Chemical space is so large that brute force searches for new interesting molecules are infeasible. High-throughput virtual screening via computer cluster simulations can speed up the discovery process by collecting very large amounts of data in parallel, e.g., up to hundreds or thousands of parallel measurements. Bayesian optimization (BO) can produce additional acceleration by sequentially identifying the most useful simulations or experiments to be performed next. However, current BO methods cannot scale to the large numbers of parallel measurements and the massive libraries of molecules currently used in high-throughput screening. Here, we propose a scalable solution based on a parallel and distributed implementation of Thompson sampling (PDTS). We show that, in small scale problems, PDTS performs similarly as parallel expected improvement (EI), a batch version of the most widely used BO heuristic. Additionally, in settings where parallel EI does not scale, PDTS outperforms other scalable baselines such as a greedy search, @math -greedy approaches and a random search method. These results show that PDTS is a successful solution for large-scale parallel BO.
@cite_29: We consider parallel global optimization of derivative-free expensive-to-evaluate functions, and propose an efficient method based on stochastic approximation for implementing a conceptual Bayesian optimization algorithm proposed by (2007). To accomplish this, we use infinitessimal perturbation analysis (IPA) to construct a stochastic gradient estimator and show that this estimator is unbiased. We also show that the stochastic gradient ascent algorithm using the constructed gradient estimator converges to a stationary point of the q-EI surface, and therefore, as the number of multiple starts of the gradient ascent algorithm and the number of steps for each start grow large, the one-step Bayes optimal set of points is recovered. We show in numerical experiments that our method for maximizing the q-EI is faster than methods based on closed-form evaluation using high-dimensional integration, when considering many parallel function evaluations, and is comparable in speed when considering few. We also show that the resulting one-step Bayes optimal algorithm for parallel global optimization finds high quality solutions with fewer evaluations that a heuristic based on approximately maximizing the q-EI. A high quality open source implementation of this algorithm is available in the open source Metrics Optimization Engine (MOE).
@cite_16: This work deals with parallel optimization of expensive objective functions which are modeled as sample realizations of Gaussian processes. The study is formalized as a Bayesian optimization problem, or continuous multi-armed bandit problem, where a batch of q > 0 arms is pulled in parallel at each iteration. Several algorithms have been developed for choosing batches by trading off exploitation and exploration. As of today, the maximum Expected Improvement (EI) and Upper Confidence Bound (UCB) selection rules appear as the most prominent approaches for batch selection. Here, we build upon recent work on the multipoint Expected Improvement criterion, for which an analytic expansion relying on Tallis' formula was recently established. The computational burden of this selection rule being still an issue in application, we derive a closed-form expression for the gradient of the multipoint Expected Improvement, which aims at facilitating its maximization using gradient-based ascent algorithms. Substantial computational savings are shown in application. In addition, our algorithms are tested numerically and compared to state-of-the-art UCB-based batch-sequential algorithms. Combining starting designs relying on UCB with gradient-based EI local optimization finally appears as a sound option for batch design in distributed Gaussian Process optimization.
@cite_8: The Multi-points Expected Improvement criterion or @math -EI has recently been studied in batch-sequential Bayesian Optimization. This paper deals with a new way of computing @math -EI, without using Monte-Carlo simulations, through a closed-form formula. The latter allows a very fast computation of @math -EI for reasonably low values of @math typically, less than 10. New parallel kriging-based optimization strategies, tested on different toy examples, show promising results.
compute a Monte Carlo approximation of the expected acquisition function over potential fantasies sampled from the model's predictive distribution. Recent methods have been proposed to modify the parallel EI procedure to recommend points jointly @cite_8 @cite_16 @cite_29 .