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In this article we study the treewidth of the \emph{display graph}, an auxiliary graph structure obtained from the fusion of phylogenetic (i.e., evolutionary) trees at their leaves. Earlier work has shown that the treewidth of the display…
The mutational heterogeneity of tumours can be described with a tree representing the evolutionary history of the tumour. With noisy sequencing data there may be uncertainty in the inferred tree structure, while we may also wish to study…
Due to hybridization events in evolution, studying two different genes of a set of species may yield two related but different phylogenetic trees for the set of species. In this case, we want to measure the dissimilarity of the two trees.…
Maximum consensus estimation plays a critically important role in robust fitting problems in computer vision. Currently, the most prevalent algorithms for consensus maximization draw from the class of randomized hypothesize-and-verify…
The Matching Augmentation Problem (MAP) has recently received significant attention as an important step towards better approximation algorithms for finding cheap $2$-edge connected subgraphs. This has culminated in a…
Connected acyclic graphs (trees) are data objects that hierarchically organize categories. Collections of trees arise in a diverse variety of fields, including evolutionary biology, public health, machine learning, social sciences and…
As Artificial Intelligence (AI) is used in more applications, the need to consider and mitigate biases from the learned models has followed. Most works in developing fair learning algorithms focus on the offline setting. However, in many…
When performing an analysis on a collection of molecular sequences, it can be convenient to reduce the number of sequences under consideration while maintaining some characteristic of a larger collection of sequences. For example, one may…
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…
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…
A matching $M$ in a graph $G$ is an \emph{acyclic matching} if the subgraph of $G$ induced by the endpoints of the edges of $M$ is a forest. Given a graph $G$ and a positive integer $\ell$, Acyclic Matching asks whether $G$ has an acyclic…
We obtain new parameterized algorithms for the classical problem of determining whether a directed acyclic graph admits an upward planar drawing. Our results include a new fixed-parameter algorithm parameterized by the number of sources, an…
Random cut forest (RCF) algorithms have been developed for anomaly detection, particularly in time series data. The RCF algorithm is an improved version of the isolation forest (IF) algorithm. Unlike the IF algorithm, the RCF algorithm can…
Tree ensembles are powerful models that achieve excellent predictive performances, but can grow to unwieldy sizes. These ensembles are often post-processed (pruned) to reduce memory footprint and improve interpretability. We present…
We propose a novel method designed for large-scale regression problems, namely the two-stage best-scored random forest (TBRF). "Best-scored" means to select one regression tree with the best empirical performance out of a certain number of…
We present four novel approximation algorithms for finding triangulation of minimum treewidth. Two of the algorithms improve on the running times of algorithms by Robertson and Seymour, and Becker and Geiger that approximate the optimum by…
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…
In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…
We describe a $\frac{3}{2}$-approximation algorithm for the Forest Augmentation Problem (\textsf{FAP}), which is a special case of the Weighted 2-Edge-Connected Spanning Subgraph Problem (\textsf{Weighted 2-ECSS}). This significantly…
We consider the stochastic geometry model where the location of each node is a random point in a given metric space, or the existence of each node is uncertain. We study the problems of computing the expected lengths of several…