{"paper":{"title":"MEM-finding with run-length compressed strings","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":[],"primary_cat":"cs.DS","authors_text":"Davide Cozzi, Paola Bonizzoni, Ragnar Groot Koerkamp, Travis Gagie, Younan Gao","submitted_at":"2026-08-02T17:07:47Z","abstract_excerpt":"We show how to store a text $T [1..n]$ consisting of $\\rho_T$ runs in $O (\\rho_T + \\chi)$ space, where $\\chi$ is the size of the smallest suffixient set for $T$, such that when we are given a pattern $P [1..m]$ consisting of $\\rho_P$ runs we can find the maximal exact matches (MEMs) of $P$ with respect to $T$ in $O (\\rho_P \\log m)$ time plus constant time for each edge we would fully or partially descend in the suffix tree for $T$ while finding those MEMs. We then adapt and optimize our result to finding set-maximal exact matches (SMEMs) of query haplotypes with respect to stored haplotype pan"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2608.01387","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/2608.01387/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"}