{"id":"W4412834425","doi":"10.1101/2025.07.29.667561","title":"AmalgaMo: flexible DNA motif merging","year":2025,"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":"McGill University; Mila - Quebec Artificial Intelligence Institute; McGill University Health Centre","funders":"","keywords":"Motif (music); DNA; Computational biology; Computer science; Biology; Genetics; Art","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":[0.002982928,0.002373557,0.001802553,0.002858942,0.001472648,0.002541064,0.004928559,0.001600861,0.01894175],"category_scores_gemma":[0.01111079,0.001725495,0.002723521,0.002588217,0.0007419194,0.002504049,0.003895141,0.002415984,0.009034676],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0007194154,"about_ca_system_score_gemma":0.001182617,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002122554,"about_ca_topic_score_gemma":0.002967159,"domain_scores_codex":[0.9980888,0.0003430774,0.000145254,0.0007307962,0.0005428881,0.0001491693],"domain_scores_gemma":[0.9974036,0.001321694,0.0002243201,0.0006002677,0.0002675276,0.0001825542],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.004529734,0.0005551663,0.01519312,0.002681184,0.001241736,0.001072343,0.001299257,0.05578598,0.09531385,0.02809227,0.1913064,0.6029289],"study_design_scores_gemma":[0.0007070299,0.0002973271,0.003851383,0.0002787052,0.0002609332,0.00121838,0.0003064071,0.6533099,0.1468655,0.06393281,0.1286287,0.0003428332],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.01699957,0.0004499823,0.6862011,0.0002491596,0.0001415433,0.0002139085,0.00745928,0.2865914,0.001694026],"genre_scores_gemma":[0.07059357,0.0002023935,0.8873986,0.0003208146,0.00005940861,0.0007673621,0.01377236,0.02508717,0.001798243],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.01894175,"threshold_uncertainty_score":0.06336647,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.00731113344912562,"score_gpt":0.2131226027848796,"score_spread":0.2058114693357539,"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."}}