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We study the hierarchy of communities in real-world networks under a generic stochastic block model, in which the connection probabilities are structured in a binary tree. Under such model, a standard recursive bi-partitioning algorithm is dividing the network into two communities based on the Fiedler vector of the unnormalized graph Laplacian and repeating the split until a stopping rule indicates no further community structures. We prove the strong consistency of this method under a wide range of model parameters, which include sparse networks with node degrees as small as $O(\log n)$. In addition, unlike most of existing work, our theory covers multiscale networks where the connection probabilities may differ by orders of magnitude, which comprise an important class of models that are practically relevant but technically challenging to deal with. Finally we demonstrate the performance of our algorithm on synthetic data and real-world examples.

Key to effective generic, or "black-box", variational inference is the selection of an approximation to the target density that balances accuracy and calibration speed. Copula models are promising options, but calibration of the approximation can be slow for some choices. Smith et al. (2020) suggest using "implicit copula" models that are formed by element-wise transformation of the target parameters. We show here why these are a tractable and scalable choice, and propose adjustments to increase their accuracy. We also show how a sub-class of elliptical copulas have a generative representation that allows easy application of the re-parameterization trick and efficient first order optimization methods. We demonstrate the estimation methodology using two statistical models as examples. The first is a mixed effects logistic regression, and the second is a regularized correlation matrix. For the latter, standard Markov chain Monte Carlo estimation methods can be slow or difficult to implement, yet our proposed variational approach provides an effective and scalable estimator. We illustrate by estimating a regularized Gaussian copula model for income inequality in U.S. states between 1917 and 2018.

This article introduces a new instrumental variable approach for estimating unknown population parameters with data having nonrandom missing values. With coarse and discrete instruments, Shao and Wang (2016) proposed a semiparametric method that uses the added information to identify the tilting parameter from the missing data propensity model. A naive application of this idea to continuous instruments through arbitrary discretizations is apt to be inefficient, and maybe questionable in some settings. We propose a nonparametric method not requiring arbitrary discretizations but involves scanning over continuous dichotomizations of the instrument; and combining scan statistics to estimate the unknown parameters via weighted integration. We establish the asymptotic normality of the proposed integrated estimator and that of the underlying scan processes uniformly across the instrument sample space. Simulation studies and the analysis of a real data set demonstrate the gains of the methodology over procedures that rely either on arbitrary discretizations or moments of the instrument.

This paper presents an efficient variational inference framework for deriving a family of structured gaussian process regression network (SGPRN) models. The key idea is to incorporate auxiliary inducing variables in latent functions and jointly treats both the distributions of the inducing variables and hyper-parameters as variational parameters. Then we propose structured variable distributions and marginalize latent variables, which enables the decomposability of a tractable variational lower bound and leads to stochastic optimization. Our inference approach is able to model data in which outputs do not share a common input set with a computational complexity independent of the size of the inputs and outputs and thus easily handle datasets with missing values. We illustrate the performance of our method on synthetic data and real datasets and show that our model generally provides better imputation results on missing data than the state-of-the-art. We also provide a visualization approach for time-varying correlation across outputs in electrocoticography data and those estimates provide insight to understand the neural population dynamics.

Cryo-Electron Tomography (cryo-ET) is a 3D imaging technology that enables the visualization of subcellular structures in situ at near-atomic resolution. Cellular cryo-ET images help in resolving the structures of macromolecules and determining their spatial relationship in a single cell, which has broad significance in cell and structural biology. Subtomogram classification and recognition constitute a primary step in the systematic recovery of these macromolecular structures. Supervised deep learning methods have been proven to be highly accurate and efficient for subtomogram classification, but suffer from limited applicability due to scarcity of annotated data. While generating simulated data for training supervised models is a potential solution, a sizeable difference in the image intensity distribution in generated data as compared to real experimental data will cause the trained models to perform poorly in predicting classes on real subtomograms. In this work, we present Cryo-Shift, a fully unsupervised domain adaptation and randomization framework for deep learning-based cross-domain subtomogram classification. We use unsupervised multi-adversarial domain adaption to reduce the domain shift between features of simulated and experimental data. We develop a network-driven domain randomization procedure with `warp' modules to alter the simulated data and help the classifier generalize better on experimental data. We do not use any labeled experimental data to train our model, whereas some of the existing alternative approaches require labeled experimental samples for cross-domain classification. Nevertheless, Cryo-Shift outperforms the existing alternative approaches in cross-domain subtomogram classification in extensive evaluation studies demonstrated herein using both simulated and experimental data.

