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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…
Gene tree/species tree reconciliation is a recent decisive progress in phylo-genetic methods, accounting for the possible differences between gene histories and species histories. Reconciliation consists in explaining these differences by…
There has been a variety of crossover operators proposed for Real-Coded Genetic Algorithms (RCGAs), which recombine values from the same location in pairs of strings. In this article we present a recombination operator for RC- GAs that…
Two completely new algorithms for generating permutations, shift-cursor algorithm and level algorithm, and their efficient implementations are presented in this paper. One implementation of the shift cursor algorithm gives an optimal…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
Evolutionary algorithms are metaheuristic techniques that derive inspiration from the natural process of evolution. They can efficiently solve (generate acceptable quality of solution in reasonable time) complex optimization (NP-Hard)…
This paper analyzes the relative advantages between crossover and mutation on a class of deterministic and stochastic additively separable problems. This study assumes that the recombination and mutation operators have the knowledge of the…
Given a graph drawn in the plane, the degenerate crossing number of the drawing is the number of points in the plane which are contained in the relative interior of at least two edges, where each edge is required to be drawn as a simple…
A tandem duplication denotes the process of inserting a copy of a segment of DNA adjacent to its original position. More formally, a tandem duplication can be thought of as an operation that converts a string $S = AXB$ into a string $T =…
Best match graphs (BMGs) are a class of colored digraphs that naturally appear in mathematical phylogenetics and can be approximated with the help of similarity measures between gene sequences, albeit not without errors. The corresponding…
A schema is a naturally defined subset of the space of fixed-length binary strings. The Holland Schema Theorem gives a lower bound on the expected fraction of a population in a schema after one generation of a simple genetic algorithm. This…
Exploration of task mappings plays a crucial role in achieving high performance in heterogeneous multi-processor system-on-chip (MPSoC) platforms. The problem of optimally mapping a set of tasks onto a set of given heterogeneous processors…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
This paper proposes a hybrid genetic algorithm for solving the Multiple Traveling Salesman Problem (mTSP) to minimize the length of the longest tour. The genetic algorithm utilizes a TSP sequence as the representation of each individual,…
We describe a new algorithm to compute the geometric intersection number between two curves, given as edge vectors on an ideal triangulation. Most importantly, this algorithm runs in polynomial time in the bit-size of the two edge vectors.…
An applied problem facing all areas of data science is harmonizing data sources. Joining data from multiple origins with unmapped and only partially overlapping features is a prerequisite to developing and testing robust, generalizable…
Phylogenetic trees illustrate the evolutionary history of genes and species. In most cases, although genes evolve along with the species they belong to, a species tree and gene tree are not identical, because of evolutionary events at the…
Early literature on genome rearrangement modelling views the problem of computing evolutionary distances as an inherently combinatorial one. In particular, attention was given to estimating distances using the minimum number of events…
We combined the genetic crossover, which is one of the operations of genetic algorithm, and replica-exchange method in parallel molecular dynamics simulations. The genetic crossover and replica-exchange method can search the global…
The crossing matrix of a braid on $N$ strands is the $N\times N$ integer matrix with zero diagonal whose $i,j$ entry is the algebraic number (positive minus negative) of crossings by strand $i$ over strand $j$ . When restricted to the…