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In domains where sample sizes are limited, efficient learning algorithms are critical. Learning using privileged information (LuPI) offers increased sample efficiency by allowing prediction models access to auxiliary information at training time which is unavailable when the models are used. In recent work, it was shown that for prediction in linear-Gaussian dynamical systems, a LuPI learner with access to intermediate time series data is never worse and often better in expectation than any unbiased classical learner. We provide new insights into this analysis and generalize it to nonlinear prediction tasks in latent dynamical systems, extending theoretical guarantees to the case where the map connecting latent variables and observations is known up to a linear transform. In addition, we propose algorithms based on random features and representation learning for the case when this map is unknown. A suite of empirical results confirm theoretical findings and show the potential of using privileged time-series information in nonlinear prediction.

Deep neural networks are powerful tools to model observations over time with non-linear patterns. Despite the widespread use of neural networks in such settings, most theoretical developments of deep neural networks are under the assumption of independent observations, and theoretical results for temporally dependent observations are scarce. To bridge this gap, we study theoretical properties of deep neural networks on modeling non-linear time series data. Specifically, non-asymptotic bounds for prediction error of (sparse) feed-forward neural network with ReLU activation function is established under mixing-type assumptions. These assumptions are mild such that they include a wide range of time series models including auto-regressive models. Compared to independent observations, established convergence rates have additional logarithmic factors to compensate for additional complexity due to dependence among data points. The theoretical results are supported via various numerical simulation settings as well as an application to a macroeconomic data set.

We propose a Bayesian tensor-on-tensor regression approach to predict a multidimensional array (tensor) of arbitrary dimensions from another tensor of arbitrary dimensions, building upon the Tucker decomposition of the regression coefficient tensor. Traditional tensor regression methods making use of the Tucker decomposition either assume the dimension of the core tensor to be known or estimate it via cross-validation or some model selection criteria. However, no existing method can simultaneously estimate the model dimension (the dimension of the core tensor) and other model parameters. To fill this gap, we develop an efficient Markov Chain Monte Carlo (MCMC) algorithm to estimate both the model dimension and parameters for posterior inference. Besides the MCMC sampler, we also develop an ultra-fast optimization-based computing algorithm wherein the maximum a posteriori estimators for parameters are computed, and the model dimension is optimized via a simulated annealing algorithm. The proposed Bayesian framework provides a natural way for uncertainty quantification. Through extensive simulation studies, we evaluate the proposed Bayesian tensor-on-tensor regression model and show its superior performance compared to alternative methods. We also demonstrate its practical effectiveness by applying it to two real-world datasets, including facial imaging data and 3D motion data.

A simple generative model based on a continuous-time normalizing flow between any pair of base and target probability densities is proposed. The velocity field of this flow is inferred from the probability current of a time-dependent density that interpolates between the base and the target in finite time. Unlike conventional normalizing flow inference methods based the maximum likelihood principle, which require costly backpropagation through ODE solvers, our interpolant approach leads to a simple quadratic loss for the velocity itself which is expressed in terms of expectations that are readily amenable to empirical estimation. The flow can be used to generate samples from either the base or target, and to estimate the likelihood at any time along the interpolant. In addition, the flow can be optimized to minimize the path length of the interpolant density, thereby paving the way for building optimal transport maps. The approach is also contextualized in its relation to diffusions. In particular, in situations where the base is a Gaussian density, we show that the velocity of our normalizing flow can also be used to construct a diffusion model to sample the target as well as estimating its score. This allows one to map methods based on stochastic differential equations to those using ordinary differential equations, simplifying the mechanics of the model, but capturing equivalent dynamics. Benchmarking on density estimation tasks illustrates that the learned flow can match and surpass maximum likelihood continuous flows at a fraction of the conventional ODE training costs.

Graph neural networks (GNNs) have shown superiority in many prediction tasks over graphs due to their impressive capability of capturing nonlinear relations in graph-structured data. However, for node classification tasks, often, only marginal improvement of GNNs over their linear counterparts has been observed. Previous works provide very few understandings of this phenomenon. In this work, we resort to Bayesian learning to deeply investigate the functions of non-linearity in GNNs for node classification tasks. Given a graph generated from the statistical model CSBM, we observe that the max-a-posterior estimation of a node label given its own and neighbors' attributes consists of two types of non-linearity, a possibly non-linear transformation of node attributes and a ReLU-activated feature aggregation from neighbors. The latter surprisingly matches the type of non-linearity used in many GNN models. By further imposing Gaussian assumption on node attributes, we prove that the superiority of those ReLU activations is only significant when the node attributes are far more informative than the graph structure, which nicely matches many previous empirical observations. A similar argument can be achieved when there is a distribution shift of node attributes between the training and testing datasets. Finally, we verify our theory on both synthetic and real-world networks.

Diffusion models (DMs) have achieved state-of-the-art results for image synthesis tasks as well as density estimation. Applied in the latent space of a powerful pretrained autoencoder (LDM), their immense computational requirements can be significantly reduced without sacrificing sampling quality. However, DMs and LDMs lack a semantically meaningful representation space as the diffusion process gradually destroys information in the latent variables. We introduce a framework for learning such representations with diffusion models (LRDM). To that end, a LDM is conditioned on the representation extracted from the clean image by a separate encoder. In particular, the DM and the representation encoder are trained jointly in order to learn rich representations specific to the generative denoising process. By introducing a tractable representation prior, we can efficiently sample from the representation distribution for unconditional image synthesis without training of any additional model. We demonstrate that i) competitive image generation results can be achieved with image-parameterized LDMs, ii) LRDMs are capable of learning semantically meaningful representations, allowing for faithful image reconstructions and semantic interpolations. Our implementation is available at //github.com/jeremiastraub/diffusion.

