Phase transition in the two star Exponential Random Graph Model

This paper gives a way to simulate from the two star probability distribution on the space of simple graphs via auxiliary variables. Using this simulation scheme, the model is explored for various domains of the parameter values, and the phase transition boundaries are identified, and shown to be similar as that of the Curie-Weiss model of statistical physics. Concentration results are obtained for all the degrees, which further validate the phase transition predictions.Comment: 21 pages, 7 figure

edge2vec: Representation learning using edge semantics for biomedical knowledge discovery

Representation learning provides new and powerful graph analytical approaches and tools for the highly valued data science challenge of mining knowledge graphs. Since previous graph analytical methods have mostly focused on homogeneous graphs, an important current challenge is extending this methodology for richly heterogeneous graphs and knowledge domains. The biomedical sciences are such a domain, reflecting the complexity of biology, with entities such as genes, proteins, drugs, diseases, and phenotypes, and relationships such as gene co-expression, biochemical regulation, and biomolecular inhibition or activation. Therefore, the semantics of edges and nodes are critical for representation learning and knowledge discovery in real world biomedical problems. In this paper, we propose the edge2vec model, which represents graphs considering edge semantics. An edge-type transition matrix is trained by an Expectation-Maximization approach, and a stochastic gradient descent model is employed to learn node embedding on a heterogeneous graph via the trained transition matrix. edge2vec is validated on three biomedical domain tasks: biomedical entity classification, compound-gene bioactivity prediction, and biomedical information retrieval. Results show that by considering edge-types into node embedding learning in heterogeneous graphs, \textbf{edge2vec}\ significantly outperforms state-of-the-art models on all three tasks. We propose this method for its added value relative to existing graph analytical methodology, and in the real world context of biomedical knowledge discovery applicability.Comment: 10 page

Dynamically generated cyclic dominance in spatial prisoner's dilemma games

We have studied the impact of time-dependent learning capacities of players in the framework of spatial prisoner's dilemma game. In our model, this capacity of players may decrease or increase in time after strategy adoption according to a step-like function. We investigated both possibilities separately and observed significantly different mechanisms that form the stationary pattern of the system. The time decreasing learning activity helps cooperator domains to recover the possible intrude of defectors hence supports cooperation. In the other case the temporary restrained learning activity generates a cyclic dominance between defector and cooperator strategies, which helps to maintain the diversity of strategies via propagating waves. The results are robust and remain valid by changing payoff values, interaction graphs or functions characterizing time-dependence of learning activity. Our observations suggest that dynamically generated mechanisms may offer alternative ways to keep cooperators alive even at very larger temptation to defect.Comment: 7 pages, 6 figures, accepted for publication in Physical Review