{"id":"W4413377109","doi":"10.1101/2025.08.13.669859","title":"Human outbreak detection and best practice MPXV analysis and interpretation with squirrel","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Bacteriophages and microbial interactions","field":"Environmental Science","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"McMaster University; Public Health Agency of Canada","funders":"","keywords":"Interpretation (philosophy); Outbreak; Geography; Biology; Virology; Linguistics; Philosophy","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":[0.007051251,0.0009772591,0.0005564884,0.001981365,0.0008299577,0.001950055,0.0008783462,0.0008142088,0.007079126],"category_scores_gemma":[0.007990984,0.0006024727,0.0007755932,0.0007899571,0.0004161512,0.0008250567,0.001684753,0.0006188437,0.003710454],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000574818,"about_ca_system_score_gemma":0.0008840136,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.005941779,"about_ca_topic_score_gemma":0.01088473,"domain_scores_codex":[0.9981438,0.0005680277,0.0001366983,0.0006379486,0.000373964,0.000139561],"domain_scores_gemma":[0.9971771,0.0009276916,0.0003203339,0.0005951671,0.0006927128,0.0002870324],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.004999132,0.0004460262,0.3563742,0.002004898,0.000921385,0.003715041,0.007695776,0.01732638,0.2013653,0.002671293,0.07193177,0.3305488],"study_design_scores_gemma":[0.0005241111,0.001838849,0.4061741,0.001642415,0.000662564,0.006851439,0.004710749,0.1672486,0.2236671,0.01603918,0.1697834,0.0008575459],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.719549,0.001696242,0.1520286,0.002858164,0.000453282,0.0006166363,0.02724267,0.07436877,0.02118662],"genre_scores_gemma":[0.6899633,0.0003955022,0.2854088,0.0007395067,0.00009500521,0.0001738333,0.01564519,0.004644172,0.002934738],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.007079126,"threshold_uncertainty_score":0.03729099,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0061559035273479,"score_gpt":0.2301536582723392,"score_spread":0.2239977547449913,"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."}}