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While many optimization problems work with a fixed number of decision variables and thus a fixed-length representation of possible solutions, genetic programming (GP) works on variable-length representations. A naturally occurring problem…

Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…

In this paper we consider the problem of finding a vector that can be written as a nonnegative integer linear combination of given 0-1 vectors, the generators, such that the l_1-distance between this vector and a given target vector is…

Restricted Boltzmann Machines (RBMs) are a common family of undirected graphical models with latent variables. An RBM is described by a bipartite graph, with all observed variables in one layer and all latent variables in the other. We…

Network alignment generalizes and unifies several approaches for forming a matching or alignment between the vertices of two graphs. We study a mathematical programming framework for network alignment problem and a sparse variation of it…

While Mixed-integer linear programming (MILP) is NP-hard in general, practical MILP has received roughly 100--fold speedup in the past twenty years. Still, many classes of MILPs quickly become unsolvable as their sizes increase, motivating…

This paper considers scheduling on identical machines. The scheduling objective considered in this paper generalizes most scheduling minimization problems. In the problem, there are $n$ jobs and each job $j$ is associated with a…

We design a heuristic method, a genetic algorithm, for the computation of an upper bound of the minimum distance of a linear code over a finite field. By the use of the row reduced echelon form, we obtain a permutation encoding of the…

Some experimental investigations have shown that evolutionary algorithms (EAs) are efficient for the minimum label spanning tree (MLST) problem. However, we know little about that in theory. As one step towards this issue, we theoretically…

Finding the minimum distance of linear codes is an NP-hard problem. Traditionally, this computation has been addressed by means of the design of algorithms that find, by a clever exhaustive search, a linear combination of some generating…

The Stable Marriage problem (SM), solved by the famous deferred acceptance algorithm of Gale and Shapley (GS), has many natural generalizations. If we allow ties in preferences, then the problem of finding a maximum stable matching becomes…

In this article, we investigate different parsimony-based approaches towards finding recombination breakpoints in a multiple sequence alignment. This recombination detection task is crucial in order to avoid errors in evolutionary analyses…

We investigate the Minimum Eccentricity Shortest Path problem in some structured graph classes. It asks for a given graph to find a shortest path with minimum eccentricity. Although it is NP-hard in general graphs, we demonstrate that a…

Partial label learning (PLL) aims to solve the problem where each training instance is associated with a set of candidate labels, one of which is the correct label. Most PLL algorithms try to disambiguate the candidate label set, by either…

Given a digraph $D$, the Minimum Leaf Out-Branching problem (MinLOB) is the problem of finding in $D$ an out-branching with the minimum possible number of leaves, i.e., vertices of out-degree 0. We prove that MinLOB is polynomial-time…

We give algorithms for geometric graph problems in the modern parallel models inspired by MapReduce. For example, for the Minimum Spanning Tree (MST) problem over a set of points in the two-dimensional space, our algorithm computes a…

Codes over permutations under the infinity norm have been recently suggested as a coding scheme for correcting limited-magnitude errors in the rank modulation scheme. Given such a code, we show that a simple relabeling operation, which…

In this paper, we present new efficiently solvable cases of the Minimum Uncovering Branching problem, an optimization problem with applications in cancer genomics introduced by Hujdurovi\'c, Husi\'c, Milani\v{c}, Rizzi, and Tomescu in 2018.…

In recent years there has been a growing interest in developing "streaming algorithms" for efficient processing and querying of continuous data streams. These algorithms seek to provide accurate results while minimizing the required storage…

Minimum Bayes Risk (MBR) decoding is a powerful decoding strategy widely used for text generation tasks, but its quadratic computational complexity limits its practical application. This paper presents a novel approach for approximating MBR…