{"id":"W4393861186","doi":"10.20517/mrr.2023.57","title":"RapidAIM 2.0: a high-throughput assay to study functional response of human gut microbiome to xenobiotics","year":2024,"lang":"en","type":"article","venue":"Microbiome Research Reports","topic":"Gut microbiota and health","field":"Biochemistry, Genetics and Molecular Biology","cited_by":6,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Ottawa","funders":"Government of Canada; Genome Canada","keywords":"Xenobiotic; Microbiome; Gut microbiome; Computational biology; Biology; Microbiology; Bioinformatics; Biochemistry","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.008916616,0.0003736062,0.0004766665,0.00121492,0.0003874161,0.0001829281,0.0004120057,0.0003065481,0.0003882128],"category_scores_gemma":[0.0005271505,0.0003603216,0.0002052302,0.001729878,0.0002246692,0.00001206576,0.0009214341,0.0004434649,0.0002428886],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002701387,"about_ca_system_score_gemma":0.001077248,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0003554243,"about_ca_topic_score_gemma":0.0001435072,"domain_scores_codex":[0.9948341,0.0009401159,0.00101985,0.001471891,0.0006507624,0.001083333],"domain_scores_gemma":[0.9969267,0.0001172003,0.0001145622,0.001381656,0.0009851425,0.0004747899],"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":[0.0005537809,0.0006581395,0.0006140827,0.0001659892,0.0002185298,0.0005574497,0.0005200641,0.00001382666,0.9130006,0.00002471241,0.08321778,0.0004550713],"study_design_scores_gemma":[0.0005133682,0.003725887,0.02089916,0.0001816931,0.00003457732,0.0006948405,0.0003773978,8.257203e-7,0.7766005,0.00006151973,0.1964361,0.0004741071],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9944978,0.0007643834,0.0005296853,0.001316227,0.0006725349,0.001808502,0.0001794276,0.00005940696,0.0001720514],"genre_scores_gemma":[0.9907848,0.00002251881,0.001314932,0.0002413403,0.0003499448,0.00008048621,0.000285788,0.0001023269,0.006817852],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1364,"threshold_uncertainty_score":0.9998849,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05651326206312624,"score_gpt":0.4034440881024889,"score_spread":0.3469308260393627,"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."}}