This work presents a deep learning-based framework for the solution of partial differential equations on complex computational domains described with computer-aided design tools. To account for the underlying distribution of the training data caused by spline-based projections from the reference to the physical domain, a variational neural solver equipped with an importance sampling scheme is developed, such that the loss function based on the discretized energy functional obtained after the weak formulation is modified according to the sample distribution. To tackle multi-patch domains possibly leading to solution discontinuities, the variational neural solver is additionally combined with a domain decomposition approach based on the Discontinuous Galerkin formulation. The proposed neural solver is verified on a toy problem and then applied to a real-world engineering test case, namely that of electric machine simulation. The numerical results show clearly that the neural solver produces physics-conforming solutions of significantly improved accuracy.

Variable importance measures are the main tools to analyze the black-box mechanisms of random forests. Although the mean decrease accuracy (MDA) is widely accepted as the most efficient variable importance measure for random forests, little is known about its statistical properties. In fact, the exact MDA definition varies across the main random forest software. In this article, our objective is to rigorously analyze the behavior of the main MDA implementations. Consequently, we mathematically formalize the various implemented MDA algorithms, and then establish their limits when the sample size increases. In particular, we break down these limits in three components: the first one is related to Sobol indices, which are well-defined measures of a covariate contribution to the response variance, widely used in the sensitivity analysis field, as opposed to thethird term, whose value increases with dependence within covariates. Thus, we theoretically demonstrate that the MDA does not target the right quantity when covariates are dependent, a fact that has already been noticed experimentally. To address this issue, we define a new importance measure for random forests, the Sobol-MDA, which fixes the flaws of the original MDA. We prove the consistency of the Sobol-MDA and show thatthe Sobol-MDA empirically outperforms its competitors on both simulated and real data. An open source implementation in R and C++ is available online.

There has been a growing interest in unsupervised domain adaptation (UDA) to alleviate the data scalability issue, while the existing works usually focus on classifying independently discrete labels. However, in many tasks (e.g., medical diagnosis), the labels are discrete and successively distributed. The UDA for ordinal classification requires inducing non-trivial ordinal distribution prior to the latent space. Target for this, the partially ordered set (poset) is defined for constraining the latent vector. Instead of the typically i.i.d. Gaussian latent prior, in this work, a recursively conditional Gaussian (RCG) set is proposed for ordered constraint modeling, which admits a tractable joint distribution prior. Furthermore, we are able to control the density of content vectors that violate the poset constraint by a simple "three-sigma rule". We explicitly disentangle the cross-domain images into a shared ordinal prior induced ordinal content space and two separate source/target ordinal-unrelated spaces, and the self-training is worked on the shared space exclusively for ordinal-aware domain alignment. Extensive experiments on UDA medical diagnoses and facial age estimation demonstrate its effectiveness.

A new prior is proposed for learning representations of high-level concepts of the kind we manipulate with language. This prior can be combined with other priors in order to help disentangling abstract factors from each other. It is inspired by cognitive neuroscience theories of consciousness, seen as a bottleneck through which just a few elements, after having been selected by attention from a broader pool, are then broadcast and condition further processing, both in perception and decision-making. The set of recently selected elements one becomes aware of is seen as forming a low-dimensional conscious state. This conscious state is combining the few concepts constituting a conscious thought, i.e., what one is immediately conscious of at a particular moment. We claim that this architectural and information-processing constraint corresponds to assumptions about the joint distribution between high-level concepts. To the extent that these assumptions are generally true (and the form of natural language seems consistent with them), they can form a useful prior for representation learning. A low-dimensional thought or conscious state is analogous to a sentence: it involves only a few variables and yet can make a statement with very high probability of being true. This is consistent with a joint distribution (over high-level concepts) which has the form of a sparse factor graph, i.e., where the dependencies captured by each factor of the factor graph involve only very few variables while creating a strong dip in the overall energy function. The consciousness prior also makes it natural to map conscious states to natural language utterances or to express classical AI knowledge in a form similar to facts and rules, albeit capturing uncertainty as well as efficient search mechanisms implemented by attention mechanisms.

Stochastic gradient Markov chain Monte Carlo (SGMCMC) has become a popular method for scalable Bayesian inference. These methods are based on sampling a discrete-time approximation to a continuous time process, such as the Langevin diffusion. When applied to distributions defined on a constrained space, such as the simplex, the time-discretisation error can dominate when we are near the boundary of the space. We demonstrate that while current SGMCMC methods for the simplex perform well in certain cases, they struggle with sparse simplex spaces; when many of the components are close to zero. However, most popular large-scale applications of Bayesian inference on simplex spaces, such as network or topic models, are sparse. We argue that this poor performance is due to the biases of SGMCMC caused by the discretization error. To get around this, we propose the stochastic CIR process, which removes all discretization error and we prove that samples from the stochastic CIR process are asymptotically unbiased. Use of the stochastic CIR process within a SGMCMC algorithm is shown to give substantially better performance for a topic model and a Dirichlet process mixture model than existing SGMCMC approaches.