{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0008113691,0.00039586,0.0004177092,0.001267483,0.0003231822,0.0005917061,0.0003567199,0.0004800723,0.0006606448],"category_scores_gemma":[0.001500732,0.0001295496,0.0004700717,0.0007386259,0.0002189868,0.0003748392,0.0005786082,0.0003672951,0.0002237338],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0006615477,"about_ca_system_score_gemma":0.0005650201,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.009701171,"about_ca_topic_score_gemma":0.007216563,"domain_scores_codex":[0.9996928,0.00008561718,0.00001697667,0.00008119951,0.00004363944,0.00007991129],"domain_scores_gemma":[0.999665,0.000112064,0.00007465042,0.00003055594,0.00006396036,0.00005380007],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.002811381,0.001021593,0.5620974,0.0002911742,0.0006803756,0.002482102,0.0004339645,0.2174861,0.02579554,0.002480638,0.01302024,0.1713995],"study_design_scores_gemma":[0.00001491472,0.0001072857,0.1037558,0.00002225056,0.00005117499,0.0002349737,0.0001414119,0.8909542,0.001764468,0.002170522,0.0007632222,0.0000196612],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9883649,0.0006096213,0.007627476,0.0004240635,0.00003131435,0.00002657262,0.00189139,0.0001821444,0.0008424438],"genre_scores_gemma":[0.9936275,0.0001756634,0.003266536,0.00005245479,0.00001199281,0.00002172409,0.002327667,0.000006977503,0.0005094332],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.009701171,"threshold_uncertainty_score":0.01928937,"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."}}