{"id":"W4416441178","doi":"10.1101/2025.11.20.687681","title":"Inferring and Evaluating Network Medicine-Based Disease Modules with Nextflow","year":2025,"lang":"","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Bioinformatics and Genomic Networks","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"Discovery Centre","funders":"HORIZON EUROPE Framework Programme; Deutsche Forschungsgemeinschaft","keywords":"Pipeline (software); Context (archaeology); Resource (disambiguation); Human disease; Precision medicine; Biological network","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":[0.004390414,0.001579275,0.000851454,0.006372414,0.0008745147,0.001936589,0.00139971,0.001056531,0.004667266],"category_scores_gemma":[0.01184374,0.0006258666,0.001994188,0.001434819,0.0005924778,0.001691843,0.002037977,0.0009353782,0.00102667],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001261894,"about_ca_system_score_gemma":0.002102905,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003661443,"about_ca_topic_score_gemma":0.004225755,"domain_scores_codex":[0.999045,0.0003287641,0.00007521849,0.0002502255,0.0002168338,0.00008385407],"domain_scores_gemma":[0.9954594,0.002864956,0.0004494233,0.0004689066,0.0004979318,0.0002594623],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.001998588,0.0006553343,0.1083478,0.003657522,0.001800542,0.001630002,0.001143215,0.3715579,0.0488314,0.02867159,0.0538513,0.3778549],"study_design_scores_gemma":[0.00009701728,0.0002014757,0.007018235,0.0001974327,0.0002308125,0.0004004113,0.00009224934,0.9285751,0.02178201,0.02767492,0.01366302,0.00006735693],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.1868825,0.002770413,0.7268673,0.001550964,0.0003100831,0.0007335783,0.02112784,0.05573054,0.00402676],"genre_scores_gemma":[0.4192885,0.001108288,0.5352862,0.0005158569,0.000114378,0.0006458736,0.0397061,0.001725317,0.001609543],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.006372414,"threshold_uncertainty_score":0.02321905,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01235305484855457,"score_gpt":0.2344427335251693,"score_spread":0.2220896786766147,"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."}}