{"id":"W3017020108","doi":"10.1093/bioinformatics/btaa756","title":"HLA predictions from the bronchoalveolar lavage fluid and blood samples of eight COVID-19 patients at the pandemic onset","year":2020,"lang":"en","type":"article","venue":"Bioinformatics","topic":"SARS-CoV-2 and COVID-19 Research","field":"Medicine","cited_by":33,"is_retracted":false,"has_abstract":true,"ca_institutions":"Genome British Columbia","funders":"National Human Genome Research Institute; National Institutes of Health; Genome British Columbia; Genome Canada","keywords":"Bronchoalveolar lavage; Human leukocyte antigen; Immunology; Allele; Pandemic; Biology; Population; Coronavirus disease 2019 (COVID-19); Allele frequency; Transcriptome; Disease; Gene; Medicine; Antigen; Genetics; Internal medicine; Infectious disease (medical specialty); Gene expression; Lung","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":[0.0002529107,0.0001450107,0.0002267015,0.00003798851,0.0002699002,0.0000336196,0.000246399,0.00009865366,0.00004586806],"category_scores_gemma":[0.001154267,0.00007816308,0.00008698009,0.0001939802,0.0003094371,0.0001041477,0.0002533087,0.0002423851,0.00005063],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00005861654,"about_ca_system_score_gemma":0.000284692,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002353128,"about_ca_topic_score_gemma":0.00007017022,"domain_scores_codex":[0.9986505,0.00006151552,0.0004307022,0.0001284395,0.0005061732,0.0002226914],"domain_scores_gemma":[0.9984791,0.0007726685,0.000131567,0.0004120754,0.0000872922,0.0001172814],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0002379905,0.000100683,0.9522027,0.0003104324,0.0002317059,0.000002940788,0.01074972,0.000002593757,0.0016377,0.00002485229,0.0331006,0.001398132],"study_design_scores_gemma":[0.006502621,0.000889242,0.2065488,0.0001139081,0.0006193339,0.00003414636,0.003102992,0.008750093,0.01138761,0.000135531,0.7616442,0.0002714297],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9938713,0.0008097127,0.0005933032,0.002171878,0.00006062774,0.0006682054,0.001144688,0.0000584243,0.0006218096],"genre_scores_gemma":[0.8986887,0.0002222772,0.0005590132,0.1000862,0.0001508341,0.00003363128,0.0002121481,0.00002101681,0.00002618638],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.7456538,"threshold_uncertainty_score":0.3187398,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05237294114448221,"score_gpt":0.3052391455710094,"score_spread":0.2528662044265272,"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."}}