{"id":"W4401385491","doi":"10.1093/nargab/lqae098","title":"Evaluating cell type deconvolution in FFPE breast tissue: application to benign breast disease","year":2024,"lang":"en","type":"review","venue":"NAR Genomics and Bioinformatics","topic":"Single-cell and spatial transcriptomics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Alberta","funders":"National Cancer Institute; National Institutes of Health; Mayo Clinic","keywords":"Deconvolution; Transcriptome; Computational biology; Cell type; RNA; Computer science; Cell; Pattern recognition (psychology); Artificial intelligence; Biology; Gene expression; Gene; Algorithm; Genetics","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":[0.001633987,0.0008999299,0.001157038,0.001994302,0.0001581142,0.0009906522,0.0008745635,0.001102172,0.001495489],"category_scores_gemma":[0.001996812,0.0003203441,0.0007375171,0.001267943,0.0004598571,0.0007606488,0.0006164907,0.001232471,0.001201541],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0006564886,"about_ca_system_score_gemma":0.0009064366,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001228769,"about_ca_topic_score_gemma":0.001955178,"domain_scores_codex":[0.9996537,0.00008001904,0.00003115456,0.00008581197,0.0001265097,0.00002279488],"domain_scores_gemma":[0.9992647,0.0004018714,0.00006504037,0.0000255301,0.0002094883,0.00003338656],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"not_applicable","study_design_scores_codex":[0.00007819411,0.00002743081,0.0004772911,0.007385355,0.0001742895,0.0001396752,0.00004180682,0.001369347,0.004616138,0.002803397,0.008149654,0.9747373],"study_design_scores_gemma":[0.00005606124,0.0004099418,0.005368592,0.005309742,0.000704196,0.004268414,0.0001247231,0.004497235,0.02160604,0.008839966,0.9486786,0.0001365485],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"review","genre_gemma":"review","genre_scores_codex":[0.0008690496,0.9911826,0.005620904,0.0003813032,0.0002041302,0.00001576541,0.00007411997,0.00004407474,0.001608121],"genre_scores_gemma":[0.008536041,0.9831655,0.005721737,0.0005177065,0.0002060032,0.00003537272,0.0002034353,0.00003098222,0.001583155],"genre_candidate":"review","genre_consensus":"review","teacher_disagreement_score":0.001994302,"threshold_uncertainty_score":0.008641422,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03001953645356214,"score_gpt":0.3274310347500039,"score_spread":0.2974114982964418,"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."}}