Papers › On the Maximal Independent Sets of k-mers with the Edit Distance
On the Maximal Independent Sets of k-mers with the Edit Distance
Leran Ma, Ke Chen, Mingfu Shao
The archive published only this paper's code-link row. Authors, date and abstract are from arXiv's metadata (CC0), read from the Kaggle arXiv metadata snapshot of 2026-09-12 where its title matched the archive's; the title is the archive's.
In computational biology, k-mers and edit distance are fundamental concepts. However, little is known about the metric space of all k-mers equipped with the edit distance. In this work, we explore the structure of the k-mer space by studying its maximal independent sets (MISs). An MIS is a sparse sketch of all k-mers with nice theoretical properties, and therefore admits critical applications in clustering, indexing, hashing, and sketching large-scale sequencing data, particularly those with high error-rates. Finding an MIS is a challenging problem, as the size of a k-mer space grows geometrically with respect to k. We propose three algorithms for this problem. The first and the most intuitive one uses a greedy strategy. The second method implements two techniques to avoid redundant comparisons by taking advantage of the locality-property of the k-mer space and the estimated bounds on the edit distance. The last algorithm avoids expensive calculations of the edit distance by translating the edit distance into the shortest path in a specifically designed graph. These algorithms are implemented and the calculated MISs of k-mer spaces and their statistical properties are reported and analyzed for k up to 15. Source code is freely available at https://github.com/Shao-Group/kmerspace .
Code
Repository list and official/mentioned flags are the archive's, frozen 2025-07-28. Reachability, where shown, is from one Syntology probe window (2026-09-16 to 2026-09-18); repositories not probed show nothing. GitHub stars are not tracked.
Code Syntology ran Syntology
Not run by Syntology. Nothing on this page verifies that the listed code works.
Results from the paper archive 2025-07-28
No leaderboard rows for this paper in the archive.
Report a problem or propose a change · a person checks every report against the paper or source before anything changes; decisions are listed on /corrections