Related papers: The Binary Perfect Phylogeny with Persistent chara…
Phylogenetic mixture models are statistical models of character evolution allowing for heterogeneity. Each of the classes in some unknown partition of the characters may evolve by different processes, or even along different trees. The…
We study the graphs formed from instances of the stable matching problem by connecting pairs of elements with an edge when there exists a stable matching in which they are matched. Our results include the NP-completeness of recognizing…
This paper examines the effect of mimicking discontinuous heredity caused by carrying more than one chromosome in some living organisms cells in Evolutionary Multi-Objective Optimization algorithms. In this representation, the phenotype may…
Recently, the minimum number of reticulation events that is required to simultaneously embed a collection P of rooted binary phylogenetic trees into a so-called temporal network has been characterized in terms of cherry-picking sequences.…
Near-duplicate images are often generated when applying repeated photometric and geometric transformations that produce imperceptible variants of the original image. Consequently, a deluge of near-duplicates can be circulated online posing…
We analyze the bit complexity of efficient algorithms for fundamental optimization problems, such as linear regression, $p$-norm regression, and linear programming (LP). State-of-the-art algorithms are iterative, and in terms of the number…
In this paper we present a collection of results pertaining to haplotyping. The first set of results concerns the combinatorial problem of reconstructing haplotypes from incomplete and/or imperfectly sequenced haplotype data. More…
The order preserving pattern matching (OPPM) problem is, given a pattern string $p$ and a text string $t$, find all substrings of $t$ which have the same relative orders as $p$. In this paper, we consider two variants of the OPPM problem…
In this paper, we consider a probabilistic set covering problem (PSCP) in which each 0-1 row of the constraint matrix is random with a finite discrete distribution, and the objective is to minimize the total cost of the selected columns…
The Exact Circular Pattern Matching (ECPM) problem consists of reporting every occurrence of a rotation of a pattern $P$ in a text $T$. In many real-world applications, specifically in computational biology, circular rotations are of…
In this work we study approximation algorithms for the \textit{Bounded Color Matching} problem (a.k.a. Restricted Matching problem) which is defined as follows: given a graph in which each edge $e$ has a color $c_e$ and a profit $p_e \in…
Forward-time models of diversification (i.e., speciation and extinction) produce phylogenetic trees that grow "vertically" as time goes by. Pruning the extinct lineages out of such trees leads to natural models for reconstructed trees…
We study the algorithmic complexity of partitioning the vertex set of a given (di)graph into a small number of paths. The Path Partition problem (PP) has been studied extensively, as it includes Hamiltonian Path as a special case. The…
Storyline drawings are a popular visualization of interactions of a set of characters over time, e.g., to show participants of scenes in a book or movie. Characters are represented as $x$-monotone curves that converge vertically for…
Finding the most parsimonious tree inside a phylogenetic network with respect to a given character is an NP-hard combinatorial optimization problem that for many network topologies is essentially inapproximable. In contrast, if the network…
A mathematical characterization of serially-pruned permutations (SPPs) employed in variable-length permuters and their associated fast pruning algorithms and architectures are proposed. Permuters are used in many signal processing systems…
The problem of reconstructing a sequence of independent and identically distributed symbols from a set of equal size, consecutive, fragments, as well as a dependent reference sequence, is considered. First, in the regime in which the…
Binarized neural networks (BNNs) are feedforward neural networks with binary weights and activation functions. In the context of using a BNN for classification, the verification problem seeks to determine whether a small perturbation of a…
This contribution is concerned with mathematical models for the dynamics of the genetic composition of populations evolving under recombination. Recombination is the genetic mechanism by which two parent individuals create the mixed type of…
Overlapping genes exist in all domains of life and are much more abundant than expected at their first discovery in the late 1970s. Assuming that the reference gene is read in frame +0, an overlapping gene can be encoded in two reading…