{"paper":{"title":"Parse indexing for choosing pseudo-MEMs","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"Parse indexing selects pseudo-MEMs guaranteed to contain every long MEM without picking k.","cross_cats":[],"primary_cat":"cs.DS","authors_text":"Travis Gagie","submitted_at":"2026-05-17T18:01:33Z","abstract_excerpt":"Brown et al.\\ (2025) recently proposed a pre-processing step, called $k$-mer based breaking (KeBaB), to speed up searches for long maximal exact matches (MEMs) between patterns and an indexed repetitive text. They fix a parameter $k$ and build a Bloom filter for the distinct $k$-mers in the text. When given a pattern, they quickly separate the $k$-mers in it into those that probably occur in the text and those that certainly do not. They call the maximal substrings of the pattern consisting only of the former $k$-mers {\\em pseudo-MEMs}. These pseudo-MEMs are guaranteed to contain all the MEMs "},"claims":{"count":4,"items":[{"kind":"strongest_claim","text":"We show how to use parse indexing to choose pseudo-MEMs to eliminate this risk, with the added benefit that we need not choose k.","source":"verdict.strongest_claim","status":"machine_extracted","claim_id":"C1","attestation":"unclaimed"},{"kind":"weakest_assumption","text":"That the properties of an existing parse index on the text are sufficient to identify a set of pseudo-MEMs that is guaranteed to contain every MEM of length at least k without introducing new parameters or post-hoc filters.","source":"verdict.weakest_assumption","status":"machine_extracted","claim_id":"C2","attestation":"unclaimed"},{"kind":"one_line_summary","text":"The paper shows how parse indexing can select pseudo-MEMs that contain every MEM of length at least k while eliminating the need to choose k and the risk of discarding important matches.","source":"verdict.one_line_summary","status":"machine_extracted","claim_id":"C3","attestation":"unclaimed"},{"kind":"headline","text":"Parse indexing selects pseudo-MEMs guaranteed to contain every long MEM without picking k.","source":"verdict.pith_extraction.headline","status":"machine_extracted","claim_id":"C4","attestation":"unclaimed"}],"snapshot_sha256":"1ff545324ad907884ee022461cb3ee31493cfd0bd7f422791a909c93598844bb"},"source":{"id":"2605.17574","kind":"arxiv","version":1},"verdict":{"id":"2a700a06-80a6-4189-a363-cf35a47ad8f0","model_set":{"reader":"grok-4.3"},"created_at":"2026-05-19T22:01:57.223425Z","strongest_claim":"We show how to use parse indexing to choose pseudo-MEMs to eliminate this risk, with the added benefit that we need not choose k.","one_line_summary":"The paper shows how parse indexing can select pseudo-MEMs that contain every MEM of length at least k while eliminating the need to choose k and the risk of discarding important matches.","pipeline_version":"pith-pipeline@v0.9.0","weakest_assumption":"That the properties of an existing parse index on the text are sufficient to identify a set of pseudo-MEMs that is guaranteed to contain every MEM of length at least k without introducing new parameters or post-hoc filters.","pith_extraction_headline":"Parse indexing selects pseudo-MEMs guaranteed to contain every long MEM without picking k."},"integrity":{"clean":true,"summary":{"advisory":0,"critical":0,"by_detector":{},"informational":0},"endpoint":"/pith/2605.17574/integrity.json","findings":[],"available":true,"detectors_run":[{"name":"doi_title_agreement","ran_at":"2026-05-19T22:31:19.564987Z","status":"completed","version":"1.0.0","findings_count":0},{"name":"doi_compliance","ran_at":"2026-05-19T22:12:21.011885Z","status":"completed","version":"1.0.0","findings_count":0},{"name":"ai_meta_artifact","ran_at":"2026-05-19T21:33:23.592787Z","status":"skipped","version":"1.0.0","findings_count":0},{"name":"claim_evidence","ran_at":"2026-05-19T21:21:57.523849Z","status":"completed","version":"1.0.0","findings_count":0}],"snapshot_sha256":"e86ff0fedb5e0e330d4ef368e33eec0f8be4bdad0d79c9c4ce3e3708867d6e01"},"references":{"count":16,"sample":[{"doi":"","year":2025,"title":"KeBaB: k-mer based breaking for finding long MEMs","work_id":"ca78d1ed-b7bc-4381-a54c-311fc0602773","ref_index":1,"cited_arxiv_id":"","is_internal_anchor":false},{"doi":"","year":2025,"title":"Faster run-length compressed suffix arrays","work_id":"0fef654e-4f95-4cc9-a557-c8ed6175a2a1","ref_index":2,"cited_arxiv_id":"","is_internal_anchor":false},{"doi":"","year":2025,"title":"Fast and small subsampled r-indexes","work_id":"97efe6e6-8e13-43c4-a050-0a21648e9046","ref_index":3,"cited_arxiv_id":"","is_internal_anchor":false},{"doi":"","year":2022,"title":"FM-indexing gram- mars induced by suffix sorting for long patterns","work_id":"22d3b93c-fa34-4d73-be24-d88704f07a9e","ref_index":4,"cited_arxiv_id":"","is_internal_anchor":false},{"doi":"","year":2000,"title":"Summary cache: a scalable wide-area web cache sharing protocol.IEEE/ACM Transactions on Networking, 8, 2000","work_id":"82672f92-ae7e-489c-9c36-316d018c0052","ref_index":5,"cited_arxiv_id":"","is_internal_anchor":false}],"resolved_work":16,"snapshot_sha256":"83fcd1b1b53d3765eb3c365746c74309dcbe873e2604fb0d34ae5b35aeccd35f","internal_anchors":1},"formal_canon":{"evidence_count":2,"snapshot_sha256":"89ba0ce410713d8e5bf339ce633f7c222804cde1ffb01fb39258a4e622aa6576"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"}