{"id":"W4405180280","doi":"10.1101/2024.12.05.626978","title":"Integrated population clustering and genomic epidemiology with PopPIPE","year":2024,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Influenza Virus Research Studies","field":"Medicine","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"Institute of Infection and Immunity","funders":"Biotechnology and Biological Sciences Research Council","keywords":"Cluster analysis; Population; Data science; Geography; Computational biology; Computer science; Evolutionary biology; Biology; Medicine; Environmental health; Artificial intelligence","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":[0.005044519,0.002615947,0.002616588,0.003066701,0.001248602,0.002599784,0.003537609,0.001426305,0.01681189],"category_scores_gemma":[0.01119416,0.002097152,0.003590616,0.002157256,0.0008184762,0.001847467,0.003763726,0.003199237,0.005537648],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0008097566,"about_ca_system_score_gemma":0.002693269,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.004351893,"about_ca_topic_score_gemma":0.00620407,"domain_scores_codex":[0.9987035,0.000406609,0.0001025218,0.0004216327,0.0002641546,0.0001015916],"domain_scores_gemma":[0.9954542,0.003059026,0.0003362529,0.0005173761,0.0004291231,0.0002039775],"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":[0.004066712,0.001058543,0.0388142,0.009302218,0.008287553,0.002120829,0.004239933,0.244571,0.03806874,0.03673952,0.254685,0.3580458],"study_design_scores_gemma":[0.000651359,0.0002382249,0.00863904,0.0002990062,0.0004871908,0.0004402468,0.0002940902,0.8300965,0.01706372,0.03464851,0.10678,0.0003621581],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.03078729,0.0009924722,0.6312408,0.0009684448,0.0006071005,0.0008470816,0.04000305,0.2912794,0.003274362],"genre_scores_gemma":[0.07096832,0.0005318166,0.8575771,0.0004942192,0.0001560957,0.002356647,0.04266342,0.02284664,0.002405664],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.01681189,"threshold_uncertainty_score":0.05624133,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05866909530130664,"score_gpt":0.3173412688324871,"score_spread":0.2586721735311805,"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."}}