{"id":"W4412683887","doi":"10.1101/2025.07.23.666343","title":"Protein Embeddings and Local Alignments","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Protein Structure and Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"McMaster University; Western University","funders":"Natural Sciences and Engineering Research Council of Canada; Alliance de recherche numérique du Canada","keywords":"Computer science; Computational biology; Biology","routes":{"ca_aff":true,"ca_fund":true,"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":[0.001698782,0.001301568,0.001037416,0.004624921,0.0006694573,0.002151108,0.001421889,0.001750931,0.006387803],"category_scores_gemma":[0.01296877,0.0005173233,0.0008018658,0.004594398,0.001289672,0.00402326,0.002031372,0.001344187,0.002284471],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001095498,"about_ca_system_score_gemma":0.0005524723,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0008608945,"about_ca_topic_score_gemma":0.001127836,"domain_scores_codex":[0.9966815,0.000835093,0.0002989056,0.001055321,0.0009312884,0.0001978553],"domain_scores_gemma":[0.9920456,0.003500147,0.001717357,0.001237303,0.001244886,0.0002545817],"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":[0.0008155267,0.0003380248,0.02513725,0.001561839,0.0003542769,0.0005892559,0.0003776438,0.4127807,0.01667884,0.106028,0.02157547,0.4137631],"study_design_scores_gemma":[0.00004931414,0.0001983588,0.004080482,0.0001016336,0.00005281954,0.0005028297,0.0001578805,0.8600697,0.009030216,0.1163189,0.009394458,0.0000434766],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.2078564,0.005217436,0.7612589,0.001447116,0.0002647705,0.0002219857,0.006005467,0.007667423,0.01006046],"genre_scores_gemma":[0.7489555,0.001263825,0.2317042,0.0002825086,0.0002363478,0.0002875626,0.01203533,0.0007622962,0.004472426],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.006387803,"threshold_uncertainty_score":0.02136934,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.005148957874356748,"score_gpt":0.2150123228464395,"score_spread":0.2098633649720827,"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."}}