{"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":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.000332834,0.0003887708,0.000524454,0.0001744934,0.00007791628,0.0001139903,0.0002387066,0.0003466039,0.000004708066],"category_scores_gemma":[0.00001562921,0.000341922,0.0001401296,0.0002595131,0.00003776542,0.000008721546,0.0001620283,0.0002214199,0.0001066994],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001100826,"about_ca_system_score_gemma":0.0003560603,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002230582,"about_ca_topic_score_gemma":0.00003182842,"domain_scores_codex":[0.9984146,0.0000387432,0.0007103063,0.0003900776,0.0001447721,0.0003014885],"domain_scores_gemma":[0.9991089,0.00001216708,0.000187381,0.0003861639,0.00008424475,0.000221196],"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":[0.00004508648,0.00005631947,0.00001726304,0.007694665,0.00004197945,0.00000202673,0.0001342537,0.00007965664,0.001174539,0.00002357387,0.0003345943,0.990396],"study_design_scores_gemma":[0.0003869186,0.0002764431,0.00003897206,0.001634841,0.0006910455,0.0001245922,0.00006318749,0.01449058,0.00006993916,0.00004791445,0.9813074,0.0008681306],"study_design_candidate":"design_other","study_design_consensus":null,"genre_codex":"review","genre_gemma":"review","genre_scores_codex":[0.005094885,0.9904845,0.00174433,0.00004162067,0.0003565085,0.001294223,0.0007266488,0.00002328421,0.0002340099],"genre_scores_gemma":[0.002115108,0.9917395,0.003602833,0.00010055,0.0003351682,0.00006158047,0.00174401,0.00006941539,0.0002318005],"genre_candidate":"review","genre_consensus":"review","teacher_disagreement_score":0.9895279,"threshold_uncertainty_score":0.9999033,"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."}}