{"id":"W4390042673","doi":"10.1101/2023.12.20.572682","title":"A validated pangenome-scale metabolic model for the <i>Klebsiella pneumoniae</i> species complex","year":2023,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Microbial Metabolic Engineering and Bioproduction","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Impact","funders":"Monash University","keywords":"Klebsiella pneumoniae; In silico; Biology; Model organism; Computational biology; Gene; Genetics; Escherichia coli","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":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0006412583,0.0005710595,0.0005217757,0.0001229922,0.0002501147,0.0001734107,0.0007465211,0.0005090221,0.000007623833],"category_scores_gemma":[0.0001585393,0.0004921861,0.0003297836,0.000314947,0.0001380389,0.000005992863,0.000554814,0.0003677825,0.00002916235],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003658438,"about_ca_system_score_gemma":0.0002321949,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003059468,"about_ca_topic_score_gemma":0.00001064428,"domain_scores_codex":[0.9975426,0.0000659257,0.000470046,0.001095512,0.000224507,0.0006014472],"domain_scores_gemma":[0.9975932,0.00001775853,0.0002594155,0.001575847,0.0004087521,0.0001450849],"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":[0.00003175941,0.0000509619,0.0001508406,0.0001427024,0.00027489,0.000001077891,0.000009165882,0.009535896,0.9843954,0.00009577808,0.005308742,0.00000273893],"study_design_scores_gemma":[0.000370848,0.00003844652,0.006001767,0.00004985444,0.000285836,4.925544e-8,0.00000392742,0.01051395,0.7910807,0.000002295197,0.1909245,0.0007278179],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.863099,0.007553644,0.1170913,0.00186158,0.004075618,0.002651389,0.003005899,0.000652763,0.000008818535],"genre_scores_gemma":[0.9863928,0.003360344,0.006529774,0.0002852168,0.00225021,0.0005120917,0.00001593294,0.0002428485,0.0004107872],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1933147,"threshold_uncertainty_score":0.999753,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03275234033977093,"score_gpt":0.229871456348704,"score_spread":0.1971191160089331,"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."}}