Related papers: Solving the Minimum Common String Partition Proble…
The partition of a problem into smaller sub-problems satisfying certain properties is often a key ingredient in the design of divide-and-conquer algorithms. For questions related to location, the partition problem can be modeled, in…
The alternating minimization (AM) method is a fundamental method for minimizing convex functions whose variable consists of two blocks. How to efficiently solve each subproblems when applying the AM method is the most concerned task. In…
Maximum bipartite matching is a fundamental algorithmic problem which can be solved in polynomial time. We consider a natural variant in which there is a separation constraint: the vertices on one side lie on a path or a grid, and two…
The minimizers sampling mechanism is a popular mechanism for string sampling introduced independently by Schleimer et al. [SIGMOD 2003] and by Roberts et al. [Bioinf. 2004]. Given two positive integers $w$ and $k$, it selects the…
Minimum connected dominating set problem is an NP-hard combinatorial optimization problem in graph theory. Finding connected dominating set is of high interest in various domains such as wireless sensor networks, optical networks, and…
The most commonly used method to tackle the graph partitioning problem in practice is the multilevel approach. During a coarsening phase, a multilevel graph partitioning algorithm reduces the graph size by iteratively contracting nodes and…
In this paper we study the fundamental problem of maintaining a dynamic collection of strings under the following operations: concat - concatenates two strings, split - splits a string into two at a given position, compare - finds the…
The Kemeny aggregation problem consists of computing the consensus rankings of an election with respect to the well-known Kemeny-Young voting method. These consensus rankings satisfy various fundamental properties and are the geometric…
In this paper, we introduce the Maximum Matrix Contraction problem, where we aim to contract as much as possible a binary matrix in order to maximize its density. We study the complexity and the polynomial approximability of the problem.…
We consider running-time optimization for band-joins in a distributed system, e.g., the cloud. To balance load across worker machines, input has to be partitioned, which causes duplication. We explore how to resolve this tension between…
Repeat finding in strings has important applications in subfields such as computational biology. The challenge of finding the longest repeats covering particular string positions was recently proposed and solved by \.{I}leri et al., using a…
Computing an optimal chain of fragments is a classical problem in string algorithms, with important applications in computational biology. There exist two efficient dynamic programming algorithms solving this problem, based on different…
We consider the rank reduction problem for matroids: Given a matroid M and an integer k, find a minimum size subset of elements of M whose removal reduces the rank of M by at least k. When M is a graphical matroid this problem is the…
We present a general method for obtaining strong bounds for discrete optimization problems that is based on a concept of branching duality. It can be applied when no useful integer programming model is available, and we illustrate this with…
Extremal optimization is a new general-purpose method for approximating solutions to hard optimization problems. We study the method in detail by way of the NP-hard graph partitioning problem. We discuss the scaling behavior of extremal…
We explore the relation between memcomputing, namely computing with and in memory, and swarm intelligence algorithms. In particular, we show that one can design memristive networks to solve short-path optimization problems that can also be…
In ongoing work to define a principled method for syntenic block discovery and structuring, work based on homology-derived constraints and a generalization of common intervals, we faced a fundamental computational problem: how to determine…
We present theoretical guarantees for an alternating minimization algorithm for the dictionary learning/sparse coding problem. The dictionary learning problem is to factorize vector samples $y^{1},y^{2},\ldots, y^{n}$ into an appropriate…
String matching is a fundamental problem in computer science, with critical applications in text retrieval, bioinformatics, and data analysis. Among the numerous solutions that have emerged for this problem in recent decades,…
Minimizers sampling is one of the most widely-used mechanisms for sampling strings [Roberts et al., Bioinformatics 2004]. Let $S=S[1]\ldots S[n]$ be a string over a totally ordered alphabet $\Sigma$. Further let $w\geq 2$ and $k\geq 1$ be…