{"id":"W4377565341","doi":"10.1021/acs.jproteome.2c00563","title":"Deep Proteomics Network and Machine Learning Analysis of Human Cerebrospinal Fluid in Japanese Encephalitis Virus Infection","year":2023,"lang":"en","type":"article","venue":"Journal of Proteome Research","topic":"Mosquito-borne diseases and control","field":"Medicine","cited_by":10,"is_retracted":false,"has_abstract":true,"ca_institutions":"Discovery Centre","funders":"Medical Research Council; Liverpool University Hospitals NHS Foundation Trust; Institut Pasteur; Liverpool School of Tropical Medicine; Institut National de la Santé et de la Recherche Médicale; University of Oxford; Wellcome; Imperial College London; Chinese Academy of Medical Sciences; National Institute for Health and Care Research; National Institute for Health Research Health Protection Research Unit; Horizon 2020 Framework Programme; Aix-Marseille Université; Fondation Mérieux; Wellcome Trust","keywords":"Proteomics; Proteome; Tandem mass spectrometry; Quantitative proteomics; Cerebrospinal fluid; Tandem mass tag; Encephalitis; Mass spectrometry; Medicine; Computational biology; Virology; Biology; Virus; Bioinformatics; Pathology; Chemistry; Chromatography; Biochemistry","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":[0.003897415,0.0001200393,0.0006250823,0.001602394,0.0001622007,0.0000475973,0.0001193704,0.0001010531,0.0001887439],"category_scores_gemma":[0.0007090026,0.00009877109,0.0002300081,0.00321044,0.0001238272,0.0001359592,0.000101613,0.0009226459,0.000004715911],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001307592,"about_ca_system_score_gemma":0.0001510089,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001635155,"about_ca_topic_score_gemma":0.0004512758,"domain_scores_codex":[0.997273,0.0004691357,0.0006790108,0.0002042785,0.0009215372,0.0004530192],"domain_scores_gemma":[0.9985946,0.0001333904,0.0002727644,0.0001820246,0.000577507,0.0002397556],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.001865891,0.0002969347,0.7543934,0.0005099111,0.0009934299,0.000391294,0.0009336055,0.006874217,0.2282484,0.0001095257,0.00007312461,0.00531022],"study_design_scores_gemma":[0.002631977,0.003101722,0.9315996,0.0004262511,0.0004872147,0.00006553272,0.0003831513,0.05912024,0.001576473,0.0003426732,0.0001372522,0.000127879],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9975753,0.001052249,0.0001928218,0.0003301172,0.0000301935,0.0006955341,0.000003935568,0.00001192718,0.000107951],"genre_scores_gemma":[0.9981658,0.001014963,0.0001509622,0.00001159882,0.0002888287,0.00005356361,0.00001399954,0.00001857481,0.0002816581],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.226672,"threshold_uncertainty_score":0.4027768,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05669279188796712,"score_gpt":0.3835042939206799,"score_spread":0.3268115020327128,"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."}}