{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.002308484,0.001071186,0.001107136,0.00201793,0.0005922768,0.001243671,0.001533221,0.0009741306,0.003162802],"category_scores_gemma":[0.01010989,0.0007322036,0.001257767,0.002325054,0.001545457,0.002426668,0.002572179,0.001531216,0.0008212501],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001191786,"about_ca_system_score_gemma":0.001335348,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002963557,"about_ca_topic_score_gemma":0.003888776,"domain_scores_codex":[0.9981934,0.0005716504,0.0001329204,0.0003766515,0.0005357135,0.0001896208],"domain_scores_gemma":[0.9938019,0.004571686,0.0005243321,0.0005484163,0.0004316108,0.0001220815],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"theoretical_or_conceptual","study_design_scores_codex":[0.000171785,0.0001366952,0.002829728,0.0004623721,0.00006356578,0.0002213496,0.0003042446,0.6959214,0.02414687,0.129865,0.001664905,0.1442121],"study_design_scores_gemma":[0.0000424435,0.0002432685,0.001165891,0.0001229784,0.00004873226,0.0001567672,0.0001215523,0.8356105,0.01796196,0.1356242,0.008864447,0.00003721986],"study_design_candidate":"theoretical_or_conceptual","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.02586106,0.0001965743,0.9718551,0.0001263338,0.00001046765,0.00007642434,0.0002066841,0.0002023687,0.001464961],"genre_scores_gemma":[0.1276611,0.0003889664,0.8675416,0.0001136702,0.00003648456,0.0003281496,0.001427016,0.0003647304,0.002138372],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.003162802,"threshold_uncertainty_score":0.01220858,"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."}}