{"id":"W4396604611","doi":"10.1101/2024.04.30.591963","title":"PlasEval: a framework for comparing and evaluating plasmid detection tools","year":2024,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Antibiotic Resistance in Bacteria","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"Dalhousie University; Agriculture and Agri-Food Canada; University of Saskatchewan; Simon Fraser University","funders":"","keywords":"Plasmid; Contig; Set (abstract data type); Genome; Computer science; Biology; Computational biology; Benchmarking; Genetics; 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":[0.01771992,0.004319909,0.002732926,0.01472697,0.001466222,0.008300665,0.007348964,0.003465934,0.005179494],"category_scores_gemma":[0.04749548,0.002139246,0.006153007,0.005643297,0.002397284,0.006819125,0.009397472,0.003319,0.002264799],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.003132639,"about_ca_system_score_gemma":0.002764921,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.005688822,"about_ca_topic_score_gemma":0.006658793,"domain_scores_codex":[0.9837149,0.005623789,0.002281913,0.003071272,0.004590107,0.0007180366],"domain_scores_gemma":[0.9774178,0.01361489,0.002149474,0.003372972,0.002464591,0.0009802115],"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":[0.004237522,0.001633759,0.02985931,0.00969473,0.004003279,0.001431217,0.002116021,0.3746504,0.02436071,0.07258778,0.0687141,0.4067112],"study_design_scores_gemma":[0.0005123104,0.0009016787,0.005701702,0.0009845491,0.0004170893,0.0004042175,0.0006594492,0.8652003,0.01492285,0.05352887,0.05644049,0.0003265296],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.04613506,0.003300871,0.7546573,0.0007539019,0.0003662548,0.001754946,0.02084646,0.1667436,0.005441614],"genre_scores_gemma":[0.1218929,0.0007016914,0.8224509,0.0003427529,0.00009281385,0.002082825,0.04091083,0.0104295,0.001095871],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.01771992,"threshold_uncertainty_score":0.09371299,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0297315459692603,"score_gpt":0.2849251221666163,"score_spread":0.255193576197356,"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."}}