Related papers: Combining Networks using Cherry Picking Sequences
Convolutional Neural Networks (CNNs) have achieved significant breakthroughs in various fields. However, these advancements have led to a substantial increase in the complexity and size of these networks. This poses a challenge when…
A binary phylogenetic network may or may not be obtainable from a tree by the addition of directed edges (arcs) between tree arcs. Here, we establish a precise and easily tested criterion (based on `2-SAT') that efficiently determines…
The evolution processes of complex systems carry key information in the systems' functional properties. Applying machine learning algorithms, we demonstrate that the historical formation process of various networked complex systems can be…
As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…
We consider the problem of uniformly generating a spanning tree, of a connected undirected graph. This process is useful to compute statistics, namely for phylogenetic trees. We describe a Markov chain for producing these trees. For cycle…
We present a learning-based approach to computing solutions for certain NP-hard problems. Our approach combines deep learning techniques with useful algorithmic elements from classic heuristics. The central component is a graph…
We propose a new method for hierarchical clustering based on the optimisation of a cost function over trees of limited depth, and we derive a message--passing method that allows to solve it efficiently. The method and algorithm can be…
Phylogenetic networks are a generalization of phylogenetic trees that are used to represent reticulate evolution. Unrooted phylogenetic networks form a special class of such networks, which naturally generalize unrooted phylogenetic trees.…
The evolution of molecular and phenotypic traits is commonly modelled using Markov processes along a phylogeny. This phylogeny can be a tree, or a network if it includes reticulations, representing events such as hybridization or admixture.…
Reconstructing the evolutionary past of a family of genes is an important aspect of many genomic studies. To help with this, simple operations on a set of sequences called orthology relations may be employed. In addition to being…
In this paper we present a novel tool to evaluate problem solving systems. Instead of using a system to solve a problem, we suggest using the problem to evaluate the system. By finding a numerical representation of a problem's complexity,…
Along with the development of manufacture and services, the problem of distribution network optimization has been growing in importance, thus receiving much attention from the research community. One of the most recently introduced network…
Seeding then expanding is a commonly used scheme to discover overlapping communities in a network. Most seeding methods are either too complex to scale to large networks or too simple to select high-quality seeds, and the non-principled…
The Steiner tree problem aims to determine a minimum edge-weighted tree that spans a given set of terminal vertices from a given graph. In the past decade, a considerable number of algorithms have been developed to solve this…
We consider the classic problem of Network Reliability. A network is given together with a source vertex, one or more target vertices, and probabilities assigned to each of the edges. Each edge appears in the network with its associated…
Phylogenetic trees illustrate the evolutionary history of genes and species. In most cases, although genes evolve along with the species they belong to, a species tree and gene tree are not identical, because of evolutionary events at the…
Network reconstruction lies at the heart of phylogenetic research. Two well studied classes of phylogenetic networks include tree-child networks and level-$k$ networks. In a tree-child network, every non-leaf node has a child that is a tree…
A large class of phylogenetic networks can be obtained from trees by the addition of horizontal edges between the tree edges. These networks are called tree based networks. Reticulation-visible networks and child-sibling networks are all…
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…
Phylogenetics begins with reconstructing biological family trees from genetic data. Since Nature is not limited to tree-like histories, we use networks to organize our data, and have discovered new polytopes, metric spaces, and simplicial…