2021/06/16 by Jonathan Larson, Larson, Jonathan, Jukka‐Pekka Onnela +1 · 2 citations
Biochemistry, Genetics and Molecular Biology · Physics and Astronomy · #Bioinformatics and Genomic Networks #Complex Network Analysis Techniques #FOS: Computer and information sciences #Gene Regulatory Network Analysis #Methodology (stat.ME)
paper · pdf · doi:10.48550/arxiv.2106.09100
openalex publication_date 2021/06/16 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
Mechanistic network models specify the mechanisms by which networks grow and change, allowing researchers to investigate complex systems using both simulation and analytical techniques. Unfortunately, it is difficult to write likelihoods for instances of graphs generated with mechanistic models because of a combinatorial explosion in outcomes of repeated applications of the mechanism. Thus it is near impossible to estimate the parameters using maximum likelihood estimation. In this paper, we propose treating node sequence in a growing network model as an additional parameter, or as a missing random variable, and maximizing over the resulting likelihood. We develop this framework in the context of a simple mechanistic network model, used to study gene duplication and divergence, and test a variety of algorithms for maximizing the likelihood in simulated graphs. We also run the best-performing algorithm on a human protein-protein interaction network and four non-human protein-protein interaction networks. Although we focus on a specific mechanistic network model here, the proposed framework is more generally applicable to reversible models.