Related papers: Essential metrics for Life on graphs
To test generalization ability of a class of deep neural networks, we randomly generate a large number of different rule sets for 2-D cellular automata (CA), based on John Conway's Game of Life. Using these rules, we compute several…
What is aging? Mechanistic answers to this question remain elusive despite decades of research. Here, we propose a mathematical model of cellular aging based on a model gene interaction network. Our network model is made of only non-aging…
Topological metrics of graphs provide a natural way to describe the prominent features of various types of networks. Graph metrics describe the structure and interplay of graph edges and have found applications in many scientific fields. In…
The two most fundamental processes describing change in biology, development and evolu-tion, occur over drastically different timescales, difficult to reconcile within a unified framework. Development involves temporal sequences of cell…
Both external environmental selection and internal lower-level evolution are essential for an integral picture of evolution. This paper proposes that the division of internal evolution into DNA/RNA pattern formation (genotype) and protein…
Cellular automata are discrete and computational models thatcan be shown as general models of complexity. They are used in varied applications to derive the generalized behavior of the presented model. In this paper we have took one such…
We study metanetworks arising in genotype and phenotype spaces, in the context of a model population of Boolean graphs evolved under selection for short dynamical attractors. We define the adjacency matrix of a graph as its genotype, which…
Identifying disease-associated genes enables the development of precision medicine and the understanding of biological processes. Genome-wide association studies (GWAS), gene expression data, biological pathway analysis, and protein network…
Exponential-family random graph models (ERGMs) provide a principled and flexible way to model and simulate features common in social networks, such as propensities for homophily, mutuality, and friend-of-a-friend triad closure, through…
Evolutionary games on graphs play an important role in the study of evolution of cooperation in applied biology. Using rigorous mathematical concepts from a dynamical systems and graph theoretical point of view, we formalize the notions of…
Biomolecular networks have already found great utility in characterizing complex biological systems arising from pair-wise interactions amongst biomolecules. Here, we review how graph theoretical approaches can be applied not only for a…
Graph generation is integral to various engineering and scientific disciplines. Nevertheless, existing methodologies tend to overlook the generation of edge attributes. However, we identify critical applications where edge attributes are…
We construct a time-optimal quasi-solution of the firing mob synchronisation problem over finite, connected, and undirected multigraphs whose maximum degrees are uniformly bounded by a constant. It is only a quasi-solution because its…
The edge-degeneracy model is an exponential random graph model that uses the graph degeneracy, a measure of the graph's connection density, and number of edges in a graph as its sufficient statistics. We show this model is relatively…
The spread of an epidemic disease and the population's collective behavioural response are deeply intertwined, influencing each other's evolution. Such a co-evolution typically has been overlooked in mathematical models, limiting their…
Cellular automata can simulate many complex physical phenomena using the power of simple rules. The presented methodological platform expresses the concept of programmable matter in which Newtons laws of motion are one of examples. Energy…
In this paper, we advance the network theory of aging and mortality by developing a causal mathematical model for the mortality rate. First, we show that in large networks, where health deficits accumulate at nodes representing health…
The genotype-phenotype map is an essential object in our understanding of organismal complexity and adaptive properties, determining at once genomic plasticity and those constraints that may limit the ability of genomes to attain…
Given a network, the critical node detection problem finds a subset of nodes whose removal disrupts the network connectivity. Since many real-world systems are naturally modeled as graphs, assessing the vulnerability of the network is…
Graph games provide the foundation for modeling and synthesizing reactive processes. In the synthesis of stochastic reactive processes, the traditional model is perfect-information stochastic games, where some transitions of the game graph…