Symbolic regression with polynomial neural networks and polynomial neural ordinary differential equations (ODEs) are two recent and powerful approaches for equation recovery of many science and engineering problems. However, these methods provide point estimates for the model parameters and are currently unable to accommodate noisy data. We address this challenge by developing and validating the following Bayesian inference methods: the Laplace approximation, Markov Chain Monte Carlo (MCMC) sampling methods, and variational inference. We have found the Laplace approximation to be the best method for this class of problems. Our work can be easily extended to the broader class of symbolic neural networks to which the polynomial neural network belongs.

This paper introduces the Fusemate probabilistic logic programming system. Fusemate's inference engine comprises a grounding component and a variable elimination method for probabilistic inference. Fusemate differs from most other systems by grounding the program in a bottom-up way instead of the common top-down way. While bottom-up grounding is attractive for a number of reasons, e.g., for dynamically creating distributions of varying support sizes, it makes it harder to control the amount of ground clauses generated. We address this problem by interleaving grounding with a query-guided relevance test which prunes rules whose bodies are inconsistent with the query. We present our method in detail and demonstrate it with examples that involve "time", such as (hidden) Markov models. Our experiments demonstrate competitive or better performance compared to a state-of-the art probabilistic logic programming system, in particular for high branching problems.

This paper introduces a novel approach to probabilistic deep learning, kernel density matrices, which provide a simpler yet effective mechanism for representing joint probability distributions of both continuous and discrete random variables. In quantum mechanics, a density matrix is the most general way to describe the state of a quantum system. This work extends the concept of density matrices by allowing them to be defined in a reproducing kernel Hilbert space. This abstraction allows the construction of differentiable models for density estimation, inference, and sampling, and enables their integration into end-to-end deep neural models. In doing so, we provide a versatile representation of marginal and joint probability distributions that allows us to develop a differentiable, compositional, and reversible inference procedure that covers a wide range of machine learning tasks, including density estimation, discriminative learning, and generative modeling. The broad applicability of the framework is illustrated by two examples: an image classification model that can be naturally transformed into a conditional generative model, and a model for learning with label proportions that demonstrates the framework's ability to deal with uncertainty in the training samples.

Passive acoustic monitoring can be an effective way of monitoring wildlife populations that are acoustically active but difficult to survey visually. Digital recorders allow surveyors to gather large volumes of data at low cost, but identifying target species vocalisations in these data is non-trivial. Machine learning (ML) methods are often used to do the identification. They can process large volumes of data quickly, but they do not detect all vocalisations and they do generate some false positives (vocalisations that are not from the target species). Existing wildlife abundance survey methods have been designed specifically to deal with the first of these mistakes, but current methods of dealing with false positives are not well-developed. They do not take account of features of individual vocalisations, some of which are more likely to be false positives than others. We propose three methods for acoustic spatial capture-recapture inference that integrate individual-level measures of confidence from ML vocalisation identification into the likelihood and hence integrate ML uncertainty into inference. The methods include a mixture model in which species identity is a latent variable. We test the methods by simulation and find that in a scenario based on acoustic data from Hainan gibbons, in which ignoring false positives results in 17% positive bias, our methods give negligible bias and coverage probabilities that are close to the nominal 95% level.

Some applications of deep learning require not only to provide accurate results but also to quantify the amount of confidence in their prediction. The management of an electric power grid is one of these cases: to avoid risky scenarios, decision-makers need both precise and reliable forecasts of, for example, power loads. For this reason, point forecasts are not enough hence it is necessary to adopt methods that provide an uncertainty quantification. This work focuses on reservoir computing as the core time series forecasting method, due to its computational efficiency and effectiveness in predicting time series. While the RC literature mostly focused on point forecasting, this work explores the compatibility of some popular uncertainty quantification methods with the reservoir setting. Both Bayesian and deterministic approaches to uncertainty assessment are evaluated and compared in terms of their prediction accuracy, computational resource efficiency and reliability of the estimated uncertainty, based on a set of carefully chosen performance metrics.

Automatic differentiation variational inference (ADVI) offers fast and easy-to-use posterior approximation in multiple modern probabilistic programming languages. However, its stochastic optimizer lacks clear convergence criteria and requires tuning parameters. Moreover, ADVI inherits the poor posterior uncertainty estimates of mean-field variational Bayes (MFVB). We introduce "deterministic ADVI" (DADVI) to address these issues. DADVI replaces the intractable MFVB objective with a fixed Monte Carlo approximation, a technique known in the stochastic optimization literature as the "sample average approximation" (SAA). By optimizing an approximate but deterministic objective, DADVI can use off-the-shelf second-order optimization, and, unlike standard mean-field ADVI, is amenable to more accurate posterior covariances via linear response (LR). In contrast to existing worst-case theory, we show that, on certain classes of common statistical problems, DADVI and the SAA can perform well with relatively few samples even in very high dimensions, though we also show that such favorable results cannot extend to variational approximations that are too expressive relative to mean-field ADVI. We show on a variety of real-world problems that DADVI reliably finds good solutions with default settings (unlike ADVI) and, together with LR covariances, is typically faster and more accurate than standard ADVI.

