{"id":"W2166542841","doi":"10.1093/bioinformatics/btq562","title":"GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop","year":2010,"lang":"en","type":"article","venue":"Bioinformatics","topic":"Bioinformatics and Genomic Networks","field":"Biochemistry, Genetics and Molecular Biology","cited_by":661,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto","funders":"Ontario Genomics; Ontario Genomics Institute; Genome Canada","keywords":"Plug-in; Computer science; Function (biology); Complement (music); Java; Set (abstract data type); Gene; Programming language; 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":[0.0002997757,0.0002058761,0.0001168939,0.00004753696,0.0003307995,0.00009308058,0.000309788,0.0002503232,0.00011746],"category_scores_gemma":[0.00004560072,0.0001436547,0.0001126536,0.0001132604,0.0001121944,0.0000117827,0.0001207547,0.0003094226,0.0002262943],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001103821,"about_ca_system_score_gemma":0.00007561409,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000003530469,"about_ca_topic_score_gemma":0.00003847812,"domain_scores_codex":[0.9989569,0.00001530693,0.0003933179,0.0001381561,0.0001876846,0.0003086353],"domain_scores_gemma":[0.9989277,0.00002198055,0.000169111,0.0006888948,0.00008313894,0.0001091687],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0005943195,0.0005268953,0.001835854,0.0002264556,0.0009387692,0.00000387602,0.002136505,0.00543018,0.4789933,0.04733384,0.3281898,0.1337902],"study_design_scores_gemma":[0.001853961,0.001533643,0.008589058,0.00004320667,0.0001878823,0.0001867341,0.001279901,0.1374743,0.0751906,0.001345063,0.7710359,0.001279785],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.7784215,0.0001570589,0.1287857,0.001226673,0.003715359,0.00116347,0.0002197129,0.000139991,0.08617061],"genre_scores_gemma":[0.989897,0.00009582756,0.005546142,0.002264481,0.000933772,0.00004878765,0.000303084,0.00002849512,0.0008824035],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4428461,"threshold_uncertainty_score":0.585807,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.007931295299022024,"score_gpt":0.200528499500222,"score_spread":0.1925972042011999,"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."}}