{"id":"W2990895847","doi":"10.1101/856591","title":"RepeatModeler2: automated genomic discovery of transposable element families","year":2019,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Chromosomal and Genetic Variations","field":"Agricultural and Biological Sciences","cited_by":264,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"National Human Genome Research Institute; Natural Sciences and Engineering Research Council of Canada; National Institutes of Health","keywords":"Genome; Annotation; Transposable element; Computational biology; Biology; Identification (biology); Genome project; Genomics; Tree (set theory); Genetics; Computer science; Gene","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":[0.0002435901,0.0003906203,0.0005365891,0.00003606529,0.0001244048,0.0001283704,0.0005469897,0.0003449731,0.0001162338],"category_scores_gemma":[0.0000261378,0.0001982172,0.0002434705,0.0003399634,0.00007046203,0.0001225671,0.0002781736,0.0002656722,0.00005021093],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001106331,"about_ca_system_score_gemma":0.0001542353,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002875217,"about_ca_topic_score_gemma":0.00004843209,"domain_scores_codex":[0.9978461,0.00009132514,0.0005903355,0.0007448447,0.0003141421,0.0004132437],"domain_scores_gemma":[0.9988579,0.00007849534,0.0003663876,0.0003754695,0.0002157556,0.0001060516],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.00002018442,0.0001617641,0.01745291,0.0001267584,0.000105659,0.000003577798,0.000009881222,0.001438177,0.980323,0.0002851864,0.00006793856,0.000005010896],"study_design_scores_gemma":[0.0003940853,0.0002141359,0.687053,0.0003221037,0.0001776124,1.354693e-8,0.00001363957,0.008362543,0.2988027,0.00001052882,0.003774678,0.0008749674],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9961108,0.0005429125,0.00006000516,0.0002403422,0.0005308462,0.0006852336,0.001436405,0.0003693774,0.00002405204],"genre_scores_gemma":[0.9983007,0.0003865292,0.0008731281,0.00006366584,0.0002638903,0.00008046032,0.000005004087,0.000007716932,0.00001886381],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.6815202,"threshold_uncertainty_score":0.8083062,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01281386883890619,"score_gpt":0.1962674532148998,"score_spread":0.1834535843759936,"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."}}