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State-space models (SSMs) are a powerful statistical tool for modelling time-varying systems via a latent state. In these models, the latent state is never directly observed. Instead, a sequence of data points related to the state are obtained. The linear-Gaussian state-space model is widely used, since it allows for exact inference when all model parameters are known, however this is rarely the case. The estimation of these parameters is a very challenging but essential task to perform inference and prediction. In the linear-Gaussian model, the state dynamics are described via a state transition matrix. This model parameter is known to behard to estimate, since it encodes the relationships between the state elements, which are never observed. In many applications, this transition matrix is sparse since not all state components directly affect all other state components. However, most parameter estimation methods do not exploit this feature. In this work we propose SpaRJ, a fully probabilistic Bayesian approach that obtains sparse samples from the posterior distribution of the transition matrix. Our method explores sparsity by traversing a set of models that exhibit differing sparsity patterns in the transition matrix. Moreover, we also design new effective rules to explore transition matrices within the same level of sparsity. This novel methodology has strong theoretical guarantees, and unveils the latent structure of the data generating process, thereby enhancing interpretability. The performance of SpaRJ is showcased in example with dimension 144 in the parameter space, and in a numerical example with real data.

Response time has attracted increased interest in educational and psychological assessment for, e.g., measuring test takers' processing speed, improving the measurement accuracy of ability, and understanding aberrant response behavior. Most models for response time analysis are based on a parametric assumption about the response time distribution. The Cox proportional hazard model has been utilized for response time analysis for the advantages of not requiring a distributional assumption of response time and enabling meaningful interpretations with respect to response processes. In this paper, we present a new version of the proportional hazard model, called a latent space accumulator model, for cognitive assessment data based on accumulators for two competing response outcomes, such as correct vs. incorrect responses. The proposed model extends a previous accumulator model by capturing dependencies between respondents and test items across accumulators in the form of distances in a two-dimensional Euclidean space. A fully Bayesian approach is developed to estimate the proposed model. The utilities of the proposed model are illustrated with two real data examples.

This article derives and validates three principles for initialization and architecture selection in finite width graph neural networks (GNNs) with ReLU activations. First, we theoretically derive what is essentially the unique generalization to ReLU GNNs of the well-known He-initialization. Our initialization scheme guarantees that the average scale of network outputs and gradients remains order one at initialization. Second, we prove in finite width vanilla ReLU GNNs that oversmoothing is unavoidable at large depth when using fixed aggregation operator, regardless of initialization. We then prove that using residual aggregation operators, obtained by interpolating a fixed aggregation operator with the identity, provably alleviates oversmoothing at initialization. Finally, we show that the common practice of using residual connections with a fixup-type initialization provably avoids correlation collapse in final layer features at initialization. Through ablation studies we find that using the correct initialization, residual aggregation operators, and residual connections in the forward pass significantly and reliably speeds up early training dynamics in deep ReLU GNNs on a variety of tasks.

This work proposes ``jointly amortized neural approximation'' (JANA) of intractable likelihood functions and posterior densities arising in Bayesian surrogate modeling and simulation-based inference. We train three complementary networks in an end-to-end fashion: 1) a summary network to compress individual data points, sets, or time series into informative embedding vectors; 2) a posterior network to learn an amortized approximate posterior; and 3) a likelihood network to learn an amortized approximate likelihood. Their interaction opens a new route to amortized marginal likelihood and posterior predictive estimation -- two important ingredients of Bayesian workflows that are often too expensive for standard methods. We benchmark the fidelity of JANA on a variety of simulation models against state-of-the-art Bayesian methods and propose a powerful and interpretable diagnostic for joint calibration. In addition, we investigate the ability of recurrent likelihood networks to emulate complex time series models without resorting to hand-crafted summary statistics.

Learning interpretable representations of neural dynamics at a population level is a crucial first step to understanding how observed neural activity relates to perception and behavior. Models of neural dynamics often focus on either low-dimensional projections of neural activity, or on learning dynamical systems that explicitly relate to the neural state over time. We discuss how these two approaches are interrelated by considering dynamical systems as representative of flows on a low-dimensional manifold. Building on this concept, we propose a new decomposed dynamical system model that represents complex non-stationary and nonlinear dynamics of time series data as a sparse combination of simpler, more interpretable components. Our model is trained through a dictionary learning procedure, where we leverage recent results in tracking sparse vectors over time. The decomposed nature of the dynamics is more expressive than previous switched approaches for a given number of parameters and enables modeling of overlapping and non-stationary dynamics. In both continuous-time and discrete-time instructional examples we demonstrate that our model can well approximate the original system, learn efficient representations, and capture smooth transitions between dynamical modes, focusing on intuitive low-dimensional non-stationary linear and nonlinear systems. Furthermore, we highlight our model's ability to efficiently capture and demix population dynamics generated from multiple independent subnetworks, a task that is computationally impractical for switched models. Finally, we apply our model to neural "full brain" recordings of C. elegans data, illustrating a diversity of dynamics that is obscured when classified into discrete states.

