相关论文: Pure Parsimony Xor Haplotyping

The homomorphism problem for relational structures is an abstract way of formulating constraint satisfaction problems (CSP) and various problems in database theory. The decision version of the homomorphism problem received a lot of…

Approximation algorithms for classical constraint satisfaction problems are one of the main research areas in theoretical computer science. Here we define a natural approximation version of the QMA-complete local Hamiltonian problem and…

This paper surveys results on complexity of the optimal recombination problem (ORP), which consists in finding the best possible offspring as a result of a recombination operator in a genetic algorithm, given two parent solutions. We…

We consider the problem of detecting and estimating the strength of association between a trait of interest and alleles or haplotypes in a small genomic region (e.g. a gene or a gene complex), when no direct information on that region is…

Genome assembly is a prominent problem studied in bioinformatics, which computes the source string using a set of its overlapping substrings. Classically, genome assembly uses assembly graphs built using this set of substrings to compute…

A useful approach to the mathematical analysis of large-scale biological networks is based upon their decompositions into monotone dynamical systems. This paper deals with two computational problems associated to finding decompositions…

Recently-developed genotype imputation methods are a powerful tool for detecting untyped genetic variants that affect disease susceptibility in genetic association studies. However, existing imputation methods require individual-level…

A homomorphism from a graph $G$ to a graph $H$ is an edge-preserving mapping from $V(G)$ to $V(H)$. For a fixed graph $H$, in the list homomorphism problem, denoted by LHom($H$), we are given a graph $G$, whose every vertex $v$ is equipped…

X-ray spectral imaging provides quantitative imaging of trace elements in biological sample with high sensitivity. We propose a novel algorithm to promote the signal-to-noise ratio (SNR) of X-ray spectral images that have low photon counts.…

Phenomics is an emerging branch of modern biology that uses high throughput phenotyping tools to capture multiple environmental and phenotypic traits, often at massive spatial and temporal scales. The resulting high dimensional data…

A phylogeny describes the evolutionary history of an evolving population. Evolutionary search algorithms can perfectly track the ancestry of candidate solutions, illuminating a population's trajectory through the search space. However,…

This work investigates the hardness of computing sparse solutions to systems of linear equations over F_2. Consider the k-EvenSet problem: given a homogeneous system of linear equations over F_2 on n variables, decide if there exists a…

The identification of homologous gene families across multiple genomes is a central task in bacterial pangenomics traditionally requiring computationally demanding all-against-all comparisons. PanDelos addresses this challenge with an…

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…

First, we study geometric variants of the standard set cover motivated by assignment of directional antenna and shipping with deadlines, providing the first known polynomial-time exact solutions. Next, we consider the following general…

In this paper, we study the sparsity-adapted complex moment-Hermitian sum of squares (moment-HSOS) hierarchy for complex polynomial optimization problems, where the sparsity includes correlative sparsity and term sparsity. We compare the…

This paper deals with a method for solving Poisson Equation (PE) based on genetic algorithms and grammatical evolution. The method forms generations of solutions expressed in an analytical form. Several examples of PE are tested and in most…

Stochastic Multi-Objective Optimization (SMOO) is critical for decision-making trading off multiple potentially conflicting objectives in uncertain environments. SMOO aims at identifying the Pareto frontier, which contains all mutually…

In this paper we consider the problem of computing an mRNA sequence of maximal similarity for a given mRNA of secondary structure constraints, introduced by Backofen et al. in [BNS02] denoted as the MRSO problem. The problem is known to be…

We present several sparsification lower and upper bounds for classic problems in graph theory and logic. For the problems 4-Coloring, (Directed) Hamiltonian Cycle, and (Connected) Dominating Set, we prove that there is no polynomial-time…