{"id":"W6958790779","doi":"10.6084/m9.figshare.c.6791261","title":"BamQuery: a proteogenomic tool to explore the immunopeptidome and prioritize actionable tumor antigens","year":2023,"lang":"en","type":"other","venue":"Figshare","topic":"Legal and Regulatory Analysis","field":"Social Sciences","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Montréal","funders":"","keywords":"Proteogenomics; Immunogenicity; Antigen; RNA; Genomics; Genome; Transcriptome; Expression (computer science)","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":["insufficient_payload"],"consensus_categories":["insufficient_payload"],"category_scores_codex":[0.0001318363,0.0001791942,0.0002378569,0.0001157743,0.0005488184,0.0001937007,0.0003457454,0.0001627258,0.1899221],"category_scores_gemma":[0.000375957,0.0001261044,0.0001203522,0.0003839084,0.00004115923,0.0000648001,0.0001522324,0.0001760076,0.006312351],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00008412615,"about_ca_system_score_gemma":0.0002374939,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001334276,"about_ca_topic_score_gemma":0.002327331,"domain_scores_codex":[0.9988328,0.00009055717,0.0001320619,0.0003276507,0.000300583,0.0003163344],"domain_scores_gemma":[0.9994043,0.00006170315,0.0001107101,0.0002779115,0.00004756354,0.00009784209],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"not_applicable","study_design_scores_codex":[0.000002970785,0.000006212831,0.000009031023,0.00005471038,0.00007555979,0.00001466853,0.001682938,0.000001164237,0.00002609308,0.00004575385,0.9970775,0.001003408],"study_design_scores_gemma":[0.00005803486,0.00001011833,0.0003996155,0.0007725329,0.00002121446,0.000001263349,0.00112562,0.000001196699,0.00001645761,0.00003388731,0.997346,0.0002141044],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"other","genre_gemma":"other","genre_scores_codex":[0.001406909,0.003431764,4.343151e-7,0.003452452,0.0007559278,0.005321151,0.1234337,0.002182078,0.8600156],"genre_scores_gemma":[0.001390878,0.00007129375,0.00002986584,0.0002498724,0.001362732,0.0007819791,0.002130164,0.000321204,0.993662],"genre_candidate":"other","genre_consensus":"other","teacher_disagreement_score":0.1836097,"threshold_uncertainty_score":0.9944614,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05006097195386889,"score_gpt":0.295759877451265,"score_spread":0.2456989054973961,"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."}}