Related papers: Pure Parsimony Xor Haplotyping
Motivated by a non-random but clustered distribution of SNPs, we introduce a phenomenological model to account for the clustering properties of SNPs in the human genome. The phenomenological model is based on a preferential mutation to the…
The increased availability of time series genetic variation data from experimental evolution studies and ancient DNA samples has created new opportunities to identify genomic regions under selective pressure and to estimate their associated…
Symmetry is a guiding principle in physics that allows to generalize conclusions between many physical systems. In the ongoing search for new topological phases of matter, symmetry plays a crucial role because it protects topological…
We study the problem of computing the isolated regular solutions of a system \((f_1,\ldots,f_n)\) of \(n\) polynomial equations in \(n\) variables \((X_1, \dots, X_n)\) over a field of characteristic zero \(k\). We focus on systems with a…
Polynomial systems occur in many areas of science and engineering. Unlike general nonlinear systems, the algebraic structure enables to compute all solutions of a polynomial system. We describe our massive parallel predictor-corrector…
One of the main aims in phylogenetics is the estimation of ancestral sequences based on present-day data like, for instance, DNA alignments. One way to estimate the data of the last common ancestor of a given set of species is to first…
We consider a class of pattern matching problems where a normalising transformation is applied at every alignment. Normalised pattern matching plays a key role in fields as diverse as image processing and musical information processing…
We examine ordered graphs, defined as graphs with linearly ordered vertices, from the perspective of homomorphisms (and colorings) and their complexities. We demonstrate the corresponding computational and parameterized complexities, along…
We give a new general approach for designing exact exponential-time algorithms for subset problems. In a subset problem the input implicitly describes a family of sets over a universe of size n and the task is to determine whether the…
We introduce a parsimonious model-based framework for clustering time course data. In these applications the computational burden becomes often an issue due to the number of available observations. The measured time series can also be very…
Determining whether two STRIPS planning instances are isomorphic is the simplest form of comparison between planning instances. It is also a particular case of the problem concerned with finding an isomorphism between a planning instance…
The human genotope is the convex hull of all allele frequency vectors that can be obtained from the genotypes present in the human population. In this paper we take a few initial steps towards a description of this object, which may be…
Background: Advances in high throughput sequencing technologies provide a huge number of genomes to be analyzed. Thus, computational methods play a crucial role in analyzing and extracting knowledge from the data generated. Investigating…
The problem of counting the number of models of a given Boolean formula has numerous applications, including computing the leakage of deterministic programs in Quantitative Information Flow. Model counting is a hard, #P-complete problem.…
One of the main aims of phylogenetics is to reconstruct the \enquote{Tree of Life}. In this respect, different methods and criteria are used to analyze DNA sequences of different species and to compare them in order to derive the…
Consider the problem of determining whether there exists a spanning hypertree in a given k-uniform hypergraph. This problem is trivially in P for k=2, and is NP-complete for k>= 4, whereas for k=3, there exists a polynomial-time algorithm…
Given a quadratic map Q : K^n -> K^k defined over a computable subring D of a real closed field K, and a polynomial p(Y_1,...,Y_k) of degree d, we consider the zero set Z=Z(p(Q(X)),K^n) of the polynomial p(Q(X_1,...,X_n)). We present a…
We propose a consistent polynomial-time method for the unseeded node matching problem for networks with smooth underlying structures. Despite widely conjectured by the research community that the structured graph matching problem to be…
We consider the problem of finding a homomorphism from an input digraph $G$ to a fixed digraph $H$. We show that if $H$ admits a weak-near-unanimity polymorphism $\phi$ then deciding whether $G$ admits a homomorphism to $H$ (HOM($H$)) is…
In an earlier paper of Cadek, Vokrinek, Wagner, and the present authors, we investigated an algorithmic problem in computational algebraic topology, namely, the computation of all possible homotopy classes of maps between two topological…