{"id":"W4415268940","doi":"10.1101/2025.10.15.682631","title":"IDBac: an open-access web platform to identify bacteria and analyze relationships in culture collections using MALDI-TOF mass spectrometry","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Bacterial Identification and Susceptibility Testing","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"Simon Fraser University","funders":"National Science Foundation Graduate Research Fellowship Program; National Institute of General Medical Sciences; National Institutes of Health","keywords":"Identification (biology); Subspecies; Metadata; Bacteria; Web application; Metabolite","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":[0.004862498,0.002658152,0.001784627,0.007424892,0.001077993,0.00418551,0.003731708,0.002073562,0.01438374],"category_scores_gemma":[0.006644568,0.001412457,0.001467449,0.00334018,0.0009413384,0.003286429,0.00714828,0.002209379,0.02060529],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0009557333,"about_ca_system_score_gemma":0.002657263,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003455209,"about_ca_topic_score_gemma":0.004958931,"domain_scores_codex":[0.9981902,0.0001908575,0.0001672119,0.0003667532,0.0009395832,0.0001453641],"domain_scores_gemma":[0.9954376,0.001016582,0.0005288965,0.001423651,0.0006027562,0.0009905797],"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":[0.003231379,0.001317434,0.01455505,0.003537589,0.0009784681,0.003086835,0.001427275,0.00702626,0.1641419,0.01467076,0.52809,0.2579371],"study_design_scores_gemma":[0.0009819922,0.0004424472,0.03561273,0.001094876,0.0003516403,0.002300003,0.0007044495,0.09141293,0.09977192,0.04439296,0.7219262,0.001007876],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"software","genre_gemma":"software","genre_scores_codex":[0.0186374,0.001308941,0.2462202,0.0009464919,0.0005433033,0.0008158224,0.1691855,0.5527227,0.009619692],"genre_scores_gemma":[0.0586569,0.001448438,0.3910019,0.001117002,0.0002890431,0.001261046,0.500528,0.03525046,0.01044722],"genre_candidate":"software","genre_consensus":"software","teacher_disagreement_score":0.01438374,"threshold_uncertainty_score":0.04811835,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05488303216128337,"score_gpt":0.3331743381509265,"score_spread":0.2782913059896431,"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."}}