{"id":"W2808064078","doi":"10.1371/journal.pcbi.1006174","title":"Identifying functional groups among the diverse, recombining antigenic var genes of the malaria parasite Plasmodium falciparum from a local community in Ghana","year":2018,"lang":"en","type":"article","venue":"PLoS Computational Biology","topic":"Malaria Research and Control","field":"Medicine","cited_by":6,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"National Institute of Allergy and Infectious Diseases; Fogarty International Center; National Institutes of Health; University of Melbourne; York University","keywords":"Biology; Phylogenetic tree; Evolutionary biology; Antigenic variation; Genetics; Sequence (biology); Gene; Plasmodium falciparum; Computational biology; Phylogenetics; Malaria","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0005042684,0.0001265655,0.0002713283,0.0001101596,0.0003633524,0.0000169295,0.0003050701,0.0001182362,0.000317106],"category_scores_gemma":[0.0002061898,0.0000800583,0.0001070144,0.0002652139,0.0007608612,0.00006272682,0.0002648528,0.0005343205,0.00003848944],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0000583179,"about_ca_system_score_gemma":0.0001594843,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001689763,"about_ca_topic_score_gemma":0.001068869,"domain_scores_codex":[0.9981143,0.0008008613,0.0003329624,0.0002031087,0.0002749892,0.0002737864],"domain_scores_gemma":[0.998261,0.001038645,0.0001422224,0.0002651609,0.0002278478,0.00006506067],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.001167096,0.0004326115,0.972819,0.00003386735,0.0006441048,0.000008179094,0.001149419,0.0008791662,0.006948411,0.01367007,0.0002176931,0.002030359],"study_design_scores_gemma":[0.001641833,0.000210135,0.9338627,0.000059614,0.00005502793,0.000008526325,0.0008431465,0.05226924,0.0006985827,0.01025359,0.00002165883,0.00007592],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9822084,0.0001189976,0.0148818,0.001835643,0.0002829609,0.0003607042,0.00005825555,0.00001863536,0.0002345798],"genre_scores_gemma":[0.9986553,0.000004799892,0.0005233029,0.0003656939,0.0001759223,0.00002956959,0.0002015551,0.000009549152,0.00003436631],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.05139008,"threshold_uncertainty_score":0.3472088,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05816536980501256,"score_gpt":0.2977375491782994,"score_spread":0.2395721793732868,"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."}}