{"id":"W4386767918","doi":"10.1101/2023.09.11.557209","title":"A Unified Framework to Analyze Transposable Element Insertion Polymorphisms using Graph Genomes","year":2023,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Chromosomal and Genetic Variations","field":"Agricultural and Biological Sciences","cited_by":6,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University","funders":"","keywords":"Transposable element; Mobile genetic elements; Genome; Biology; Computational biology; Genetics; Pipeline (software); Genomics; Benchmarking; Computer science; DNA sequencing; Gene","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.002320763,0.001941108,0.001207604,0.006973336,0.0007952444,0.003428721,0.002291953,0.001260312,0.006083514],"category_scores_gemma":[0.008147983,0.001152248,0.003435622,0.003595589,0.0009992932,0.002718094,0.002528718,0.001959398,0.002632142],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0009075834,"about_ca_system_score_gemma":0.001457275,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.006756388,"about_ca_topic_score_gemma":0.0103087,"domain_scores_codex":[0.9989246,0.000278188,0.00009008407,0.000339934,0.0002925722,0.00007470525],"domain_scores_gemma":[0.9974363,0.00141695,0.0001911846,0.0005238552,0.0003121425,0.0001195475],"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":[0.0005728772,0.0003771218,0.01730202,0.002835926,0.00168186,0.001280046,0.00106387,0.2977748,0.02877228,0.1902275,0.06889868,0.389213],"study_design_scores_gemma":[0.0001163918,0.00009144656,0.002910597,0.0001653625,0.0001442897,0.0004548747,0.0001792808,0.672692,0.006776789,0.2454972,0.07086222,0.0001095473],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.002963943,0.0003334975,0.9635846,0.0002064722,0.0000420345,0.0001034201,0.007195716,0.02479609,0.000774223],"genre_scores_gemma":[0.04299253,0.0005406307,0.9309109,0.0001724767,0.00006641572,0.0003417813,0.02055128,0.003426848,0.0009970727],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.006973336,"threshold_uncertainty_score":0.02035141,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03015772945940026,"score_gpt":0.2287315632630304,"score_spread":0.1985738338036301,"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."}}