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Kondo et al. (DS 2014) proposed methods for computing distances between unordered rooted trees by transforming an instance of the distance computing problem into an instance of the integer programming problem. They showed that the tree edit…
N-fold integer programming is a fundamental problem with a variety of natural applications in operations research and statistics. Moreover, it is universal and provides a new, variable-dimension, parametrization of all of integer…
In the $k$-cut problem, we are given an edge-weighted graph $G$ and an integer $k$, and have to remove a set of edges with minimum total weight so that $G$ has at least $k$ connected components. The current best algorithms are an…
We describe algorithms to efficiently compute minimum $(s,t)$-cuts and global minimum cuts of undirected surface-embedded graphs. Given an edge-weighted undirected graph $G$ with $n$ vertices embedded on an orientable surface of genus $g$,…
Finding the length of the longest increasing subsequence (LIS) is a classic algorithmic problem. Let $n$ denote the size of the array. Simple $O(n\log n)$ algorithms are known for this problem. We develop a polylogarithmic time randomized…
We study dynamic $(1+\epsilon)$-approximation algorithms for the all-pairs shortest paths problem in unweighted undirected $n$-node $m$-edge graphs under edge deletions. The fastest algorithm for this problem is a randomized algorithm with…
We study Geometric Graph Edit Distance (GGED), a graph-editing model to compute the minimum edit distance of intersection graphs that uses moving objects as an edit operation. We first show an $O(n\log n)$-time algorithm that minimises the…
We give an $\tilde O(n^2)$ time algorithm for computing the exact Dynamic Time Warping distance between two strings whose run-length encoding is of size at most $n$. This matches (up to log factors) the known (conditional) lower bound, and…
We consider the classic problem of computing the Longest Common Subsequence (LCS) of two strings of length $n$. While a simple quadratic algorithm has been known for the problem for more than 40 years, no faster algorithm has been found…
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…
Longest Increasing Subsequence (LIS) is a fundamental statistic of a sequence, and has been studied for decades. While the LIS of a sequence of length $n$ can be computed exactly in time $O(n\log n)$, the complexity of estimating the…
Given a graph $G=(V,E)$ with two distinguished vertices $s,t\in V$ and an integer parameter $L>0$, an {\em $L$-bounded cut} is a subset $F$ of edges (vertices) such that the every path between $s$ and $t$ in $G\setminus F$ has length more…
In the presented paper we study the Length-Bounded Cut problem for special graph classes as well as from a parameterized-complexity viewpoint. Here, we are given a graph $G$, two vertices $s$ and $t$, and positive integers $\beta$ and…
In the decades-old Pattern Matching with Edits problem, given a length-$n$ string $T$ (the text), a length-$m$ string $P$ (the pattern), and a positive integer $k$ (the threshold), the task is to list the $k$-error occurrences of $P$ in…
In this paper, we develop deterministic fully dynamic algorithms for computing approximate distances in a graph with worst-case update time guarantees. In particular, we obtain improved dynamic algorithms that, given an unweighted and…
The Longest Common Subsequence (LCS) is a fundamental string similarity measure, and computing the LCS of two strings is a classic algorithms question. A textbook dynamic programming algorithm gives an exact algorithm in quadratic time, and…
In the Min $k$-Cut problem, input is an edge weighted graph $G$ and an integer $k$, and the task is to partition the vertex set into $k$ non-empty sets, such that the total weight of the edges with endpoints in different parts is minimized.…
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 study the problem of computing the minimum cut in a weighted distributed message-passing networks (the CONGEST model). Let $\lambda$ be the minimum cut, $n$ be the number of nodes in the network, and $D$ be the network diameter. Our…
We study the classic Text-to-Pattern Hamming Distances problem: given a pattern $P$ of length $m$ and a text $T$ of length $n$, both over a polynomial-size alphabet, compute the Hamming distance between $P$ and $T[i\, .\, . \, i+m-1]$ for…