Related papers: Selection, recombination, and the ancestral initia…
We introduce the notion of a network's conduciveness, a probabilistically interpretable measure of how the network's structure allows it to be conducive to roaming agents, in certain conditions, from one portion of the network to another.…
We use the combination of ideas and results from the theory of graph limits and nonlinear evolution equations to provide a rigorous mathematical justification for taking continuum limit for certain nonlocally coupled networks and to extend…
Research shows that gene duplication followed by either repurposing or removal of duplicated genes is an important contributor to evolution of gene and protein interaction networks. We aim to identify which characteristics of a network can…
We consider the population dynamics of a set of species whose network of catalytic interactions is described by a directed graph. The relationship between the attractors of this dynamics and the underlying graph theoretic structures like…
The origin of diversification and coexistence of genes and species have been traditionally studied in isolated biological levels. Ecological and evolutionary views have focused on the mechanisms that enable or constrain species coexistence,…
This paper studies graphical model selection, i.e., the problem of estimating a graph of statistical relationships among a collection of random variables. Conventional graphical model selection algorithms are passive, i.e., they require all…
To a given gene tree topology $G$ and species tree topology $S$ with leaves labeled bijectively from a fixed set $X$, one can associate a set of ancestral configurations, each of which encodes a set of gene lineages that can be found at a…
Besides the complexity in time or in number of messages, a common approach for analyzing distributed algorithms is to look at the assumptions they make on the underlying network. We investigate this question from the perspective of network…
We are looking at local protein interaction networks from the perspective of directed, labeled graphs with quantitative values for monotonic changes in concentrations. These systems can be used to perform stability analysis for a stable…
A probability model is presented for the dynamics of mutation-selection balance in a haploid infinite-population infinite-sites setting sufficiently general to cover mutation-driven changes in full age-specific demographic schedules. The…
In a (two-type) Wright-Fisher diffusion with directional selection and two-way mutation, let $x$ denote today's frequency of the beneficial type, and given $x$, let $h(x)$ be the probability that, among all individuals of today's…
In stochastic evolutionary dynamics, the replacement of an existing genotype or cultural trait by a newly introduced mutant is typically characterized by the quantities of fixation probability and fixation time. But in a structured…
Graph representation learning (a.k.a. network embedding) is a significant topic of network analysis, due to its effectiveness to support various graph inference tasks. In this paper, we study the representation learning with multiple…
We consider the discrete-time migration-recombination equation, a deterministic, nonlinear dynamical system that describes the evolution of the genetic type distribution of a population evolving under migration and recombination in a law of…
Representation learning is central to graph machine learning, powering tasks such as link prediction and node classification. However, most graph embeddings are hard to interpret, offering limited insight into how learned features relate to…
Prediction of protein-ligand complexes for flexible proteins remains still a challenging problem in computational structural biology and drug design. Here we present two novel deep neural network approaches with significant improvement in…
We consider the Wright-Fisher model for a population of $N$ individuals, each identified with a sequence of a finite number of sites, and single-crossover recombination between them. We trace back the ancestry of single individuals from the…
We study the problem of robustly reconnecting habitats via the placement of green bridges at minimum total cost. Habitats are fragmented into patches and we seek to reconnect each habitat such that it remains connected even if any of its…
Random intersection graphs have received much interest and been used in diverse applications. They are naturally induced in modeling secure sensor networks under random key predistribution schemes, as well as in modeling the topologies of…
When long-lived, balancing selection can lead to trans-species polymorphisms that are shared by two or more species identical by descent. In this case, the gene genealogies at the selected sites cluster by allele instead of by species and,…