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    Olofsson S, Mehrian M, Geris L, Calandra R, Deisenroth MP, Misener Ret al., 2017,

    Bayesian multi-objective optimisation of neotissue growth in a perfusion bioreactor set-up

    , European Symposium on Computer Aided Process Engineering (ESCAPE 27), Publisher: Elsevier

    We consider optimising bone neotissue growth in a 3D scaffold during dynamic perfusionbioreactor culture. The goal is to choose design variables by optimising two conflictingobjectives: (i) maximising neotissue growth and (ii) minimising operating cost. Our con-tribution is a novel extension of Bayesian multi-objective optimisation to the case of oneblack-box (neotissue growth) and one analytical (operating cost) objective function, thathelps determine, within a reasonable amount of time, what design variables best managethe trade-off between neotissue growth and operating cost. Our method is tested againstand outperforms the most common approach in literature, genetic algorithms, and showsits important real-world applicability to problems that combine black-box models witheasy-to-quantify objectives like cost.

    Salimbeni H, Deisenroth M, 2017,

    Doubly Stochastic Variational Inference for Deep Gaussian Processes

    , Advances in Neural Information Processing Systems (NIPS)

    Gaussian processes (GPs) are a good choice for function approximation as theyare flexible, robust to over-fitting, and provide well-calibrated predictiveuncertainty. Deep Gaussian processes (DGPs) are multi-layer generalisations ofGPs, but inference in these models has proved challenging. Existing approachesto inference in DGP models assume approximate posteriors that forceindependence between the layers, and do not work well in practice. We present adoubly stochastic variational inference algorithm, which does not forceindependence between layers. With our method of inference we demonstrate that aDGP model can be used effectively on data ranging in size from hundreds to abillion points. We provide strong empirical evidence that our inference schemefor DGPs works well in practice in both classification and regression.

    Tiwari K, Honore V, Jeong S, Chong NY, Deisenroth MPet al., 2017,

    Resource-constrained decentralized active sensing for multi-robot systems using distributed Gaussian processes

    , Pages: 13-18, ISSN: 1598-7833

    © 2016 Institute of Control, Robotics and Systems - ICROS. We consider the problem of area coverage for robot teams operating under resource constraints, while modeling spatio-temporal environmental phenomena. The aim of the mobile robot team is to avoid exhaustive search and only visit the most important locations that can improve the prediction accuracy of a spatio-temporal model. We use a Gaussian Process (GP) to model spatially varying and temporally evolving dynamics of the target phenomenon. Each robot of the team is allocated a dedicated search area wherein the robot autonomously optimizes its prediction accuracy. We present this as a Decentralized Computation and Centralized Data Fusion approach wherein the trajectory sampled by the robot is generated using our proposed Resource-Constrained Decentralized Active Sensing (RC-DAS). Since each robot possesses its own independent prediction model, at the end of robot's mission time, we fuse all the prediction models from all robots to have a global model of the spatio-temporal phenomenon. Previously, all robots and GPs needed to be synchronized, such that the GPs can be jointly trained. However, doing so defeats the purpose of a fully decentralized mobile robot team. Thus, we allow the robots to independently gather new measurements and update their model parameters irrespective of other members of the team. To evaluate the performance of our model, we compare the trajectory traced by the robot using active and passive (e.g., nearest neighbor selection) sensing. We compare the performance and cost incurred by a resource constrained optimization with the unconstrained entropy maximization version.

    Zhang Q, Filippi S, Gretton A, Sejdinovic Det al., 2017,

    Large-Scale Kernel Methods for Independence Testing

    , Statistics and Computing, ISSN: 1573-1375

    Representations of probability measures in reproducing kernel Hilbert spacesprovide a flexible framework for fully nonparametric hypothesis tests ofindependence, which can capture any type of departure from independence,including nonlinear associations and multivariate interactions. However, theseapproaches come with an at least quadratic computational cost in the number ofobservations, which can be prohibitive in many applications. Arguably, it isexactly in such large-scale datasets that capturing any type of dependence isof interest, so striking a favourable tradeoff between computational efficiencyand test performance for kernel independence tests would have a direct impacton their applicability in practice. In this contribution, we provide anextensive study of the use of large-scale kernel approximations in the contextof independence testing, contrasting block-based, Nystrom and random Fourierfeature approaches. Through a variety of synthetic data experiments, it isdemonstrated that our novel large scale methods give comparable performancewith existing methods whilst using significantly less computation time andmemory.

