相关论文: Perfect Phylogeny Haplotyping is Complete for Logs…

This paper categorizes the parameterized complexity of the algorithmic problems Perfect Phylogeny and Triangulating Colored Graphs when parameterized by the number of genes and colors, respectively. We show that they are complete for the…

The linking genotype to phenotype is the fundamental aim of modern genetics. We focus on study of links between gene expression data and phenotype data through integrative analysis. We propose three approaches. 1) The inherent complexity of…

Nowadays hybrid evolutionary algorithms, i.e, heuristic search algorithms combining several mutation operators some of which are meant to implement stochastically a well known technique designed for the specific problem in question while…

Haxell's condition is a natural hypergraph analog of Hall's condition, which is a well-known necessary and sufficient condition for a bipartite graph to admit a perfect matching. That is, when Haxell's condition holds it forces the…

Among the evolutionary methods, one that is quite prominent is Genetic Programming, and, in recent years, a variant called Geometric Semantic Genetic Programming (GSGP) has shown to be successfully applicable to many real-world problems.…

This paper presents a genetic-based hybrid algorithm that combines the exploration power of Genetic Algorithm (GA) with the exploitation capacity of a phenotypical probabilistic local search algorithm. Though not limited to a certain class…

The variation graph toolkit (VG) represents genetic variation as a graph. Each path in the graph is a potential haplotype, though most paths are unlikely recombinations of true haplotypes. We augment the VG model with haplotype information…

HyperParameter Optimization (HPO) aims at finding the best HyperParameters (HPs) of learning models, such as neural networks, in the fastest and most efficient way possible. Most recent HPO algorithms try to optimize HPs regardless of the…

We describe, for the first time, a completely rigorous homotopy (path--following) algorithm (in the Turing machine model) to find approximate zeros of systems of polynomial equations. If the coordinates of the input systems and the initial…

Valiant introduced matchgate computation and holographic algorithms. A number of seemingly exponential time problems can be solved by this novel algorithmic paradigm in polynomial time. We show that, in a very strong sense, matchgate…

A probabilistic reconstruction of genealogies in a polyploid population (from 2x to 4x) is investigated, by considering genetic data analyzed as the probability of allele presence in a given genotype. Based on the likelihood of all possible…

Several algorithms build on the perfect phylogeny model to infer evolutionary trees. This problem is particularly hard when evolutionary trees are inferred from the fraction of genomes that have mutations in different positions, across…

This note presents a simple and effective variation of genetic algorithm (GA) for solving RCPSP, denoted as 2-Phase Genetic Algorithm (2PGA). The 2PGA implements GA parent selection in two phases: Phase-1 includes the best current solutions…

Genotype-to-phenotype mappings translate genotypic variations such as mutations into phenotypic changes. Neutrality is the observation that some mutations do not lead to phenotypic changes. Studying the search trajectories in genotypic and…

A geophylogeny is a phylogenetic tree (or dendrogram) where each leaf (e.g. biological taxon) has an associated geographic location (site). To clearly visualize a geophylogeny, the tree is typically represented as a crossing-free drawing…

In the counting Graph Homomorphism problem (#GraphHom) the question is: Given graphs G,H, find the number of homomorphisms from G to H. This problem is generally #P-complete, moreover, Cygan et al. proved that unless the ETH is false there…

Genetic programming (GP) is an evolutionary computation technique to solve problems in an automated, domain-independent way. Rather than identifying the optimum of a function as in more traditional evolutionary optimization, the aim of GP…

In this paper we propose a new approach for developing a proof that P=NP. We propose to use a polynomial-time reduction of a NP-complete problem to Linear Programming. Earlier such attempts used polynomial-time transformation which is a…

Phylogenetic networks are necessary to represent the tree of life expanded by edges to represent events such as horizontal gene transfers, hybridizations or gene flow. Not all species follow the paradigm of vertical inheritance of their…

The overarching goal of this paper is to solve the word problem for a class of idempotent commutative monoids whose elements model population haplotypes. More specifically, we design an algebraic framework in which it is possible to unravel…