Related papers: Comparing and simplifying distinct-cluster phyloge…
Understanding the origins of complexity is a fundamental challenge with implications for biological and technological systems. Network theory emerges as a powerful tool to model complex systems. Networks are an intuitive framework to…
An important part of the analysis of bio-molecular networks is to detect different functional units. Different functions are reflected in a different evolutionary dynamics, and hence in different statistical characteristics of network…
Binets and trinets are phylogenetic networks with two and three leaves, respectively. Here we consider the problem of deciding if there exists a binary level-1 phylogenetic network displaying a given set $\mathcal{T}$ of binary binets or…
Phylogenetic trees (i.e. evolutionary trees, additive trees or X-trees) play a key role in the processes of modeling and representing species evolution. Genome evolution of a given group of species is usually modeled by a species…
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…
Clustering is a fundamental problem in network analysis that finds closely connected groups of nodes and separates them from other nodes in the graph, while link prediction is to predict whether two nodes in a network are likely to have a…
Phylogenetic networks provide a more general description of evolutionary relationships than rooted phylogenetic trees. One way to produce a phylogenetic network is to randomly place $k$ arcs between the edges of a rooted binary phylogenetic…
Given any complex directed network, a set of acyclic subgraphs - the hierarchical backbone of the network - can be extracted that will provide valuable information about its hierarchical structure. The current paper presents how the…
Rooted phylogenetic networks are often constructed by combining trees, clusters, triplets or characters into a single network that in some well-defined sense simultaneously represents them all. We review these four models and investigate…
Network classification aims to group networks (or graphs) into distinct categories based on their structure. We study the connection between classification of a network and of its constituent nodes, and whether nodes from networks in…
Arboreal networks are multi-rooted phylogenetic networks whose underlying graph is a tree. We give an encoding of stack-free arboreal networks in terms of triplets and the novel concept of a duet. This yields a polynomial time algorithm to…
Plants are fundamentally important to life. Key research areas in plant science include plant species identification, weed classification using hyper spectral images, monitoring plant health and tracing leaf growth, and the semantic…
A phylogenetic tree is a way to organize a finite set of species, individuals or other sources of related data. The species for which we have existing DNA data make up the set of leaves of the tree. The balanced minimal evolution method of…
Phylogenetic networks describe the evolution of a set of taxa for which reticulate events have occurred at some point in their evolutionary history. Of particular interest is when the evolutionary history between a set of just three taxa…
We study the enumeration of spinal tree-child phylogenetic networks, a rigid family of tree-child networks in which all internal vertices lie on a single root--to--leaf path. We provide two complementary combinatorial frameworks. First, we…
Fixed effects models are very flexible because they do not make assumptions on the distribution of effects and can also be used if the heterogeneity component is correlated with explanatory variables. A disadvantage is the large number of…
We present new algorithms for inference in credal networks --- directed acyclic graphs associated with sets of probabilities. Credal networks are here interpreted as encoding strong independence relations among variables. We first present a…
Driven by the need for better models that allow one to shed light into the question how life's diversity has evolved, phylogenetic networks have now joined phylogenetic trees in the center of phylogenetics research. Like phylogenetic trees,…
Classifying large scale networks into several categories and distinguishing them according to their fine structures is of great importance with several applications in real life. However, most studies of complex networks focus on properties…
In the present paper we discuss the clustering procedure in the case where instead of a single metric we have a family of metrics. In this case we can obtain a partially ordered graph of clusters which is not necessarily a tree. We discuss…