Related papers: Approximation algorithms for nonbinary agreement f…
We consider the problem of approximating the arboricity of a graph $G= (V,E)$, which we denote by $\mathsf{arb}(G)$, in sublinear time, where the arboricity of a graph is the minimal number of forests required to cover its edges. An…
Compatibility of unrooted phylogenetic trees is a well studied problem in phylogenetics. It asks to determine whether for a set of k input trees there exists a larger tree (called a supertree) that contains the topologies of all k input…
A rearrangement operation makes a small graph-theoretical change to a phylogenetic network to transform it into another one. For unrooted phylogenetic trees and networks, popular rearrangement operations are tree bisection and reconnection…
This paper summarizes the work on implementing few solutions for the Steiner Tree problem which we undertook in the PAAL project. The main focus of the project is the development of generic implementations of approximation algorithms…
The Aho, Hopcroft and Ullman (AHU) algorithm has been the state of the art since the 1970s for determining in linear time whether two unordered rooted trees are isomorphic or not. However, it has been criticized (by Campbell and Radford)…
Sequence alignment is common nowadays as it is used in many fields to determine how closely two sequences are related and at times to see how little they differ. In computational biology / Bioinformatics, there are many algorithms developed…
Moss and Rabani[12] study constrained node-weighted Steiner tree problems with two independent weight values associated with each node, namely, cost and prize (or penalty). They give an O(log n)-approximation algorithm for the…
Scheduling with assignment restrictions is an important special case of scheduling unrelated machines which has attracted much attention in the recent past. While a lower bound on approximability of 3/2 is known for its most general…
Phylogenetic trees are frequently used to model evolution. Such trees are typically reconstructed from data like DNA, RNA, or protein alignments using methods based on criteria like maximum parsimony (amongst others). Maximum parsimony has…
We present the first fixed-parameter algorithm for constructing a tree-child phylogenetic network that displays an arbitrary number of binary input trees and has the minimum number of reticulations among all such networks. The algorithm…
In this paper, we introduce the notion of Cartesian Forest, which generalizes Cartesian Trees, in order to deal with partially ordered sequences. We show that algorithms that solve both exact and approximate Cartesian Tree Matching can be…
We introduce canonical correlation forests (CCFs), a new decision tree ensemble method for classification and regression. Individual canonical correlation trees are binary decision trees with hyperplane splits based on local canonical…
Agreement forests continue to play a central role in the comparison of phylogenetic trees since their introduction more than 25 years ago. More specifically, they are used to characterise several distances that are based on tree…
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…
In this paper we introduce and study three new measures for efficient discriminative comparison of phylogenetic trees. The NNI navigation dissimilarity $d_{nav}$ counts the steps along a "combing" of the Nearest Neighbor Interchange (NNI)…
In this paper we present a novel probabilistic sampling-based motion planning algorithm called the Fast Marching Tree algorithm (FMT*). The algorithm is specifically aimed at solving complex motion planning problems in high-dimensional…
Phylogenetic trees are leaf-labelled trees used to model the evolution of species. Here we explore the practical impact of kernelization (i.e. data reduction) on the NP-hard problem of computing the TBR distance between two unrooted binary…
A common subgraph of two graphs $G_1$ and $G_2$ is a graph that is isomorphic to subgraphs of $G_1$ and $G_2$. In the largest common subgraph problem the task is to determine a common subgraph for two given graphs $G_1$ and $G_2$ that is of…
We show the first conditionally optimal deterministic algorithm for $3$-coloring forests in the low-space massively parallel computation (MPC) model. Our algorithm runs in $O(\log \log n)$ rounds and uses optimal global space. The best…
Phylogenetic trees describe the relationships between species in the evolutionary process, and provide information about the rates of diversification. To understand the mechanisms behind macroevolution, we consider a class of multitype…