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This study investigates whether reoptimization can help in solving the closest substring problem. We are dealing with the following reoptimization scenario. Suppose, we have an optimal l-length closest substring of a given set of sequences…
Finding the longest common subsequence in $k$-length substrings (LCS$k$) is a recently proposed problem motivated by computational biology. This is a generalization of the well-known LCS problem in which matching symbols from two sequences…
The {\em shortest common superstring} and the {\em shortest common supersequence} are two well studied problems having a wide range of applications. In this paper we consider both problems with resource constraints, denoted as the…
Many problems in signal processing and machine learning can be formalized as weak submodular optimization tasks. For such problems, a simple greedy algorithm (\textsc{Greedy}) is guaranteed to find a solution achieving the objective with a…
We present SimultaneousGreedys, a deterministic algorithm for constrained submodular maximization. At a high level, the algorithm maintains $\ell$ solutions and greedily updates them in a simultaneous fashion. SimultaneousGreedys achieves…
In this paper, we consider the ``Shortest Superstring Problem''(SSP) or the ``Shortest Common Superstring Problem''(SCS). The problem is as follows. For a positive integer $n$, a sequence of n strings $S=(s^1,\dots,s^n)$ is given. We should…
Given a set ${\cal R}=\{R_1,R_2,..., R_n\}$ of $n$ randomly positioned axis parallel rectangles in 2D, the problem of computing the minimum clique cover (MCC) and maximum independent set (MIS) for the intersection graph $G({\cal R})$ of the…
Finding an Approximate Longest Common Substring (ALCS) within a given set $S=\{s_1,s_2,\ldots,s_m\}$ of $m \ge 2$ strings is a key problem in computational biology, such as identifying related mutations across multiple genetic sequences. We…
In this paper, we propose a new greedy algorithm for sparse approximation, called SLS for Single L_1 Selection. SLS essentially consists of a greedy forward strategy, where the selection rule of a new component at each iteration is based on…
Longest Common Subsequence ($LCS$) deals with the problem of measuring similarity of two strings. While this problem has been analyzed for decades, the recent interest stems from a practical observation that considering single characters is…
Motivated by an application in kidney exchange, we study the following query-commit problem: we are given the set of vertices of a non-bipartite graph G. The set of edges in this graph are not known ahead of time. We can query any pair of…
The submodular maximization problem is widely applicable in many engineering problems where objectives exhibit diminishing returns. While this problem is known to be NP-hard for certain subclasses of objective functions, there is a greedy…
In this paper, we consider two versions of the Text Assembling problem. We are given a sequence of strings $s^1,\dots,s^n$ of total length $L$ that is a dictionary, and a string $t$ of length $m$ that is texts. The first version of the…
The Longest Common Subsequence (LCS) is the problem of finding a subsequence among a set of strings that has two properties of being common to all and is the longest. The LCS has applications in computational biology and text editing, among…
The Set Cover problem (SCP) and Set Packing problem (SPP) are standard NP-hard combinatorial optimization problems. Their decision problem versions are shown to be NP-Complete in Karp's 1972 paper. We specify a rough guide to constructing…
We study greedy-type algorithms such that at a greedy step we pick several dictionary elements contrary to a single dictionary element in standard greedy-type algorithms. We call such greedy algorithms {\it super greedy algorithms}. The…
For many popular graph metric sparsifiers, such as spanners, emulators, and preservers, simple and elegant greedy algorithms are known that achieve state-of-the-art or existentially optimal tradeoffs between size and quality. The goal of…
Finding the common subsequences of $L$ multiple strings has many applications in the area of bioinformatics, computational linguistics, and information retrieval. A well-known result states that finding a Longest Common Subsequence (LCS)…
The Longest Common Subsequence (LCS) of two strings is a fundamental string similarity measure with a classical dynamic programming solution taking quadratic time. Despite significant efforts, little progress was made in improving the…
String matching is the problem of finding all the substrings of a text which match a given pattern. It is one of the most investigated problems in computer science, mainly due to its very diverse applications in several fields. Recently,…