Averaging predictions from multiple competing inferential models frequently outperforms predictions from any single model, providing that models are optimally weighted to maximize predictive performance. This is particularly the case in so-called $\mathcal{M}$-open settings where the true model is not in the set of candidate models, and may be neither mathematically reifiable nor known precisely. This practice of model averaging has a rich history in statistics and machine learning, and there are currently a number of methods to estimate the weights for constructing model-averaged predictive distributions. Nonetheless, there are few existing software packages that can estimate model weights from the full variety of methods available, and none that blend model predictions into a coherent predictive distribution according to the estimated weights. In this paper, we introduce the BayesBlend Python package, which provides a user-friendly programming interface to estimate weights and blend multiple (Bayesian) models' predictive distributions. BayesBlend implements pseudo-Bayesian model averaging, stacking and, uniquely, hierarchical Bayesian stacking to estimate model weights. We demonstrate the usage of BayesBlend with examples of insurance loss modeling.

Deep generative models have been accelerating the inverse design process in material and drug design. Unlike their counterpart property predictors in typical molecular design frameworks, generative molecular design models have seen fewer efforts on uncertainty quantification (UQ) due to computational challenges in Bayesian inference posed by their large number of parameters. In this work, we focus on the junction-tree variational autoencoder (JT-VAE), a popular model for generative molecular design, and address this issue by leveraging the low dimensional active subspace to capture the uncertainty in the model parameters. Specifically, we approximate the posterior distribution over the active subspace parameters to estimate the epistemic model uncertainty in an extremely high dimensional parameter space. The proposed UQ scheme does not require alteration of the model architecture, making it readily applicable to any pre-trained model. Our experiments demonstrate the efficacy of the AS-based UQ and its potential impact on molecular optimization by exploring the model diversity under epistemic uncertainty.

Addressing real-world optimization problems becomes particularly challenging when analytic objective functions or constraints are unavailable. While numerous studies have addressed the issue of unknown objectives, limited research has focused on scenarios where feasibility constraints are not given explicitly. Overlooking these constraints can lead to spurious solutions that are unrealistic in practice. To deal with such unknown constraints, we propose to perform optimization within the data manifold using diffusion models. To constrain the optimization process to the data manifold, we reformulate the original optimization problem as a sampling problem from the product of the Boltzmann distribution defined by the objective function and the data distribution learned by the diffusion model. To enhance sampling efficiency, we propose a two-stage framework that begins with a guided diffusion process for warm-up, followed by a Langevin dynamics stage for further correction. Theoretical analysis shows that the initial stage results in a distribution focused on feasible solutions, thereby providing a better initialization for the later stage. Comprehensive experiments on a synthetic dataset, six real-world black-box optimization datasets, and a multi-objective optimization dataset show that our method achieves better or comparable performance with previous state-of-the-art baselines.

Constrained optimization plays a crucial role in the fields of quantum physics and quantum information science and becomes especially challenging for high-dimensional complex structure problems. One specific issue is that of quantum process tomography, in which the goal is to retrieve the underlying quantum process based on a given set of measurement data. In this paper, we introduce a modified version of stochastic gradient descent on a Riemannian manifold that integrates recent advancements in numerical methods for Riemannian optimization. This approach inherently supports the physically driven constraints of a quantum process, takes advantage of state-of-the-art large-scale stochastic objective optimization, and has superior performance to traditional approaches such as maximum likelihood estimation and projected least squares. The data-driven approach enables accurate, order-of-magnitude faster results, and works with incomplete data. We demonstrate our approach on simulations of quantum processes and in hardware by characterizing an engineered process on quantum computers.

Synthetic microbiomes offer new possibilities for modulating microbiota, to address the barriers in multidtug resistance (MDR) research. We present a Bayesian optimization approach to enable efficient searching over the space of synthetic microbiome variants to identify candidates predictive of reduced MDR. Microbiome datasets were encoded into a low-dimensional latent space using autoencoders. Sampling from this space allowed generation of synthetic microbiome signatures. Bayesian optimization was then implemented to select variants for biological screening to maximize identification of designs with restricted MDR pathogens based on minimal samples. Four acquisition functions were evaluated: expected improvement, upper confidence bound, Thompson sampling, and probability of improvement. Based on each strategy, synthetic samples were prioritized according to their MDR detection. Expected improvement, upper confidence bound, and probability of improvement consistently produced synthetic microbiome candidates with significantly fewer searches than Thompson sampling. By combining deep latent space mapping and Bayesian learning for efficient guided screening, this study demonstrated the feasibility of creating bespoke synthetic microbiomes with customized MDR profiles.

