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_26 proposed the following framework for parallel BO: given a set of current observations @math and pending experiments @math , an additional set of fantasies @math can be assumed to be the result of those pending experiments. A step of Bayesian optimization can then be performed using the augmented dataset @math and the acquisition function @math . Two different values are proposed for the fantasies: the , where @math for some constant @math and all @math , and the , where @math is given by the GP predictive mean at @math .
@cite_26
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Scientists often express their understanding of the world through a computationally demanding simulation program. Analyzing the posterior distribution of the parameters given observations (the inverse problem) can be extremely challenging. The Approximate Bayesian Computation (ABC) framework is the standard statistical tool to handle these likelihood free problems, but they require a very large number of simulations. In this work we develop two new ABC sampling algorithms that significantly reduce the number of simulations necessary for posterior inference. Both algorithms use confidence estimates for the accept probability in the Metropolis Hastings step to adaptively choose the number of necessary simulations. Our GPS-ABC algorithm stores the information obtained from every simulation in a Gaussian process which acts as a surrogate function for the simulated statistics. Experiments on a challenging realistic biological problem illustrate the potential of these algorithms. Recently, Bayesian Optimization (BO) has been used to successfully optimize parametric policies in several challenging Reinforcement Learning (RL) applications. BO is attractive for this problem because it exploits Bayesian prior information about the expected return and exploits this knowledge to select new policies to execute. Effectively, the BO framework for policy search addresses the exploration-exploitation tradeoff. In this work, we show how to more effectively apply BO to RL by exploiting the sequential trajectory information generated by RL agents. Our contributions can be broken into two distinct, but mutually beneficial, parts. The first is a new Gaussian process (GP) kernel for measuring the similarity between policies using trajectory data generated from policy executions. This kernel can be used in order to improve posterior estimates of the expected return thereby improving the quality of exploration. The second contribution, is a new GP mean function which uses learned transition and reward functions to approximate the surface of the objective. We show that the model-based approach we develop can recover from model inaccuracies when good transition and reward models cannot be learned. We give empirical results in a standard set of RL benchmarks showing that both our model-based and model-free approaches can speed up learning compared to competing methods. Further, we show that our contributions can be combined to yield synergistic improvement in some domains. These lecture notes highlight the mathematical and computational structure relating to the formulation of, and development of algorithms for, the Bayesian approach to inverse problems in differential equations. This approach is fundamental in the quantification of uncertainty within applications in volving the blending of mathematical models with data. The finite dimensional situation is described first, along with some motivational examples. Then the development of probability measures on separable Banach space is undertaken, using a random series over an infinite set of functions to construct draws; these probability measures are used as priors in the Bayesian approach to inverse problems. Regularity of draws from the priors is studied in the natural Sobolev or Besov spaces implied by the choice of functions in the random series construction, and the Kolmogorov continuity theorem is used to extend regularity considerations to the space of Holder continuous functions. Bayes’ theorem is de rived in this prior setting, and here interpreted as finding conditions under which the posterior is absolutely continuous with respect to the prior, and determining a formula for the Radon-Nikodym derivative in terms of the likelihood of the data. Having established the form of the posterior, we then describe various properties common to it in the infinite dimensional setting. These properties include well-posedness, approximation theory, and the existence of maximum a posteriori estimators. We then describe measure-preserving dynamics, again on the infinite dimensional space, including Markov chain-Monte C arlo and sequential Monte Carlo methods, and measure-preserving reversible stochastic differential equations. By formulating the theory and algorithms on the underlying infinite dimensional space, we obtain a framework suitable for rigorous analysis of the accuracy of reconstructions, of computational complexity, as well as naturally constructing algorithms which perform well under mesh refinement, since they are inherently well-defined in infinite dimensions. We consider the problem of 20 questions with noise for multiple players under the minimum entropy criterion in the setting of stochastic search, with application to target localization. Each player yields a noisy response to a binary query governed by a certain error probability. First, we propose a sequential policy for constructing questions that queries each player in sequence and refines the posterior of the target location. Second, we consider a joint policy that asks all players questions in parallel at each time instant and characterize the structure of the optimal policy for constructing the sequence of questions. This generalizes the single player probabilistic bisection method for stochastic search problems. Third, we prove an equivalence between the two schemes showing that, despite the fact that the sequential scheme has access to a more refined filtration, the joint scheme performs just as well on average. Fourth, we establish convergence rates of the mean-square error and derive error exponents. Finally, we obtain an extension to the case of unknown error probabilities. This framework provides a mathematical model for incorporating a human in the loop for active machine learning systems.