A novel machine learning optimization process coined Restrictive Federated Model Selection (RFMS) is proposed under the scenario, for example, when data from healthcare units can not leave the site it is situated on and it is forbidden to carry out training algorithms on remote data sites due to either technical or privacy and trust concerns. To carry out a clinical research under this scenario, an analyst could train a machine learning model only on local data site, but it is still possible to execute a statistical query at a certain cost in the form of sending a machine learning model to some of the remote data sites and get the performance measures as feedback, maybe due to prediction being usually much cheaper. Compared to federated learning, which is optimizing the model parameters directly by carrying out training across all data sites, RFMS trains model parameters only on one local data site but optimizes hyper-parameters across other data sites jointly since hyper-parameters play an important role in machine learning performance. The aim is to get a Pareto optimal model with respective to both local and remote unseen prediction losses, which could generalize well across data sites. In this work, we specifically consider high dimensional data with shifted distributions over data sites. As an initial investigation, Bayesian Optimization especially multi-objective Bayesian Optimization is used to guide an adaptive hyper-parameter optimization process to select models under the RFMS scenario. Empirical results show that solely using the local data site to tune hyper-parameters generalizes poorly across data sites, compared to methods that utilize the local and remote performances. Furthermore, in terms of dominated hypervolumes, multi-objective Bayesian Optimization algorithms show increased performance across multiple data sites among other candidates.
We consider the problem of learning from sparse and underspecified rewards, where an agent receives a complex input, such as a natural language instruction, and needs to generate a complex response, such as an action sequence, while only receiving binary success-failure feedback. Such success-failure rewards are often underspecified: they do not distinguish between purposeful and accidental success. Generalization from underspecified rewards hinges on discounting spurious trajectories that attain accidental success, while learning from sparse feedback requires effective exploration. We address exploration by using a mode covering direction of KL divergence to collect a diverse set of successful trajectories, followed by a mode seeking KL divergence to train a robust policy. We propose Meta Reward Learning (MeRL) to construct an auxiliary reward function that provides more refined feedback for learning. The parameters of the auxiliary reward function are optimized with respect to the validation performance of a trained policy. The MeRL approach outperforms our alternative reward learning technique based on Bayesian Optimization, and achieves the state-of-the-art on weakly-supervised semantic parsing. It improves previous work by 1.2% and 2.4% on WikiTableQuestions and WikiSQL datasets respectively.
High throughput sequencing of RNA (RNA-Seq) can provide us with millions of short fragments of RNA transcripts from a sample. How to better recover the original RNA transcripts from those fragments (RNA-Seq assembly) is still a difficult task. For example, RNA-Seq assembly tools typically require hyper-parameter tuning to achieve good performance for particular datasets. This kind of tuning is usually unintuitive and time-consuming. Consequently, users often resort to default parameters, which do not guarantee consistent good performance for various datasets. Here we propose BOAssembler (https://github.com/olivomao/boassembler), a framework that enables end-to-end automatic tuning of RNA-Seq assemblers, based on Bayesian Optimization principles. Experiments show this data-driven approach is effective to improve the overall assembly performance. The approach would be helpful for downstream (e.g. gene, protein, cell) analysis, and more broadly, for future bioinformatics benchmark studies.
We propose a method to incrementally learn an embedding space over the domain of network architectures, to enable the careful selection of architectures for evaluation during compressed architecture search. Given a teacher network, we search for a compressed network architecture by using Bayesian Optimization (BO) with a kernel function defined over our proposed embedding space to select architectures for evaluation. We demonstrate that our search algorithm can significantly outperform various baseline methods, such as random search and reinforcement learning (Ashok et al., 2018). The compressed architectures found by our method are also better than the state-of-the-art manually-designed compact architecture ShuffleNet (Zhang et al., 2018). We also demonstrate that the learned embedding space can be transferred to new settings for architecture search, such as a larger teacher network or a teacher network in a different architecture family, without any training. Code is publicly available here: https://github.com/Friedrich1006/ESNAC .
