{"id":"W4400647996","doi":"10.1371/journal.pone.0298564","title":"Puzzle Hi-C: An accurate scaffolding software","year":2024,"lang":"en","type":"article","venue":"PLoS ONE","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Waterloo","funders":"National Key Research and Development Program of China; Yunnan University; National Natural Science Foundation of China","keywords":"Genomics; Genome; Software; Contig; Computational biology; Computer science; Sequence assembly; Scaffold; Cluster analysis; Comparative genomics; Scaffold protein; Biology; Genetics; Artificial intelligence; Gene","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":[0.003475468,0.002228982,0.001890909,0.002592005,0.001391161,0.002608832,0.006759185,0.00164652,0.04426167],"category_scores_gemma":[0.008019342,0.002332076,0.001878867,0.00207405,0.000705005,0.002681248,0.003938668,0.003810387,0.02456788],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001100212,"about_ca_system_score_gemma":0.002387287,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00414361,"about_ca_topic_score_gemma":0.003962441,"domain_scores_codex":[0.9983113,0.0002339209,0.0001897883,0.0003765335,0.000736998,0.0001514811],"domain_scores_gemma":[0.9959175,0.001512185,0.00038288,0.0009030386,0.000959349,0.0003250046],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"not_applicable","study_design_scores_codex":[0.002620881,0.0002289615,0.004663285,0.002517762,0.0007968033,0.0008802142,0.0008509137,0.01856814,0.06853379,0.01645895,0.5421057,0.3417747],"study_design_scores_gemma":[0.0008905045,0.0003575259,0.007175027,0.000376746,0.0003557971,0.001468625,0.0002310274,0.3553286,0.1579602,0.0239364,0.4511707,0.0007488502],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"methods","genre_gemma":"software","genre_scores_codex":[0.006158245,0.0004280709,0.553641,0.0002309144,0.0002279172,0.0003079168,0.01721098,0.4162565,0.005538485],"genre_scores_gemma":[0.04629151,0.0006554279,0.8031663,0.0004702519,0.0001131944,0.001722768,0.05335351,0.08296506,0.01126196],"genre_candidate":"software","genre_consensus":null,"teacher_disagreement_score":0.04426167,"threshold_uncertainty_score":0.14807,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02608947046259043,"score_gpt":0.2372393526100059,"score_spread":0.2111498821474155,"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."}}