{"paper":{"title":"Bridging the Gaps in Statistical Models of Protein Alignment","license":"http://creativecommons.org/licenses/by-nc-sa/4.0/","headline":"","cross_cats":["q-bio.BM","stat.ML"],"primary_cat":"cs.LG","authors_text":"Arun S. Konagurthu, Dinithi Sumanaweera, Lloyd Allison","submitted_at":"2020-10-02T08:36:24Z","abstract_excerpt":"This work demonstrates how a complete statistical model quantifying the evolution of pairs of aligned proteins can be constructed from a time-parameterised substitution matrix and a time-parameterised 3-state alignment machine. All parameters of such a model can be inferred from any benchmark data-set of aligned protein sequences. This allows us to examine nine well-known substitution matrices on six benchmarks curated using various structural alignment methods; any matrix that does not explicitly model a \"time\"-dependent Markov process is converted to a corresponding base-matrix that does. In"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2010.00855","kind":"arxiv","version":1},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"integrity":{"clean":true,"summary":{"advisory":0,"critical":0,"by_detector":{},"informational":0},"endpoint":"/pith/2010.00855/integrity.json","findings":[],"available":true,"detectors_run":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938"},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"}