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We present FlowMO: an open-source Python library for molecular property prediction with Gaussian Processes. Built upon GPflow and RDKit, FlowMO enables the user to make predictions with well-calibrated uncertainty estimates, an output central to active learning and molecular design applications. Gaussian Processes are particularly attractive for modelling small molecular datasets, a characteristic of many real-world virtual screening campaigns where high-quality experimental data is scarce. Computational experiments across three small datasets demonstrate comparable predictive performance to deep learning methods but with superior uncertainty calibration.
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Variational autoencoders (VAE) are a powerful and widely-used class of models to learn complex data distributions in an unsupervised fashion. One important limitation of VAEs is the prior assumption that latent sample representations are independent and identically distributed. However, for many important datasets, such as time-series of images, this assumption is too strong: accounting for covariances between samples, such as those in time, can yield to a more appropriate model specification and improve performance in downstream tasks. In this work, we introduce a new model, the Gaussian Process (GP) Prior Variational Autoencoder (GPPVAE), to specifically address this issue. The GPPVAE aims to combine the power of VAEs with the ability to model correlations afforded by GP priors. To achieve efficient inference in this new class of models, we leverage structure in the covariance matrix, and introduce a new stochastic backpropagation strategy that allows for computing stochastic gradients in a distributed and low-memory fashion. We show that our method outperforms conditional VAEs (CVAEs) and an adaptation of standard VAEs in two image data applications.
This paper analyzes the problem of Gaussian process (GP) bandits with deterministic observations. The analysis uses a branch and bound algorithm that is related to the UCB algorithm of (Srinivas et al, 2010). For GPs with Gaussian observation noise, with variance strictly greater than zero, Srinivas et al proved that the regret vanishes at the approximate rate of $O(1/sqrt{t})$, where t is the number of observations. To complement their result, we attack the deterministic case and attain a much faster exponential convergence rate. Under some regularity assumptions, we show that the regret decreases asymptotically according to $O(e^{-frac{tau t}{(ln t)^{d/4}}})$ with high probability. Here, d is the dimension of the search space and tau is a constant that depends on the behaviour of the objective function near its global maximum.
Currently, multi-output Gaussian process regression models either do not model nonstationarity or are associated with severe computational burdens and storage demands. Nonstationary multi-variate Gaussian process models (NMGP) use a nonstationary covariance function with an input-dependent linear model of coregionalisation to jointly model input-dependent correlation, scale, and smoothness of outputs. Variational sparse approximation relies on inducing points to enable scalable computations. Here, we take the best of both worlds: considering an inducing variable framework on the underlying latent functions in NMGP, we propose a novel model called the collaborative nonstationary Gaussian process model(CNMGP). For CNMGP, we derive computationally tractable variational bounds amenable to doubly stochastic variational inference. Together, this allows us to model data in which outputs do not share a common input set, with a computational complexity that is independent of the size of the inputs and outputs. We illustrate the performance of our method on synthetic data and three real datasets and show that our model generally pro-vides better predictive performance than the state-of-the-art, and also provides estimates of time-varying correlations that differ across outputs.
This paper analyses the problem of Gaussian process (GP) bandits with deterministic observations. The analysis uses a branch and bound algorithm that is related to the UCB algorithm of (Srinivas et al., 2010). For GPs with Gaussian observation noise, with variance strictly greater than zero, (Srinivas et al., 2010) proved that the regret vanishes at the approximate rate of $O(frac{1}{sqrt{t}})$, where t is the number of observations. To complement their result, we attack the deterministic case and attain a much faster exponential convergence rate. Under some regularity assumptions, we show that the regret decreases asymptotically according to $O(e^{-frac{tau t}{(ln t)^{d/4}}})$ with high probability. Here, d is the dimension of the search space and $tau$ is a constant that depends on the behaviour of the objective function near its global maximum.
Many applications require a learner to make sequential decisions given uncertainty regarding both the systems payoff function and safety constraints. In safety-critical systems, it is paramount that the learners actions do not violate the safety constraints at any stage of the learning process. In this paper, we study a stochastic bandit optimization problem where the unknown payoff and constraint functions are sampled from Gaussian Processes (GPs) first considered in [Srinivas et al., 2010]. We develop a safe variant of GP-UCB called SGP-UCB, with necessary modifications to respect safety constraints at every round. The algorithm has two distinct phases. The first phase seeks to estimate the set of safe actions in the decision set, while the second phase follows the GP-UCB decision rule. Our main contribution is to derive the first sub-linear regret bounds for this problem. We numerically compare SGP-UCB against existing safe Bayesian GP optimization algorithms.
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