515408,8.631333e-7,0.00004767755,0.00005765078,0.000005486654],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000007594962,"about_ca_system_score_gemma":0.00001692213,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001155955,"about_ca_topic_score_gemma":0.000006720363,"domain_scores_codex":[0.9992462,0.00006774909,0.0001176478,0.0003643817,0.00003630698,0.0001677037],"domain_scores_gemma":[0.999731,0.000009793373,0.00003902638,0.0001442512,0.00002839352,0.00004755528],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.00007970178,0.0000179163,0.01362654,0.000008737535,0.00003630866,4.177702e-7,0.00004026866,0.00007589427,0.9737917,0.001988679,0.00001052642,0.01032333],"study_design_scores_gemma":[0.003079087,0.004265688,0.5705445,0.00006909847,0.0001245517,0.00007131007,0.0001884956,0.00129841,0.3409664,0.01266259,0.06560122,0.001128637],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9793183,0.006406354,0.01345154,0.0001230024,0.00009226319,0.0001835502,0.00001655631,0.000004440733,0.0004040506],"genre_scores_gemma":[0.9980316,0.0005986253,0.0009544613,0.0001780701,0.00006446001,0.00001316902,0.00007782222,0.00001123172,0.00007054666],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.6328253,"threshold_uncertainty_score":0.5016968,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.006917321649544127,"score_gpt":0.243310725991547,"score_spread":0.2363934043420029,"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."}}