Bayesian variable selection methods are powerful techniques for fitting and inferring on sparse high-dimensional linear regression models. However, many are computationally intensive or require restrictive prior distributions on model parameters. Likelihood based penalization methods are more computationally friendly, but resource intensive refitting techniques are needed for inference. In this paper, we proposed an efficient and powerful Bayesian approach for sparse high-dimensional linear regression. Minimal prior assumptions on the parameters are required through the use of plug-in empirical Bayes estimates of hyperparameters. Efficient maximum a posteriori probability (MAP) estimation is completed through the use of a partitioned and extended expectation conditional maximization (ECM) algorithm. The result is a PaRtitiOned empirical Bayes Ecm (PROBE) algorithm applied to sparse high-dimensional linear regression. We propose methods to estimate credible and prediction intervals for predictions of future values. We compare the empirical properties of predictions and our predictive inference to comparable approaches with numerous simulation studies and an analysis of cancer cell lines drug response study. The proposed approach is implemented in the R package probe.

Nowadays, differential privacy (DP) has become a well-accepted standard for privacy protection, and deep neural networks (DNN) have been immensely successful in machine learning. The combination of these two techniques, i.e., deep learning with differential privacy, promises the privacy-preserving release of high-utility models trained with sensitive data such as medical records. A classic mechanism for this purpose is DP-SGD, which is a differentially private version of the stochastic gradient descent (SGD) optimizer commonly used for DNN training. Subsequent approaches have improved various aspects of the model training process, including noise decay schedule, model architecture, feature engineering, and hyperparameter tuning. However, the core mechanism for enforcing DP in the SGD optimizer remains unchanged ever since the original DP-SGD algorithm, which has increasingly become a fundamental barrier limiting the performance of DP-compliant machine learning solutions. Motivated by this, we propose DPIS, a novel mechanism for differentially private SGD training that can be used as a drop-in replacement of the core optimizer of DP-SGD, with consistent and significant accuracy gains over the latter. The main idea is to employ importance sampling (IS) in each SGD iteration for mini-batch selection, which reduces both sampling variance and the amount of random noise injected to the gradients that is required to satisfy DP. Integrating IS into the complex mathematical machinery of DP-SGD is highly non-trivial. DPIS addresses the challenge through novel mechanism designs, fine-grained privacy analysis, efficiency enhancements, and an adaptive gradient clipping optimization. Extensive experiments on four benchmark datasets, namely MNIST, FMNIST, CIFAR-10 and IMDb, demonstrate the superior effectiveness of DPIS over existing solutions for deep learning with differential privacy.

We explore using neural operators, or neural network representations of nonlinear maps between function spaces, to accelerate infinite-dimensional Bayesian inverse problems (BIPs) with models governed by nonlinear parametric partial differential equations (PDEs). Neural operators have gained significant attention in recent years for their ability to approximate the parameter-to-solution maps defined by PDEs using as training data solutions of PDEs at a limited number of parameter samples. The computational cost of BIPs can be drastically reduced if the large number of PDE solves required for posterior characterization are replaced with evaluations of trained neural operators. However, reducing error in the resulting BIP solutions via reducing the approximation error of the neural operators in training can be challenging and unreliable. We provide an a priori error bound result that implies certain BIPs can be ill-conditioned to the approximation error of neural operators, thus leading to inaccessible accuracy requirements in training. To reliably deploy neural operators in BIPs, we consider a strategy for enhancing the performance of neural operators, which is to correct the prediction of a trained neural operator by solving a linear variational problem based on the PDE residual. We show that a trained neural operator with error correction can achieve a quadratic reduction of its approximation error, all while retaining substantial computational speedups of posterior sampling when models are governed by highly nonlinear PDEs. The strategy is applied to two numerical examples of BIPs based on a nonlinear reaction--diffusion problem and deformation of hyperelastic materials. We demonstrate that posterior representations of the two BIPs produced using trained neural operators are greatly and consistently enhanced by error correction.

The adaptive processing of structured data is a long-standing research topic in machine learning that investigates how to automatically learn a mapping from a structured input to outputs of various nature. Recently, there has been an increasing interest in the adaptive processing of graphs, which led to the development of different neural network-based methodologies. In this thesis, we take a different route and develop a Bayesian Deep Learning framework for graph learning. The dissertation begins with a review of the principles over which most of the methods in the field are built, followed by a study on graph classification reproducibility issues. We then proceed to bridge the basic ideas of deep learning for graphs with the Bayesian world, by building our deep architectures in an incremental fashion. This framework allows us to consider graphs with discrete and continuous edge features, producing unsupervised embeddings rich enough to reach the state of the art on several classification tasks. Our approach is also amenable to a Bayesian nonparametric extension that automatizes the choice of almost all model's hyper-parameters. Two real-world applications demonstrate the efficacy of deep learning for graphs. The first concerns the prediction of information-theoretic quantities for molecular simulations with supervised neural models. After that, we exploit our Bayesian models to solve a malware-classification task while being robust to intra-procedural code obfuscation techniques. We conclude the dissertation with an attempt to blend the best of the neural and Bayesian worlds together. The resulting hybrid model is able to predict multimodal distributions conditioned on input graphs, with the consequent ability to model stochasticity and uncertainty better than most works. Overall, we aim to provide a Bayesian perspective into the articulated research field of deep learning for graphs.