Arash A. Amini

Qiaoling Ye, Arash A. Amini, Qing Zhou

We consider the task of learning causal structures from data stored on multiple machines, and propose a novel structure learning method called distributed annealing on regularized likelihood score (DARLS) to solve this problem. We model causal structures by a directed acyclic graph that is parameterized with generalized linear models, so that our method is applicable to various types of data. To obtain a high-scoring causal graph, DARLS simulates an annealing process to search over the space of topological sorts, where the optimal graphical structure compatible with a sort is found by a distributed optimization method. This distributed optimization relies on multiple rounds of communication between local and central machines to estimate the optimal structure. We establish its convergence to a global optimizer of the overall score that is computed on all data across local machines. To the best of our knowledge, DARLS is the first distributed method for learning causal graphs with such theoretical guarantees. Through extensive simulation studies, DARLS has shown competing performance against existing methods on distributed data, and achieved comparable structure learning accuracy and test-data likelihood with competing methods applied to pooled data across all local machines. In a real-world application for modeling protein-DNA binding networks with distributed ChIP-Sequencing data, DARLS also exhibits higher predictive power than other methods, demonstrating a great advantage in estimating causal networks from distributed data.

Linfan Zhang, Arash A. Amini

We propose a goodness-of-fit test for degree-corrected stochastic block models (DCSBM). The test is based on an adjusted chi-square statistic for measuring equality of means among groups of $n$ multinomial distributions with $d_1,\dots,d_n$ observations. In the context of network models, the number of multinomials, $n$, grows much faster than the number of observations, $d_i$, corresponding to the degree of node $i$, hence the setting deviates from classical asymptotics. We show that a simple adjustment allows the statistic to converge in distribution, under null, as long as the harmonic mean of $\{d_i\}$ grows to infinity. When applied sequentially, the test can also be used to determine the number of communities. The test operates on a compressed version of the adjacency matrix, conditional on the degrees, and as a result is highly scalable to large sparse networks. We incorporate a novel idea of compressing the rows based on a $(K+1)$-community assignment when testing for $K$ communities. This approach increases the power in sequential applications without sacrificing computational efficiency, and we prove its consistency in recovering the number of communities. Since the test statistic does not rely on a specific alternative, its utility goes beyond sequential testing and can be used to simultaneously test against a wide range of alternatives outside the DCSBM family. In particular, we prove that the test is consistent against a general family of latent-variable network models with community structure.

Arash A. Amini, Zahra S. Razaee

We study the concentration of random kernel matrices around their mean. We derive nonasymptotic exponential concentration inequalities for Lipschitz kernels assuming that the data points are independent draws from a class of multivariate distributions on $\mathbb R^d$, including the strongly log-concave distributions under affine transformations. A feature of our result is that the data points need not have identical distributions or zero mean, which is key in certain applications such as clustering. Our bound for the Lipschitz kernels is dimension-free and sharp up to constants. For comparison, we also derive the companion result for the Euclidean (inner product) kernel for a class of sub-Gaussian distributions. A notable difference between the two cases is that, in contrast to the Euclidean kernel, in the Lipschitz case, the concentration inequality does not depend on the mean of the underlying vectors. As an application of these inequalities, we derive a bound on the misclassification rate of a kernel spectral clustering (KSC) algorithm, under a perturbed nonparametric mixture model. We show an example where this bound establishes the high-dimensional consistency (as $d \to \infty$) of the KSC, when applied with a Gaussian kernel, to a noisy model of nested nonlinear manifolds.

Arash A. Amini, Bryon Aragam, Qing Zhou

Knowing when a graphical model is perfect to a distribution is essential in order to relate separation in the graph to conditional independence in the distribution, and this is particularly important when performing inference from data. When the model is perfect, there is a one-to-one correspondence between conditional independence statements in the distribution and separation statements in the graph. Previous work has shown that almost all models based on linear directed acyclic graphs as well as Gaussian chain graphs are perfect, the latter of which subsumes Gaussian graphical models (i.e., the undirected Gaussian models) as a special case. However, the complexity of chain graph models leads to a proof of this result which is indirect and mired by the complications of parameterizing this general class. In this paper, we directly approach the problem of perfectness for the Gaussian graphical models, and provide a new proof, via a more transparent parametrization, that almost all such models are perfect. Our approach is based on, and substantially extends, a construction of Lněnička and Matúš showing the existence of a perfect Gaussian distribution for any graph.

