Related papers: On Cherry-picking and Network Containment
Phylogenetic networks are mathematical structures for modeling and visualization of reticulation processes in the study of evolution. Galled networks, reticulation visible networks, nearly-stable networks and stable-child networks are the…
In this paper, a 1d convolutional neural network is designed for classification tasks of plant leaves. This network based classifier is analyzed in two directions. In the forward direction, the proposed network can be used in two ways: a…
Tree-child networks, one of the prominent network classes in phylogenetics, have been introduced for the purpose of modeling reticulate evolution. Recently, the first author together with Gittenberger and Mansouri (2019) showed that the…
The structure of an evolving network contains information about its past. Extracting this information efficiently, however, is, in general, a difficult challenge. We formulate a fast and efficient method to estimate the most likely history…
Complex networks representing social interactions, brain activities, molecular structures have been studied widely to be able to understand and predict their characteristics as graphs. Models and algorithms for these networks are used in…
Phylogenetic networks have gained prominence over the years due to their ability to represent complex non-treelike evolutionary events such as recombination or hybridization. Popular combinatorial objects used to construct them are triplet…
Tree-child networks are one of the most prominent network classes for modeling evolutionary processes which contain reticulation events. Several recent studies have addressed counting questions for {\it bicombining tree-child networks}…
Orchards are a biologically relevant class of phylogenetic networks as they can describe treelike evolutionary histories augmented with horizontal transfer events. Moreover, the class has attractive mathematical characterizations that can…
Recent genomic and bioinformatic advances have motivated the development of numerous random network models purporting to describe graphs of biological, technological, and sociological origin. The success of a model has been evaluated by how…
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…
An important problem in phylogenetics is the construction of phylogenetic trees. One way to approach this problem, known as the supertree method, involves inferring a phylogenetic tree with leaves consisting of a set $X$ of species from a…
Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for…
Decompositions of networks are useful not only for structural exploration. They also have implications and use in analysis and computational solution of processes (such as the Ising model, percolation, SIR model) running on a given network.…
A contemporary and fundamental problem faced by many evolutionary biologists is how to puzzle together a collection $\mathcal P$ of partial trees (leaf-labelled trees whose leaves are bijectively labelled by species or, more generally,…
Real networks exhibit nontrivial topological features such as heavy-tailed degree distribution, high clustering, and small-worldness. Researchers have developed several generative models for synthesizing artificial networks that are…
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…
Designing algorithms that generate networks with a given degree sequence while varying both subgraph composition and distribution of subgraphs around nodes is an important but challenging research problem. Current algorithms lack control of…
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…
Phylogenetic networks are a generalization of evolutionary or phylogenetic trees that are commonly used to represent the evolution of species which cross with one another. A special type of phylogenetic network is an {\em $X$-cactus}, which…
Finding the most parsimonious tree inside a phylogenetic network with respect to a given character is an NP-hard combinatorial optimization problem that for many network topologies is essentially inapproximable. In contrast, if the network…