New network models facilitate analysis of biological networks

no code implementations • 11 Dec 2023 • Alex Stivala

I find that the Tapered ERGM and the LOLOG are able to estimate models for networks for which it was not possible to estimate a conventional ERGM, and are able to do so using only simple model parameters.

Testing biological network motif significance with exponential random graph models

1 code implementation • 29 Jan 2020 • Alex Stivala, Alessandro Lomi

ERGM models indicate over-representation of triangles in the PPI network, and confirm results from previous research as to over-representation of transitive triangles (feed-forward loop) in an E. coli and a yeast regulatory network.

Exponential random graph model parameter estimation for very large directed networks

1 code implementation • 17 Apr 2019 • Alex Stivala, Garry Robins, Alessandro Lomi

In the case of undirected networks, snowball sampling can be used to find ERGM parameter estimates of larger networks via network samples, and recently published improvements in ERGM network distribution sampling and ERGM estimation algorithms have allowed ERGM parameter estimates of undirected networks with over one hundred thousand nodes to be made.

Methodology Applications

Fast Maximum Likelihood estimation via Equilibrium Expectation for Large Network Data

2 code implementations • 28 Feb 2018 • Maksym Byshkin, Alex Stivala, Antonietta Mira, Garry Robins, Alessandro Lomi

We demonstrate the performance of the EE algorithm in the context of exponential random graphmodels (ERGMs) a family of statistical models commonly used in empirical research based on network data observed at a single period in time.

Another phase transition in the Axelrod model

1 code implementation • 8 Dec 2016 • Alex Stivala, Paul Keeler

Axelrod's model of cultural dissemination, despite its apparent simplicity, demonstrates complex behavior that has been of much interest in statistical physics.

Physics and Society Statistical Mechanics