Arash A. Amini

Kernel ridge regression (KRR) is a well-known and popular nonparametric regression approach with many desirable properties, including minimax rate-optimality in estimating functions that belong to common reproducing kernel Hilbert spaces (RKHS). The approach, however, is computationally intensive for large data sets, due to the need to operate on a dense $n \times n$ kernel matrix, where $n$ is the sample size. Recently, various approximation schemes for solving KRR have been considered, and some analyzed. Some approaches such as Nyström approximation and sketching have been shown to preserve the rate optimality of KRR. In this paper, we consider the simplest approximation, namely, spectrally truncating the kernel matrix to its largest $r < n$ eigenvalues. We derive an exact expression for the maximum risk of this truncated KRR, over the unit ball of the RKHS. This result can be used to study the exact trade-off between the level of spectral truncation and the regularization parameter. We show that, as long as the RKHS is infinite-dimensional, there is a threshold on $r$, above which, the spectrally-truncated KRR surprisingly outperforms the full KRR in terms of the minimax risk, where the minimum is taken over the regularization parameter. This strengthens the existing results on approximation schemes, by showing that not only one does not lose in terms of the rates, truncation can in fact improve the performance, for all finite samples (above the threshold). Moreover, we show that the implicit regularization achieved by spectral truncation is not a substitute for Hilbert norm regularization. Both are needed to achieve the best performance.

Qiaoling Ye, Arash A. Amini, Qing Zhou

Bayesian networks are a class of popular graphical models that encode causal and conditional independence relations among variables by directed acyclic graphs (DAGs). We propose a novel structure learning method, annealing on regularized Cholesky score (ARCS), to search over topological sorts, or permutations of nodes, for a high-scoring Bayesian network. Our scoring function is derived from regularizing Gaussian DAG likelihood, and its optimization gives an alternative formulation of the sparse Cholesky factorization problem from a statistical viewpoint, which is of independent interest. We combine global simulated annealing over permutations with a fast proximal gradient algorithm, operating on triangular matrices of edge coefficients, to compute the score of any permutation. Combined, the two approaches allow us to quickly and effectively search over the space of DAGs without the need to verify the acyclicity constraint or to enumerate possible parent sets given a candidate topological sort. The annealing aspect of the optimization is able to consistently improve the accuracy of DAGs learned by local search algorithms. In addition, we develop several techniques to facilitate the structure learning, including pre-annealing data-driven tuning parameter selection and post-annealing constraint-based structure refinement. Through extensive numerical comparisons, we show that ARCS achieves substantial improvements over existing methods, demonstrating its great potential to learn Bayesian networks from both observational and experimental data.

Arash A. Amini, Marina S. Paez, Lizhen Lin

Multiplex networks have become increasingly more prevalent in many fields, and have emerged as a powerful tool for modeling the complexity of real networks. There is a critical need for developing inference models for multiplex networks that can take into account potential dependencies across different layers, particularly when the aim is community detection. We add to a limited literature by proposing a novel and efficient Bayesian model for community detection in multiplex networks. A key feature of our approach is the ability to model varying communities at different network layers. In contrast, many existing models assume the same communities for all layers. Moreover, our model automatically picks up the necessary number of communities at each layer (as validated by real data examples). This is appealing, since deciding the number of communities is a challenging aspect of community detection, and especially so in the multiplex setting, if one allows the communities to change across layers. Borrowing ideas from hierarchical Bayesian modeling, we use a hierarchical Dirichlet prior to model community labels across layers, allowing dependency in their structure. Given the community labels, a stochastic block model (SBM) is assumed for each layer. We develop an efficient slice sampler for sampling the posterior distribution of the community labels as well as the link probabilities between communities. In doing so, we address some unique challenges posed by coupling the complex likelihood of SBM with the hierarchical nature of the prior on the labels. An extensive empirical validation is performed on simulated and real data, demonstrating the superior performance of the model over single-layer alternatives, as well as the ability to uncover interesting structures in real networks.

Arash A. Amini, Marina Paez, Lizhen Lin et al.

We propose an exact slice sampler for Hierarchical Dirichlet process (HDP) and its associated mixture models (Teh et al., 2006). Although there are existing MCMC algorithms for sampling from the HDP, a slice sampler has been missing from the literature. Slice sampling is well-known for its desirable properties including its fast mixing and its natural potential for parallelization. On the other hand, the hierarchical nature of HDPs poses challenges to adopting a full-fledged slice sampler that automatically truncates all the infinite measures involved without ad-hoc modifications. In this work, we adopt the powerful idea of Bayesian variable augmentation to address this challenge. By introducing new latent variables, we obtain a full factorization of the joint distribution that is suitable for slice sampling. Our algorithm has several appealing features such as (1) fast mixing; (2) remaining exact while allowing natural truncation of the underlying infinite-dimensional measures, as in (Kalli et al., 2011), resulting in updates of only a finite number of necessary atoms and weights in each iteration; and (3) being naturally suited to parallel implementations. The underlying principle for joint factorization of the full likelihood is simple and can be applied to many other settings, such as designing sampling algorithms for general dependent Dirichlet process (DDP) models.

