Related papers: Heading in the right direction? Using head moves t…
A nearest-neighbor-interchange (NNI) walk is a sequence of unrooted phylogenetic trees, T_0, T_1, T_2,... where each consecutive pair of trees differ by a single NNI move. We give tight bounds on the length of the shortest NNI-walks that…
A directed phylogenetic network is tree-child if every non-leaf vertex has a child that is not a reticulation. As a class of directed phylogenetic networks, tree-child networks are very useful from a computational perspective. For example,…
A fundamental problem in the study of phylogenetic networks is to determine whether or not a given phylogenetic network contains a given phylogenetic tree. We develop a quadratic-time algorithm for this problem for binary nearly-stable…
We study the temporal co-variation of network co-evolution via the cross-link structure of networks, for which we take advantage of the formalism of hypergraphs to map cross-link structures back to network nodes. We investigate two sets of…
The aim of this paper is to highlight and explore a traditional problem, which is the minimum spanning tree, and finding the shortest-path in network routing, by using Swarm Intelligence. This work to be considered as an investigation topic…
Neural networks are a group of neurons stacked together in multiple layers to mimic the biological neurons in a human brain. Neural networks have been trained using the backpropagation algorithm based on gradient descent strategy for…
Rooted phylogenetic networks allow biologists to represent evolutionary relationships between present-day species by revealing ancestral speciation and hybridization events. A convenient and well-studied class of such networks are…
Phylogenetic networks are an important way to represent evolutionary histories that involve reticulations such as hybridization or horizontal gene transfer, yet fundamental questions such as how many networks there are that satisfy certain…
Substring kernels are classical tools for representing biological sequences or text. However, when large amounts of annotated data are available, models that allow end-to-end training such as neural networks are often preferred. Links…
Segmentation in arthropod embryogenesis represents a well-known example of body plan diversity. Striped patterns of gene expression that lead to the future body segments appear simultaneously or sequentially in long and short germ-band…
The dynamical evolution of complex networks underpins the structure-function relationships in natural and artificial systems. Yet, restoring a network's formation from a single static snapshot remains challenging. Here, we present a…
Mode connectivity is a phenomenon where trained models are connected by a path of low loss. We reframe this in the context of Information Geometry, where neural networks are studied as spaces of parameterized distributions with curved…
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…
Orthologous genes, which arise through speciation, play a key role in comparative genomics and functional inference. In particular, graph-based methods allow for the inference of orthology estimates without prior knowledge of the underlying…
In this work, we answer an open problem in the study of phylogenetic networks. Phylogenetic trees are rooted binary trees in which all edges are directed away from the root, whereas phylogenetic networks are rooted acyclic digraphs. For the…
Network dynamics offers critical insights into the behavior and evolution of complex systems. Here, we focus on the topological dynamics of networks to explore a unique process for reducing the average distance: topological compression. The…
Self-avoiding random walks were performed on protein residue networks. Compared with protein residue networks with randomized links, the probability of a walk being successful is lower and the length of successful walks shorter in…
Recordings of increasingly large neural populations have revealed that the firing of individual neurons is highly coordinated. When viewed in the space of all possible patterns, the collective activity forms non-linear structures called…
Tree-child networks are an important network class which are used in phylogenetics to model reticulate evolution. In a recent paper, Pons and Batle (2021) conjectured a relation between tree-child networks and certain words. In this short…
Decades of research on the neural code underlying spatial navigation have revealed a diverse set of neural response properties. The Entorhinal Cortex (EC) of the mammalian brain contains a rich set of spatial correlates, including grid…