Deep Transformed Gaussian Processes

Transformed Gaussian Processes (TGPs) are stochastic processes specified by transforming samples from the joint distribution from a prior process (typically a GP) using an invertible transformation; increasing the flexibility of the base process. Furthermore, they achieve competitive results compared with Deep Gaussian Processes (DGPs), which are another generalization constructed by a hierarchical concatenation of GPs. In this work, we propose a generalization of TGPs named Deep Transformed Gaussian Processes (DTGPs), which follows the trend of concatenating layers of stochastic processes. More precisely, we obtain a multi-layer model in which each layer is a TGP. This generalization implies an increment of flexibility with respect to both TGPs and DGPs. Exact inference in such a model is intractable. However, we show that one can use variational inference to approximate the required computations yielding a straightforward extension of the popular DSVI inference algorithm Salimbeni et al (2017). The experiments conducted evaluate the proposed novel DTGPs in multiple regression datasets, achieving good scalability and performance.

Variational Linearized Laplace Approximation for Bayesian Deep Learning

Pre-trained deep neural networks can be adapted to perform uncertainty estimation by transforming them into Bayesian neural networks via methods such as Laplace approximation (LA) or its linearized form (LLA), among others. To make these methods more tractable, the generalized Gauss-Newton (GGN) approximation is often used. However, due to complex inefficiency difficulties, both LA and LLA rely on further approximations, such as Kronecker-factored or diagonal approximate GGN matrices, which can affect the results. To address these issues, we propose a new method for scaling LLA using a variational sparse Gaussian Process (GP) approximation based on the dual RKHS of GPs. Our method retains the predictive mean of the original model while allowing for efficient stochastic optimization and scalability in both the number of parameters and the size of the training dataset. Moreover, its training cost is independent of the number of training points, improving over previously existing methods. Our preliminary experiments indicate that it outperforms already existing efficient variants of LLA, such as accelerated LLA (ELLA), based on the Nystr\"om approximation.

Correcting Model Bias with Sparse Implicit Processes

Model selection in machine learning (ML) is a crucial part of the Bayesian learning procedure. Model choice may impose strong biases on the resulting predictions, which can hinder the performance of methods such as Bayesian neural networks and neural samplers. On the other hand, newly proposed approaches for Bayesian ML exploit features of approximate inference in function space with implicit stochastic processes (a generalization of Gaussian processes). The approach of Sparse Implicit Processes (SIP) is particularly successful in this regard, since it is fully trainable and achieves flexible predictions. Here, we expand on the original experiments to show that SIP is capable of correcting model bias when the data generating mechanism differs strongly from the one implied by the model. We use synthetic datasets to show that SIP is capable of providing predictive distributions that reflect the data better than the exact predictions of the initial, but wrongly assumed model.

Deep Variational Implicit Processes

Implicit processes (IPs) are a generalization of Gaussian processes (GPs). IPs may lack a closed-form expression but are easy to sample from. Examples include, among others, Bayesian neural networks or neural samplers. IPs can be used as priors over functions, resulting in flexible models with well-calibrated prediction uncertainty estimates. Methods based on IPs usually carry out function-space approximate inference, which overcomes some of the difficulties of parameter-space approximate inference. Nevertheless, the approximations employed often limit the expressiveness of the final model, resulting, \emph{e.g.}, in a Gaussian predictive distribution, which can be restrictive. We propose here a multi-layer generalization of IPs called the Deep Variational Implicit process (DVIP). This generalization is similar to that of deep GPs over GPs, but it is more flexible due to the use of IPs as the prior distribution over the latent functions. We describe a scalable variational inference algorithm for training DVIP and show that it outperforms previous IP-based methods and also deep GPs. We support these claims via extensive regression and classification experiments. We also evaluate DVIP on large datasets with up to several million data instances to illustrate its good scalability and performance.

Efficient Transformed Gaussian Processes for Non-Stationary Dependent Multi-class Classification

This work introduces the Efficient Transformed Gaussian Process (ETGP), a new way of creating C stochastic processes characterized by: 1) the C processes are non-stationary, 2) the C processes are dependent by construction without needing a mixing matrix, 3) training and making predictions is very efficient since the number of Gaussian Processes (GP) operations (e.g. inverting the inducing point's covariance matrix) do not depend on the number of processes. This makes the ETGP particularly suited for multi-class problems with a very large number of classes, which are the problems studied in this work. ETGPs exploit the recently proposed Transformed Gaussian Process (TGP), a stochastic process specified by transforming a Gaussian Process using an invertible transformation. However, unlike TGPs, ETGPs are constructed by transforming a single sample from a GP using C invertible transformations. We derive an efficient sparse variational inference algorithm for the proposed model and demonstrate its utility in 5 classification tasks which include low/medium/large datasets and a different number of classes, ranging from just a few to hundreds. Our results show that ETGPs, in general, outperform state-of-the-art methods for multi-class classification based on GPs, and have a lower computational cost (around one order of magnitude smaller).

