{"id":"W2619023647","doi":"10.1089/aid.2017.0061","title":"HIV-1 Full-Genome Phylogenetics of Generalized Epidemics in Sub-Saharan Africa: Impact of Missing Nucleotide Characters in Next-Generation Sequences","year":2017,"lang":"en","type":"article","venue":"AIDS Research and Human Retroviruses","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":29,"is_retracted":false,"has_abstract":true,"ca_institutions":"Institute of Infection and Immunity","funders":"National Institute of Allergy and Infectious Diseases; Medical Research Council; Klaus Tschira Stiftung; Engineering and Physical Sciences Research Council; NHLBI Division of Intramural Research; Ministry of Business, Innovation and Employment; Fogarty International Center; Department for International Development; Imperial College London; Bill and Melinda Gates Foundation; Austrian Science Fund; National Institutes of Health; University of Auckland; Division of Intramural Research, National Institute of Allergy and Infectious Diseases","keywords":"Phylogenetics; Genome; Human immunodeficiency virus (HIV); Virology; Biology; Genetics; Evolutionary biology; Computational biology; 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":[0.001425373,0.0001790987,0.0005167708,0.0006546372,0.0003968024,0.00008504511,0.0004221188,0.0001721089,0.0001249507],"category_scores_gemma":[0.00047827,0.0001472362,0.00009894183,0.0001729365,0.001219828,0.0002432714,0.0001736597,0.0004260295,0.00003461135],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001572944,"about_ca_system_score_gemma":0.0002124606,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003371868,"about_ca_topic_score_gemma":0.001084298,"domain_scores_codex":[0.9976483,0.0006147798,0.0005040073,0.0003520819,0.0001505781,0.0007302809],"domain_scores_gemma":[0.9988269,0.0002217553,0.0002062347,0.0004910268,0.0001675045,0.00008657514],"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":[0.0002499134,0.0001678254,0.3141297,0.0000325675,0.0000884614,0.0000235658,0.0002608471,0.000005761035,0.6828409,0.0001550904,0.0001549639,0.001890316],"study_design_scores_gemma":[0.00218608,0.002324353,0.8810169,0.0000982758,0.00001031855,0.000007268069,0.00007831303,0.000008442039,0.1132402,0.0006444665,0.0002341176,0.0001513516],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9926187,0.006478892,0.000004418296,0.00007372449,0.00002841584,0.000361295,0.0002182009,0.000006155136,0.0002101672],"genre_scores_gemma":[0.996137,0.003366188,0.0001077902,0.000004247581,0.00003341148,0.00002590371,0.0001707175,0.00001602144,0.0001387313],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5696008,"threshold_uncertainty_score":0.6004118,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1778245725768024,"score_gpt":0.3869087264383318,"score_spread":0.2090841538615294,"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."}}