16,500 research outputs found

    Sequential stopping for high-throughput experiments

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    In high-throughput experiments, the sample size is typically chosen informally. Most formal sample-size calculations depend critically on prior knowledge. We propose a sequential strategy that, by updating knowledge when new data are available, depends less critically on prior assumptions. Experiments are stopped or continued based on the potential benefits in obtaining additional data. The underlying decision-theoretic framework guarantees the design to proceed in a coherent fashion. We propose intuitively appealing, easy-to-implement utility functions. As in most sequential design problems, an exact solution is prohibitive. We propose a simulation-based approximation that uses decision boundaries. We apply the method to RNA-seq, microarray, and reverse-phase protein array studies and show its potential advantages. The approach has been added to the Bioconductor package gaga

    An Entropy Search Portfolio for Bayesian Optimization

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    Bayesian optimization is a sample-efficient method for black-box global optimization. How- ever, the performance of a Bayesian optimization method very much depends on its exploration strategy, i.e. the choice of acquisition function, and it is not clear a priori which choice will result in superior performance. While portfolio methods provide an effective, principled way of combining a collection of acquisition functions, they are often based on measures of past performance which can be misleading. To address this issue, we introduce the Entropy Search Portfolio (ESP): a novel approach to portfolio construction which is motivated by information theoretic considerations. We show that ESP outperforms existing portfolio methods on several real and synthetic problems, including geostatistical datasets and simulated control tasks. We not only show that ESP is able to offer performance as good as the best, but unknown, acquisition function, but surprisingly it often gives better performance. Finally, over a wide range of conditions we find that ESP is robust to the inclusion of poor acquisition functions.Comment: 10 pages, 5 figure

    Planning with Information-Processing Constraints and Model Uncertainty in Markov Decision Processes

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    Information-theoretic principles for learning and acting have been proposed to solve particular classes of Markov Decision Problems. Mathematically, such approaches are governed by a variational free energy principle and allow solving MDP planning problems with information-processing constraints expressed in terms of a Kullback-Leibler divergence with respect to a reference distribution. Here we consider a generalization of such MDP planners by taking model uncertainty into account. As model uncertainty can also be formalized as an information-processing constraint, we can derive a unified solution from a single generalized variational principle. We provide a generalized value iteration scheme together with a convergence proof. As limit cases, this generalized scheme includes standard value iteration with a known model, Bayesian MDP planning, and robust planning. We demonstrate the benefits of this approach in a grid world simulation.Comment: 16 pages, 3 figure

    A principled information valuation for communications during multi-agent coordination

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    Decentralised coordination in multi-agent systems is typically achieved using communication. However, in many cases, communication is expensive to utilise because there is limited bandwidth, it may be dangerous to communicate, or communication may simply be unavailable at times. In this context, we argue for a rational approach to communication --- if it has a cost, the agents should be able to calculate a value of communicating. By doing this, the agents can balance the need to communicate with the cost of doing so. In this research, we present a novel model of rational communication that uses information theory to value communications, and employ this valuation in a decision theoretic coordination mechanism. A preliminary empirical evaluation of the benefits of this approach is presented in the context of the RoboCupRescue simulator
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