{"id":"W3017049640","doi":"10.1073/pnas.1921046117","title":"RepeatModeler2 for automated genomic discovery of transposable element families","year":2020,"lang":"en","type":"article","venue":"Proceedings of the National Academy of Sciences","topic":"Chromosomal and Genetic Variations","field":"Agricultural and Biological Sciences","cited_by":3983,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"National Institute of General Medical Sciences; National Human Genome Research Institute; Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada","keywords":"Annotation; Genome; Transposable element; Computational biology; Biology; Identification (biology); Genome project; Genomics; Comparative genomics; Computer science; Genetics; 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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.002120877,0.002399066,0.001197952,0.001730613,0.0009433684,0.001523998,0.002179995,0.001064713,0.01372577],"category_scores_gemma":[0.003712464,0.001100589,0.001975768,0.001326461,0.0004697453,0.001767535,0.001700166,0.001694565,0.006338642],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0008995715,"about_ca_system_score_gemma":0.002007763,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.004039666,"about_ca_topic_score_gemma":0.006230638,"domain_scores_codex":[0.9989576,0.000161197,0.00007295319,0.0004527857,0.000275623,0.00007970294],"domain_scores_gemma":[0.9992166,0.0004197152,0.0000822085,0.0001093763,0.0001111862,0.00006095053],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.004742763,0.0006160653,0.02283787,0.003435948,0.001573274,0.001778078,0.001682578,0.07110093,0.1725668,0.0188893,0.3472371,0.3535393],"study_design_scores_gemma":[0.0006407453,0.0003015499,0.006423486,0.0001518552,0.0002193872,0.0008771579,0.0002173889,0.7136408,0.1089566,0.01657645,0.1517214,0.0002731623],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"software","genre_gemma":"software","genre_scores_codex":[0.04157703,0.0008164014,0.4307464,0.0004477302,0.0001629291,0.0002747602,0.04079011,0.4801746,0.005010168],"genre_scores_gemma":[0.1041271,0.0005252821,0.7572984,0.0004718929,0.0000498171,0.001073664,0.09831855,0.03254466,0.005590724],"genre_candidate":"software","genre_consensus":"software","teacher_disagreement_score":0.01372577,"threshold_uncertainty_score":0.04591733,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0482309174198915,"score_gpt":0.2642692087111527,"score_spread":0.2160382912912612,"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."}}