Related papers: Beating O(nm) in approximate LZW-compressed patter…
We revisit the complexity of one of the most basic problems in pattern matching. In the k-mismatch problem we must compute the Hamming distance between a pattern of length m and every m-length substring of a text of length n, as long as…
The regular expression matching problem asks whether a given regular expression of length $m$ matches a given string of length $n$. As is well known, the problem can be solved in $O(nm)$ time using Thompson's algorithm. Moreover, recent…
Although real-world text datasets, such as DNA sequences, are far from being uniformly random, average-case string searching algorithms perform significantly better than worst-case ones in most applications of interest. In this paper, we…
Internal Pattern Matching (IPM) queries on a text $T$, given two fragments $X$ and $Y$ of $T$ such that $|Y|<2|X|$, ask to compute all exact occurrences of $X$ within $Y$. IPM queries have been introduced by Kociumaka, Radoszewski, Rytter,…
Given $d$ strings over the alphabet $\{0,1,\ldots,\sigma{-}1\}$, the classical Aho--Corasick data structure allows us to find all $occ$ occurrences of the strings in any text $T$ in $O(|T| + occ)$ time using $O(m\log m)$ bits of space,…
Computation on compressed strings is one of the key approaches to processing massive data sets. We consider local subsequence recognition problems on strings compressed by straight-line programs (SLP), which is closely related to…
We propose algorithms that, given the input string of length $n$ over integer alphabet of size $\sigma$, construct the Burrows-Wheeler transform (BWT), the permuted longest-common-prefix (PLCP) array, and the LZ77 parsing in…
The edit distance of two strings is the minimum number of insertions, deletions, and substitutions of characters needed to transform one string into the other. The textbook dynamic-programming algorithm computes the edit distance of two…
The random access problem for compressed strings is to build a data structure that efficiently supports accessing the character in position $i$ of a string given in compressed form. Given a grammar of size $n$ compressing a string of size…
We present a near-linear time algorithm that approximates the edit distance between two strings within a polylogarithmic factor; specifically, for strings of length n and every fixed epsilon>0, it can compute a (log n)^O(1/epsilon)…
We show how to determine whether a given pattern p of length m occurs in a given text t of length n in ${\tilde O}(\sqrt{n}+\sqrt{m})$\footnote{${\tilde O}$ allows for logarithmic factors in m and $n/m$} time, with inverse polynomial…
In this paper we give an algorithm for streaming $k$-edit approximate pattern matching which uses space $\widetilde{O}(k^2)$ and time $\widetilde{O}(k^2)$ per arriving symbol. This improves substantially on the recent algorithm of…
We study here the so called subsequence pattern matching also known as hidden pattern matching in which one searches for a given pattern $w$ of length $m$ as a subsequence in a random text of length $n$. The quantity of interest is the…
Let G be an edge-weighted hypergraph on n vertices, m edges of size \le s, where the edges have real weights in an interval [1,W]. We show that if we can approximate a maximum weight matching in G within factor alpha in time T(n,m,W) then…
Computing the LZ factorization (or LZ77 parsing) of a string is a computational bottleneck in many diverse applications, including data compression, text indexing, and pattern discovery. We describe new linear time LZ factorization…
A Random Access query to a string $T\in [0..\sigma)^n$ asks for the character $T[i]$ at a given position $i\in [0..n)$. In $O(n\log\sigma)$ bits of space, this fundamental task admits constant-time queries. While this is optimal in the…
Given two strings $S$ and $P$, the Episode Matching problem is to find the shortest substring of $S$ that contains $P$ as a subsequence. The best known upper bound for this problem is $\tilde O(nm)$ by Das et al. (1997) , where $n,m$ are…
We show tight bounds for online Hamming distance computation in the cell-probe model with word size w. The task is to output the Hamming distance between a fixed string of length n and the last n symbols of a stream. We give a lower bound…
We consider the problem of querying a string (or, a database) of length $N$ bits to determine all the locations where a substring (query) of length $M$ appears either exactly or is within a Hamming distance of $K$ from the query. We assume…
Two recent lower bounds on the compressibility of repetitive sequences, $\delta \le \gamma$, have received much attention. It has been shown that a length-$n$ string $S$ over an alphabet of size $\sigma$ can be represented within the…