{"id":"W2121091764","doi":"10.1016/j.gene.2008.06.015","title":"High rates of lateral gene transfer are not due to false diagnosis of gene absence","year":2008,"lang":"en","type":"article","venue":"Gene","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":8,"is_retracted":false,"has_abstract":false,"ca_institutions":"McMaster University","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Biology; Gene; Genome; Genetics; Gene prediction; Cutoff; Gene dosage; Human genome; Gene density; Computational biology; Gene expression","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":[0.00008157603,0.0001748106,0.0003216255,0.00004258904,0.00006062595,0.000004011524,0.0002369146,0.0001009338,0.00001913615],"category_scores_gemma":[0.00002283847,0.0001652756,0.0001200238,0.00009304289,0.00009616148,7.254704e-7,0.00009037765,0.00003611751,0.000006214],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000006042389,"about_ca_system_score_gemma":0.00003463168,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001292968,"about_ca_topic_score_gemma":0.00004563222,"domain_scores_codex":[0.9989727,0.00002928149,0.0003129155,0.0003172816,0.0001382102,0.0002296826],"domain_scores_gemma":[0.999347,0.00001445201,0.0000633441,0.0003467948,0.0001454981,0.00008287858],"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":[0.0000871397,0.00008200726,0.04892476,0.00001796806,0.0001017964,0.00001186782,0.0001748659,0.0004755152,0.9495527,0.000006693008,0.0002605715,0.0003041523],"study_design_scores_gemma":[0.0003277511,0.0002144103,0.2297277,0.000006593857,0.00001684465,0.00001493441,0.00001173718,0.000001730145,0.7688146,0.00001692583,0.0007057834,0.0001410139],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9967596,0.002022813,0.0003859724,0.0001472245,0.0001476544,0.0001829219,0.000333181,0.000002493936,0.0000181361],"genre_scores_gemma":[0.9940458,0.001956714,0.00335752,0.0002705283,0.0001575215,0.00004679043,0.00003726292,0.00002188216,0.0001060102],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1808029,"threshold_uncertainty_score":0.6739742,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01812124295107378,"score_gpt":0.2284144677353676,"score_spread":0.2102932247842938,"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."}}