{"id":"W4409079926","doi":"10.1103/prxlife.3.022001","title":"Constraints on Metabolic Network Analysis in Bacterial Physiology","year":2025,"lang":"en","type":"article","venue":"PRX Life","topic":"Microbial Metabolic Engineering and Bioproduction","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Waterloo","funders":"","keywords":"Metabolic network; Computational biology; Network analysis; Computer science; Biology; Physiology; Engineering","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":[0.001846281,0.001211159,0.0007138014,0.001193529,0.0005584254,0.002059797,0.001019237,0.0009055103,0.00398206],"category_scores_gemma":[0.008984273,0.0004182826,0.0008126117,0.001498719,0.001232339,0.00371599,0.001591983,0.001808476,0.001020203],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0015307,"about_ca_system_score_gemma":0.0009476732,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002554246,"about_ca_topic_score_gemma":0.002047961,"domain_scores_codex":[0.9989653,0.0004495049,0.00005886923,0.0001549874,0.0003083912,0.00006304246],"domain_scores_gemma":[0.9972826,0.002072552,0.0001671134,0.0001600476,0.0002338333,0.00008380918],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"theoretical_or_conceptual","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0000277561,0.00001425233,0.000547539,0.0002035823,0.00002231987,0.0001659016,0.00009457306,0.1225046,0.002950176,0.846702,0.002299964,0.02446728],"study_design_scores_gemma":[0.000004346031,0.000009154057,0.0003885896,0.00008790706,0.000007436747,0.00006446236,0.00003901976,0.1975789,0.0009092509,0.7831722,0.01772095,0.00001773669],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.0165382,0.007840092,0.9337275,0.00272478,0.0002232121,0.00006270769,0.0006828211,0.0002034184,0.03799726],"genre_scores_gemma":[0.5230648,0.02978259,0.4256357,0.001021154,0.001169731,0.0007925563,0.001747401,0.0006089311,0.01617716],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.00398206,"threshold_uncertainty_score":0.01332134,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.004852718140277195,"score_gpt":0.2273304485949628,"score_spread":0.2224777304546857,"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."}}