Related papers: Faster Algorithms for Text-to-Pattern Hamming Dist…
In Pattern Matching with Weighted Edits (PMWED), we are given a pattern $P$ of length $m$, a text $T$ of length $n$, a positive threshold $k$, and oracle access to a weight function that specifies the costs of edits (depending on the…
We study algorithms for solving the problem of constructing a text (long string) from a dictionary (sequence of small strings). The problem has an application in bioinformatics and has a connection with the Sequence assembly method for…
We present parallel algorithms for exact and approximate pattern matching with suffix arrays, using a CREW-PRAM with $p$ processors. Given a static text of length $n$, we first show how to compute the suffix array interval of a given…
We present the first $m\,\text{polylog}(n)$ work, $\text{polylog}(n)$ time algorithm in the PRAM model that computes $(1+\epsilon)$-approximate single-source shortest paths on weighted, undirected graphs. This improves upon the breakthrough…
The tree edit distance is a natural dissimilarity measure between rooted ordered trees whose nodes are labeled over an alphabet $\Sigma$. It is defined as the minimum number of node edits (insertions, deletions, and relabelings) required to…
Two strings are considered to have parameterized matching when there exists a bijection of the parameterized alphabet onto itself such that it transforms one string to another. Parameterized matching has application in software duplication…
In this paper we study the classical problem of throughput maximization. In this problem we have a collection $J$ of $n$ jobs, each having a release time $r_j$, deadline $d_j$, and processing time $p_j$. They have to be scheduled…
Given two strings of length $n$ over alphabet $\Sigma$, and an upper bound $k$ on their edit distance, the algorithm of Myers (Algorithmica'86) and Landau and Vishkin (JCSS'88) computes the unweighted string edit distance in…
We describe a distributed randomized algorithm computing approximate distances and routes that approximate shortest paths. Let n denote the number of nodes in the graph, and let HD denote the hop diameter of the graph, i.e., the diameter of…
The edit distance between strings classically assigns unit cost to every character insertion, deletion, and substitution, whereas the Hamming distance only allows substitutions. In many real-life scenarios, insertions and deletions…
In this paper, a fully compressed pattern matching problem is studied. The compression is represented by straight-line programs (SLPs), i.e. a context-free grammars generating exactly one string; the term fully means that both the pattern…
This paper revisits the ordered statistics decoding (OSD). It provides a comprehensive analysis of the OSD algorithm by characterizing the statistical properties, evolution and the distribution of the Hamming distance and weighted Hamming…
We study several questions related to diversifying search results. We give improved approximation algorithms in each of the following problems, together with some lower bounds. - We give a polynomial-time approximation scheme (PTAS) for a…
In this paper we study lower bounds for the fundamental problem of text indexing with mismatches and differences. In this problem we are given a long string of length $n$, the "text", and the task is to preprocess it into a data structure…
Schoening presents a simple randomized algorithm for (d,k)-CSP problems with running time (d(k-1)/k)^n poly(n). Here, d is the number of colors, k is the size of the constraints, and n is the number of variables. A derandomized version of…
The classical pattern matching asks for locating all occurrences of one string, called the pattern, in another, called the text, where a string is simply a sequence of characters. Due to the potential practical applications, it is desirable…
We improve the running times of $O(1)$-approximation algorithms for the set cover problem in geometric settings, specifically, covering points by disks in the plane, or covering points by halfspaces in three dimensions. In the unweighted…
We study approximation algorithms for the following geometric version of the maximum coverage problem: Let $\mathcal{P}$ be a set of $n$ weighted points in the plane. Let $D$ represent a planar object, such as a rectangle, or a disk. We…
Let $(\{1,2,\ldots,n\},d)$ be a metric space. We analyze the expected value and the variance of $\sum_{i=1}^{\lfloor n/2\rfloor}\,d({\boldsymbol{\pi}}(2i-1),{\boldsymbol{\pi}}(2i))$ for a uniformly random permutation ${\boldsymbol{\pi}}$ of…
The $k$-mappability problem has two integers parameters $m$ and $k$. For every subword of size $m$ in a text $S$, we wish to report the number of indices in $S$ in which the word occurs with at most $k$ mismatches. The problem was lately…