{"id":"W4417448051","doi":"10.64898/2025.12.15.694404","title":"On Deriving Synteny Blocks by Compacting Elements","year":2025,"lang":"","type":"article","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Genome Rearrangement Algorithms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Simon Fraser University","funders":"","keywords":"Synteny; Genome; Block (permutation group theory); Breakpoint; Sequence (biology); Comparative genomics","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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.000779441,0.0008279407,0.000601858,0.0002928975,0.0005336704,0.0003089163,0.000781949,0.0005550545,0.000144784],"category_scores_gemma":[0.0004743775,0.000985341,0.0002452761,0.0008117377,0.0001772464,0.00002083972,0.000435286,0.0005104789,0.00009509509],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003064734,"about_ca_system_score_gemma":0.0004550222,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002130201,"about_ca_topic_score_gemma":0.000001897009,"domain_scores_codex":[0.9956638,0.0002120249,0.0008854297,0.001498577,0.0004664075,0.001273823],"domain_scores_gemma":[0.9972312,0.00007189164,0.0004506735,0.001453718,0.0004254679,0.0003670339],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.00007230295,0.0004270916,0.01394854,0.00018027,0.0006971656,0.00001727026,0.000003953312,0.00002239023,0.9783146,0.0001310265,0.006153879,0.00003145868],"study_design_scores_gemma":[0.001757214,0.0003297407,0.007580653,0.000553103,0.0002338255,1.613881e-8,0.00001827446,0.0005982614,0.9156811,9.608981e-7,0.07221591,0.001030955],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9855254,0.005782009,0.005060055,0.0004774861,0.001554055,0.0009642236,0.000223587,0.0001122265,0.0003009112],"genre_scores_gemma":[0.9959888,0.0007046228,0.001704489,0.0008991762,0.0003128969,0.00008497581,0.000001326592,0.0001353065,0.000168379],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.06606203,"threshold_uncertainty_score":0.9992597,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.006094927196160357,"score_gpt":0.216999188829563,"score_spread":0.2109042616334027,"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."}}