{"id":"W3006949621","doi":"10.1021/acs.jproteome.9b00859","title":"MAPDP: A Cloud-Based Computational Platform for Immunopeptidomics Analyses","year":2020,"lang":"en","type":"article","venue":"Journal of Proteome Research","topic":"vaccines and immunoinformatics approaches","field":"Biochemistry, Genetics and Molecular Biology","cited_by":18,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Montréal; Institute for Research in Immunology and Cancer","funders":"Natural Sciences and Engineering Research Council of Canada; Canadian Cancer Society Research Institute; Canada Foundation for Innovation; Fonds de Recherche du Québec - Santé; Genome Canada","keywords":"Computational biology; Major histocompatibility complex; Proteome; Human leukocyte antigen; Biology; Computer science; Proteomics; Antigen; Bioinformatics; Immunology; Genetics; Gene","routes":{"ca_aff":true,"ca_fund":true,"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":[0.001086701,0.00009960344,0.0002024536,0.0001175291,0.0001279404,0.00007972055,0.0003619889,0.00008993939,0.00001723301],"category_scores_gemma":[0.0004813021,0.00007764437,0.0002035023,0.0002015597,0.00005521745,0.00001395189,0.00009576586,0.0002703751,0.000006252388],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002692121,"about_ca_system_score_gemma":0.0004331104,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000002466296,"about_ca_topic_score_gemma":3.792468e-7,"domain_scores_codex":[0.9987291,0.00004936706,0.0004708462,0.0001091254,0.0003883435,0.0002532569],"domain_scores_gemma":[0.998629,0.00006237289,0.0002219465,0.0001290395,0.000833513,0.0001241172],"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":[0.003730816,0.0001968581,0.0002695847,0.0004071199,0.0004375408,0.000006005576,0.0002963895,0.01979183,0.9544705,0.0003196422,0.01689895,0.003174714],"study_design_scores_gemma":[0.0126415,0.01341625,0.001101448,0.0001805291,0.00009135356,0.0001357496,0.001859072,0.1627902,0.691639,0.003537833,0.1119391,0.0006680136],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8218257,0.00130682,0.1721309,0.003270974,0.00009797898,0.0009876337,0.00004177241,0.000005414102,0.0003328593],"genre_scores_gemma":[0.9543592,0.00006110211,0.04456868,0.0002240421,0.0006183005,0.00002816946,0.00006072348,0.00002154386,0.00005818883],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2628315,"threshold_uncertainty_score":0.3166246,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.2122234474346346,"score_gpt":0.4187389652143857,"score_spread":0.2065155177797512,"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."}}