arXiv subjects

Edwin V. Bonilla

Publications and source records attributed to Edwin V. Bonilla.

At least 37 records · Page 2Linked to original sources

arXiv2024

Contextual Directed Acyclic Graphs

Estimating the structure of directed acyclic graphs (DAGs) from observational data remains a significant challenge in machine learning. Most research in this area concentrates on learning a single DAG for the entire population. This paper considers an alternative setting where the graph structure varies across individuals based on available "contextual" features. We tackle this contextual DAG problem via a neural network that maps the contextual features to a DAG, represented as a weighted adjacency matrix. The neural network is equipped with a novel projection layer that ensures the output matrices are sparse and satisfy a recently developed characterization of acyclicity. We devise a scalable computational framework for learning contextual DAGs and provide a convergence guarantee and an analytical gradient for backpropagating through the projection layer. Our experiments suggest that the new approach can recover the true context-specific graph where existing approaches fail.

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arXiv2024

Statistically Efficient Bayesian Sequential Experiment Design via Reinforcement Learning with Cross-Entropy Estimators

Reinforcement learning can learn amortised design policies for designing sequences of experiments. However, current amortised methods rely on estimators of expected information gain (EIG) that require an exponential number of samples on the magnitude of the EIG to achieve an unbiased estimation. We propose the use of an alternative estimator based on the cross-entropy of the joint model distribution and a flexible proposal distribution. This proposal distribution approximates the true posterior of the model parameters given the experimental history and the design policy. Our method overcomes the exponential-sample complexity of previous approaches and provide more accurate estimates of high EIG values. More importantly, it allows learning of superior design policies, and is compatible with continuous and discrete design spaces, non-differentiable likelihoods and even implicit probabilistic models.

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arXiv2023

Free-Form Variational Inference for Gaussian Process State-Space Models

Gaussian process state-space models (GPSSMs) provide a principled and flexible approach to modeling the dynamics of a latent state, which is observed at discrete-time points via a likelihood model. However, inference in GPSSMs is computationally and statistically challenging due to the large number of latent variables in the model and the strong temporal dependencies between them. In this paper, we propose a new method for inference in Bayesian GPSSMs, which overcomes the drawbacks of previous approaches, namely over-simplified assumptions, and high computational requirements. Our method is based on free-form variational inference via stochastic gradient Hamiltonian Monte Carlo within the inducing-variable formalism. Furthermore, by exploiting our proposed variational distribution, we provide a collapsed extension of our method where the inducing variables are marginalized analytically. We also showcase results when combining our framework with particle MCMC methods. We show that, on six real-world datasets, our approach can learn transition dynamics and latent states more accurately than competing methods.

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arXiv2023

Recurrent Neural Networks and Universal Approximation of Bayesian Filters

We consider the Bayesian optimal filtering problem: i.e. estimating some conditional statistics of a latent time-series signal from an observation sequence. Classical approaches often rely on the use of assumed or estimated transition and observation models. Instead, we formulate a generic recurrent neural network framework and seek to learn directly a recursive mapping from observational inputs to the desired estimator statistics. The main focus of this article is the approximation capabilities of this framework. We provide approximation error bounds for filtering in general non-compact domains. We also consider strong time-uniform approximation error bounds that guarantee good long-time performance. We discuss and illustrate a number of practical concerns and implications of these results.

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arXiv2022

Optimizing Sequential Experimental Design with Deep Reinforcement Learning

Bayesian approaches developed to solve the optimal design of sequential experiments are mathematically elegant but computationally challenging. Recently, techniques using amortization have been proposed to make these Bayesian approaches practical, by training a parameterized policy that proposes designs efficiently at deployment time. However, these methods may not sufficiently explore the design space, require access to a differentiable probabilistic model and can only optimize over continuous design spaces. Here, we address these limitations by showing that the problem of optimizing policies can be reduced to solving a Markov decision process (MDP). We solve the equivalent MDP with modern deep reinforcement learning techniques. Our experiments show that our approach is also computationally efficient at deployment time and exhibits state-of-the-art performance on both continuous and discrete design spaces, even when the probabilistic model is a black box.

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arXiv2022

Addressing Over-Smoothing in Graph Neural Networks via Deep Supervision

Learning useful node and graph representations with graph neural networks (GNNs) is a challenging task. It is known that deep GNNs suffer from over-smoothing where, as the number of layers increases, node representations become nearly indistinguishable and model performance on the downstream task degrades significantly. To address this problem, we propose deeply-supervised GNNs (DSGNNs), i.e., GNNs enhanced with deep supervision where representations learned at all layers are used for training. We show empirically that DSGNNs are resilient to over-smoothing and can outperform competitive benchmarks on node and graph property prediction problems.

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arXiv2021

SigGPDE: Scaling Sparse Gaussian Processes on Sequential Data

Making predictions and quantifying their uncertainty when the input data is sequential is a fundamental learning challenge, recently attracting increasing attention. We develop SigGPDE, a new scalable sparse variational inference framework for Gaussian Processes (GPs) on sequential data. Our contribution is twofold. First, we construct inducing variables underpinning the sparse approximation so that the resulting evidence lower bound (ELBO) does not require any matrix inversion. Second, we show that the gradients of the GP signature kernel are solutions of a hyperbolic partial differential equation (PDE). This theoretical insight allows us to build an efficient back-propagation algorithm to optimize the ELBO. We showcase the significant computational gains of SigGPDE compared to existing methods, while achieving state-of-the-art performance for classification tasks on large datasets of up to 1 million multivariate time series.

