Related papers: A Minimal Periods Algorithm with Applications
Detecting all the strings that occur in a text more frequently or less frequently than expected according to an IID or a Markov model is a basic problem in string mining, yet current algorithms are based on data structures that are either…
The k-Tree algorithm [Wagner 02] is a non-trivial algorithm for the average-case k-SUM problem that has found widespread use in cryptanalysis. Its input consists of k lists, each containing n integers from a range of size m. Wagner's…
We revisit the exact shortest unique substring (SUS) finding problem, and propose its approximate version where mismatches are allowed, due to its applications in subfields such as computational biology. We design a generic in-place…
A simple linear-time algorithm for constructing a linear context-free tree grammar of size O(rg + r g log (n/r g))for a given input tree T of size n is presented, where g is the size of a minimal linear context-free tree grammar for T, and…
A palindromic substring $T[i.. j]$ of a string $T$ is said to be a shortest unique palindromic substring (SUPS) in $T$ for an interval $[p, q]$ if $T[i.. j]$ is a shortest palindromic substring such that $T[i.. j]$ occurs only once in $T$,…
We consider the following problem: given an unsorted array of $n$ elements, and a sequence of intervals in the array, compute the median in each of the subarrays defined by the intervals. We describe a simple algorithm which uses O(n) space…
We present linear-space data structures for several frequency queries on trees, namely: path mode, path least frequent element, and path $\alpha$-minority queries. We present the first linear-space data structures, requiring $O(n…
We consider directed graphs where each edge is labeled with an integer weight and study the fundamental algorithmic question of computing the value of a cycle with minimum mean weight. Our contributions are twofold: (1) First we show that…
A minimax tree is similar to a Huffman tree except that, instead of minimizing the weighted average of the leaves' depths, it minimizes the maximum of any leaf's weight plus its depth. Golumbic (1976) introduced minimax trees and gave a…
Suppose we want to seek the longest common subsequences (LCSs) of two strings as informative patterns that explain the relationship between the strings. The dynamic programming algorithm gives us a table from which all LCSs can be extracted…
Regularities in strings are often related to periods and covers, which have extensively been studied, and algorithms for their efficient computation have broad application. In this paper we concentrate on computing cyclic regularities of…
A $k$-mismatch square is a string of the form $XY$ where $X$ and $Y$ are two equal-length strings that have at most $k$ mismatches. Kolpakov and Kucherov [Theor. Comput. Sci., 2003] defined two notions of $k$-mismatch repeats, called…
We consider the problem of constructing a sparse suffix tree (or suffix array) for $b$ suffixes of a given text $T$ of size $n$, using only $O(b)$ words of space during construction time. Breaking the naive bound of $\Omega(nb)$ time for…
We revisit two well-known algorithmic problems on strings: computing a shortest unique substring (SUS) and a shortest absent substring (SAS) of a string $S$ of length $n$. Both problems admit folklore $\mathcal{O}(n)$-time solutions using…
It is known that the Wadge reducibility of regular $\omega$-languages is efficiently decidable (Krishnan et al., 1995), (Wilke, Yoo, 1995). In this paper we study analogous problem for regular k-partitions of $\omega$-languages. In the…
Given a weighted $n$-vertex graph $G$ with integer edge-weights taken from a range $[-M,M]$, we show that the minimum-weight simple path visiting $k$ vertices can be found in time $\tilde{O}(2^k \poly(k) M n^\omega) = O^*(2^k M)$. If the…
A string is said to be closed if its length is one, or if it has a non-empty factor that occurs both as a prefix and as a suffix of the string, but does not occur elsewhere. The notion of closed words was introduced by [Fici, WORDS 2011].…
We continue the line of research started in "Broadword Implementation of Rank/Select Queries" proposing broadword (a.k.a. SWAR, "SIMD Within A Register") algorithms for finding matching closed parentheses and the k-th far closed…
We propose a linear algorithm for determining two function parameters by their linear combination. These functions must satisfy the first order differential equations with polynomial coefficients and our parameters are the coefficients of…
The parameterized matching problem is a variant of string matching, which is to search for all parameterized occurrences of a pattern $P$ in a text $T$. In considering matching algorithms, the combinatorial natures of strings, especially…