{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002294508,0.0001161725,0.0001126612,0.0000346034,0.00011649,0.0001248791,0.00006305151,0.0001019136,0.00000134203],"category_scores_gemma":[0.0002256981,0.0001057141,0.00005968548,0.00004875629,0.00003658413,0.000002637341,0.00008895155,0.00006101058,0.000005331048],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000009852481,"about_ca_system_score_gemma":0.00004217492,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000001442908,"about_ca_topic_score_gemma":0.00001629965,"domain_scores_codex":[0.9993899,0.000009964822,0.0002207268,0.0001392347,0.00007318814,0.0001669811],"domain_scores_gemma":[0.9996282,0.0001143257,0.0000460065,0.0001309073,0.0000399538,0.00004053826],"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":[0.0007621024,0.00009647624,0.00968255,0.006405302,0.001069839,0.000001894289,0.005486776,0.01347101,0.3843254,0.01490767,0.002900879,0.5608901],"study_design_scores_gemma":[0.0005580378,0.0006413879,0.002178159,0.0001407571,0.00009763607,0.00003692549,0.0007962392,0.9279359,0.04062563,0.00303833,0.02356951,0.0003814931],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.6169585,0.001540296,0.3804253,0.0000220143,0.0003402606,0.0002957071,0.00003479524,0.00001395313,0.0003691541],"genre_scores_gemma":[0.7770757,0.0001439542,0.2223643,0.000076469,0.0002036224,0.00005340403,0.00002592697,0.00001632399,0.0000402652],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.9144649,"threshold_uncertainty_score":0.4310896,"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."}}