In statistical network analysis, we often assume either the full network is available or multiple subgraphs can be sampled to estimate various global properties of the network. However, in a real social network, people frequently make decisions based on their local view of the network alone. Here, we consider a partial information framework that characterizes the local network centered at a given individual by path length $L$ and gives rise to a partial adjacency matrix. Under $L=2$, we focus on the problem of (global) community detection using the popular stochastic block model (SBM) and its degree-corrected variant (DCSBM). We derive theoretical properties of the eigenvalues and eigenvectors from the signal term of the partial adjacency matrix and propose new spectral-based community detection algorithms that achieve consistency under appropriate conditions. Our analysis also allows us to propose a new centrality measure that assesses the importance of an individual's partial information in determining global community structure. Using simulated and real networks, we demonstrate the performance of our algorithms and compare our centrality measure with other popular alternatives to show it captures unique nodal information. Our results illustrate that the partial information framework enables us to compare the viewpoints of different individuals regarding the global structure.

Variational approximation has been widely used in large-scale Bayesian inference recently, the simplest kind of which involves imposing a mean field assumption to approximate complicated latent structures. Despite the computational scalability of mean field, theoretical studies of its loss function surface and the convergence behavior of iterative updates for optimizing the loss are far from complete. In this paper, we focus on the problem of community detection for a simple two-class Stochastic Blockmodel (SBM) with equal class sizes. Using batch co-ordinate ascent (BCAVI) for updates, we show different convergence behavior with respect to different initializations. When the parameters are known or estimated within a reasonable range and held fixed, we characterize conditions under which an initialization can converge to the ground truth. On the other hand, when the parameters need to be estimated iteratively, a random initialization will converge to an uninformative local optimum.

Mean-field variational inference (MFVI) has been widely applied in large scale Bayesian inference. However, MFVI assumes independent distribution on the latent variables, which often leads to objective functions with many local optima, making optimization algorithms sensitive to initialization. In this paper, we study the advantage of structured variational inference in the context of the two-class Stochastic Blockmodel. To facilitate theoretical analysis, the variational distribution is constructed to have a simple pairwise dependency structure on the nodes of the network. We prove that, in a broad density regime and for general random initializations, unlike MFVI, the estimated class labels by structured VI converge to the ground truth with high probability, when the model parameters are known, estimated within a reasonable range or jointly optimized with the variational parameters. In addition, empirically we demonstrate structured VI is more robust compared with MFVI when the graph is sparse and the signal to noise ratio is low. The paper takes a first step towards understanding the importance of dependency structure in variational inference for community detection.

Tuning hyperparameters for unsupervised learning problems is difficult in general due to the lack of ground truth for validation. However, the success of most clustering methods depends heavily on the correct choice of the involved hyperparameters. Take for example the Lagrange multipliers of penalty terms in semidefinite programming (SDP) relaxations of community detection in networks, or the bandwidth parameter needed in the Gaussian kernel used to construct similarity matrices for spectral clustering. Despite the popularity of these clustering algorithms, there are not many provable methods for tuning these hyperparameters. In this paper, we provide an overarching framework with provable guarantees for tuning hyperparameters in the above class of problems under two different models. Our framework can be augmented with a cross validation procedure to do model selection as well. In a variety of simulation and real data experiments, we show that our framework outperforms other widely used tuning procedures in a broad range of parameter settings.

Variational approximation has been widely used in large-scale Bayesian inference recently, the simplest kind of which involves imposing a mean field assumption to approximate complicated latent structures. Despite the computational scalability of mean field, theoretical studies of its loss function surface and the convergence behavior of iterative updates for optimizing the loss are far from complete. In this paper, we focus on the problem of community detection for a simple two-class Stochastic Blockmodel (SBM). Using batch co-ordinate ascent (BCAVI) for updates, we give a complete characterization of all the critical points and show different convergence behaviors with respect to initializations. When the parameters are known, we show a significant proportion of random initializations will converge to ground truth. On the other hand, when the parameters themselves need to be estimated, a random initialization will converge to an uninformative local optimum.

Motivation: The three-dimensional organization of chromatin plays a critical role in gene regulation and disease. High-throughput chromosome conformation capture experiments such as Hi-C are used to obtain genome-wide maps of three-dimensional chromatin contacts. However, robust estimation of data quality and systematic comparison of these contact maps is challenging due to the multi-scale, hierarchical structure of chromatin contacts and the resulting properties of experimental noise in the data. Measuring concordance of contact maps is important for assessing reproducibility of replicate experiments and for modeling variation between different cellular contexts. Results: We introduce a concordance measure called DIfferences between Smoothed COntact maps (GenomeDISCO) for assessing the similarity of a pair of contact maps obtained from chromosome conformation capture experiments. The key idea is to smooth contact maps using random walks on the contact map graph, before estimating concordance. We use simulated datasets to benchmark GenomeDISCO's sensitivity to different types of noise that affect chromatin contact maps. When applied to a large collection of Hi-C datasets, GenomeDISCO accurately distinguishes biological replicates from samples obtained from different cell types. GenomeDISCO also generalizes to other chromosome conformation capture assays, such as HiChIP. Availability and implementation: Software implementing GenomeDISCO is available at https://github.com/kundajelab/genomedisco. Supplementary information: Supplementary data are available at Bioinformatics online.

Motivation: Capturing association patterns in gene expression levels under different conditions or time points is important for inferring gene regulatory interactions. In practice, temporal changes in gene expression may result in complex association patterns that require more sophisticated detection methods than simple correlation measures. For instance, the effect of regulation may lead to time-lagged associations and interactions local to a subset of samples. Furthermore, expression profiles of interest may not be aligned or directly comparable (e.g. gene expression profiles from two species). Results: We propose a count statistic for measuring association between pairs of gene expression profiles consisting of ordered samples (e.g. time-course), where correlation may only exist locally in subsequences separated by a position shift. The statistic is simple and fast to compute, and we illustrate its use in two applications. In a cross-species comparison of developmental gene expression levels, we show our method not only measures association of gene expressions between the two species, but also provides alignment between different developmental stages. In the second application, we applied our statistic to expression profiles from two distinct phenotypic conditions, where the samples in each profile are ordered by the associated phenotypic values. The detected associations can be useful in building correspondence between gene association networks under different phenotypes. On the theoretical side, we provide asymptotic distributions of the statistic for different regions of the parameter space and test its power on simulated data. Availability and implementation: The code used to perform the analysis is available as part of the Supplementary Material. Contact: [email protected] or [email protected]. Supplementary information: Supplementary data are available at Bioinformatics online.