Related papers: Pattern matching in Lempel-Ziv compressed strings:…
In this paper we compare the difference in performance of two of the Prediction by Partial Matching (PPM) family of compressors (PPM$^*$ and the original Bounded PPM algorithm) and the Lempel-Ziv 78 (LZ) algorithm. We construct an infinite…
The Binary Jumbled String Matching problem is defined as: Given a string $s$ over $\{a,b\}$ of length $n$ and a query $(x,y)$, with $x,y$ non-negative integers, decide whether $s$ has a substring $t$ with exactly $x$ $a$'s and $y$ $b$'s.…
To store and search genomic databases efficiently, researchers have recently started building compressed self-indexes based on grammars. In this paper we show how, given a straight-line program with $r$ rules for a string (S [1..n]) whose…
We consider the problem of maintaining a collection of strings while efficiently supporting splits and concatenations on them, as well as comparing two substrings, and computing the longest common prefix between two suffixes. This problem…
Unbalanced translocations are among the most frequent chromosomal alterations, accounted for 30\% of all losses of heterozygosity, a major genetic event causing inactivation of tumor suppressor genes. Despite of their central role in…
Many services today massively and continuously produce log files of different and varying formats. These logs are important since they contain information about the application activities, which is necessary for improvements by analyzing…
A weighted string over an alphabet of size $\sigma$ is a string in which a set of letters may occur at each position with respective occurrence probabilities. Weighted strings, also known as position weight matrices or uncertain sequences,…
We consider the approximate pattern matching problem under the edit distance. Given a text $T$ of length $n$, a pattern $P$ of length $m$, and a threshold $k$, the task is to find the starting positions of all substrings of $T$ that can be…
In the classic longest common substring (LCS) problem, we are given two strings $S$ and $T$, each of length at most $n$, over an alphabet of size $\sigma$, and we are asked to find a longest string occurring as a fragment of both $S$ and…
Because of the vast volume of data being produced by today's scientific simulations, lossy compression allowing user-controlled information loss can significantly reduce the data size and the I/O burden. However, for large-scale cosmology…
In this paper, we revisit the much studied problem of Pattern Matching with Swaps (Swap Matching problem, for short). We first present a graph-theoretic model, which opens a new and so far unexplored avenue to solve the problem. Then, using…
A popular approach to sentence compression is to formulate the task as a constrained optimization problem and solve it with integer linear programming (ILP) tools. Unfortunately, dependence on ILP may make the compressor prohibitively slow,…
A Longest Common Extension (LCE) query on a text $T$ of length $N$ asks for the length of the longest common prefix of suffixes starting at given two positions. We show that the signature encoding $\mathcal{G}$ of size $w = O(\min(z \log N…
This paper gives new results for synchronization strings, a powerful combinatorial object that allows to efficiently deal with insertions and deletions in various communication settings: $\bullet$ We give a deterministic, linear time…
The dictionary matching problem is to locate occurrences of any pattern among a set of patterns in a given text. Massive data sets abound and at the same time, there are many settings in which working space is extremely limited. We…
A suffix tree is able to efficiently locate a pattern in an indexed string, but not in general the most recent copy of the pattern in an online stream, which is desirable in some applications. We study the most general version of the…
Tokenization efficiency plays a critical role in the performance and cost of large language models (LLMs), yet most models rely on static tokenizers optimized on general-purpose corpora. These tokenizers' fixed vocabularies often fail to…
Recently Kubica et al. (Inf. Process. Let., 2013) and Kim et al. (submitted to Theor. Comp. Sci.) introduced order-preserving pattern matching. In this problem we are looking for consecutive substrings of the text that have the same "shape"…
The currently fastest algorithm for regular expression pattern matching and membership improves the classical O(nm) time algorithm by a factor of about log^{3/2}n. Instead of focussing on general patterns we analyse homogeneous patterns of…
The compression-complexity trade-off of lossy compression algorithms that are based on a random codebook or a random database is examined. Motivated, in part, by recent results of Gupta-Verd\'{u}-Weissman (GVW) and their underlying…