{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.01046569,0.0007545976,0.001756315,0.003427627,0.001228329,0.002234817,0.002734156,0.001705319,0.003639108],"category_scores_gemma":[0.05727917,0.001032949,0.001537362,0.003280757,0.001639777,0.004598135,0.00304676,0.002660502,0.001107609],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001239745,"about_ca_system_score_gemma":0.001623274,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002166195,"about_ca_topic_score_gemma":0.003245024,"domain_scores_codex":[0.9954967,0.002437035,0.0003351867,0.0006513154,0.0007588184,0.0003209444],"domain_scores_gemma":[0.9670553,0.02635555,0.001185859,0.003256941,0.001560972,0.0005854267],"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":[0.001026696,0.000241743,0.02406449,0.0009649643,0.0002766871,0.000729746,0.001571096,0.518566,0.01355055,0.1958269,0.006272978,0.2369082],"study_design_scores_gemma":[0.00007029944,0.00006285318,0.001368067,0.00007889459,0.00002792369,0.0002552051,0.0001077925,0.8690747,0.00217153,0.1238309,0.002923761,0.00002809687],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.04209103,0.0002741636,0.9553052,0.0001712572,0.00002426842,0.0001368234,0.0005165108,0.0006402214,0.0008405201],"genre_scores_gemma":[0.1841974,0.0003922739,0.8100508,0.0001106762,0.00007773794,0.000568497,0.002829251,0.0004061234,0.00136725],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.01046569,"threshold_uncertainty_score":0.05534858,"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."}}