Related papers: An Efficient Dynamic Programming Algorithm for STR…
We present a deterministic algorithm for solving a wide range of dynamic programming problems in trees in $O(\log D)$ rounds in the massively parallel computation model (MPC), with $O(n^\delta)$ words of local memory per machine, for any…
This paper studies parallel algorithms for the longest increasing subsequence (LIS) problem. Let $n$ be the input size and $k$ be the LIS length of the input. Sequentially, LIS is a simple problem that can be solved using dynamic…
This paper describes a linear-time algorithm that finds the longest stretch in a sequence of real numbers (``scores'') in which the sum exceeds an input parameter. The algorithm also solves the problem of finding the longest interval in…
The equidistant subsequence pattern matching problem is considered. Given a pattern string $P$ and a text string $T$, we say that $P$ is an \emph{equidistant subsequence} of $T$ if $P$ is a subsequence of the text such that consecutive…
The Multiobjective Minimum Spanning Tree (MO-MST) problem is a variant of the Minimum Spanning Tree problem, in which the costs associated with every edge of the input graph are vectors. In this paper, we design a new dynamic programming…
Longest common subsequence ($\mathsf{LCS}$) is a classic and central problem in combinatorial optimization. While $\mathsf{LCS}$ admits a quadratic time solution, recent evidence suggests that solving the problem may be impossible in truly…
While in many graph mining applications it is crucial to handle a stream of updates efficiently in terms of {\em both} time and space, not much was known about achieving such type of algorithm. In this paper we study this issue for a…
In numerical linear algebra, considerable effort has been devoted to obtaining faster algorithms for linear systems whose underlying matrices exhibit structural properties. A prominent success story is the method of generalized nested…
In this paper, we provide new approximation algorithms for dynamic variations of the longest increasing subsequence (\textsf{LIS}) problem, and the complementary distance to monotonicity (\textsf{DTM}) problem. In this setting, operations…
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…
The Longest Common Subsequence Problem (LCS) deals with finding the longest subsequence among a given set of strings. The LCS problem is an NP-hard problem which makes it a target for lots of effort to find a better solution with heuristics…
We study approximation algorithms for the following three string measures that are widely used in practice: edit distance (ED), longest common subsequence (LCS), and longest increasing sequence (LIS). All three problems can be solved…
We study the generalized minimum Manhattan network (GMMN) problem: given a set $P$ of pairs of two points in the Euclidean plane $\mathbb{R}^2$, we are required to find a minimum-length geometric network which consists of axis-aligned…
Multiple sequence alignment (MSA) is a ubiquitous problem in computational biology. Although it is NP-hard to find an optimal solution for an arbitrary number of sequences, due to the importance of this problem researchers are trying to…
The Binary Jumbled String Matching problem is defined as: Given a string $s$ over $\{a,b\}$ of length $n$ and a query $(x,y)$, with $x,y$ non-negative integers, decide whether $s$ has a substring $t$ with exactly $x$ $a$'s and $y$ $b$'s.…
We study the fundamental problem of sampling independent events, called subset sampling. Specifically, consider a set of $n$ events $S=\{x_1, \ldots, x_n\}$, where each event $x_i$ has an associated probability $p(x_i)$. The subset sampling…
Given a graph, the sparsest cut problem asks for a subset of vertices whose edge expansion (the normalized cut given by the subset) is minimized. In this paper, we study a generalization of this problem seeking for $ k $ disjoint subsets of…
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…
In this work, we present a constant-round algorithm for the $2$-ruling set problem in the Congested Clique model. As a direct consequence, we obtain a constant round algorithm in the MPC model with linear space-per-machine and optimal total…
Suppose an oracle knows a string $S$ that is unknown to us and that we want to determine. The oracle can answer queries of the form "Is $s$ a substring of $S$?". In 1995, Skiena and Sundaram showed that, in the worst case, any algorithm…