Related papers: Fast Compatibility Testing for Rooted Phylogenetic…
Motivated by an application in computational topology, we consider a novel variant of the problem of efficiently maintaining dynamic rooted trees. This variant requires merging two paths in a single operation. In contrast to the standard…
Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…
Given a collection $\tau$ of subsets of a finite set $X$, we say that $\tau$ is {\em phylogenetically flexible} if, for any collection $R$ of rooted phylogenetic trees whose leaf sets comprise the collection $\tau$, $R$ is compatible (i.e.…
Label tree-based algorithms are widely used to tackle multi-class and multi-label problems with a large number of labels. We focus on a particular subclass of these algorithms that use probabilistic classifiers in the tree nodes. Examples…
Tree alignment graphs (TAGs) provide an intuitive data structure for storing phylogenetic trees that exhibits the relationships of the individual input trees and can potentially account for nested taxonomic relationships. This paper…
There is a long tradition of the axiomatic study of consensus methods in phylogenetics that satisfy certain desirable properties. One recently-introduced property is associative stability, which is desirable because it confers a…
The phylogenetic tree construction is to infer the evolutionary relationship between species from the experimental data. However, the experimental data are often imperfect and conflicting each others. Therefore, it is important to extract…
Consider a tree $T=(V,E)$ with root $\circ$ and edge length function $\ell:E\to\mathbb{R}_+$. The phylogenetic covariance matrix of $T$ is the matrix $C$ with rows and columns indexed by $L$, the leaf set of $T$, with entries…
A T-graph (a special case of a chordal graph) is the intersection graph of connected subtrees of a suitable subdivision of a fixed tree T . We deal with the isomorphism problem for T-graphs which is GI-complete in general - when T is a part…
Phylogenetic networks generalize phylogenetic trees by representing reticulate evolution. Tree-based networks and their support trees have been extensively studied, but not all networks are tree-based. To measure how far such networks are…
In this paper we address the problem of testing whether two observed trees $(t,t')$ are sampled either independently or from a joint distribution under which they are correlated. This problem, which we refer to as correlation detection in…
We study the natural problem of Triplet Reconstruction (also Rooted Triplets Consistency or Triplet Clustering), originally motivated in computational biology and relational databases (Aho, Sagiv, Szymanski, and Ullman, 1981): given $n$…
We compare the phylogenetic tensors for various trees and networks for two, three and four taxa. If the probability spaces between one tree or network and another are not identical then there will be phylogenetic tensors that could have…
Network Phylogenetic Diversity (Network-PD) is a measure for the diversity of a set of species based on a rooted phylogenetic network (with branch lengths and inheritance probabilities on the reticulation edges) describing the evolution of…
An $\alpha$-thin tree $T$ of a graph $G$ is a spanning tree such that every cut of $G$ has at most an $\alpha$ proportion of its edges in $T$. The Thin Tree Conjecture proposes that there exists a function $f$ such that for any $\alpha >…
Comparing and computing distances between phylogenetic trees are important biological problems, especially for models where edge lengths play an important role. The geodesic distance measure between two phylogenetic trees with edge lengths…
Given a text $T$ of length $n$ and a pattern $P$ of length $m$, the string matching problem is a task to find all occurrences of $P$ in $T$. In this study, we propose an algorithm that solves this problem in $O((n + m)q)$ time considering…
An important problem in evolutionary genomics is to investigate whether a certain trait measured on each sample is associated with the sample phylogenetic tree. The phylogenetic tree represents the shared evolutionary history of the samples…
Quartet Reconstruction, the task of recovering a phylogenetic tree from smaller trees on four species called \textit{quartets}, is a well-studied problem in theoretical computer science with far-reaching connections to statistics, graph…
In the laminar-constrained spanning tree problem, the goal is to find a minimum-cost spanning tree which respects upper bounds on the number of times each cut in a given laminar family is crossed. This generalizes the well-studied…