Gaussian Processes for Missing Value Imputation

Missing values are common in many real-life datasets. However, most of the current machine learning methods can not handle missing values. This means that they should be imputed beforehand. Gaussian Processes (GPs) are non-parametric models with accurate uncertainty estimates that combined with sparse approximations and stochastic variational inference scale to large data sets. Sparse GPs can be used to compute a predictive distribution for missing data. Here, we present a hierarchical composition of sparse GPs that is used to predict missing values at each dimension using all the variables from the other dimensions. We call the approach missing GP (MGP). MGP can be trained simultaneously to impute all observed missing values. Specifically, it outputs a predictive distribution for each missing value that is then used in the imputation of other missing values. We evaluate MGP in one private clinical data set and four UCI datasets with a different percentage of missing values. We compare the performance of MGP with other state-of-the-art methods for imputing missing values, including variants based on sparse GPs and deep GPs. The results obtained show a significantly better performance of MGP.

Inference over radiative transfer models using variational and expectation maximization methods

Earth observation from satellites offers the possibility to monitor our planet with unprecedented accuracy. Radiative transfer models (RTMs) encode the energy transfer through the atmosphere, and are used to model and understand the Earth system, as well as to estimate the parameters that describe the status of the Earth from satellite observations by inverse modeling. However, performing inference over such simulators is a challenging problem. RTMs are nonlinear, non-differentiable and computationally costly codes, which adds a high level of difficulty in inference. In this paper, we introduce two computational techniques to infer not only point estimates of biophysical parameters but also their joint distribution. One of them is based on a variational autoencoder approach and the second one is based on a Monte Carlo Expectation Maximization (MCEM) scheme. We compare and discuss benefits and drawbacks of each approach. We also provide numerical comparisons in synthetic simulations and the real PROSAIL model, a popular RTM that combines land vegetation leaf and canopy modeling. We analyze the performance of the two approaches for modeling and inferring the distribution of three key biophysical parameters for quantifying the terrestrial biosphere.

Sparse Implicit Processes for Approximate Inference

Implicit Processes (IPs) are flexible priors that can describe models such as Bayesian neural networks, neural samplers and data generators. IPs allow for approximate inference in function-space. This avoids some degenerate problems of parameter-space approximate inference due to the high number of parameters and strong dependencies. For this, an extra IP is often used to approximate the posterior of the prior IP. However, simultaneously adjusting the parameters of the prior IP and the approximate posterior IP is a challenging task. Existing methods that can tune the prior IP result in a Gaussian predictive distribution, which fails to capture important data patterns. By contrast, methods producing flexible predictive distributions by using another IP to approximate the posterior process cannot fit the prior IP to the observed data. We propose here a method that can carry out both tasks. For this, we rely on an inducing-point representation of the prior IP, as often done in the context of sparse Gaussian processes. The result is a scalable method for approximate inference with IPs that can tune the prior IP parameters to the data, and that provides accurate non-Gaussian predictive distributions.

Input Dependent Sparse Gaussian Processes

Gaussian Processes (GPs) are Bayesian models that provide uncertainty estimates associated to the predictions made. They are also very flexible due to their non-parametric nature. Nevertheless, GPs suffer from poor scalability as the number of training instances N increases. More precisely, they have a cubic cost with respect to $N$. To overcome this problem, sparse GP approximations are often used, where a set of $M \ll N$ inducing points is introduced during training. The location of the inducing points is learned by considering them as parameters of an approximate posterior distribution $q$. Sparse GPs, combined with variational inference for inferring $q$, reduce the training cost of GPs to $\mathcal{O}(M^3)$. Critically, the inducing points determine the flexibility of the model and they are often located in regions of the input space where the latent function changes. A limitation is, however, that for some learning tasks a large number of inducing points may be required to obtain a good prediction performance. To address this limitation, we propose here to amortize the computation of the inducing points locations, as well as the parameters of the variational posterior approximation q. For this, we use a neural network that receives the observed data as an input and outputs the inducing points locations and the parameters of $q$. We evaluate our method in several experiments, showing that it performs similar or better than other state-of-the-art sparse variational GP approaches. However, with our method the number of inducing points is reduced drastically due to their dependency on the input data. This makes our method scale to larger datasets and have faster training and prediction times.

Max-value Entropy Search for Multi-objective Bayesian Optimization with Constraints

We present MESMOC, a Bayesian optimization method that can be used to solve constrained multi-objective problems when the objectives and the constraints are expensive to evaluate. MESMOC works by minimizing the entropy of the solution of the optimization problem in function space, i.e., the Pareto frontier, to guide the search for the optimum. The execution cost of MESMOC is linear in the number of objectives and constraints. Furthermore, it is often significantly smaller than the cost of alternative methods based on minimizing the entropy of the Pareto set. The reason for this is that it is easier to approximate the required computations in MESMOC. Moreover, MESMOC's acquisition function is expressed as the sum of one acquisition per each black-box (objective or constraint). Thus, it can be used in a decoupled evaluation setting in which one chooses not only the next input location to evaluate, but also which black-box to evaluate there. We compare MESMOC with related methods in synthetic and real optimization problems. These experiments show that MESMOC is competitive with other information-based methods for constrained multi-objective Bayesian optimization, but its execution time is smaller.