This paper focuses on Bayesian Optimization (BO) for objectives on combinatorial search spaces, including ordinal and categorical variables. Despite the abundance of potential applications of Combinatorial BO, including chipset configuration search and neural architecture search, only a handful of methods have been proposed. We introduce COMBO, a new Gaussian Process (GP) BO. COMBO quantifies "smoothness" of functions on combinatorial search spaces by utilizing a combinatorial graph. The vertex set of the combinatorial graph consists of all possible joint assignments of the variables, while edges are constructed using the graph Cartesian product of the sub-graphs that represent the individual variables. On this combinatorial graph, we propose an ARD diffusion kernel with which the GP is able to model high-order interactions between variables leading to better performance. Moreover, using the Horseshoe prior for the scale parameter in the ARD diffusion kernel results in an effective variable selection procedure, making COMBO suitable for high dimensional problems. Computationally, in COMBO the graph Cartesian product allows the Graph Fourier Transform calculation to scale linearly instead of exponentially. We validate COMBO in a wide array of realistic benchmarks, including weighted maximum satisfiability problems and neural architecture search. COMBO outperforms consistently the latest state-of-the-art while maintaining computational and statistical efficiency.
Optimizing an expensive-to-query function is a common task in science and engineering, where it is beneficial to keep the number of queries to a minimum. A popular strategy is Bayesian optimization (BO), which leverages probabilistic models for this task. Most BO today uses Gaussian processes (GPs), or a few other surrogate models. However, there is a broad set of Bayesian modeling techniques that could be used to capture complex systems and reduce the number of queries in BO. Probabilistic programming languages (PPLs) are modern tools that allow for flexible model definition, prior specification, model composition, and automatic inference. In this paper, we develop ProBO, a BO procedure that uses only standard operations common to most PPLs. This allows a user to drop in a model built with an arbitrary PPL and use it directly in BO. We describe acquisition functions for ProBO, and strategies for efficiently optimizing these functions given complex models or costly inference procedures. Using existing PPLs, we implement new models to aid in a few challenging optimization settings, and demonstrate these on model hyperparameter and architecture search tasks.
This paper investigates lung nodule classification by using deep neural networks (DNNs). Hyperparameter optimization in DNNs is a computationally expensive problem, where evaluating a hyperparameter configuration may take several hours or even days. Bayesian optimization has been recently introduced for the automatically searching of optimal hyperparameter configurations of DNNs. It applies probabilistic surrogate models to approximate the validation error function of hyperparameter configurations, such as Gaussian processes, and reduce the computational complexity to a large extent. However, most existing surrogate models adopt stationary covariance functions to measure the difference between hyperparameter points based on spatial distance without considering its spatial locations. This distance-based assumption together with the condition of constant smoothness throughout the whole hyperparameter search space clearly violates the property that the points far away from optimal points usually get similarly poor performance even though each two of them have huge spatial distance between them. In this paper, a non-stationary kernel is proposed which allows the surrogate model to adapt to functions whose smoothness varies with the spatial location of inputs, and a multi-level convolutional neural network (ML-CNN) is built for lung nodule classification whose hyperparameter configuration is optimized by using the proposed non-stationary kernel based Gaussian surrogate model. Our algorithm searches the surrogate for optimal setting via hyperparameter importance based evolutionary strategy, and the experiments demonstrate our algorithm outperforms manual tuning and well-established hyperparameter optimization methods such as Random search, Gaussian processes with stationary kernels, and recently proposed Hyperparameter Optimization via RBF and Dynamic coordinate search.
Learning by integrating multiple heterogeneous data sources is a common requirement in many tasks. Collective Matrix Factorization (CMF) is a technique to learn shared latent representations from arbitrary collections of matrices. It can be used to simultaneously complete one or more matrices, for predicting the unknown entries. Classical CMF methods assume linearity in the interaction of latent factors which can be restrictive and fails to capture complex non-linear interactions. In this paper, we develop the first deep-learning based method, called dCMF, for unsupervised learning of multiple shared representations, that can model such non-linear interactions, from an arbitrary collection of matrices. We address optimization challenges that arise due to dependencies between shared representations through Multi-Task Bayesian Optimization and design an acquisition function adapted for collective learning of hyperparameters. Our experiments show that dCMF significantly outperforms previous CMF algorithms in integrating heterogeneous data for predictive modeling. Further, on two tasks - recommendation and prediction of gene-disease association - dCMF outperforms state-of-the-art matrix completion algorithms that can utilize auxiliary sources of information.
Bayesian optimization usually assumes that a Bayesian prior is given. However, the strong theoretical guarantees in Bayesian optimization are often regrettably compromised in practice because of unknown parameters in the prior. In this paper, we adopt a variant of empirical Bayes and show that, by estimating the Gaussian process prior from offline data sampled from the same prior and constructing unbiased estimators of the posterior, variants of both GP-UCB and probability of improvement achieve a near-zero regret bound, which decreases to a constant proportional to the observational noise as the number of offline data and the number of online evaluations increase. Empirically, we have verified our approach on challenging simulated robotic problems featuring task and motion planning.
