{"id":"W4415906417","doi":"10.21203/rs.3.rs-7906379/v1","title":"Molecular epidemiology, evolution and transmission dynamics of HIV-1 in Ghana, West Africa","year":2025,"lang":"","type":"preprint","venue":"Research Square","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":0,"is_retracted":false,"has_abstract":false,"ca_institutions":"Western University","funders":"","keywords":"Transmission (telecommunications); Phylogeography; Population; Molecular clock; Human immunodeficiency virus (HIV); Phylogenetic tree; Molecular epidemiology; Phylogenetics; Viral phylodynamics","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":[0.0006088768,0.000271368,0.000251458,0.001298552,0.0004654452,0.0006844583,0.0004060573,0.0005589366,0.001598436],"category_scores_gemma":[0.002464875,0.0002569685,0.0001024824,0.001764765,0.0008503032,0.0007402093,0.000396138,0.0005119194,0.0001753984],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001251634,"about_ca_system_score_gemma":0.0006944262,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.03734198,"about_ca_topic_score_gemma":0.0242587,"domain_scores_codex":[0.9995965,0.0001651145,0.00002397138,0.00005973805,0.00003240189,0.0001223228],"domain_scores_gemma":[0.9989296,0.0003245646,0.0004834729,0.00003360093,0.00008896888,0.0001398289],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0003604383,0.00008073504,0.9730068,0.0001204169,0.00003260563,0.0006985387,0.00418329,0.0004963765,0.003792259,0.00068534,0.0003299885,0.01621318],"study_design_scores_gemma":[0.00001053968,0.00009424156,0.9939836,0.00006653868,0.00001402349,0.0006592169,0.003780796,0.0003266932,0.0001802149,0.0002250468,0.0006520241,0.000007056148],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.998072,0.001198448,0.00006897807,0.0001643485,0.000003479147,0.00001008503,0.0001873349,0.000002365397,0.0002929102],"genre_scores_gemma":[0.9986017,0.001021001,0.0001494434,0.00002438038,0.000006328068,0.000005446569,0.00008456484,0.000001376798,0.0001057082],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.03734198,"threshold_uncertainty_score":0.07424927,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0404523918732486,"score_gpt":0.3666240694022533,"score_spread":0.3261716775290047,"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."}}