We present AutoOED, an Optimal Experiment Design platform powered with automated machine learning to accelerate the discovery of optimal solutions. The platform solves multi-objective optimization problems in time- and data-efficient manner by automatically guiding the design of experiments to be evaluated. To automate the optimization process, we implement several multi-objective Bayesian optimization algorithms with state-of-the-art performance. AutoOED is open-source and written in Python. The codebase is modular, facilitating extensions and tailoring the code, serving as a testbed for machine learning researchers to easily develop and evaluate their own multi-objective Bayesian optimization algorithms. An intuitive graphical user interface (GUI) is provided to visualize and guide the experiments for users with little or no experience with coding, machine learning, or optimization. Furthermore, a distributed system is integrated to enable parallelized experimental evaluations by independent workers in remote locations. The platform is available at https://autooed.org.
It is commonly believed that Bayesian optimization (BO) algorithms are highly efficient for optimizing numerically costly functions. However, BO is not often compared to widely different alternatives, and is mostly tested on narrow sets of problems (multimodal, low-dimensional functions), which makes it difficult to assess where (or if) they actually achieve state-of-the-art performance. Moreover, several aspects in the design of these algorithms vary across implementations without a clear recommendation emerging from current practices, and many of these design choices are not substantiated by authoritative test campaigns. This article reports a large investigation about the effects on the performance of (Gaussian process based) BO of common and less common design choices. The experiments are carried out with the established COCO (COmparing Continuous Optimizers) software. It is found that a small initial budget, a quadratic trend, high-quality optimization of the acquisition criterion bring consistent progress. Using the GP mean as an occasional acquisition contributes to a negligible additional improvement. Warping degrades performance. The Mat\'ern 5/2 kernel is a good default but it may be surpassed by the exponential kernel on irregular functions. Overall, the best EGO variants are competitive or improve over state-of-the-art algorithms in dimensions less or equal to 5 for multimodal functions. The code developed for this study makes the new version (v2.1.1) of the R package DiceOptim available on CRAN. The structure of the experiments by function groups allows to define priorities for future research on Bayesian optimization.
We consider the problem of chance constrained optimization where it is sought to optimize a function and satisfy constraints, both of which are affected by uncertainties. The real world declinations of this problem are particularly challenging because of their inherent computational cost. To tackle such problems, we propose a new Bayesian optimization method. It applies to the situation where the uncertainty comes from some of the inputs, so that it becomes possible to define an acquisition criterion in the joint controlled-uncontrolled input space. The main contribution of this work is an acquisition criterion that accounts for both the average improvement in objective function and the constraint reliability. The criterion is derived following the Stepwise Uncertainty Reduction logic and its maximization provides both optimal controlled and uncontrolled parameters. Analytical expressions are given to efficiently calculate the criterion. Numerical studies on test functions are presented. It is found through experimental comparisons with alternative sampling criteria that the adequation between the sampling criterion and the problem contributes to the efficiency of the overall optimization. As a side result, an expression for the variance of the improvement is given.
Bayesian optimization has emerged as a powerful strategy to accelerate scientific discovery by means of autonomous experimentation. However, expensive measurements are required to accurately estimate materials properties, and can quickly become a hindrance to exhaustive materials discovery campaigns. Here, we introduce Gemini: a data-driven model capable of using inexpensive measurements as proxies for expensive measurements by correcting systematic biases between property evaluation methods. We recommend using Gemini for regression tasks with sparse data and in an autonomous workflow setting where its predictions of expensive to evaluate objectives can be used to construct a more informative acquisition function, thus reducing the number of expensive evaluations an optimizer needs to achieve desired target values. In a regression setting, we showcase the ability of our method to make accurate predictions of DFT calculated bandgaps of hybrid organic-inorganic perovskite materials. We further demonstrate the benefits that Gemini provides to autonomous workflows by augmenting the Bayesian optimizer Phoenics to yeild a scalable optimization framework leveraging multiple sources of measurement. Finally, we simulate an autonomous materials discovery platform for optimizing the activity of electrocatalysts for the oxygen evolution reaction. Realizing autonomous workflows with Gemini, we show that the number of measurements of a composition space comprising expensive and rare metals needed to achieve a target overpotential is significantly reduced when measurements from a proxy composition system with less expensive metals are available.
