{"id":"W4296536574","doi":"10.1016/j.xpro.2022.101706","title":"Reconstructing cancer phylogenies using Pairtree, a clone tree reconstruction algorithm","year":2022,"lang":"en","type":"article","venue":"STAR Protocols","topic":"Cancer Genomics and Diagnostics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":11,"is_retracted":false,"has_abstract":true,"ca_institutions":"Ontario Genomics","funders":"National Cancer Institute; National Institutes of Health","keywords":"clone (Java method); Tree (set theory); Biology; Mutation; Computational biology; Computer science; Algorithm; Genetics; Gene; Mathematics; Combinatorics","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":[0.004908034,0.001718755,0.002200919,0.006002747,0.002314591,0.003427677,0.003138049,0.002135316,0.01574454],"category_scores_gemma":[0.01474445,0.002604365,0.003829954,0.004741569,0.0009324445,0.00327529,0.003414766,0.004097183,0.005952243],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001286395,"about_ca_system_score_gemma":0.002173335,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003122108,"about_ca_topic_score_gemma":0.005460932,"domain_scores_codex":[0.9979835,0.0005517869,0.000157485,0.0007250266,0.0004345605,0.0001475652],"domain_scores_gemma":[0.9963251,0.001925331,0.0002871374,0.0007342136,0.0005708112,0.0001573389],"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":[0.002288906,0.0005739364,0.03795378,0.003552494,0.003339446,0.002184998,0.003846638,0.09296357,0.09209445,0.07450189,0.1424019,0.544298],"study_design_scores_gemma":[0.0004891893,0.0003272263,0.01099681,0.0003466564,0.0008997226,0.002535814,0.0006112056,0.7150809,0.04201439,0.07961447,0.1468261,0.0002575529],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.03226151,0.0008554313,0.9176954,0.0003063786,0.0001621953,0.0003451805,0.01344472,0.03247459,0.002454543],"genre_scores_gemma":[0.04880531,0.0004230896,0.9162652,0.0001467321,0.00004430435,0.0005191659,0.0257076,0.006593099,0.001495441],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.01574454,"threshold_uncertainty_score":0.05267072,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02754533702232974,"score_gpt":0.3023880071025223,"score_spread":0.2748426700801926,"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."}}