{"id":"W6902683378","doi":"10.6084/m9.figshare.c.6791261.v1","title":"BamQuery: a proteogenomic tool to explore the immunopeptidome and prioritize actionable tumor antigens","year":2023,"lang":"en","type":"other","venue":"Figshare","topic":"","field":"","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001740648,0.003124906,0.001533829,0.002226323,0.00101812,0.002496933,0.002541931,0.001357251,0.08704263],"category_scores_gemma":[0.002123888,0.001620019,0.001107883,0.001151659,0.0006309583,0.002099779,0.001694549,0.002217611,0.04704247],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0008138357,"about_ca_system_score_gemma":0.0007680419,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0009515288,"about_ca_topic_score_gemma":0.001328905,"domain_scores_codex":[0.9994703,0.00007512361,0.0000390207,0.0001458877,0.0001967678,0.00007290916],"domain_scores_gemma":[0.9991985,0.0004453063,0.00008196246,0.00009293172,0.00007755271,0.0001038158],"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":[0.003096971,0.0004669979,0.002197595,0.003154072,0.0003568151,0.001487488,0.000565763,0.003052047,0.3340342,0.01181222,0.4866611,0.1531148],"study_design_scores_gemma":[0.001254321,0.000367461,0.004919193,0.0003659869,0.0001664707,0.001473617,0.0001364988,0.04789978,0.3852179,0.01473423,0.5430334,0.0004311567],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"software","genre_gemma":"software","genre_scores_codex":[0.01284218,0.001122527,0.3768677,0.0007231704,0.0003312735,0.0005333712,0.09174008,0.5008618,0.01497795],"genre_scores_gemma":[0.07928107,0.001802154,0.4208586,0.001085313,0.0001632126,0.002924218,0.2243142,0.2339558,0.03561549],"genre_candidate":"software","genre_consensus":"software","teacher_disagreement_score":0.08704263,"threshold_uncertainty_score":0.2911866,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.07139268231385726,"score_gpt":0.2910955573713018,"score_spread":0.2197028750574445,"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."}}