Related papers: An Approximation Algorithm for Ancestral Maximum-L…
Phylogenetic networks are leaf-labelled directed acyclic graphs that are used to describe non-treelike evolutionary histories and are thus a generalization of phylogenetic trees. The hybridization number of a phylogenetic network is the sum…
We develop a stochastic approximation-type algorithm to solve finite state/action, infinite-horizon, risk-aware Markov decision processes. Our algorithm has two loops. The inner loop computes the risk by solving a stochastic saddle-point…
In this paper, we address the inverse problem, or the statistical machine learning problem, in Markov random fields with a non-parametric pair-wise energy function with continuous variables. The inverse problem is formulated by maximum…
In evolutionary biology, genetic sequences carry with them a trace of the underlying tree that describes their evolution from a common ancestral sequence. The question of how many sequence sites are required to recover this evolutionary…
For an $m$-edge connected simple graph $G$, finding a spanning tree of $G$ with the maximum number of leaves is MAXSNP-complete. The problem remains NP-complete even if $G$ is planar and the maximal degree of $G$ is at most four. Lu and…
In this paper, we present two approximation algorithms for the directed multi-multiway cut and directed multicut problems. The so called region growing paradigm \cite{1} is modified and used for these two cut problems on directed graphs. By…
The \emph{Tree Augmentation Problem (TAP)} is given a tree $T=(V,E_T)$ and additional set of {\em links} $E$ on $V\times V$, find $F \subseteq E$ such that $T \cup F$ is $2$-edge-connected, and $|F|$ is minimum. The problem is APX-hard…
Reticulate evolution gives rise to complex phylogenetic networks, making their interpretation challenging. A typical approach is to extract trees within such networks. Since Francis and Steel's seminal paper, "Which Phylogenetic Networks…
Calculation of the log-likelihood stands as the computational bottleneck for many statistical phylogenetic algorithms. Even worse is its gradient evaluation, often used to target regions of high probability. Order ${\cal…
The reconstruction of phylogenetic trees from discrete character data typically relies on models that assume the characters evolve under a continuous-time Markov process operating at some overall rate $\lambda$. When $\lambda$ is too high…
Resource allocation problems are a family of problems in which resources must be selected to satisfy given demands. This paper focuses on the two-stage stochastic generalization of resource allocation problems where future demands are…
Determining the interaction partners among protein/domain families poses hard computational problems, in particular in the presence of paralogous proteins. Available approaches aim to identify interaction partners among protein/domain…
We present a computational model to reconstruct trees of ancestors for animals with sexual reproduction. Through a recursive algorithm combined with a random number generator, it is possible to reproduce the number of ancestors for each…
We present approximation algorithms for the following NP-hard optimization problems related to bottleneck spanning trees in metric spaces. 1. The disjoint bottleneck spanning tree problem: Given $n$ pairs of points in a metric space, find…
Accurate estimation of evolutionary distances between taxa is important for many phylogenetic reconstruction methods. In the case of bacteria, distances can be estimated using a range of different evolutionary models, from single nucleotide…
Markov chains are a common framework for individual-based state and time discrete models in ecology and evolution. Their use, however, is largely limited to systems with a low number of states, since the transition matrices involved pose…
Let $T$ be a tree space (or tree network) represented by a weighted tree with $t$ vertices, and $S$ be a set of $n$ stochastic points in $T$, each of which has a fixed location with an independent existence probability. We investigate two…
Bayesian inference methods rely on numerical algorithms for both model selection and parameter inference. In general, these algorithms require a high computational effort to yield reliable estimates. One of the major challenges in…
Motivation: Word-based or `alignment-free' methods for phylogeny reconstruction are much faster than traditional approaches, but they are generally less accurate. Most of these methods calculate pairwise distances for a set of input…
Reconstructing the tree of life from molecular sequences is a fundamental problem in computational biology. Modern data sets often contain a large number of genes, which can complicate the reconstruction problem due to the fact that…