{"id":"W3133670677","doi":"10.1111/jeb.13771","title":"Variable routes to genomic and host adaptation among coronaviruses","year":2021,"lang":"en","type":"article","venue":"Journal of Evolutionary Biology","topic":"SARS-CoV-2 and COVID-19 Research","field":"Medicine","cited_by":11,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia; AIDS Vancouver","funders":"Canadian Institutes of Health Research","keywords":"Biology; Nonsynonymous substitution; Host adaptation; Negative selection; Adaptation (eye); Genetics; Host (biology); Coronavirus; Evolutionary biology; Natural selection; Gene; Genome; Selection (genetic algorithm); Coronavirus disease 2019 (COVID-19)","routes":{"ca_aff":true,"ca_fund":true,"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":[0.0002168575,0.00007424626,0.000224755,0.0001538736,0.0000601904,0.000009572141,0.00006295056,0.00009194474,0.0000436612],"category_scores_gemma":[0.0004084704,0.00006119845,0.00005238111,0.0001769767,0.00008931845,0.00008792907,0.00006300684,0.0001876302,0.0000185755],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001279709,"about_ca_system_score_gemma":0.0005886681,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0000922844,"about_ca_topic_score_gemma":0.00001987763,"domain_scores_codex":[0.9992203,0.00008467882,0.0002736068,0.0001326167,0.0001185317,0.0001703382],"domain_scores_gemma":[0.9991755,0.0001727555,0.00009809743,0.00009599685,0.0003994231,0.00005820118],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0003602575,0.00008994384,0.5550706,0.00001717671,0.00009019511,0.000123253,0.0001069694,0.000007792962,0.4407767,0.001302056,0.001109394,0.0009456965],"study_design_scores_gemma":[0.001000692,0.0008522014,0.8886535,0.00006397907,0.00005186961,0.001339244,0.0002975468,0.0003720881,0.005338356,0.001339983,0.1006081,0.00008240291],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9908013,0.005005723,0.002472566,0.0008123643,0.0002140242,0.00008173552,0.00001004611,0.000006821561,0.0005954366],"genre_scores_gemma":[0.9814761,0.00004890042,0.008244687,0.009763993,0.0003745682,0.000003504994,0.000003799293,0.000008929499,0.00007549993],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4354383,"threshold_uncertainty_score":0.2495601,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04308126076211744,"score_gpt":0.3336108289411712,"score_spread":0.2905295681790538,"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."}}