Related papers: A 3-approximation algorithm for computing a parsim…
Motivation: Gene selection has become a common task in most gene expression studies. The objective of such research is often to identify the smallest possible set of genes that can still achieve good predictive performance. The problem of…
In this paper we present a collection of results pertaining to haplotyping. The first set of results concerns the combinatorial problem of reconstructing haplotypes from incomplete and/or imperfectly sequenced haplotype data. More…
This paper addresses the following questions for a given tree $T$ and integer $d\geq2$: (1) What is the minimum number of degree-$d$ subtrees that partition $E(T)$? (2) What is the minimum number of degree-$d$ subtrees that cover $E(T)$? We…
We design a 3/2 approximation algorithm for the Generalized Steiner Tree problem (GST) in metrics with distances 1 and 2. This is the first polynomial time approximation algorithm for a wide class of non-geometric metric GST instances with…
We propose a method to reduce the computational effort to solve a partial differential equation on a given domain. The main idea is to split the domain of interest in two subdomains, and to use different approximation methods in each of the…
Computing and storing probabilities is a hard problem as soon as one has to deal with complex distributions over multiple random variables. The problem of efficient representation of probability distributions is central in term of…
We present a fast randomized algorithm that computes a low rank LU decomposition. Our algorithm uses random projections type techniques to efficiently compute a low rank approximation of large matrices. The randomized LU algorithm can be…
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…
Problems with solutions represented by permutations are very prominent in combinatorial optimization. Thus, in recent decades, a number of evolutionary algorithms have been proposed to solve them, and among them, those based on probability…
The ancestral maximum-likelihood and phylogeography problems are two fundamental problems involving evolutionary studies. The ancestral maximum-likelihood problem involves identifying a rooted tree alongside internal node sequences that…
Pedigrees, or family trees, are graphs of family relationships that are used to study inheritance. A fundamental problem in computational biology is to find, for a pedigree with $n$ individuals genotyped at every site, a set of…
We formalize the problem of selecting the optimal set of options for planning as that of computing the smallest set of options so that planning converges in less than a given maximum of value-iteration passes. We first show that the problem…
We propose to prune a random forest (RF) for resource-constrained prediction. We first construct a RF and then prune it to optimize expected feature cost & accuracy. We pose pruning RFs as a novel 0-1 integer program with linear constraints…
We study a general class of bicriteria network design problems. A generic problem in this class is as follows: Given an undirected graph and two minimization objectives (under different cost functions), with a budget specified on the first,…
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…
Approximating Subset Sum is a classic and fundamental problem in computer science and mathematical optimization. The state-of-the-art approximation scheme for Subset Sum computes a $(1-\varepsilon)$-approximation in time…
We significantly improve known time bounds for solving the minimum cut problem on undirected graphs. We use a ``semi-duality'' between minimum cuts and maximum spanning tree packings combined with our previously developed random sampling…
In this paper, we consider the problem of finding a minimum common partition of two strings. The problem has its application in genome comparison. As it is an NP-hard, discrete combinatorial optimization problem, we employ a metaheuristic…
Given a finite metric space $(X\cup Y, \mathbf{d})$ the $k$-median problem is to find a set of $k$ centers $C\subseteq Y$ that minimizes $\sum_{p\in X} \min_{c\in C} \mathbf{d}(p,c)$. In general metrics, the best polynomial time algorithm…
We present subquadratic algorithms in the algebraic decision-tree model for several \textsc{3Sum}-hard geometric problems, all of which can be reduced to the following question: Given two sets $A$, $B$, each consisting of $n$ pairwise…