Gaussian processes (GPs) provide a gold standard for performance in online settings, such as sample-efficient control and black box optimization, where we need to update a posterior distribution as we acquire data in a sequential fashion. However, updating a GP posterior to accommodate even a single new observation after having observed $n$ points incurs at least $O(n)$ computations in the exact setting. We show how to use structured kernel interpolation to efficiently recycle computations for constant-time $O(1)$ online updates with respect to the number of points $n$, while retaining exact inference. We demonstrate the promise of our approach in a range of online regression and classification settings, Bayesian optimization, and active sampling to reduce error in malaria incidence forecasting. Code is available at https://github.com/wjmaddox/online_gp.
Bayesian optimization (BO) is a powerful paradigm for efficient optimization of black-box objective functions. High-dimensional BO presents a particular challenge, in part because the curse of dimensionality makes it difficult to define -- as well as do inference over -- a suitable class of surrogate models. We argue that Gaussian process surrogate models defined on sparse axis-aligned subspaces offer an attractive compromise between flexibility and parsimony. We demonstrate that our approach, which relies on Hamiltonian Monte Carlo for inference, can rapidly identify sparse subspaces relevant to modeling the unknown objective function, enabling sample-efficient high-dimensional BO. In an extensive suite of experiments comparing to existing methods for high-dimensional BO we demonstrate that our algorithm, Sparse Axis-Aligned Subspace BO (SAASBO), achieves excellent performance on several synthetic and real-world problems without the need to set problem-specific hyperparameters.
In this work we propose a batch Bayesian optimization method for combinatorial problems on permutations, which is well suited for expensive-to-evaluate objectives. We first introduce LAW, an efficient batch acquisition method based on determinantal point processes using the acquisition weighted kernel. Relying on multiple parallel evaluations, LAW enables accelerated search on combinatorial spaces. We then apply the framework to permutation problems, which have so far received little attention in the Bayesian Optimization literature, despite their practical importance. We call this method LAW2ORDER. On the theoretical front, we prove that LAW2ORDER has vanishing simple regret by showing that the batch cumulative regret is sublinear. Empirically, we assess the method on several standard combinatorial problems involving permutations such as quadratic assignment, flowshop scheduling and the traveling salesman, as well as on a structure learning task.
We study methods for estimating model uncertainty for neural networks (NNs) in regression. To isolate the effect of model uncertainty, we focus on a noiseless setting with scarce training data. We introduce five important desiderata regarding model uncertainty that any method should satisfy. However, we find that established benchmarks often fail to reliably capture some of these desiderata, even those that are required by Bayesian theory. To address this, we introduce a new approach for capturing model uncertainty for NNs, which we call Neural Optimization-based Model Uncertainty (NOMU). The main idea of NOMU is to design a network architecture consisting of two connected sub-NNs, one for model prediction and one for model uncertainty, and to train it using a carefully-designed loss function. Importantly, our design enforces that NOMU satisfies our five desiderata. Due to its modular architecture, NOMU can provide model uncertainty for any given (previously trained) NN if given access to its training data. We evaluate NOMU in various regressions tasks and noiseless Bayesian optimization (BO) with costly evaluations. In regression, NOMU performs at least as well as state-of-the-art methods. In BO, NOMU even outperforms all considered benchmarks.
