{"id":"W4408553729","doi":"10.1101/2025.03.17.643783","title":"ImmuniT Platform for Improved Neoantigen Prediction in Lung Cancer","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"vaccines and immunoinformatics approaches","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Simon Fraser University","funders":"","keywords":"Lung cancer; Computer science; Medicine; Computational biology; Oncology; Biology","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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0003969635,0.0004313173,0.0004128274,0.0001957641,0.0001230549,0.0001133244,0.0005249743,0.0006972706,0.00001360698],"category_scores_gemma":[0.0001024494,0.000458792,0.0001887494,0.0002063719,0.00003339224,0.00001658609,0.0005771702,0.0004066115,0.000001947716],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001434205,"about_ca_system_score_gemma":0.0007283612,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001360672,"about_ca_topic_score_gemma":0.00001679862,"domain_scores_codex":[0.9982403,0.00002581491,0.000607793,0.0005602138,0.00009918985,0.000466668],"domain_scores_gemma":[0.998329,0.00001492487,0.0003080716,0.0009687787,0.0002979265,0.00008130337],"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":[0.0002057546,0.000117009,0.006180669,0.001426314,0.0004257984,7.233494e-7,0.00002090384,0.0005802038,0.98907,0.0001241228,0.001820513,0.0000279754],"study_design_scores_gemma":[0.0031491,0.0002091272,0.04959689,0.0009900277,0.000295929,1.883674e-8,0.0000246426,0.05539433,0.8497596,0.00000466943,0.03918266,0.00139295],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9833219,0.006337648,0.005048466,0.0001467857,0.001330216,0.002036668,0.001658274,0.00008023436,0.00003980937],"genre_scores_gemma":[0.991086,0.002317667,0.004192655,0.0002178509,0.0005025115,0.001453851,0.00002188014,0.0000847394,0.000122822],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1393104,"threshold_uncertainty_score":0.9997864,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01192752768204733,"score_gpt":0.2358402324867905,"score_spread":0.2239127048047432,"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."}}