Large neural networks trained on large datasets have become the dominant paradigm in machine learning. These systems rely on maximum likelihood point estimates of their parameters, precluding them from expressing model uncertainty. This may result in overconfident predictions and it prevents the use of deep learning models for sequential decision making. This thesis develops scalable methods to equip neural networks with model uncertainty. In particular, we leverage the linearised Laplace approximation to equip pre-trained neural networks with the uncertainty estimates provided by their tangent linear models. This turns the problem of Bayesian inference in neural networks into one of Bayesian inference in conjugate Gaussian-linear models. Alas, the cost of this remains cubic in either the number of network parameters or in the number of observations times output dimensions. By assumption, neither are tractable. We address this intractability by using stochastic gradient descent (SGD) -- the workhorse algorithm of deep learning -- to perform posterior sampling in linear models and their convex duals: Gaussian processes. With this, we turn back to linearised neural networks, finding the linearised Laplace approximation to present a number of incompatibilities with modern deep learning practices -- namely, stochastic optimisation, early stopping and normalisation layers -- when used for hyperparameter learning. We resolve these and construct a sample-based EM algorithm for scalable hyperparameter learning with linearised neural networks. We apply the above methods to perform linearised neural network inference with ResNet-50 (25M parameters) trained on Imagenet (1.2M observations and 1000 output dimensions). Additionally, we apply our methods to estimate uncertainty for 3d tomographic reconstructions obtained with the deep image prior network.

We study the problem of learning mixtures of $k$ Gaussians in $d$ dimensions. We make no separation assumptions on the underlying mixture components: we only require that the covariance matrices have bounded condition number and that the means and covariances lie in a ball of bounded radius. We give an algorithm that draws $d^{\mathrm{poly}(k/\varepsilon)}$ samples from the target mixture, runs in sample-polynomial time, and constructs a sampler whose output distribution is $\varepsilon$-far from the unknown mixture in total variation. Prior works for this problem either (i) required exponential runtime in the dimension $d$, (ii) placed strong assumptions on the instance (e.g., spherical covariances or clusterability), or (iii) had doubly exponential dependence on the number of components $k$. Our approach departs from commonly used techniques for this problem like the method of moments. Instead, we leverage a recently developed reduction, based on diffusion models, from distribution learning to a supervised learning task called score matching. We give an algorithm for the latter by proving a structural result showing that the score function of a Gaussian mixture can be approximated by a piecewise-polynomial function, and there is an efficient algorithm for finding it. To our knowledge, this is the first example of diffusion models achieving a state-of-the-art theoretical guarantee for an unsupervised learning task.

Why is language vague? Vagueness may be explained and rationalized if it can be shown that vague language is more useful to speaker and hearer than precise language. In a well-known paper, Lipman proposes a game-theoretic account of vagueness in terms of mixed strategy that leads to a puzzle: vagueness cannot be strictly better than precision at equilibrium. More recently, \'Egr\'e, Spector, Mortier and Verheyen have put forward a Bayesian account of vagueness establishing that using vague words can be strictly more informative than using precise words. This paper proposes to compare both results and to explain why they are not in contradiction. Lipman's definition of vagueness relies exclusively on a property of signaling strategies, without making any assumptions about the lexicon, whereas \'Egr\'e et al.'s involves a layer of semantic content. We argue that the semantic account of vagueness is needed, and more adequate and explanatory of vagueness.

Predictive uncertainty quantification is crucial for reliable decision-making in various applied domains. Bayesian neural networks offer a powerful framework for this task. However, defining meaningful priors and ensuring computational efficiency remain significant challenges, especially for complex real-world applications. This paper addresses these challenges by proposing a novel neural adaptive empirical Bayes (NA-EB) framework. NA-EB leverages a class of implicit generative priors derived from low-dimensional distributions. This allows for efficient handling of complex data structures and effective capture of underlying relationships in real-world datasets. The proposed NA-EB framework combines variational inference with a gradient ascent algorithm. This enables simultaneous hyperparameter selection and approximation of the posterior distribution, leading to improved computational efficiency. We establish the theoretical foundation of the framework through posterior and classification consistency. We demonstrate the practical applications of our framework through extensive evaluations on a variety of tasks, including the two-spiral problem, regression, 10 UCI datasets, and image classification tasks on both MNIST and CIFAR-10 datasets. The results of our experiments highlight the superiority of our proposed framework over existing methods, such as sparse variational Bayesian and generative models, in terms of prediction accuracy and uncertainty quantification.

Machines that can replicate human intelligence with type 2 reasoning capabilities should be able to reason at multiple levels of spatio-temporal abstractions and scales using internal world models. Devising formalisms to develop such internal world models, which accurately reflect the causal hierarchies inherent in the dynamics of the real world, is a critical research challenge in the domains of artificial intelligence and machine learning. This thesis identifies several limitations with the prevalent use of state space models (SSMs) as internal world models and propose two new probabilistic formalisms namely Hidden-Parameter SSMs and Multi-Time Scale SSMs to address these drawbacks. The structure of graphical models in both formalisms facilitates scalable exact probabilistic inference using belief propagation, as well as end-to-end learning via backpropagation through time. This approach permits the development of scalable, adaptive hierarchical world models capable of representing nonstationary dynamics across multiple temporal abstractions and scales. Moreover, these probabilistic formalisms integrate the concept of uncertainty in world states, thus improving the system's capacity to emulate the stochastic nature of the real world and quantify the confidence in its predictions. The thesis also discuss how these formalisms are in line with related neuroscience literature on Bayesian brain hypothesis and predicitive processing. Our experiments on various real and simulated robots demonstrate that our formalisms can match and in many cases exceed the performance of contemporary transformer variants in making long-range future predictions. We conclude the thesis by reflecting on the limitations of our current models and suggesting directions for future research.