Today, deep learning is increasingly applied in security-critical situations such as autonomous driving and medical diagnosis. Despite its success, the behavior and robustness of deep networks are not fully understood yet, posing a significant risk. In particular, researchers recently found that neural networks are overly confident in their predictions, even on data they have never seen before. To tackle this issue, one can differentiate two approaches in the literature. One accounts for uncertainty in the predictions, while the second estimates the underlying density of the training data to decide whether a given input is close to the training data, and thus the network is able to perform as expected.In this thesis, we investigate the capabilities of EBMs at the task of fitting the training data distribution to perform detection of out-of-distribution (OOD) inputs. We find that on most datasets, EBMs do not inherently outperform other density estimators at detecting OOD data despite their flexibility. Thus, we additionally investigate the effects of supervision, dimensionality reduction, and architectural modifications on the performance of EBMs. Further, we propose Energy-Prior Network (EPN) which enables estimation of various uncertainties within an EBM for classification, bridging the gap between two approaches for tackling the OOD detection problem. We identify a connection between the concentration parameters of the Dirichlet distribution and the joint energy in an EBM. Additionally, this allows optimization without a held-out OOD dataset, which might not be available or costly to collect in some applications. Finally, we empirically demonstrate that Energy-Prior Network (EPN) is able to detect OOD inputs, datasets shifts, and adversarial examples. Theoretically, EPN offers favorable properties for the asymptotic case when inputs are far from the training data.

In many areas of the observational and experimental sciences data is scarce. Data observation in high-energy astrophysics is disrupted by celestial occlusions and limited telescope time while data derived from laboratory experiments in synthetic chemistry and materials science is time and cost-intensive to collect. On the other hand, knowledge about the data-generation mechanism is often available in the sciences, such as the measurement error of a piece of laboratory apparatus. Both characteristics, small data and knowledge of the underlying physics, make Gaussian processes (GPs) ideal candidates for fitting such datasets. GPs can make predictions with consideration of uncertainty, for example in the virtual screening of molecules and materials, and can also make inferences about incomplete data such as the latent emission signature from a black hole accretion disc. Furthermore, GPs are currently the workhorse model for Bayesian optimisation, a methodology foreseen to be a guide for laboratory experiments in scientific discovery campaigns. The first contribution of this thesis is to use GP modelling to reason about the latent emission signature from the Seyfert galaxy Markarian 335, and by extension, to reason about the applicability of various theoretical models of black hole accretion discs. The second contribution is to extend the GP framework to molecular and chemical reaction representations and to provide an open-source software library to enable the framework to be used by scientists. The third contribution is to leverage GPs to discover novel and performant photoswitch molecules. The fourth contribution is to introduce a Bayesian optimisation scheme capable of modelling aleatoric uncertainty to facilitate the identification of material compositions that possess intrinsic robustness to large scale fabrication processes.

This paper demonstrates that some non-classical models of human decision-making can be run successfully as circuits on quantum computers. Since the 1960s, many observed cognitive behaviors have been shown to violate rules based on classical probability and set theory. For example, the order in which questions are posed in a survey affects whether participants answer 'yes' or 'no', so the population that answers 'yes' to both questions cannot be modeled as the intersection of two fixed sets. It can, however, be modeled as a sequence of projections carried out in different orders. This and other examples have been described successfully using quantum probability, which relies on comparing angles between subspaces rather than volumes between subsets. Now in the early 2020s, quantum computers have reached the point where some of these quantum cognitive models can be implemented and investigated on quantum hardware, by representing the mental states in qubit registers, and the cognitive operations and decisions using different gates and measurements. This paper develops such quantum circuit representations for quantum cognitive models, focusing particularly on modeling order effects and decision-making under uncertainty. The claim is not that the human brain uses qubits and quantum circuits explicitly (just like the use of Boolean set theory does not require the brain to be using classical bits), but that the mathematics shared between quantum cognition and quantum computing motivates the exploration of quantum computers for cognition modeling. Key quantum properties include superposition, entanglement, and collapse, as these mathematical elements provide a common language between cognitive models, quantum hardware, and circuit implementations.

Many autonomous agents, such as intelligent vehicles, are inherently required to interact with one another. Game theory provides a natural mathematical tool for robot motion planning in such interactive settings. However, tractable algorithms for such problems usually rely on a strong assumption, namely that the objectives of all players in the scene are known. To make such tools applicable for ego-centric planning with only local information, we propose an adaptive model-predictive game solver, which jointly infers other players' objectives online and computes a corresponding generalized Nash equilibrium (GNE) strategy. The adaptivity of our approach is enabled by a differentiable trajectory game solver whose gradient signal is used for maximum likelihood estimation (MLE) of opponents' objectives. This differentiability of our pipeline facilitates direct integration with other differentiable elements, such as neural networks (NNs). Furthermore, in contrast to existing solvers for cost inference in games, our method handles not only partial state observations but also general inequality constraints. In two simulated traffic scenarios, we find superior performance of our approach over both existing game-theoretic methods and non-game-theoretic model-predictive control (MPC) approaches. We also demonstrate our approach's real-time planning capabilities and robustness in two hardware experiments.