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arXiv2021

Distribution Regression for Sequential Data

Distribution regression refers to the supervised learning problem where labels are only available for groups of inputs instead of individual inputs. In this paper, we develop a rigorous mathematical framework for distribution regression where inputs are complex data streams. Leveraging properties of the expected signature and a recent signature kernel trick for sequential data from stochastic analysis, we introduce two new learning techniques, one feature-based and the other kernel-based. Each is suited to a different data regime in terms of the number of data streams and the dimensionality of the individual streams. We provide theoretical results on the universality of both approaches and demonstrate empirically their robustness to irregularly sampled multivariate time-series, achieving state-of-the-art performance on both synthetic and real-world examples from thermodynamics, mathematical finance and agricultural science.

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arXiv2021

Learning ODEs via Diffeomorphisms for Fast and Robust Integration

Advances in differentiable numerical integrators have enabled the use of gradient descent techniques to learn ordinary differential equations (ODEs). In the context of machine learning, differentiable solvers are central for Neural ODEs (NODEs), a class of deep learning models with continuous depth, rather than discrete layers. However, these integrators can be unsatisfactorily slow and inaccurate when learning systems of ODEs from long sequences, or when solutions of the system vary at widely different timescales in each dimension. In this paper we propose an alternative approach to learning ODEs from data: we represent the underlying ODE as a vector field that is related to another base vector field by a differentiable bijection, modelled by an invertible neural network. By restricting the base ODE to be amenable to integration, we can drastically speed up and improve the robustness of integration. We demonstrate the efficacy of our method in training and evaluating continuous neural networks models, as well as in learning benchmark ODE systems. We observe improvements of up to two orders of magnitude when integrating learned ODEs with GPUs computation.

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arXiv2021

Model Selection for Bayesian Autoencoders

We develop a novel method for carrying out model selection for Bayesian autoencoders (BAEs) by means of prior hyper-parameter optimization. Inspired by the common practice of type-II maximum likelihood optimization and its equivalence to Kullback-Leibler divergence minimization, we propose to optimize the distributional sliced-Wasserstein distance (DSWD) between the output of the autoencoder and the empirical data distribution. The advantages of this formulation are that we can estimate the DSWD based on samples and handle high-dimensional problems. We carry out posterior estimation of the BAE parameters via stochastic gradient Hamiltonian Monte Carlo and turn our BAE into a generative model by fitting a flexible Dirichlet mixture model in the latent space. Consequently, we obtain a powerful alternative to variational autoencoders, which are the preferred choice in modern applications of autoencoders for representation learning with uncertainty. We evaluate our approach qualitatively and quantitatively using a vast experimental campaign on a number of unsupervised learning tasks and show that, in small-data regimes where priors matter, our approach provides state-of-the-art results, outperforming multiple competitive baselines.

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arXiv2021

Sparse Gaussian Processes Revisited: Bayesian Approaches to Inducing-Variable Approximations

Variational inference techniques based on inducing variables provide an elegant framework for scalable posterior estimation in Gaussian process (GP) models. Besides enabling scalability, one of their main advantages over sparse approximations using direct marginal likelihood maximization is that they provide a robust alternative for point estimation of the inducing inputs, i.e. the location of the inducing variables. In this work we challenge the common wisdom that optimizing the inducing inputs in the variational framework yields optimal performance. We show that, by revisiting old model approximations such as the fully-independent training conditionals endowed with powerful sampling-based inference methods, treating both inducing locations and GP hyper-parameters in a Bayesian way can improve performance significantly. Based on stochastic gradient Hamiltonian Monte Carlo, we develop a fully Bayesian approach to scalable GP and deep GP models, and demonstrate its state-of-the-art performance through an extensive experimental campaign across several regression and classification problems.

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arXiv2021

BORE: Bayesian Optimization by Density-Ratio Estimation

Bayesian optimization (BO) is among the most effective and widely-used blackbox optimization methods. BO proposes solutions according to an explore-exploit trade-off criterion encoded in an acquisition function, many of which are computed from the posterior predictive of a probabilistic surrogate model. Prevalent among these is the expected improvement (EI) function. The need to ensure analytical tractability of the predictive often poses limitations that can hinder the efficiency and applicability of BO. In this paper, we cast the computation of EI as a binary classification problem, building on the link between class-probability estimation and density-ratio estimation, and the lesser-known link between density-ratios and EI. By circumventing the tractability constraints, this reformulation provides numerous advantages, not least in terms of expressiveness, versatility, and scalability.

