相关论文: Identifying species network features from gene tre…

Describing a complex system is in many ways a problem akin to identifying an object, in that it involves defining boundaries, constituent parts and their relationships by the use of grouping laws. Here we propose a novel method which…

The comprehensive characterization of the structure of complex networks is essential to understand the dynamical processes which guide their evolution. The discovery of the scale-free distribution and the small world property of real…

Real world complex networks often exhibit multiplex structure, connecting entities from different aspects of physical systems such as social, transportation and biological networks. Little is known about general properties of such networks…

Gene genealogies are frequently studied by measuring properties such as their height ($H$), length ($L$), sum of external branches ($E$), sum of internal branches ($I$), and mean of their two basal branches ($B$), and the coalescence times…

Algebraic techniques in phylogenetics have historically been successful at proving identifiability results and have also led to novel reconstruction algorithms. In this paper, we study the ideal of phylogenetic invariants of the…

Bayesian networks faithfully represent the symmetric conditional independences existing between the components of a random vector. Staged trees are an extension of Bayesian networks for categorical random vectors whose graph represents…

Species trees represent the historical divergences of populations or species, while gene trees trace the ancestry of individual gene copies sampled within those populations. In cases involving rapid speciation, gene trees with topologies…

We consider a distributed detection system with communication constraints, where several nodes are arranged in an arbitrary tree topology, under the assumption of conditionally independent observations. We propose a cyclic design procedure…

We present simple deterministic algorithms for subgraph finding and enumeration in the broadcast CONGEST model of distributed computation: -- For any constant $k$, detecting $k$-paths and trees on $k$ nodes can be done in $O(1)$ rounds. --…

Phylogenetic networks provide a way to describe and visualize evolutionary histories that have undergone so-called reticulate evolutionary events such as recombination, hybridization or horizontal gene transfer. The level k of a network…

Complex networks are a powerful modeling tool, allowing the study of countless real-world systems. They have been used in very different domains such as computer science, biology, sociology, management, etc. Authors have been trying to…

Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate evolutionary processes such as hybridization. They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters,…

We propose a cyclic coefficient $R$ which represents the cyclic characteristics of complex networks. If the network forms a perfect tree-like structure then $R$ becomes zero. The larger value of $R$ represents that the network is more…

Phylogenetic networks can model more complicated evolutionary phenomena that trees fail to capture such as horizontal gene transfer and hybridization. The same Markov models that are used to model evolution on trees can also be extended to…

We propose a novel model-selection method for dynamic networks. Our approach involves training a classifier on a large body of synthetic network data. The data is generated by simulating nine state-of-the-art random graph models for dynamic…

Inference of the evolutionary histories of species, commonly represented by a species tree, is complicated by the divergent evolutionary history of different parts of the genome. Different loci on the genome can have different histories…

The multispecies coalescent model describes the generation of gene trees from a rooted metric species tree, and thus provides a framework for the inference of species trees from sampled gene trees. We prove that the STAR method of Liu et…

Deviations from the average can provide valuable insights about the organization of natural systems. This article extends this important principle to the more systematic identification and analysis of singular local connectivity patterns in…

Structural information of phylogenetic tree topologies plays an important role in phylogenetic inference. However, finding appropriate topological structures for specific phylogenetic inference tasks often requires significant design effort…

Complex networks in natural, social, and technological systems generically exhibit an abundance of rich information. Extracting meaningful structural features from data is one of the most challenging tasks in network theory. Many methods…