Related papers: Towards a Data Reduction for the Minimum Flip Supe…
Supertree methods are tree reconstruction techniques that combine several smaller gene trees (possibly on different sets of species) to build a larger species tree. The question of interest is whether the reconstructed supertree converges…
This paper addresses the problem of finding a representation of a subtree distance, which is an extension of the tree metric. We show that a minimal representation is uniquely determined by a given subtree distance, and give a linear time…
The mode of a collection of values (i.e., the most frequent value in the collection) is a key summary statistic. Finding the mode in a given range of an array of values is thus of great importance, and constructing a data structure to solve…
The Maximum Agreement Forest (Maf) problem is a well-studied problem in evolutionary biology, which asks for a largest common subforest of a given collection of phylogenetic trees with identical leaf label-set. However, the previous work…
We consider a variant of treewidth that we call clique-partitioned treewidth in which each bag is partitioned into cliques. This is motivated by the recent development of FPT-algorithms based on similar parameters for various problems. With…
Structural information of phylogenetic tree topologies plays an important role in phylogenetic inference. However, finding appropriate topological structures for specific phylogenetic inference tasks often requires significant design effort…
Decision trees are one of the most popular methods for solving classification problems, mainly because of their good interpretability properties. Moreover, due to advances in recent years in mixed-integer optimization, several models have…
The Persistent-Phylogeny Model is an extension of the widely studied Perfect-Phylogeny Model, encompassing a broader range of evolutionary phenomena. Biological and algorithmic questions concerning persistent phylogeny have been intensely…
Different sources of information might tell different stories about the evolutionary history of a given set of species. This leads to (rooted) phylogenetic trees that "disagree" on triples of species, which we call "conflict triples". An…
The problem of reconstructing evolutionary trees or phylogenies is of great interest in computational biology. A popular model for this problem assumes that we are given the set of leaves (current species) of an unknown binary tree and the…
Tree projections provide a unifying framework to deal with most structural decomposition methods of constraint satisfaction problems (CSPs). Within this framework, a CSP instance is decomposed into a number of sub-problems, called views,…
We combine two methods for the lossless compression of unlabeled graphs - entropy compressing adjacency lists and computing canonical names for vertices - and solve an ensuing novel optimisation problem: Minimum-Entropy Tree-Extraction…
The prototypical high-dimensional statistics problem entails finding a structured signal in noise. Many of these problems exhibit an intriguing phenomenon: the amount of data needed by all known computationally efficient algorithms far…
Motivation: Many inference tools use the Perfect Phylogeny Model (PPM) to learn trees from noisy variant allele frequency (VAF) data. Learning in this setting is hard, and existing tools use approximate or heuristic algorithms. An…
Phylogenetic networks provide a way to describe and visualize evolutionary histories that have undergone so-called reticulate evolutionary events such as recombination, hybridization or horizontal gene transfer. The level k of a network…
This paper addresses a class of problems under interval data uncertainty composed of min-max regret versions of classical 0-1 optimization problems with interval costs. We refer to them as interval 0-1 min-max regret problems. The…
We study the planted clique problem in which a clique of size k is planted in an Erdos-Renyi graph G(n,1/2) and one is interested in recovering this planted clique. It is widely believed that it exhibits a statistical-computational gap when…
The structure of an evolving network contains information about its past. Extracting this information efficiently, however, is, in general, a difficult challenge. We formulate a fast and efficient method to estimate the most likely history…
We consider the polyhedral properties of two spanning tree problems with additional constraints. In the first problem, it is required to find a tree with a minimum sum of edge weights among all spanning trees with the number of leaves less…
Evolutionary histories for species that cross with one another or exchange genetic material can be represented by leaf-labelled, directed graphs called phylogenetic networks. A major challenge in the burgeoning area of phylogenetic networks…