Efficient machine learning implementations optimized for inference in hardware have wide-ranging benefits, depending on the application, from lower inference latency to higher data throughput and reduced energy consumption. Two popular techniques for reducing computation in neural networks are pruning, removing insignificant synapses, and quantization, reducing the precision of the calculations. In this work, we explore the interplay between pruning and quantization during the training of neural networks for ultra low latency applications targeting high energy physics use cases. Techniques developed for this study have potential applications across many other domains. We study various configurations of pruning during quantization-aware training, which we term quantization-aware pruning, and the effect of techniques like regularization, batch normalization, and different pruning schemes on performance, computational complexity, and information content metrics. We find that quantization-aware pruning yields more computationally efficient models than either pruning or quantization alone for our task. Further, quantization-aware pruning typically performs similar to or better in terms of computational efficiency compared to other neural architecture search techniques like Bayesian optimization. Surprisingly, while networks with different training configurations can have similar performance for the benchmark application, the information content in the network can vary significantly, affecting its generalizability.
Obtaining an explanation for an SQL query result can enrich the analysis experience, reveal data errors, and provide deeper insight into the data. Inference query explanation seeks to explain unexpected aggregate query results on inference data; such queries are challenging to explain because an explanation may need to be derived from the source, training, or inference data in an ML pipeline. In this paper, we model an objective function as a black-box function and propose BOExplain, a novel framework for explaining inference queries using Bayesian optimization (BO). An explanation is a predicate defining the input tuples that should be removed so that the query result of interest is significantly affected. BO - a technique for finding the global optimum of a black-box function - is used to find the best predicate. We develop two new techniques (individual contribution encoding and warm start) to handle categorical variables. We perform experiments showing that the predicates found by BOExplain have a higher degree of explanation compared to those found by the state-of-the-art query explanation engines. We also show that BOExplain is effective at deriving explanations for inference queries from source and training data on a variety of real-world datasets. BOExplain is open-sourced as a Python package at https://github.com/sfu-db/BOExplain.
Optimization of problems with high computational power demands is a challenging task. A probabilistic approach to such optimization called Bayesian optimization lowers performance demands by solving mathematically simpler model of the problem. Selected approach, Gaussian Process, models problem using a mixture of Gaussian functions. This paper presents specific modifications of Gaussian Process optimization components from available scientific libraries. Presented modifications were submitted to BlackBox 2020 challenge, where it outperformed some conventionally available optimization libraries.
Bayesian optimization is a popular method for optimizing expensive black-box functions. Yet it oftentimes struggles in high dimensions where the computation could be prohibitively heavy. To alleviate this problem, we introduce Coordinate backoff Bayesian Optimization (CobBO) with two-stage kernels. During each round, the first stage uses a simple coarse kernel that sacrifices the approximation accuracy for computational efficiency. It captures the global landscape by purposely smoothing away local fluctuations. Then, in the second stage of the same round, past observed points in the full space are projected to the selected subspace to form virtual points. These virtual points, along with the means and variances of their unknown function values estimated using the simple kernel of the first stage, are fitted to a more sophisticated kernel model in the second stage. Within the selected low dimensional subspace, the computational cost of conducting Bayesian optimization therein becomes affordable. To further enhance the performance, a sequence of consecutive observations in the same subspace are collected, which can effectively refine the approximation of the function. This refinement lasts until a stopping rule is met determining when to back off from a certain subspace and switch to another. This decoupling significantly reduces the computational burden in high dimensions, which fully leverages the observations in the whole space rather than only relying on observations in each coordinate subspace. Extensive evaluations show that CobBO finds solutions comparable to or better than other state-of-the-art methods for dimensions ranging from tens to hundreds, while reducing both the trial complexity and computational costs.
The increasing availability of structured but high dimensional data has opened new opportunities for optimization. One emerging and promising avenue is the exploration of unsupervised methods for projecting structured high dimensional data into low dimensional continuous representations, simplifying the optimization problem and enabling the application of traditional optimization methods. However, this line of research has been purely methodological with little connection to the needs of practitioners so far. In this paper, we study the effect of different search space design choices for performing Bayesian Optimization in high dimensional structured datasets. In particular, we analyse the influence of the dimensionality of the latent space, the role of the acquisition function and evaluate new methods to automatically define the optimization bounds in the latent space. