{"id":"W3036084659","doi":"10.1186/s40168-020-00864-3","title":"Revealing the microbial assemblage structure in the human gut microbiome using latent Dirichlet allocation","year":2020,"lang":"en","type":"article","venue":"Microbiome","topic":"Gut microbiota and health","field":"Biochemistry, Genetics and Molecular Biology","cited_by":53,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Institute of Genetics; Japan Society for the Promotion of Science; Research Organization of Information and Systems","keywords":"Biology; Latent Dirichlet allocation; Microbial ecology; Microbiome; Assemblage (archaeology); Gut microbiome; Ecology; Metagenomics; Medical microbiology; Computational biology; Evolutionary biology; Microbiology; Bacteria; Genetics; Topic model","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003766286,0.0002995483,0.0002389998,0.00007507685,0.0003723959,0.0001247039,0.000728938,0.000254163,0.00003658233],"category_scores_gemma":[0.00002264142,0.0002041935,0.0001354542,0.0004602186,0.0001371593,0.000009353533,0.0002076856,0.0003337381,0.00002149276],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00006211021,"about_ca_system_score_gemma":0.0001067031,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001668046,"about_ca_topic_score_gemma":0.0001960255,"domain_scores_codex":[0.9981287,0.0002648709,0.0004543146,0.0005475818,0.00009478931,0.0005097151],"domain_scores_gemma":[0.9991626,0.00001459531,0.0001751611,0.000503907,0.00007018595,0.00007361921],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.00002370097,0.00004260936,0.0005253618,0.00006121039,0.00002872312,0.000006527413,0.0009311007,0.00007554026,0.9900336,0.00002801355,0.00816517,0.00007846066],"study_design_scores_gemma":[0.001573452,0.0002297094,0.01151863,0.00008377665,0.00008215493,0.0002712844,0.0004859843,0.00006715764,0.8784077,0.00003097189,0.106543,0.000706192],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9932479,0.0007114689,0.0002695548,0.004809802,0.0001666224,0.0005857236,0.0001508645,0.00001748836,0.00004052771],"genre_scores_gemma":[0.9905254,0.00004172314,0.0005459951,0.00754363,0.0005000986,0.000006233061,0.000705224,0.00004286045,0.00008879196],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1116259,"threshold_uncertainty_score":0.8326769,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02967842357288501,"score_gpt":0.2866335081199388,"score_spread":0.2569550845470537,"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."}}