Gaussian processes (GPs) with derivatives are useful in many applications, including Bayesian optimization, implicit surface reconstruction, and terrain reconstruction. Fitting a GP to function values and derivatives at $n$ points in $d$ dimensions requires linear solves and log determinants with an ${n(d+1) \times n(d+1)}$ positive definite matrix -- leading to prohibitive $\mathcal{O}(n^3d^3)$ computations for standard direct methods. We propose iterative solvers using fast $\mathcal{O}(nd)$ matrix-vector multiplications (MVMs), together with pivoted Cholesky preconditioning that cuts the iterations to convergence by several orders of magnitude, allowing for fast kernel learning and prediction. Our approaches, together with dimensionality reduction, enables Bayesian optimization with derivatives to scale to high-dimensional problems and large evaluation budgets.
In this paper we present a hybrid active sampling strategy for pairwise preference aggregation, which aims at recovering the underlying rating of the test candidates from sparse and noisy pairwise labelling. Our method employs Bayesian optimization framework and Bradley-Terry model to construct the utility function, then to obtain the Expected Information Gain (EIG) of each pair. For computational efficiency, Gaussian-Hermite quadrature is used for estimation of EIG. In this work, a hybrid active sampling strategy is proposed, either using Global Maximum (GM) EIG sampling or Minimum Spanning Tree (MST) sampling in each trial, which is determined by the test budget. The proposed method has been validated on both simulated and real-world datasets, where it shows higher preference aggregation ability than the state-of-the-art methods.
Deep Convolutional Networks (DCNs) have been shown to be vulnerable to adversarial examples---perturbed inputs specifically designed to produce intentional errors in the learning algorithms at test time. Existing input-agnostic adversarial perturbations exhibit interesting visual patterns that are currently unexplained. In this paper, we introduce a structured approach for generating Universal Adversarial Perturbations (UAPs) with procedural noise functions. Our approach unveils the systemic vulnerability of popular DCN models like Inception v3 and YOLO v3, with single noise patterns able to fool a model on up to 90% of the dataset. Procedural noise allows us to generate a distribution of UAPs with high universal evasion rates using only a few parameters. Additionally, we propose Bayesian optimization to efficiently learn procedural noise parameters to construct inexpensive untargeted black-box attacks. We demonstrate that it can achieve an average of less than 10 queries per successful attack, a 100-fold improvement on existing methods. We further motivate the use of input-agnostic defences to increase the stability of models to adversarial perturbations. The universality of our attacks suggests that DCN models may be sensitive to aggregations of low-level class-agnostic features. These findings give insight on the nature of some universal adversarial perturbations and how they could be generated in other applications.
Bayesian optimization is an approach to optimizing objective functions that take a long time (minutes or hours) to evaluate. It is best-suited for optimization over continuous domains of less than 20 dimensions, and tolerates stochastic noise in function evaluations. It builds a surrogate for the objective and quantifies the uncertainty in that surrogate using a Bayesian machine learning technique, Gaussian process regression, and then uses an acquisition function defined from this surrogate to decide where to sample. In this tutorial, we describe how Bayesian optimization works, including Gaussian process regression and three common acquisition functions: expected improvement, entropy search, and knowledge gradient. We then discuss more advanced techniques, including running multiple function evaluations in parallel, multi-fidelity and multi-information source optimization, expensive-to-evaluate constraints, random environmental conditions, multi-task Bayesian optimization, and the inclusion of derivative information. We conclude with a discussion of Bayesian optimization software and future research directions in the field. Within our tutorial material we provide a generalization of expected improvement to noisy evaluations, beyond the noise-free setting where it is more commonly applied. This generalization is justified by a formal decision-theoretic argument, standing in contrast to previous ad hoc modifications.
Modern deep learning methods are very sensitive to many hyperparameters, and, due to the long training times of state-of-the-art models, vanilla Bayesian hyperparameter optimization is typically computationally infeasible. On the other hand, bandit-based configuration evaluation approaches based on random search lack guidance and do not converge to the best configurations as quickly. Here, we propose to combine the benefits of both Bayesian optimization and bandit-based methods, in order to achieve the best of both worlds: strong anytime performance and fast convergence to optimal configurations. We propose a new practical state-of-the-art hyperparameter optimization method, which consistently outperforms both Bayesian optimization and Hyperband on a wide range of problem types, including high-dimensional toy functions, support vector machines, feed-forward neural networks, Bayesian neural networks, deep reinforcement learning, and convolutional neural networks. Our method is robust and versatile, while at the same time being conceptually simple and easy to implement.
