{"id":"W2048253923","doi":"10.1128/jcm.06689-11","title":"Automating HIV Drug Resistance Genotyping with RECall, a Freely Accessible Sequence Analysis Tool","year":2012,"lang":"en","type":"article","venue":"Journal of Clinical Microbiology","topic":"HIV/AIDS drug development and treatment","field":"Medicine","cited_by":191,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia; AIDS Vancouver","funders":"National Institute of Allergy and Infectious Diseases; Canadian Institutes of Health Research; School of Medicine, Stanford University; International AIDS Society","keywords":"Concordance; Genotyping; Drug resistance; Sequence analysis; Sequence (biology); Computational biology; Computer science; Bioinformatics; Medicine; Biology; Genetics; Genotype; Gene","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":[0.0025301,0.0001904619,0.001135462,0.000248031,0.00008826225,0.00002081025,0.0002003568,0.0001706671,0.0001735273],"category_scores_gemma":[0.0008098567,0.000117579,0.0003968779,0.0005230457,0.0001593462,0.0002256914,0.00005740518,0.0005547256,0.00005245696],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001059865,"about_ca_system_score_gemma":0.0003678263,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00000184263,"about_ca_topic_score_gemma":0.00002857701,"domain_scores_codex":[0.997336,0.0002823892,0.001606866,0.0002165562,0.0001431724,0.0004149722],"domain_scores_gemma":[0.9972129,0.0007150498,0.001171303,0.0002470922,0.0004131687,0.0002404846],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.001032498,0.0004767964,0.9688359,0.00005115025,0.003408251,0.0001411574,0.0004365379,0.000006736974,0.007232643,0.00005474299,0.01467997,0.003643629],"study_design_scores_gemma":[0.01331329,0.0005829291,0.6418865,0.001576614,0.01012536,0.001944364,0.0003703778,0.0001173771,0.008109679,0.0001448184,0.320896,0.0009327147],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9851923,0.0009906784,0.001514845,0.01119205,0.0003024706,0.0001451186,0.00000709624,0.000025728,0.0006297234],"genre_scores_gemma":[0.8844004,0.0001313684,0.09699805,0.0007663271,0.0006071582,0.000004097556,0.00003209935,0.00001957693,0.01704087],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3269494,"threshold_uncertainty_score":0.4794734,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05950039931131185,"score_gpt":0.3838241607718468,"score_spread":0.324323761460535,"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."}}