Related papers: A short note on the tractability of constructing p…
It is required to find an optimal order of constructing the edges of a network so as to minimize the sum of the weighted connection times of relevant pairs of vertices. Construction can be performed anytime anywhere in the network, with a…
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…
It has remained an open question for some time whether, given a set of not necessarily binary (i.e. "nonbinary") trees T on a set of taxa X, it is possible to determine in time f(r).poly(m) whether there exists a phylogenetic network that…
We call an Ising model tractable when it is possible to compute its partition function value (statistical inference) in polynomial time. The tractability also implies an ability to sample configurations of this model in polynomial time. The…
This paper introduces a hierarchical clustering algorithm, the Clustroid Hierarchical Nearest Neighbor ($\mathrm{CHN}^2$), designed for datasets with a countably infinite number of points. The method builds clusters across successive levels…
Cluster algebras are a recent topic of study and have been shown to be a useful tool to characterize structures in several knowledge fields. An important problem is to establish whether or not a given cluster algebra is of finite type.…
A rooted phylogenetic network is a directed acyclic graph with a single root, whose sinks correspond to a set of species. As such networks are useful for representing the evolution of species that have undergone reticulate evolution, there…
We give a Hasse-diagram characterization of when a clustering system $\mathcal C$ on a finite taxa set $X$ is the hardwired clustering system $C_N$ of a rooted level-$k$ network. For each non-trivial block $B$ of $H=\mathcal H[\mathcal C]$,…
A number of recent works have employed decision trees for the construction of explainable partitions that aim to minimize the $k$-means cost function. These works, however, largely ignore metrics related to the depths of the leaves in the…
This work proposes a clusterization algorithm called k-Morphological Sets (k-MS), based on morphological reconstruction and heuristics. k-MS is faster than the CPU-parallel k-Means in worst case scenarios and produces enhanced…
We have proposed a model based upon flocking on a complex network, and then developed two clustering algorithms on the basis of it. In the algorithms, firstly a \textit{k}-nearest neighbor (knn) graph as a weighted and directed graph is…
Inference of phylogenetic networks is of increasing interest in the genomic era. However, the extent to which phylogenetic networks are identifiable from various types of data remains poorly understood, despite its crucial role in…
We propose a nearest neighbor based clustering algorithm that results in a naturally defined hierarchy of clusters. In contrast to the agglomerative and divisive hierarchical clustering algorithms, our approach is not dependent on the…
Clusters of genes that have evolved by repeated segmental duplication present difficult challenges throughout genomic analysis, from sequence assembly to functional analysis. Improved understanding of these clusters is of utmost importance,…
Phylogenetics, the inference of evolutionary trees from molecular sequence data such as DNA, is an enterprise that yields valuable evolutionary understanding of many biological systems. Bayesian phylogenetic algorithms, which approximate a…
Phylogenetic networks are an extension of phylogenetic trees that allow for the representation of reticulate evolution events. One of the classes of networks that has gained the attention of the scientific community over the last years is…
Graph clustering involves the task of dividing nodes into clusters, so that the edge density is higher within clusters as opposed to across clusters. A natural, classic and popular statistical setting for evaluating solutions to this…
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…
Phylogenetic networks generalize phylogenetic trees, and have been introduced in order to describe evolution in the case of transfer of genetic material between coexisting species. There are many classes of phylogenetic networks, which can…
Phylogenetic networks generalize phylogenetic trees by allowing reticulate evolutionary events such as horizontal gene transfer and hybridization. Among the many subclasses of phylogenetic networks, orchard networks have attracted…