{"id":"W4401747011","doi":"10.1109/tcbb.2024.3447746","title":"NeoMS: Mass Spectrometry-Based Method for Uncovering Mutated MHC-I Neoantigens","year":2024,"lang":"en","type":"article","venue":"IEEE Transactions on Computational Biology and Bioinformatics","topic":"Immunotherapy and Immune Responses","field":"Immunology and Microbiology","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Waterloo","funders":"","keywords":"Mass spectrometry; Computational biology; Major histocompatibility complex; Chemistry; Computer science; Biology; Chromatography; Antigen; Genetics","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":[0.001050497,0.001087826,0.0006612852,0.002932557,0.0003667205,0.0007233915,0.0009107089,0.0007354431,0.001707455],"category_scores_gemma":[0.001466758,0.0002921578,0.0005919122,0.001228584,0.0003069794,0.0007710257,0.001008914,0.000490823,0.001245757],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003324543,"about_ca_system_score_gemma":0.0006579069,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0007347199,"about_ca_topic_score_gemma":0.001070134,"domain_scores_codex":[0.9994192,0.00006127648,0.00004259741,0.0001888095,0.0002463099,0.00004185345],"domain_scores_gemma":[0.9994924,0.0001314825,0.0001218411,0.00007520348,0.0001368645,0.00004214507],"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":[0.001219242,0.0003385336,0.01896502,0.0007958398,0.000346495,0.0008766611,0.0001518206,0.008698563,0.5839536,0.002162572,0.00754737,0.3749442],"study_design_scores_gemma":[0.0001570067,0.0004224902,0.02053079,0.00006642847,0.000211261,0.00338523,0.0002073738,0.5040444,0.4426541,0.00646688,0.02169151,0.0001624808],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.1923684,0.003037899,0.7830192,0.0003436574,0.0002056041,0.000352435,0.003783945,0.01335252,0.003536407],"genre_scores_gemma":[0.3113975,0.0009551976,0.6793891,0.0003568581,0.00007169238,0.0002589918,0.003739596,0.0004871789,0.003343955],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.002932557,"threshold_uncertainty_score":0.005712032,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01360018487492809,"score_gpt":0.2876374881180591,"score_spread":0.274037303243131,"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."}}