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Motivated by multi-subject experiments in neuroimaging studies, we develop a modeling framework for joint community detection in a group of related networks, which can be considered as a sample from a population of networks. The proposed random effects stochastic block model facilitates the study of group differences and subject-specific variations in the community structure. The model proposes a putative mean community structure which is representative of the group or the population under consideration but is not the community structure of any individual component network. Instead, the community memberships of nodes vary in each component network with a transition matrix, thus modeling the variation in community structure across a group of subjects. To estimate the quantities of interest we propose two methods, a variational EM algorithm, and a model-free "two-step" method based on either spectral or non-negative matrix factorization (NMF). Our NMF based method Co-OSNTF is of independent interest and we study its convergence properties to a stationary point. We also develop a resampling-based hypothesis test for differences in community structure in two populations both at the whole network level and node level. The methodology is applied to a publicly available fMRI dataset from multi-subject experiments involving schizophrenia patients. Our methods reveal an overall putative community structure representative of the group as well as subject-specific variations within each group. Using our network level hypothesis tests we are able to ascertain statistically significant difference in community structure between the two groups, while our node level tests help determine the nodes that are driving the difference.

A random effects stochastic block model for joint community detection in multiple networks with applications to neuroimaging