Access to complete data in large-scale networks is often infeasible. Therefore, the problem of missing data is a crucial and unavoidable issue in the analysis and modeling of real-world social networks. However, most of the research on different aspects of social networks does not consider this limitation. One effective way to solve this problem is to recover the missing data as a pre-processing step. In this paper, a model is learned from partially observed data to infer unobserved diffusion and structure networks. To jointly discover omitted diffusion activities and hidden network structures, we develop a probabilistic generative model called "DiffStru." The interrelations among links of nodes and cascade processes are utilized in the proposed method via learning coupled with low-dimensional latent factors. Besides inferring unseen data, latent factors such as community detection may also aid in network classification problems. We tested different missing data scenarios on simulated independent cascades over LFR networks and real datasets, including Twitter and Memtracker. Experiments on these synthetic and real-world datasets show that the proposed method successfully detects invisible social behaviors, predicts links, and identifies latent features.

Latent confounding has been a long-standing obstacle for causal reasoning from observational data. One popular approach is to model the data using acyclic directed mixed graphs (ADMGs), which describe ancestral relations between variables using directed and bidirected edges. However, existing methods using ADMGs are based on either linear functional assumptions or a discrete search that is complicated to use and lacks computational tractability for large datasets. In this work, we further extend the existing body of work and develop a novel gradient-based approach to learning an ADMG with non-linear functional relations from observational data. We first show that the presence of latent confounding is identifiable under the assumptions of bow-free ADMGs with non-linear additive noise models. With this insight, we propose a novel neural causal model based on autoregressive flows for ADMG learning. This not only enables us to determine complex causal structural relationships behind the data in the presence of latent confounding, but also estimate their functional relationships (hence treatment effects) simultaneously. We further validate our approach via experiments on both synthetic and real-world datasets, and demonstrate the competitive performance against relevant baselines.

Conditional Neural Processes~(CNPs) formulate distributions over functions and generate function observations with exact conditional likelihoods. CNPs, however, have limited expressivity for high-dimensional observations, since their predictive distribution is factorized into a product of unconstrained (typically) Gaussian outputs. Previously, this could be handled using latent variables or autoregressive likelihood, but at the expense of intractable training and quadratically increased complexity. Instead, we propose calibrating CNPs with an adversarial training scheme besides regular maximum likelihood estimates. Specifically, we train an energy-based model (EBM) with noise contrastive estimation, which enforces EBM to identify true observations from the generations of CNP. In this way, CNP must generate predictions closer to the ground-truth to fool EBM, instead of merely optimizing with respect to the fixed-form likelihood. From generative function reconstruction to downstream regression and classification tasks, we demonstrate that our method fits mainstream CNP members, showing effectiveness when unconstrained Gaussian likelihood is defined, requiring minimal computation overhead while preserving foundation properties of CNPs.

This article is written for pedagogical purposes aiming at practitioners trying to estimate the finite support of continuous probability distributions, i.e., the minimum and the maximum of a distribution defined on a finite domain. Generalized Pareto distribution GP({\theta}, {\sigma}, {\xi}) is a three-parameter distribution which plays a key role in Peaks-Over-Threshold framework for tail estimation in Extreme Value Theory. Estimators for GP often lack analytical solutions and the best known Bayesian methods for GP involves numerical methods. Moreover, existing literature focuses on estimating the scale {\sigma} and the shape {\xi}, lacking discussion of the estimation of the location {\theta} which is the lower support of (minimum value possible in) a GP. To fill the gap, we analyze four two-parameter subclasses of GP whose conjugate priors can be obtained analytically, although some of the results are known. Namely, we prove the conjugacy for {\xi} > 0 (Pareto), {\xi} = 0 (Shifted Exponential), {\xi} < 0 (Power), and {\xi} = -1 (Two-parameter Uniform).

When considering an invariant that gives a Bayesian generalization error, that is a real log canonical threshold, in general, papers replace a mean error function with a relatively simple polynomial whose real log canonical threshold corresponds to that of the mean error function, and obtain its real log canonical threshold by resolving its singularities through an algebraic operation called blow-up. Though it is known that the singularities of any polynomial can be resolved by a finite number of blow-up iterations, it is not clarified well whether or not it is possible to resolve singularities of a specific polynomial by applying a specific blow-up algorithm. Therefore this paper proposes a blow-up algorithm that can be applied to the polynomials called sum-of-products polynomials and proves that it halts. Furthermore, this paper considers real log canonical thresholds of sum-of-products polynomials by using the algorithm. First, this section explains the foundation of Bayesian learning theory and details the relation to a real log canonical threshold and blow-up. Then this section defines exclusive sum-of-products polynomials which is subject to previous studies and explains the novelty and utility of this paper.

An algorithm based on a deep probabilistic architecture referred to as a tree-structured sum-product network (t-SPN) is considered for cell classification. The t-SPN is constructed such that the unnormalized probability is represented as conditional probabilities of a subset of most similar cell classes. The constructed t-SPN architecture is learned by maximizing the margin, which is the difference in the conditional probability between the true and the most competitive false label. To enhance the generalization ability of the architecture, L2-regularization (REG) is considered along with the maximum margin (MM) criterion in the learning process. To highlight cell features, this paper investigates the effectiveness of two generic high-pass filters: ideal high-pass filtering and the Laplacian of Gaussian (LOG) filtering. On both HEp-2 and Feulgen benchmark datasets, the t-SPN architecture learned based on the max-margin criterion with regularization produced the highest accuracy rate compared to other state-of-the-art algorithms that include convolutional neural network (CNN) based algorithms. The ideal high-pass filter was more effective on the HEp-2 dataset, which is based on immunofluorescence staining, while the LOG was more effective on the Feulgen dataset, which is based on Feulgen staining.