相关论文: Combinatorial Topological Models for Phylogenetic …

Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…

Tanglegrams are a special class of graphs appearing in applications concerning cospeciation and coevolution in biology and computer science. They are formed by identifying the leaves of two rooted binary trees. We give an explicit formula…

Recently, considerable effort has been put into developing fast algorithms to reconstruct a rooted phylogenetic network that explains two rooted phylogenetic trees and has a minimum number of hybridization vertices. With the standard…

Deep Convolutional Neural Networks have become a Swiss knife in solving critical artificial intelligence tasks. However, deploying deep CNN models for latency-critical tasks remains to be challenging because of the complex nature of CNNs.…

Current popular methods for Magnetic Resonance Fingerprint (MRF) recovery are bottlenecked by the heavy computations of a matched-filtering step due to the growing size and complexity of the fingerprint dictionaries in multi-parametric…

'Tree-based' phylogenetic networks proposed by Francis and Steel have attracted much attention of theoretical biologists in the last few years. At the heart of the definitions of tree-based phylogenetic networks is the notion of 'support…

The paper tackles the problem of clustering multiple networks, directed or not, that do not share the same set of vertices, into groups of networks with similar topology. A statistical model-based approach based on a finite mixture of…

The inability to resolve deep node relationships of highly divergent/rapidly evolving protein families is a major factor that stymies evolutionary studies. In this manuscript, we propose a Multiple Sequence Alignment (MSA) independent…

Phylogenetic trees and networks are leaf-labelled graphs used to model evolution. Display graphs are created by identifying common leaf labels in two or more phylogenetic trees or networks. The treewidth of such graphs is bounded as a…

Genetic and comparative genomic studies indicate that extant genomes are more properly considered to be a fusion product of random mutations over generations and genomic material transfers between individuals of different lineages. This has…

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…

Graph connectivity and network design problems are among the most fundamental problems in combinatorial optimization. The minimum spanning tree problem, the two edge-connected spanning subgraph problem (2-ECSS) and the tree augmentation…

Ensembles of networks arise in various fields where multiple independent networks are observed on the same set of nodes, for example, a collection of brain networks constructed on the same brain regions for different individuals. However,…

Reticulate evolution gives rise to complex phylogenetic networks, making their interpretation challenging. A typical approach is to extract trees within such networks. Since Francis and Steel's seminal paper, "Which Phylogenetic Networks…

A common problem in phylogenetics is to try to infer a species phylogeny from gene trees. We consider different variants of this problem. The first variant, called Unrestricted Minimal Episodes Inference, aims at inferring a species tree…

We present kleuren, a novel assembly-free method to reconstruct phylogenetic trees using the Colored de Bruijn Graph. kleuren works by constructing the Colored de Bruijn Graph and then traversing it, finding bubble structures in the graph…

As a representation of relational data over time series, longitudinal networks provide opportunities to study link formation processes. However, networks at scale often exhibits community structure (i.e. clustering), which may confound…

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…

In deep neural networks, better results can often be obtained by increasing the complexity of previously developed basic models. However, it is unclear whether there is a way to boost performance by decreasing the complexity of such models.…

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…