{"id":"W4404722864","doi":"10.1186/s12859-024-05941-0","title":"Plaseval: a framework for comparing and evaluating plasmid detection tools","year":2024,"lang":"en","type":"article","venue":"BMC Bioinformatics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":5,"is_retracted":false,"has_abstract":true,"ca_institutions":"Dalhousie University; Agriculture and Agri-Food Canada; University of Saskatchewan; Simon Fraser University","funders":"Natural Sciences and Engineering Research Council of Canada; Genome Canada","keywords":"DNA microarray; Plasmid; Computational biology; Computer science; Biology; Genetics; Gene; 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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.01785909,0.004510771,0.002785853,0.01503811,0.001561914,0.008174785,0.007076024,0.003621171,0.004386129],"category_scores_gemma":[0.04181159,0.001866748,0.006414242,0.005092394,0.002411546,0.005910021,0.008397708,0.003188426,0.001663683],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.003246106,"about_ca_system_score_gemma":0.003232082,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.005124091,"about_ca_topic_score_gemma":0.006091398,"domain_scores_codex":[0.983802,0.005255927,0.002478305,0.003059029,0.004723832,0.0006808509],"domain_scores_gemma":[0.9793632,0.01151292,0.002543738,0.003138836,0.002479968,0.0009613336],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.003367869,0.001438254,0.03145551,0.008480877,0.004158983,0.001231729,0.001842738,0.3487698,0.02362807,0.06614407,0.04505436,0.4644277],"study_design_scores_gemma":[0.0004588725,0.001227209,0.006596189,0.001143854,0.0005983965,0.0005582373,0.0006456377,0.8527797,0.01578755,0.06724209,0.05262086,0.0003414127],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.02725484,0.00228889,0.8744433,0.0005138689,0.0002370524,0.00138537,0.01074729,0.07977916,0.003350257],"genre_scores_gemma":[0.09444084,0.0006512596,0.872883,0.0002739314,0.00009040305,0.001993367,0.02364591,0.005250044,0.0007712176],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.01785909,"threshold_uncertainty_score":0.09444898,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.06687434104668352,"score_gpt":0.3231134474966735,"score_spread":0.2562391064499899,"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."}}