{"id":"W4399504522","doi":"10.1186/s13059-024-03275-x","title":"CelFiE-ISH: a probabilistic model for multi-cell type deconvolution from single-molecule DNA methylation haplotypes","year":2024,"lang":"en","type":"article","venue":"Genome biology","topic":"Epigenetics and DNA Methylation","field":"Biochemistry, Genetics and Molecular Biology","cited_by":12,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Israeli Centers for Research Excellence; Horizon 2020 Framework Programme; Azrieli Foundation; Israel Science Foundation","keywords":"Deconvolution; Biology; Haplotype; Leverage (statistics); Computational biology; DNA sequencing; DNA methylation; Probabilistic logic; Human genetics; Genetics; DNA; Computer science; Gene; Algorithm; Artificial intelligence; Genotype","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.003770257,0.001059943,0.001261278,0.00097265,0.0006214515,0.001692734,0.00295692,0.001795422,0.003616766],"category_scores_gemma":[0.007317026,0.00109275,0.001575819,0.0008225462,0.001088529,0.001654389,0.001882138,0.002541817,0.001781614],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00109028,"about_ca_system_score_gemma":0.001892093,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.005355292,"about_ca_topic_score_gemma":0.008408587,"domain_scores_codex":[0.999244,0.0001706538,0.0000318373,0.0002623323,0.000213898,0.0000773205],"domain_scores_gemma":[0.9978107,0.001234159,0.0001886646,0.000358157,0.0003085166,0.00009978562],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0006763868,0.0002014787,0.01434379,0.0005034817,0.0005382167,0.0003495608,0.00041909,0.6173146,0.06667574,0.06235236,0.01083735,0.2257879],"study_design_scores_gemma":[0.0000220284,0.00002814336,0.001097941,0.00001491758,0.00003038731,0.0001118498,0.00001600285,0.9596567,0.01051109,0.02439786,0.004056066,0.00005691175],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.003699985,0.0001038395,0.9940746,0.00007062764,0.00002039112,0.00002918955,0.0003906111,0.001151919,0.0004589057],"genre_scores_gemma":[0.2101783,0.000607569,0.773403,0.0005484538,0.0001177837,0.0005664148,0.003627569,0.001157633,0.009793283],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.005355292,"threshold_uncertainty_score":0.0199393,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05255356524208168,"score_gpt":0.2999731786029038,"score_spread":0.2474196133608222,"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."}}