Literature DB >> 26120266

Improving Simulation-Based Algorithms for Fitting ERGMs.

Ruth M Hummel1, David R Hunter2, Mark S Handcock3.   

Abstract

Markov chain Monte Carlo methods can be used to approximate the intractable normalizing constants that arise in likelihood calculations for many exponential family random graph models for networks. However, in practice, the resulting approximations degrade as parameter values move away from the value used to define the Markov chain, even in cases where the chain produces perfectly efficient samples. We introduce a new approximation method along with a novel method of moving toward a maximum likelihood estimator (MLE) from an arbitrary starting parameter value in a series of steps based on alternating between the canonical exponential family parameterization and the mean-value parameterization. This technique enables us to find an approximate MLE in many cases where this was previously not possible. We illustrate these methods on a model for a transcriptional regulation network for E. coli, an example where previous attempts to approximate an MLE had failed, and a model for a well-known social network dataset involving friendships among workers in a tailor shop. These methods are implemented in the publicly available ergm package for R, and computer code to duplicate the results of this paper is included in the Supplemental Materials.

Entities:  

Keywords:  Exponential family random graph model; Markov chain Monte Carlo; Maximum likelihood estimation; Mean value parameterization

Year:  2012        PMID: 26120266      PMCID: PMC4479216          DOI: 10.1080/10618600.2012.679224

Source DB:  PubMed          Journal:  J Comput Graph Stat        ISSN: 1061-8600            Impact factor:   1.884


  7 in total

1.  RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12.

Authors:  H Salgado; A Santos-Zavaleta; S Gama-Castro; D Millán-Zárate; E Díaz-Peredo; F Sánchez-Solano; E Pérez-Rueda; C Bonavides-Martínez; J Collado-Vides
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

2.  Network motifs in the transcriptional regulation network of Escherichia coli.

Authors:  Shai S Shen-Orr; Ron Milo; Shmoolik Mangan; Uri Alon
Journal:  Nat Genet       Date:  2002-04-22       Impact factor: 38.330

3.  Exploring biological network structure using exponential random graph models.

Authors:  Zachary M Saul; Vladimir Filkov
Journal:  Bioinformatics       Date:  2007-07-20       Impact factor: 6.937

4.  Curved Exponential Family Models for Social Networks.

Authors:  David R Hunter
Journal:  Soc Networks       Date:  2007-03

5.  ergm: A Package to Fit, Simulate and Diagnose Exponential-Family Models for Networks.

Authors:  David R Hunter; Mark S Handcock; Carter T Butts; Steven M Goodreau; Martina Morris
Journal:  J Stat Softw       Date:  2008-05-01       Impact factor: 6.440

6.  A Framework for the Comparison of Maximum Pseudo Likelihood and Maximum Likelihood Estimation of Exponential Family Random Graph Models.

Authors:  Marijtje A J van Duijn; Krista J Gile; Mark S Handcock
Journal:  Soc Networks       Date:  2009-01

7.  Instability, Sensitivity, and Degeneracy of Discrete Exponential Families.

Authors:  Michael Schweinberger
Journal:  J Am Stat Assoc       Date:  2012-01-24       Impact factor: 5.033

  7 in total
  8 in total

1.  INFERENCE FOR SOCIAL NETWORK MODELS FROM EGOCENTRICALLY SAMPLED DATA, WITH APPLICATION TO UNDERSTANDING PERSISTENT RACIAL DISPARITIES IN HIV PREVALENCE IN THE US.

Authors:  Pavel N Krivitsky; Martina Morris
Journal:  Ann Appl Stat       Date:  2017-04-08       Impact factor: 2.083

2.  Computational Statistical Methods for Social Network Models.

Authors:  David R Hunter; Pavel N Krivitsky; Michael Schweinberger
Journal:  J Comput Graph Stat       Date:  2012-12-01       Impact factor: 2.302

3.  An approximation method for improving dynamic network model fitting.

Authors:  Nicole Bohme Carnegie; Pavel N Krivitsky; David R Hunter; Steven M Goodreau
Journal:  J Comput Graph Stat       Date:  2015       Impact factor: 2.302

4.  Fast Maximum Likelihood Estimation via Equilibrium Expectation for Large Network Data.

Authors:  Maksym Byshkin; Alex Stivala; Antonietta Mira; Garry Robins; Alessandro Lomi
Journal:  Sci Rep       Date:  2018-07-31       Impact factor: 4.379

5.  Testing biological network motif significance with exponential random graph models.

Authors:  Alex Stivala; Alessandro Lomi
Journal:  Appl Netw Sci       Date:  2021-11-22

6.  Complex network analysis to understand trading partnership in French swine production.

Authors:  Pachka Hammami; Stefan Widgren; Vladimir Grosbois; Andrea Apolloni; Nicolas Rose; Mathieu Andraud
Journal:  PLoS One       Date:  2022-04-07       Impact factor: 3.240

7.  Highly scalable maximum likelihood and conjugate Bayesian inference for ERGMs on graph sets with equivalent vertices.

Authors:  Fan Yin; Carter T Butts
Journal:  PLoS One       Date:  2022-08-26       Impact factor: 3.752

8.  Exponential random graph model parameter estimation for very large directed networks.

Authors:  Alex Stivala; Garry Robins; Alessandro Lomi
Journal:  PLoS One       Date:  2020-01-24       Impact factor: 3.240

  8 in total

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