2013/01/25 by Travis Gagie, Danny Hermelin, Gagie, Travis +5 · 2 citations
Biochemistry, Genetics and Molecular Biology · Computer Science · #Algorithms and Data Compression #DNA and Biological Computing #Data Structures and Algorithms (cs.DS) #FOS: Computer and information sciences #Network Packet Processing and Optimization
paper · pdf · doi:10.48550/arxiv.1301.6127
openalex publication_date 2013/01/25 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
Binary jumbled pattern matching asks to preprocess a binary string S in order to answer queries (i,j) which ask for a substring of S that is of length i and has exactly j 1-bits. This problem naturally generalizes to vertex-labeled trees and graphs by replacing "substring" with "connected subgraph". In this paper, we give an O(n2 / log2 n)-time solution for trees, matching the currently best bound for (the simpler problem of) strings. We also give an \Ohg2 / 3 n4 / 3/(log n)4/3-time solution for strings that are compressed by a grammar of size g. This solution improves the known bounds when the string is compressible under many popular compression schemes. Finally, we prove that the problem is fixed-parameter tractable with respect to the treewidth w of the graph, thus improving the previous best nO(w) algorithm [ICALP'07].