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arXiv2020

Quantile Propagation for Wasserstein-Approximate Gaussian Processes

Approximate inference techniques are the cornerstone of probabilistic methods based on Gaussian process priors. Despite this, most work approximately optimizes standard divergence measures such as the Kullback-Leibler (KL) divergence, which lack the basic desiderata for the task at hand, while chiefly offering merely technical convenience. We develop a new approximate inference method for Gaussian process models which overcomes the technical challenges arising from abandoning these convenient divergences. Our method---dubbed Quantile Propagation (QP)---is similar to expectation propagation (EP) but minimizes the $L_2$ Wasserstein distance (WD) instead of the KL divergence. The WD exhibits all the required properties of a distance metric, while respecting the geometry of the underlying sample space. We show that QP matches quantile functions rather than moments as in EP and has the same mean update but a smaller variance update than EP, thereby alleviating EP's tendency to over-estimate posterior variances. Crucially, despite the significant complexity of dealing with the WD, QP has the same favorable locality property as EP, and thereby admits an efficient algorithm. Experiments on classification and Poisson regression show that QP outperforms both EP and variational Bayes.

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arXiv2020

Variational Inference for Graph Convolutional Networks in the Absence of Graph Data and Adversarial Settings

We propose a framework that lifts the capabilities of graph convolutional networks (GCNs) to scenarios where no input graph is given and increases their robustness to adversarial attacks. We formulate a joint probabilistic model that considers a prior distribution over graphs along with a GCN-based likelihood and develop a stochastic variational inference algorithm to estimate the graph posterior and the GCN parameters jointly. To address the problem of propagating gradients through latent variables drawn from discrete distributions, we use their continuous relaxations known as Concrete distributions. We show that, on real datasets, our approach can outperform state-of-the-art Bayesian and non-Bayesian graph neural network algorithms on the task of semi-supervised classification in the absence of graph data and when the network structure is subjected to adversarial perturbations.

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arXiv2019

Scalable Grouped Gaussian Processes via Direct Cholesky Functional Representations

We consider multi-task regression models where observations are assumed to be a linear combination of several latent node and weight functions, all drawn from Gaussian process (GP) priors that allow nonzero covariance between grouped latent functions. We show that when these grouped functions are conditionally independent given a group-dependent pivot, it is possible to parameterize the prior through sparse Cholesky factors directly, hence avoiding their computation during inference. Furthermore, we establish that kernels that are multiplicatively separable over input points give rise to such sparse parameterizations naturally without any additional assumptions. Finally, we extend the use of these sparse structures to approximate posteriors within variational inference, further improving scalability on the number of functions. We test our approach on multi-task datasets concerning distributed solar forecasting and show that it outperforms several multi-task GP baselines and that our sparse specifications achieve the same or better accuracy than non-sparse counterparts.

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arXiv2019

Structured Variational Inference in Continuous Cox Process Models

We propose a scalable framework for inference in an inhomogeneous Poisson process modeled by a continuous sigmoidal Cox process that assumes the corresponding intensity function is given by a Gaussian process (GP) prior transformed with a scaled logistic sigmoid function. We present a tractable representation of the likelihood through augmentation with a superposition of Poisson processes. This view enables a structured variational approximation capturing dependencies across variables in the model. Our framework avoids discretization of the domain, does not require accurate numerical integration over the input space and is not limited to GPs with squared exponential kernels. We evaluate our approach on synthetic and real-world data showing that its benefits are particularly pronounced on multivariate input settings where it overcomes the limitations of mean-field methods and sampling schemes. We provide the state of-the-art in terms of speed, accuracy and uncertainty quantification trade-offs.

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arXiv2018

Grouped Gaussian Processes for Solar Power Prediction

We consider multi-task regression models where the observations are assumed to be a linear combination of several latent node functions and weight functions, which are both drawn from Gaussian process priors. Driven by the problem of developing scalable methods for forecasting distributed solar and other renewable power generation, we propose coupled priors over groups of (node or weight) processes to exploit spatial dependence between functions. We estimate forecast models for solar power at multiple distributed sites and ground wind speed at multiple proximate weather stations. Our results show that our approach maintains or improves point-prediction accuracy relative to competing solar benchmarks and improves over wind forecast benchmark models on all measures. Our approach consistently dominates the equivalent model without coupled priors, achieving faster gains in forecast accuracy. At the same time our approach provides better quantification of predictive uncertainties.

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arXiv2018

Generic Inference in Latent Gaussian Process Models

We develop an automated variational method for inference in models with Gaussian process (GP) priors and general likelihoods. The method supports multiple outputs and multiple latent functions and does not require detailed knowledge of the conditional likelihood, only needing its evaluation as a black-box function. Using a mixture of Gaussians as the variational distribution, we show that the evidence lower bound and its gradients can be estimated efficiently using samples from univariate Gaussian distributions. Furthermore, the method is scalable to large datasets which is achieved by using an augmented prior via the inducing-variable approach underpinning most sparse GP approximations, along with parallel computation and stochastic optimization. We evaluate our approach quantitatively and qualitatively with experiments on small datasets, medium-scale datasets and large datasets, showing its competitiveness under different likelihood models and sparsity levels. On the large-scale experiments involving prediction of airline delays and classification of handwritten digits, we show that our method is on par with the state-of-the-art hard-coded approaches for scalable GP regression and classification.

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