Related papers: Computing q-gram Non-overlapping Frequencies on SL…
Computing the diameter, and more generally, all eccentricities of an undirected graph is an important problem in algorithmic graph theory and the challenge is to identify graph classes for which their computation can be achieved in…
Much research in stringology focuses on structures that can, in a way, ``grasp'' repeats (substrings that occur multiple times) as, for example, the so-called runs, a.k.a. maximal repetitions, compactly describe all tandem repeats. In this…
Longest common extension queries (LCE queries) and runs are ubiquitous in algorithmic stringology. Linear-time algorithms computing runs and preprocessing for constant-time LCE queries have been known for over a decade. However, these…
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…
In this paper, an iterative algorithm is designed to compute the sparse graphs for traveling salesman problem (TSP) according to the frequency quadrilaterals so that the computation time of the algorithms for TSP will be lowered. At each…
Two important similarity measures between sequences are the longest common subsequence (LCS) and the dynamic time warping distance (DTWD). The computations of these measures for two given sequences are central tasks in a variety of…
We study the problem of estimating the edit distance between two $n$-character strings. While exact computation in the worst case is believed to require near-quadratic time, previous work showed that in certain regimes it is possible to…
Let $P$ and $Q$ be two simple polygons in the plane of total complexity $n$, each of which can be decomposed into at most $k$ convex parts. We present an $(1-\varepsilon)$-approximation algorithm, for finding the translation of $Q$, which…
Palindromes are important objects in strings which have been extensively studied from combinatorial, algorithmic, and bioinformatics points of views. It is known that the length of the longest palindromic substrings (LPSs) of a given string…
We investigate the problem of testing the equivalence between two discrete histograms. A {\em $k$-histogram} over $[n]$ is a probability distribution that is piecewise constant over some set of $k$ intervals over $[n]$. Histograms have been…
Given a pattern string $P$ of length $n$ and a query string $T$ of length $m$, where the characters of $P$ and $T$ are drawn from an alphabet of size $\Delta$, the {\em exact string matching} problem consists of finding all occurrences of…
We prove upper and lower bounds for the threshold of the q-overlap-k-Exact cover problem. These results are motivated by the one-step replica symmetry breaking approach of Statistical Physics, and the hope of using an approach based on that…
The compressed indexing problem is to preprocess a string $S$ of length $n$ into a compressed representation that supports pattern matching queries. That is, given a string $P$ of length $m$ report all occurrences of $P$ in $S$. We present…
An occurrence of a repeated substring $u$ in a string $S$ is called a net occurrence if extending the occurrence to the left or to the right decreases the number of occurrences to 1. The net frequency (NF) of a repeated substring $u$ in a…
The set of all $ q $-ary strings that do not contain repeated substrings of length $ \leqslant\! 3 $ (i.e., that do not contain substrings of the form $ a a $, $ a b a b $, and $ a b c a b c $) constitutes a code correcting an arbitrary…
We present algorithms for length-constrained maximum sum segment and maximum density segment problems, in particular, and the problem of finding length-constrained heaviest segments, in general, for a sequence of real numbers. Given a…
We present an algorithm computing the longest periodic subsequence of a string of length $n$ in $O(n^7)$ time with $O(n^4)$ words of space. We obtain improvements when restricting the exponents or extending the search allowing the reported…
The area of sublinear algorithms have recently received a lot of attention. In this setting, one has to choose specific access model for the input, as the algorithm does not have time to pre-process or even to see the whole input. A…
Consider a pair of plane straight-line graphs, whose edges are colored red and blue, respectively, and let n be the total complexity of both graphs. We present a O(n log n)-time O(n)-space technique to preprocess such pair of graphs, that…
Change-point problems have appeared in a great many applications for example cancer genetics, econometrics and climate change. Modern multiscale type segmentation methods are considered to be a statistically efficient approach for multiple…