{"id":"W3127513279","doi":"10.1093/bioinformatics/btab076","title":"WgLink: reconstructing whole-genome viral haplotypes using L0+L1-regularization","year":2021,"lang":"en","type":"article","venue":"Bioinformatics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":10,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Calgary; Alberta Children's Hospital","funders":"Canada Foundation for Innovation","keywords":"Haplotype; Regularization (linguistics); Computational biology; Genome; Genetics; Computer science; Biology; Virology; Artificial intelligence; Gene; Genotype","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":[0.000109482,0.000151116,0.0001527659,0.00003448054,0.0001766332,0.00006180273,0.0001115662,0.0001265841,0.00001043178],"category_scores_gemma":[0.0001152938,0.0001548725,0.00008175298,0.00009313131,0.00006454003,0.00000345868,0.0001848071,0.00006086725,0.00001581134],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001760711,"about_ca_system_score_gemma":0.0001575613,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00000310928,"about_ca_topic_score_gemma":0.00000520367,"domain_scores_codex":[0.9991447,0.00002206317,0.0003361966,0.0001637378,0.0001009187,0.0002323254],"domain_scores_gemma":[0.9993451,0.000007425383,0.0001392467,0.0002826822,0.000152098,0.00007348984],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.00001170663,0.00002170699,0.002882003,0.00006047754,0.0001176835,0.000002447337,0.0004081446,0.001146986,0.989922,0.000310894,0.000122617,0.00499336],"study_design_scores_gemma":[0.00265886,0.0004710399,0.006994354,0.0001210774,0.0002992754,0.0005650297,0.005753149,0.05629273,0.6618432,0.002357614,0.260543,0.002100655],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9825102,0.001115953,0.01279871,0.00009958793,0.0003901014,0.0001242836,0.00008796141,0.00001033958,0.00286286],"genre_scores_gemma":[0.8718504,0.0003146085,0.1253178,0.0005977778,0.0005191057,0.000006361647,0.0005078714,0.00004120902,0.0008447918],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3280787,"threshold_uncertainty_score":0.6315518,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01705181949001315,"score_gpt":0.2314050820654523,"score_spread":0.2143532625754391,"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."}}