{"id":"W4411729841","doi":"10.52843/cassyni.fmnjm6","title":"Functional archetypes in the human gut microbiome reveal metabolic diversity, stability, and confound disease-associated signatures","year":2025,"lang":"en","type":"preprint","venue":"","topic":"Gut microbiota and health","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Natural Sciences and Engineering Research Council of Canada; Vector Institute","keywords":"Microbiome; Diversity (politics); Evolutionary biology; Biology; Functional diversity; Disease; Metagenomics; Archetype; Gut microbiome; Computational biology; Ecology; Medicine; Bioinformatics; Genetics; Sociology; Internal medicine; Anthropology; Philosophy; Gene","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0009296112,0.0005140469,0.0004737326,0.0008582232,0.0003080774,0.0009527103,0.0002209773,0.0005361706,0.001833773],"category_scores_gemma":[0.002330406,0.0002114494,0.0005468936,0.0008435228,0.0007370313,0.0006241728,0.001297358,0.0008978696,0.0002929826],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003529347,"about_ca_system_score_gemma":0.0004710745,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001317527,"about_ca_topic_score_gemma":0.00199755,"domain_scores_codex":[0.9996064,0.0001152643,0.00001758577,0.0001458285,0.00004467029,0.00007015584],"domain_scores_gemma":[0.9991688,0.0002874543,0.0001869325,0.000175973,0.00006997467,0.0001110946],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.00302711,0.0002007929,0.5560096,0.0006742703,0.0010237,0.000644835,0.001140121,0.01741393,0.2400366,0.008549984,0.0034094,0.1678696],"study_design_scores_gemma":[0.00006416962,0.0003455875,0.8088334,0.0001832472,0.0003826465,0.001775063,0.0009326653,0.07086203,0.02940183,0.07914234,0.007952053,0.0001248433],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9509559,0.002354159,0.04058957,0.0006874957,0.00004726276,0.00001785498,0.00323522,0.0002629717,0.001849632],"genre_scores_gemma":[0.9883668,0.0004195744,0.009416896,0.0001640985,0.00002014537,0.00001563271,0.001174106,0.0000501983,0.0003725932],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001833773,"threshold_uncertainty_score":0.00613457,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03264642717430129,"score_gpt":0.2858159125401757,"score_spread":0.2531694853658744,"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."}}