{"id":"W4416215612","doi":"10.1101/gr.280569.125","title":"Graph-based deep reinforcement learning for haplotype assembly with Ralphi","year":2025,"lang":"en","type":"preprint","venue":"Genome Research","topic":"Genetic Associations and Epidemiology","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"Artificial Intelligence in Medicine (Canada)","funders":"National Institutes of Health; Broad Institute","keywords":"Haplotype; Genome; Reinforcement learning; Set (abstract data type); Allele; Genomics; Human genome; Fragment (logic)","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":[],"consensus_categories":[],"category_scores_codex":[0.002265918,0.0002601065,0.0003712811,0.000300068,0.0003686635,0.00005640083,0.000526714,0.0005853377,0.00002790535],"category_scores_gemma":[0.0006401445,0.0002373956,0.0001975297,0.0002194589,0.00014399,0.000001167546,0.0007015229,0.0007388494,0.00001279605],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001084997,"about_ca_system_score_gemma":0.0009643755,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001070339,"about_ca_topic_score_gemma":0.0001211098,"domain_scores_codex":[0.9972787,0.0004350273,0.0003613129,0.0007902998,0.000331467,0.0008031484],"domain_scores_gemma":[0.998002,0.0001817742,0.0001631158,0.0006977488,0.000826617,0.0001287315],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0007143178,0.0001184363,0.01076025,0.0006976421,0.000754448,0.000004419241,0.0001106465,0.9497349,0.02941215,0.0003132861,0.004269248,0.003110272],"study_design_scores_gemma":[0.007801364,0.0107896,0.04708366,0.0005552177,0.0004395776,0.000009510533,0.0009578941,0.1055464,0.01843484,0.00583378,0.799323,0.003225176],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.2141006,0.005750353,0.7603351,0.003249432,0.0004196273,0.004285106,0.0000970527,0.00007543788,0.01168736],"genre_scores_gemma":[0.9724935,0.0008145808,0.01084465,0.0002113346,0.0003812934,0.001180416,0.003074792,0.00005084824,0.01094854],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.8441885,"threshold_uncertainty_score":0.968071,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05809863799738766,"score_gpt":0.3721162728511507,"score_spread":0.314017634853763,"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."}}