{"id":"W4415931006","doi":"10.1101/2025.11.03.686425","title":"GNAT: An Interactive Web Tool for Gene Neighbourhood Analysis","year":2025,"lang":"","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"SickKids Foundation; Hospital for Sick Children; University of Toronto; University of Saskatchewan","funders":"","keywords":"Neighbourhood (mathematics); Categorical variable; Interface (matter); User interface; Visualization; Interactive visualization; Sequence (biology)","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":[0.001609285,0.002201556,0.001633135,0.004904274,0.0009842663,0.00253754,0.002677872,0.00134047,0.08712881],"category_scores_gemma":[0.004835735,0.001087713,0.001857617,0.003472251,0.0006575289,0.002752623,0.003756327,0.002328381,0.03560249],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0007824625,"about_ca_system_score_gemma":0.001227952,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002897538,"about_ca_topic_score_gemma":0.004175008,"domain_scores_codex":[0.9990731,0.0001574575,0.00008151396,0.0002107688,0.000395028,0.00008208969],"domain_scores_gemma":[0.998546,0.0008408141,0.0001083137,0.000210889,0.0001941159,0.00009985743],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0009865882,0.0002046559,0.005156625,0.002452705,0.0004469748,0.0009048915,0.00087231,0.00483381,0.01774673,0.01611295,0.8217325,0.1285492],"study_design_scores_gemma":[0.0008291206,0.000130557,0.007741809,0.0006622968,0.0002206073,0.001855074,0.0005417918,0.0913692,0.03250201,0.07893471,0.7847806,0.0004323687],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"software","genre_gemma":"software","genre_scores_codex":[0.005749602,0.0006952644,0.2633459,0.0003696489,0.0003891549,0.0002172136,0.09814988,0.6233378,0.007745488],"genre_scores_gemma":[0.07099959,0.001250845,0.5309122,0.0009983908,0.0002247375,0.002173892,0.2205712,0.1582862,0.014583],"genre_candidate":"software","genre_consensus":"software","teacher_disagreement_score":0.08712881,"threshold_uncertainty_score":0.2914749,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.009648477738430415,"score_gpt":0.2368996671187851,"score_spread":0.2272511893803547,"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."}}