Related papers: A faster algorithm for the construction of optimal…
We present an online algorithm to deal with pattern matching in strings. The problem we investigate is commonly known as string matching with mismatches in which the objective is to report the number of characters that match when a pattern…
We consider a range of simply stated dynamic data structure problems on strings. An update changes one symbol in the input and a query asks us to compute some function of the pattern of length $m$ and a substring of a longer text. We give…
This paper presents two new deterministic algorithms for constructing consensus trees. Given an input of k phylogenetic trees with identical leaf label sets and n leaves each, the first algorithm constructs the majority rule (+) consensus…
In the Longest Common Factor with $k$ Mismatches (LCF$_k$) problem, we are given two strings $X$ and $Y$ of total length $n$, and we are asked to find a pair of maximal-length factors, one of $X$ and the other of $Y$, such that their…
We study the problem of enumerating the $k$-arc-connected orientations of a graph $G$, i.e., generating each exactly once. A first algorithm using submodular flow optimization is easy to state, but intricate to implement. In a second…
We give the first O(m polylog(n)) time algorithms for approximating maximum flows in undirected graphs and constructing polylog(n) -quality cut-approximating hierarchical tree decompositions. Our algorithm invokes existing algorithms for…
We propose a new approach for calculating the Lempel-Ziv factorization of a string, based on run length encoding (RLE). We present a conceptually simple off-line algorithm based on a variant of suffix arrays, as well as an on-line algorithm…
In many applications, it is necessary to determine the string similarity. Edit distance[WF74] approach is a classic method to determine Field Similarity. A well known dynamic programming algorithm [GUS97] is used to calculate edit distance…
The algorithmic tasks of computing the Hamming distance between a given pattern of length $m$ and each location in a text of length $n$ is one of the most fundamental algorithmic tasks in string algorithms. Unfortunately, there is evidence…
We give an algorithm that decides whether the bipartite crossing number of a given graph is at most $k$. The running time of the algorithm is upper bounded by $2^{O(k)} + n^{O(1)}$, where $n$ is the number of vertices of the input graph,…
We consider two natural problems about nondeterministic finite automata. First, given such an automaton M of n states, and a length l, does M accept a word of length l? We show that the classic problem of triangle-free graph recognition…
With the development of connected filters for the last decade, many algorithms have been proposed to compute the max-tree. Max-tree allows to compute the most advanced connected operators in a simple way. However, no fair comparison of…
It has recently been shown that starting with a classical query algorithm (decision tree) and a guessing algorithm that tries to predict the query answers, we can design a quantum algorithm with query complexity $O(\sqrt{GT})$ where $T$ is…
We study the following rearrangement problem: Given $n$ words, rearrange and concatenate them so that the obtained string is lexicographically smallest (or largest, respectively). We show that this problem reduces to sorting the given words…
We describe a RAM algorithm computing all runs (maximal repetitions) of a given string of length $n$ over a general ordered alphabet in $O(n\log^{\frac{2}3} n)$ time and linear space. Our algorithm outperforms all known solutions working in…
We present a compressed representation of tries based on top tree compression [ICALP 2013] that works on a standard, comparison-based, pointer machine model of computation and supports efficient prefix search queries. Namely, we show how to…
In the moldable job scheduling problem one has to assign a set of $n$ jobs to $m$ machines, in order to minimize the time it takes to process all jobs. Each job is moldable, so it can be assigned not only to one but any number of the equal…
In this paper we present a really simple linear-time algorithm constructing a context-free grammar of size O(g log (N/g)) for the input string, where N is the size of the input string and g the size of the optimal grammar generating this…
In binary jumbled pattern matching we wish to preprocess a binary string $S$ in order to answer queries $(i,j)$ which ask for a substring of $S$ that is of size $i$ and has exactly $j$ 1-bits. The problem naturally generalizes to…
The Cartesian tree of a sequence captures the relative order of the sequence's elements. In recent years, Cartesian tree matching has attracted considerable attention, particularly due to its applications in time series analysis. Consider a…