Parthe Pandit, Mojtaba Sahraee-Ardakan, Arash A. Amini et al.

We consider the problem of estimating the parameters of a multivariate Bernoulli process with auto-regressive feedback in the high-dimensional setting where the number of samples available is much less than the number of parameters. This problem arises in learning interconnections of networks of dynamical systems with spiking or binary-valued data. We allow the process to depend on its past up to a lag $p$, for a general $p \ge 1$, allowing for more realistic modeling in many applications. We propose and analyze an $\ell_1$-regularized maximum likelihood estimator (MLE) under the assumption that the parameter tensor is approximately sparse. Rigorous analysis of such estimators is made challenging by the dependent and non-Gaussian nature of the process as well as the presence of the nonlinearities and multi-level feedback. We derive precise upper bounds on the mean-squared estimation error in terms of the number of samples, dimensions of the process, the lag $p$ and other key statistical properties of the model. The ideas presented can be used in the high-dimensional analysis of regularized $M$-estimators for other sparse nonlinear and non-Gaussian processes with long-range dependence.

Arash A. Amini, Bryon Aragam, Qing Zhou

Neighborhood regression has been a successful approach in graphical and structural equation modeling, with applications to learning undirected and directed graphical models. We extend these ideas by defining and studying an algebraic structure called the neighborhood lattice based on a generalized notion of neighborhood regression. We show that this algebraic structure has the potential to provide an economic encoding of all conditional independence statements in a Gaussian distribution (or conditional uncorrelatedness in general), even in the cases where no graphical model exists that could "perfectly" encode all such statements. We study the computational complexity of computing these structures and show that under a sparsity assumption, they can be computed in polynomial time, even in the absence of the assumption of perfectness to a graph. On the other hand, assuming perfectness, we show how these neighborhood lattices may be "graphically" computed using the separation properties of the so-called partial correlation graph. We also draw connections with directed acyclic graphical models and Bayesian networks. We derive these results using an abstract generalization of partial uncorrelatedness, called partial orthogonality, which allows us to use algebraic properties of projection operators on Hilbert spaces to significantly simplify and extend existing ideas and arguments. Consequently, our results apply to a wide range of random objects and data structures, such as random vectors, data matrices, and functions.

Zahra S. Razaee, Arash A. Amini, Jingyi Jessica Li

Community detection or clustering is a fundamental task in the analysis of network data. Many real networks have a bipartite structure which makes community detection challenging. In this paper, we consider a model which allows for matched communities in the bipartite setting, in addition to node covariates with information about the matching. We derive a simple fast algorithm for fitting the model based on variational inference ideas and show its effectiveness on both simulated and real data. A variation of the model to allow for degree-correction is also considered, in addition to a novel approach to fitting such degree-corrected models.

Bryon Aragam, Arash A. Amini, Qing Zhou

We study a family of regularized score-based estimators for learning the structure of a directed acyclic graph (DAG) for a multivariate normal distribution from high-dimensional data with $p\gg n$. Our main results establish support recovery guarantees and deviation bounds for a family of penalized least-squares estimators under concave regularization without assuming prior knowledge of a variable ordering. These results apply to a variety of practical situations that allow for arbitrary nondegenerate covariance structures as well as many popular regularizers including the MCP, SCAD, $\ell_{0}$ and $\ell_{1}$. The proof relies on interpreting a DAG as a recursive linear structural equation model, which reduces the estimation problem to a series of neighbourhood regressions. We provide a novel statistical analysis of these neighbourhood problems, establishing uniform control over the superexponential family of neighbourhoods associated with a Gaussian distribution. We then apply these results to study the statistical properties of score-based DAG estimators, learning causal DAGs, and inferring conditional independence relations via graphical models. Our results yield---for the first time---finite-sample guarantees for structure learning of Gaussian DAGs in high-dimensions via score-based estimation.

Arash A. Amini, XuanLong Nguyen

We propose a general formalism of iterated random functions with semigroup property, under which exact and approximate Bayesian posterior updates can be viewed as specific instances. A convergence theory for iterated random functions is presented. As an application of the general theory we analyze convergence behaviors of exact and approximate message-passing algorithms that arise in a sequential change point detection problem formulated via a latent variable directed graphical model. The sequential inference algorithm and its supporting theory are illustrated by simulated examples.

Arash Ali Amini, XuanLong Nguyen

We propose a probabilistic formulation that enables sequential detection of multiple change points in a network setting. We present a class of sequential detection rules for certain functionals of change points (minimum among a subset), and prove their asymptotic optimality properties in terms of expected detection delay time. Drawing from graphical model formalism, the sequential detection rules can be implemented by a computationally efficient message-passing protocol which may scale up linearly in network size and in waiting time. The effectiveness of our inference algorithm is demonstrated by simulations.