{"id":"W2007843607","doi":"10.1371/journal.pone.0013348","title":"Module Discovery by Exhaustive Search for Densely Connected, Co-Expressed Regions in Biomolecular Interaction Networks","year":2010,"lang":"en","type":"article","venue":"PLoS ONE","topic":"Bioinformatics and Genomic Networks","field":"Biochemistry, Genetics and Molecular Biology","cited_by":24,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia; BC Centre for Disease Control; Simon Fraser University","funders":"Division of Mathematical Sciences; Natural Sciences and Engineering Research Council of Canada; Canadian Institutes of Health Research; SFU Community Trust Endowment Fund; Simon Fraser University; Michael Smith Health Research BC; Pacific Institute for the Mathematical Sciences","keywords":"Computer science; Benchmarking; Benchmark (surveying); Function (biology); Computational biology; Biological network; Scale (ratio); Theoretical computer science; Artificial intelligence; Machine learning; Data mining; Biology; Genetics","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":[0.0001688076,0.0001468033,0.000171883,0.00004934553,0.0000774587,0.00007473262,0.0001698093,0.0002490855,0.00001010094],"category_scores_gemma":[0.00003682527,0.0001503327,0.00006691839,0.00008175376,0.00007466602,0.00001422232,0.00006541058,0.0002703045,0.000005091389],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001548066,"about_ca_system_score_gemma":0.00003763102,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002757676,"about_ca_topic_score_gemma":0.00006032677,"domain_scores_codex":[0.9990512,0.00002356649,0.0002340997,0.000273165,0.0001053499,0.0003125886],"domain_scores_gemma":[0.9993994,0.00003397113,0.00007759332,0.0003160722,0.00009392825,0.00007903165],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.0002221245,0.0004161232,0.0004999592,0.00003165183,0.0001328525,0.000001260829,0.00004877927,0.0002972978,0.9935791,0.0003105952,0.004150725,0.0003095322],"study_design_scores_gemma":[0.001501396,0.000363857,0.0002209763,0.00007633249,0.00005635851,0.000005051447,0.0001406589,0.04960058,0.9433594,0.0002297844,0.004066718,0.0003788424],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9150916,0.0001631084,0.08338366,0.0002135588,0.00009801922,0.000537601,0.00009436766,0.00001264605,0.0004054648],"genre_scores_gemma":[0.9961697,0.0001362525,0.001711409,0.0002425095,0.000235265,0.0001000568,0.0009620223,0.00002814197,0.0004146026],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.08167224,"threshold_uncertainty_score":0.6130388,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0208701685677656,"score_gpt":0.2513988349734896,"score_spread":0.230528666405724,"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."}}