{"id":"W4391554852","doi":"10.1101/2024.01.29.577879","title":"Puzzle Hi-C: an accurate scaffolding software","year":2024,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Toronto and Region Conservation Authority; University of Waterloo","funders":"Yunnan University","keywords":"Contig; Software; Computer science; Genomics; Scaffold; Sequence assembly; Genome; Cluster analysis; Computational biology; Window (computing); Quality (philosophy); Scaffold protein; Chromosome; Biology; Genetics; Artificial intelligence; Physics; Gene; World Wide Web","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":[0.003687923,0.002234623,0.001663442,0.00270681,0.001131674,0.002680205,0.005903393,0.001450135,0.03489049],"category_scores_gemma":[0.007808682,0.00217147,0.00144855,0.002373753,0.0007897983,0.002351017,0.003761904,0.00346997,0.02458201],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0009064305,"about_ca_system_score_gemma":0.001880823,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003590677,"about_ca_topic_score_gemma":0.002402288,"domain_scores_codex":[0.9984743,0.000237097,0.0001609167,0.0003512195,0.000648969,0.0001275666],"domain_scores_gemma":[0.9959472,0.001488128,0.0003569185,0.001075786,0.0008576683,0.0002743038],"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":[0.002232315,0.000213247,0.004422565,0.00191113,0.0005940538,0.0007982619,0.0006253261,0.02825439,0.07577372,0.02423584,0.5537297,0.3072095],"study_design_scores_gemma":[0.000747199,0.0002240939,0.004789294,0.000281922,0.0002176282,0.001054186,0.0001504265,0.5051279,0.1645117,0.02729723,0.2950764,0.0005220278],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"methods","genre_gemma":"software","genre_scores_codex":[0.005274888,0.0002572923,0.6379339,0.0001834447,0.0001581435,0.0002083899,0.01277652,0.3394721,0.003735358],"genre_scores_gemma":[0.05018847,0.000434165,0.8232224,0.0003041112,0.00009633479,0.001237282,0.04842829,0.06725793,0.008831027],"genre_candidate":"software","genre_consensus":null,"teacher_disagreement_score":0.03489049,"threshold_uncertainty_score":0.1167204,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01032586611683723,"score_gpt":0.2256788665847476,"score_spread":0.2153530004679104,"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."}}