Related papers: A Simple Linear-Time Algorithm for the Common Refi…
Partition refinement is a method for minimizing automata and transition systems of various types. Recently, we have developed a partition refinement algorithm that is generic in the transition type of the given system and matches the run…
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…
Linear model trees are regression trees that incorporate linear models in the leaf nodes. This preserves the intuitive interpretation of decision trees and at the same time enables them to better capture linear relationships, which is hard…
Partition refinement is a method for minimizing automata and transition systems of various types. Recently, we have developed a partition refinement algorithm that is generic in the transition type of the given system and matches the run…
Individualization-Refinement (IR) algorithms form the standard method and currently the only practical method for symmetry computations of graphs and combinatorial objects in general. Through backtracking, on each graph an IR-algorithm…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
We consider problems in which we are given a rooted tree as input, and must find a subtree with the same root, optimizing some objective function of the nodes in the subtree. When this function is the sum of constant node weights, the…
We give an algorithm to enumerate the results on trees of monadic second-order (MSO) queries represented by nondeterministic tree automata. After linear time preprocessing (in the input tree), we can enumerate answers with linear delay (in…
Phylogenetic trees canonically arise as embeddings of phylogenetic networks. We recently showed that the problem of deciding if two phylogenetic networks embed the same sets of phylogenetic trees is computationally hard, \blue{in…
This work proposes \textsc{H-Td}, a practical linear-time algorithm for computing an optimal-width tree decomposition of Halin graphs. Unlike state-of-the-art methods based on reduction rules or separators, \textsc{H-Td} exploits the…
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
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…
The AHU-algorithm solves the computationally difficult graph isomorphism problem for rooted trees, and does so with a linear time complexity. Although the AHU-algorithm has remained state of the art for almost 50 years, it has been…
A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…
An evolutionary tree (phylogenetic tree) is a binary, rooted, unordered tree that models the evolutionary history of currently living species in which leaves are labeled by species. In this paper, we investigate the problem of finding the…
We present an algorithm that enumerates all the minimal triangulations of a graph in incremental polynomial time. Consequently, we get an algorithm for enumerating all the proper tree decompositions, in incremental polynomial time, where…
We present a comprehensive classical and parameterized complexity analysis of decision tree pruning operations, extending recent research on the complexity of learning small decision trees. Thereby, we offer new insights into the…
This note presents an encoding and a decoding algorithms for a forest of (labelled) rooted uniform hypertrees and hypercycles in linear time, by using as few as $n - 2$ integers in the range $[1,n]$. It is a simple extension of the…
We analyze the bit complexity of efficient algorithms for fundamental optimization problems, such as linear regression, $p$-norm regression, and linear programming (LP). State-of-the-art algorithms are iterative, and in terms of the number…