Bayesian optimization has emerged as a strong candidate tool for global optimization of functions with expensive evaluation costs. However, due to the dynamic nature of research in Bayesian approaches, and the evolution of computing technology, using Bayesian optimization in a parallel computing environment remains a challenge for the non-expert. In this report, I review the state-of-the-art in parallel and scalable Bayesian optimization methods. In addition, I propose practical ways to avoid a few of the pitfalls of Bayesian optimization, such as oversampling of edge parameters and over-exploitation of high performance parameters. Finally, I provide relatively simple, heuristic algorithms, along with their open source software implementations, that can be immediately and easily deployed in any computing environment.
The optimization of expensive-to-evaluate black-box functions over combinatorial structures is an ubiquitous task in machine learning, engineering and the natural sciences. The combinatorial explosion of the search space and costly evaluations pose challenges for current techniques in discrete optimization and machine learning, and critically require new algorithmic ideas. This article proposes, to the best of our knowledge, the first algorithm to overcome these challenges, based on an adaptive, scalable model that identifies useful combinatorial structure even when data is scarce. Our acquisition function pioneers the use of semidefinite programming to achieve efficiency and scalability. Experimental evaluations demonstrate that this algorithm consistently outperforms other methods from combinatorial and Bayesian optimization.
The Java implementation of a portfolio of parameter-less evolutionary algorithms is presented. The Parameter-less Evolutionary Portfolio implements a heuristic that performs adaptive selection of parameter-less evolutionary algorithms in accordance with performance criteria that are measured during running time. At present time, the portfolio includes three parameter-less evolutionary algorithms: Parameter-less Univariate Marginal Distribution Algorithm, Parameter-less Extended Compact Genetic Algorithm, and Parameter-less Hierarchical Bayesian Optimization Algorithm. Initial experiments showed that the parameter-less portfolio can solve various classes of problems without the need for any prior parameter setting technique and with an increase in computational effort that can be considered acceptable.
The Parameter-less Genetic Algorithm was first presented by Harik and Lobo in 1999 as an alternative to the usual trial-and-error method of finding, for each given problem, an acceptable set-up of the parameter values of the genetic algorithm. Since then, the same strategy has been successfully applied to create parameter-less versions of other population-based search algorithms such as the Extended Compact Genetic Algorithm and the Hierarchical Bayesian Optimization Algorithm. This report describes a Java implementation, Parameter-less Evolutionary Algorithm (P-EAJava), that integrates several parameter-less evolutionary algorithms into a single platform. Along with a brief description of P-EAJava, we also provide detailed instructions on how to use it, how to implement new problems, and how to generate new parameter-less versions of evolutionary algorithms. At present time, P-EAJava already includes parameter-less versions of the Simple Genetic Algorithm, the Extended Compact Genetic Algorithm, the Univariate Marginal Distribution Algorithm, and the Hierarchical Bayesian Optimization Algorithm. The source and binary files of the Java implementation of P-EAJava are available for free download at https://github.com/JoseCPereira/2015ParameterlessEvolutionaryAlgorithmsJava.
The Simple Genetic Algorithm, the Univariate Marginal Distribution Algorithm, the Extended Compact Genetic Algorithm, and the Hierarchical Bayesian Optimization Algorithm are all well known Evolutionary Algorithms. In this report we present a Java implementation of these four algorithms with detailed instructions on how to use each of them to solve a given set of optimization problems. Additionally, it is explained how to implement and integrate new problems within the provided set. The source and binary files of the Java implementations are available for free download at https://github.com/JoseCPereira/2015EvolutionaryAlgorithmsJava.
Bayesian optimization techniques have been successfully applied to robotics, planning, sensor placement, recommendation, advertising, intelligent user interfaces and automatic algorithm configuration. Despite these successes, the approach is restricted to problems of moderate dimension, and several workshops on Bayesian optimization have identified its scaling to high-dimensions as one of the holy grails of the field. In this paper, we introduce a novel random embedding idea to attack this problem. The resulting Random EMbedding Bayesian Optimization (REMBO) algorithm is very simple, has important invariance properties, and applies to domains with both categorical and continuous variables. We present a thorough theoretical analysis of REMBO. Empirical results confirm that REMBO can effectively solve problems with billions of dimensions, provided the intrinsic dimensionality is low. They also show that REMBO achieves state-of-the-art performance in optimizing the 47 discrete parameters of a popular mixed integer linear programming solver.