    Arulkumaran K, Dilokthanakul N, Shanahan M, Bharath AAet al., 2016,

    Classifying Options for Deep Reinforcement Learning.

    Calandra R, Peters J, Rasmussen CE, Deisenroth MPet al., 2016,

    Manifold Gaussian Processes for Regression

    , International Joint Conference on Neural Networks

    Off-the-shelf Gaussian Process (GP) covariancefunctions encode smoothness assumptions on the structureof the function to be modeled. To model complex and nondifferentiablefunctions, these smoothness assumptions are oftentoo restrictive. One way to alleviate this limitation is to finda different representation of the data by introducing a featurespace. This feature space is often learned in an unsupervisedway, which might lead to data representations that are notuseful for the overall regression task. In this paper, we proposeManifold Gaussian Processes, a novel supervised method thatjointly learns a transformation of the data into a featurespace and a GP regression from the feature space to observedspace. The Manifold GP is a full GP and allows to learn datarepresentations, which are useful for the overall regressiontask. As a proof-of-concept, we evaluate our approach oncomplex non-smooth functions where standard GPs performpoorly, such as step functions and robotics tasks with contacts.

    Calandra R, Seyfarth A, Peters J, Deisenroth MPet al., 2016,

    Bayesian optimization for learning gaits under uncertainty: An experimental comparison on a dynamic bipedal walker

    , Annals of Mathematics and Artificial Intelligence, Vol: 76, Pages: 5-23, ISSN: 1012-2443

    © 2015, Springer International Publishing Switzerland. Designing gaits and corresponding control policies is a key challenge in robot locomotion. Even with a viable controller parametrization, finding near-optimal parameters can be daunting. Typically, this kind of parameter optimization requires specific expert knowledge and extensive robot experiments. Automatic black-box gait optimization methods greatly reduce the need for human expertise and time-consuming design processes. Many different approaches for automatic gait optimization have been suggested to date. However, no extensive comparison among them has yet been performed. In this article, we thoroughly discuss multiple automatic optimization methods in the context of gait optimization. We extensively evaluate Bayesian optimization, a model-based approach to black-box optimization under uncertainty, on both simulated problems and real robots. This evaluation demonstrates that Bayesian optimization is particularly suited for robotic applications, where it is crucial to find a good set of gait parameters in a small number of experiments.

    Eleftheriadis S, Rudovic O, Deisenroth MP, Pantic Met al., 2016,

    Gaussian Process Domain Experts for Model Adaptation in Facial Behavior Analysis

    , 29th IEEE Conference on Computer Vision and Pattern Recognition Workshops (CVPRW), Publisher: IEEE, Pages: 1469-1477, ISSN: 2160-7508
    Filippi S, Barnes CP, Kirk PDW, Kudo T, Kunida K, McMahon SS, Tsuchiya T, Wada T, Kuroda S, Stumpf MPHet al., 2016,

    Robustness of MEK-ERK Dynamics and Origins of Cell-to-Cell Variability in MAPK Signaling

    , CELL REPORTS, Vol: 15, Pages: 2524-2535, ISSN: 2211-1247
    Filippi S, Holmes C, 2016,

    A Bayesian nonparametric approach to testing for dependence between random variables

    , Bayesian Analysis, ISSN: 1931-6690

    Nonparametric and nonlinear measures of statistical dependence between pairsof random variables are important tools in modern data analysis. In particularthe emergence of large data sets can now support the relaxation of linearityassumptions implicit in traditional association scores such as correlation.Here we describe a Bayesian nonparametric procedure that leads to a tractable,explicit and analytic quantification of the relative evidence for dependence vsindependence. Our approach uses Polya tree priors on the space of probabilitymeasures which can then be embedded within a decision theoretic test fordependence. Polya tree priors can accommodate known uncertainty in the form ofthe underlying sampling distribution and provides an explicit posteriorprobability measure of both dependence and independence. Well known advantagesof having an explicit probability measure include: easy comparison of evidenceacross different studies; encoding prior information; quantifying changes independence across different experimental conditions, and; the integration ofresults within formal decision analysis.

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