Offshore wind structures are subject to deterioration mechanisms throughout their operational lifetime. Even if the deterioration evolution of structural elements can be estimated through physics-based deterioration models, the uncertainties involved in the process hurdle the selection of lifecycle management decisions. In this scenario, the collection of relevant information through an efficient monitoring system enables the reduction of uncertainties, ultimately driving more optimal lifecycle decisions. However, a full monitoring instrumentation implemented on all wind turbines in a farm might become unfeasible due to practical and economical constraints. Besides, certain load monitoring systems often become defective after a few years of marine environment exposure. Addressing the aforementioned concerns, a farm-wide virtual load monitoring scheme directed by a fleet-leader wind turbine offers an attractive solution. Fetched with data retrieved from a fully-instrumented wind turbine, a model can be trained and then deployed, thus yielding load predictions of non-fully monitored wind turbines, from which only standard data remains available. In this paper, we propose a virtual load monitoring framework formulated via Bayesian neural networks (BNNs) and we provide relevant implementation details needed for the construction, training, and deployment of BNN data-based virtual monitoring models. As opposed to their deterministic counterparts, BNNs intrinsically announce the uncertainties associated with generated load predictions and allow to detect inaccurate load estimations generated for non-fully monitored wind turbines. The proposed virtual load monitoring is thoroughly tested through an experimental campaign in an operational offshore wind farm and the results demonstrate the effectiveness of BNN models for fleet-leader-based farm-wide virtual monitoring.

We propose an optimization algorithm for Variational Inference (VI) in complex models. Our approach relies on natural gradient updates where the variational space is a Riemann manifold. We develop an efficient algorithm for Gaussian Variational Inference that implicitly satisfies the positive definite constraint on the variational covariance matrix. Our Exact manifold Gaussian Variational Bayes (EMGVB) provides exact but simple update rules and is straightforward to implement. Due to its black-box nature, EMGVB stands as a ready-to-use solution for VI in complex models. Over five datasets, we empirically validate our feasible approach on different statistical, econometric, and deep learning models, discussing its performance with respect to baseline methods.

Multiple-try Metropolis (MTM) is a popular Markov chain Monte Carlo method with the appealing feature of being amenable to parallel computing. At each iteration, it samples several candidates for the next state of the Markov chain and randomly selects one of them based on a weight function. The canonical weight function is proportional to the target density. We show both theoretically and empirically that this weight function induces pathological behaviours in high dimensions, especially during the convergence phase. We propose to instead use weight functions akin to the locally-balanced proposal distributions of Zanella (2020), thus yielding MTM algorithms that do not exhibit those pathological behaviours. To theoretically analyse these algorithms, we study the high-dimensional performance of ideal schemes that can be thought of as MTM algorithms which sample an infinite number of candidates at each iteration, as well as the discrepancy between such schemes and the MTM algorithms which sample a finite number of candidates. Our analysis unveils a strong distinction between the convergence and stationary phases: in the former, local balancing is crucial and effective to achieve fast convergence, while in the latter, the canonical and novel weight functions yield similar performance. Numerical experiments include an application in precision medicine involving a computationally-expensive forward model, which makes the use of parallel computing within MTM iterations beneficial.

In data-driven drug discovery, designing molecular descriptors is a very important task. Deep generative models such as variational autoencoders (VAEs) offer a potential solution by designing descriptors as probabilistic latent vectors derived from molecular structures. These models can be trained on large datasets, which have only molecular structures, and applied to transfer learning. Nevertheless, the approximate posterior distribution of the latent vectors of the usual VAE assumes a simple multivariate Gaussian distribution with zero covariance, which may limit the performance of representing the latent features. To overcome this limitation, we propose a novel molecular deep generative model that incorporates a hierarchical structure into the probabilistic latent vectors. We achieve this by a denoising diffusion probabilistic model (DDPM). We demonstrate that our model can design effective molecular latent vectors for molecular property prediction from some experiments by small datasets on physical properties and activity. The results highlight the superior prediction performance and robustness of our model compared to existing approaches.