{"id":"W4412481490","doi":"10.1007/s40291-025-00797-3","title":"Optimization of Metagenomic Next-Generation Sequencing Workflow with a Novel Host Depletion Method for Enhanced Pathogen Detection","year":2025,"lang":"en","type":"article","venue":"Molecular Diagnosis & Therapy","topic":"Bacterial Identification and Susceptibility Testing","field":"Biochemistry, Genetics and Molecular Biology","cited_by":7,"is_retracted":false,"has_abstract":true,"ca_institutions":"National Defence Medical Centre","funders":"Taipei Veterans General Hospital","keywords":"Metagenomics; Workflow; Human genetics; Computational biology; Host (biology); Pathogen; Biology; DNA sequencing; Computer science; Bioinformatics; Microbiology; Genetics; Gene","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":[],"consensus_categories":[],"category_scores_codex":[0.0003868394,0.0001569294,0.0001791878,0.00009346058,0.0001105081,0.00006613125,0.0001152816,0.0001346673,0.000009706854],"category_scores_gemma":[0.0001645891,0.0001549974,0.0001123405,0.0002258314,0.00002653024,0.00001336034,0.00001942692,0.00004394621,2.870556e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00005349786,"about_ca_system_score_gemma":0.00009184179,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00004788404,"about_ca_topic_score_gemma":0.0001127345,"domain_scores_codex":[0.9989145,0.0001287808,0.0002992551,0.0004200556,0.00008941883,0.0001479997],"domain_scores_gemma":[0.9991341,0.00003718293,0.000180967,0.0003282648,0.0002891386,0.00003038111],"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":[0.0001446007,0.00007945181,0.0001345943,0.00001921762,0.0001038485,1.214161e-7,0.00005938012,0.0190859,0.9600318,0.00003630361,0.000008734972,0.02029601],"study_design_scores_gemma":[0.0009114094,0.0002297496,0.0005380285,0.00002815424,0.00005398203,0.000001026249,0.00003898781,0.01434702,0.9831889,0.00002247463,0.0004893325,0.0001509878],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.4494587,0.00024562,0.5496585,0.00007007413,0.00007574464,0.0004545633,0.00001419666,0.00001245118,0.00001019121],"genre_scores_gemma":[0.8714632,0.0002363674,0.1270753,0.0003019783,0.00006191166,0.0004958615,0.0003145614,0.0000257454,0.00002508907],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.4225832,"threshold_uncertainty_score":0.6320612,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03834890060678876,"score_gpt":0.2836908920761865,"score_spread":0.2453419914693978,"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."}}