{"id":"W4310960769","doi":"10.1093/nar/gkac1112","title":"Freddie: annotation-independent detection and discovery of transcriptomic alternative splicing isoforms using long-read sequencing","year":2022,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"RNA and protein synthesis mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":17,"is_retracted":false,"has_abstract":true,"ca_institutions":"Simon Fraser University; University of British Columbia","funders":"DOD Prostate Cancer Research Program; Canadian Institutes of Health Research; Michael Smith Health Research BC","keywords":"Annotation; Biology; Computational biology; Alternative splicing; Cluster analysis; Segmentation; Exon; DNA sequencing; Gene isoform; Computer science; Bioinformatics; Genetics; Artificial intelligence; Gene","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":[0.003263706,0.001761179,0.00133879,0.001647123,0.0008390333,0.001894656,0.002754841,0.001667696,0.002156842],"category_scores_gemma":[0.006002509,0.001122149,0.001983155,0.001331481,0.0009013003,0.001224892,0.00152312,0.002140428,0.001377411],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001020352,"about_ca_system_score_gemma":0.001836765,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002739262,"about_ca_topic_score_gemma":0.006193627,"domain_scores_codex":[0.9984878,0.0002667079,0.0001008849,0.0006860859,0.0003581392,0.0001003111],"domain_scores_gemma":[0.9976422,0.001405984,0.0002443588,0.0003659186,0.000251343,0.00009015918],"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":[0.00190943,0.0003803551,0.01343402,0.001651842,0.001083405,0.001371935,0.0008742526,0.1849659,0.2212459,0.02683189,0.03918853,0.5070624],"study_design_scores_gemma":[0.0001049969,0.0001430574,0.001765342,0.00005147759,0.00007593079,0.0003096158,0.0000898982,0.8996924,0.07046112,0.01322805,0.01398685,0.00009135318],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.02072324,0.0003649819,0.9389412,0.0001963861,0.0001065676,0.0001537303,0.002696777,0.03557205,0.001245012],"genre_scores_gemma":[0.05956338,0.000187053,0.9296276,0.0002010872,0.000029956,0.000268483,0.006594375,0.002025863,0.001502235],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.003263706,"threshold_uncertainty_score":0.01726037,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04472401955337067,"score_gpt":0.3189964249739821,"score_spread":0.2742724054206114,"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."}}