{"id":"W3125312219","doi":"10.1101/2021.01.20.427493","title":"Freddie: Annotation-independent Detection and Discovery of Transcriptomic Alternative Splicing Isoforms","year":2021,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"RNA Research and Splicing","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"Simon Fraser University; University of British Columbia","funders":"Natural Sciences and Engineering Research Council of Canada; Michael Smith Health Research BC","keywords":"Annotation; Alternative splicing; Computer science; Computational biology; splice; Exon; Segmentation; Cluster analysis; Transcriptome; Gene isoform; Data mining; Biology; Artificial intelligence; Gene; Genetics","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.002579089,0.00125868,0.001180186,0.001844427,0.0006742731,0.001586686,0.002515004,0.001437289,0.002115945],"category_scores_gemma":[0.004221108,0.000946281,0.001563391,0.001226199,0.0008074151,0.00105526,0.001342094,0.00146632,0.0009087295],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001052225,"about_ca_system_score_gemma":0.00139148,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003053716,"about_ca_topic_score_gemma":0.005362157,"domain_scores_codex":[0.9988985,0.0001911409,0.00006172501,0.0005106364,0.000241278,0.00009670276],"domain_scores_gemma":[0.9979113,0.001316868,0.0001657811,0.0002930896,0.0002306165,0.00008219692],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.001629233,0.000361885,0.01462458,0.0008445745,0.0005796482,0.0009913668,0.0004353122,0.2883842,0.1507674,0.0202295,0.02092176,0.5002305],"study_design_scores_gemma":[0.00004209481,0.00005858906,0.0007470551,0.00001376433,0.00002263904,0.0001271408,0.00003631625,0.9633414,0.02613642,0.005918957,0.003527939,0.00002764581],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.0375402,0.0002967189,0.9383218,0.0002104198,0.00006035297,0.00012299,0.001606774,0.02068289,0.001157773],"genre_scores_gemma":[0.1017645,0.0001174591,0.8912681,0.0001541924,0.00002180986,0.0001644617,0.00412592,0.0009262051,0.00145746],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.003053716,"threshold_uncertainty_score":0.01363969,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.009011507757822716,"score_gpt":0.2291922027775129,"score_spread":0.2201806950196901,"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."}}