Related papers: Pure Parsimony Xor Haplotyping
We extend the concept of polynomial time approximation algorithms to apply to problems for hierarchically specified graphs, many of which are PSPACE-complete. Assuming P != PSPACE, the existence or nonexistence of such efficient…
We introduce the Cox homotopy algorithm for solving a sparse system of polynomial equations on a compact toric variety $X_\Sigma$. The algorithm lends its name from a construction, described by Cox, of $X_\Sigma$ as a GIT quotient $X_\Sigma…
Let $\K$ be a field of characteristic zero and $\Kbar$ be an algebraic closure of $\K$. Consider a sequence of polynomials$G=(g\_1,\dots,g\_s)$ in $\K[X\_1,\dots,X\_n]$, a polynomial matrix $\F=[f\_{i,j}] \in \K[X\_1,\dots,X\_n]^{p \times…
Accurate identification of haplotypes in sequenced human genomes can provide invaluable information about population demography and fine-scale correlations along the genome, thus empowering both population genomic and medical association…
We consider the following problem for a fixed graph H: given a graph G and two H-colorings of G, i.e. homomorphisms from G to H, can one be transformed (reconfigured) into the other by changing one color at a time, maintaining an H-coloring…
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…
Routine single-sample haplotype-resolved assembly remains an unresolved problem. Here we describe a new algorithm that combines PacBio HiFi reads and Hi-C chromatin interaction data to produce a haplotype-resolved assembly without the…
This paper studies the haplotype assembly problem from an information theoretic perspective. A haplotype is a sequence of nucleotide bases on a chromosome, often conveniently represented by a binary string, that differ from the bases in the…
We introduce a new generic Archetype technique for source classification and identification, based on the NP-complete set cover problem (SCP) in computer science and operations research (OR). We have developed a new heuristic SCP solver, by…
A polynomial homotopy is a family of polynomial systems, where the systems in the family depend on one parameter. If for one value of the parameter we know a regular solution, then what is the nearest value of the parameter for which the…
A polynomial homotopy is a family of polynomial systems in one parameter, which defines solution paths starting from known solutions and ending at solutions of a system that has to be solved. We consider paths leading to isolated singular…
In this paper we apply for the first time a new method for multivariate equation solving which was developed in \cite{gh1}, \cite{gh2}, \cite{gh3} for complex root determination to the {\em real} case. Our main result concerns the problem…
Given a redundant dictionary $\Phi$, represented by an $M \times N$ matrix ($\Phi \in \mathbb{R}^{M \times N}$) and a target signal $y \in \mathbb{R}^M$, the \emph{sparse approximation problem} asks to find an approximate representation of…
The problem Parsimony Haplotyping (PH) asks for the smallest set of haplotypes which can explain a given set of genotypes, and the problem Minimum Perfect Phylogeny Haplotyping (MPPH) asks for the smallest such set which also allows the…
We consider the classical problem of finding the sparse representation of a signal in a pair of bases. When both bases are orthogonal, it is known that the sparse representation is unique when the sparsity $K$ of the signal satisfies…
The objective of this paper is to show how the recently proposed method by Giusti, Heintz, Morais, Morgenstern, Pardo \cite{gihemorpar} can be applied to a case of real polynomial equation solving. Our main result concerns the problem of…
Understanding genetic variation, e.g., through mutations, in organisms is crucial to unravel their effects on the environment and human health. A fundamental characterization can be obtained by solving the haplotype assembly problem, which…
We initiate the systematic study of a recently introduced polynomial-time analogue of MaxSNP, which includes a large number of well-studied problems (including Nearest and Furthest Neighbor in the Hamming metric, Maximum Inner Product,…
We give a high precision polynomial-time approximation scheme for the supremum of any honest n-variate (n+2)-nomial with a constant term, allowing real exponents as well as real coefficients. Our complexity bounds count field operations and…
We present several new results pertaining to haplotyping. These results concern the combinatorial problem of reconstructing haplotypes from incomplete and/or imperfectly sequenced haplotype fragments. We consider the complexity of the…