{"id":"W1966813277","doi":"10.1186/1471-2105-15-205","title":"A model-based information sharing protocol for profile Hidden Markov Models used for HIV-1 recombination detection","year":2014,"lang":"en","type":"article","venue":"BMC Bioinformatics","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":5,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Guelph","funders":"National Institute of Allergy and Infectious Diseases; National Institutes of Health; Deutsche Forschungsgemeinschaft","keywords":"Hidden Markov model; Subfamily; Inference; Biology; Computer science; Subtyping; Computational biology; Markov chain; Data mining; Artificial intelligence; Genetics; Machine learning; 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":[0.0005591608,0.0001790006,0.0001992181,0.0002160766,0.0003059213,0.00007865357,0.0001807734,0.0002260994,0.0000289646],"category_scores_gemma":[0.0001882887,0.0001518398,0.0001232989,0.00009513836,0.00004115916,0.0009147479,0.0000398416,0.0001094201,0.0002907733],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001375354,"about_ca_system_score_gemma":0.0001435582,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000005889722,"about_ca_topic_score_gemma":0.00002252161,"domain_scores_codex":[0.9988574,0.00003467765,0.0005173119,0.0001276433,0.00007060693,0.0003923541],"domain_scores_gemma":[0.9990029,0.0001777342,0.0002556407,0.0002724557,0.0002517719,0.00003950158],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.008012796,0.001219014,0.001240643,0.01132661,0.0004523214,1.241405e-7,0.005514832,0.04466279,0.004916634,0.009805508,0.02791108,0.8849376],"study_design_scores_gemma":[0.008694347,0.0005572453,0.00004181873,0.00004910001,0.00002156023,0.000001957432,0.00008607974,0.9690669,0.01243058,0.001591705,0.007285156,0.0001735908],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"protocol","genre_scores_codex":[0.0007506953,0.000001275237,0.9124237,0.00005967171,0.00007049647,0.08518823,0.0002567625,0.000117804,0.001131419],"genre_scores_gemma":[0.06651113,4.136388e-7,0.3480406,0.0001212004,0.00003082509,0.5802267,0.003953439,0.00003123141,0.001084557],"genre_candidate":"methods","genre_consensus":null,"teacher_disagreement_score":0.9244041,"threshold_uncertainty_score":0.6191848,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04325172657652011,"score_gpt":0.2975769257119991,"score_spread":0.254325199135479,"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."}}