We propose a novel hierarchical Bayesian model for learning with a large (possibly infinite) number of tasks/episodes, which suits well the few-shot meta learning problem. We consider episode-wise random variables to model episode-specific target generative processes, where these local random variables are governed by a higher-level global random variate. The global variable helps memorize the important information from historic episodes while controlling how much the model needs to be adapted to new episodes in a principled Bayesian manner. Within our model framework, the prediction on a novel episode/task can be seen as a Bayesian inference problem. However, a main obstacle in learning with a large/infinite number of local random variables in online nature, is that one is not allowed to store the posterior distribution of the current local random variable for frequent future updates, typical in conventional variational inference. We need to be able to treat each local variable as a one-time iterate in the optimization. We propose a Normal-Inverse-Wishart model, for which we show that this one-time iterate optimization becomes feasible due to the approximate closed-form solutions for the local posterior distributions. The resulting algorithm is more attractive than the MAML in that it is not required to maintain computational graphs for the whole gradient optimization steps per episode. Our approach is also different from existing Bayesian meta learning methods in that unlike dealing with a single random variable for the whole episodes, our approach has a hierarchical structure that allows one-time episodic optimization, desirable for principled Bayesian learning with many/infinite tasks. The code is available at \url{//github.com/minyoungkim21/niwmeta}.

Bayesian neural networks (BNNs) provide a formalism to quantify and calibrate uncertainty in deep learning. Current inference approaches for BNNs often resort to few-sample estimation for scalability, which can harm predictive performance, while its alternatives tend to be computationally prohibitively expensive. We tackle this challenge by revealing a previously unseen connection between inference on BNNs and volume computation problems. With this observation, we introduce a novel collapsed inference scheme that performs Bayesian model averaging using collapsed samples. It improves over a Monte-Carlo sample by limiting sampling to a subset of the network weights while pairing it with some closed-form conditional distribution over the rest. A collapsed sample represents uncountably many models drawn from the approximate posterior and thus yields higher sample efficiency. Further, we show that the marginalization of a collapsed sample can be solved analytically and efficiently despite the non-linearity of neural networks by leveraging existing volume computation solvers. Our proposed use of collapsed samples achieves a balance between scalability and accuracy. On various regression and classification tasks, our collapsed Bayesian deep learning approach demonstrates significant improvements over existing methods and sets a new state of the art in terms of uncertainty estimation as well as predictive performance.

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.

Residual networks (ResNets) have displayed impressive results in pattern recognition and, recently, have garnered considerable theoretical interest due to a perceived link with neural ordinary differential equations (neural ODEs). This link relies on the convergence of network weights to a smooth function as the number of layers increases. We investigate the properties of weights trained by stochastic gradient descent and their scaling with network depth through detailed numerical experiments. We observe the existence of scaling regimes markedly different from those assumed in neural ODE literature. Depending on certain features of the network architecture, such as the smoothness of the activation function, one may obtain an alternative ODE limit, a stochastic differential equation or neither of these. These findings cast doubts on the validity of the neural ODE model as an adequate asymptotic description of deep ResNets and point to an alternative class of differential equations as a better description of the deep network limit.

We propose a Bayesian convolutional neural network built upon Bayes by Backprop and elaborate how this known method can serve as the fundamental construct of our novel, reliable variational inference method for convolutional neural networks. First, we show how Bayes by Backprop can be applied to convolutional layers where weights in filters have probability distributions instead of point-estimates; and second, how our proposed framework leads with various network architectures to performances comparable to convolutional neural networks with point-estimates weights. In the past, Bayes by Backprop has been successfully utilised in feedforward and recurrent neural networks, but not in convolutional ones. This work symbolises the extension of the group of Bayesian neural networks which encompasses all three aforementioned types of network architectures now.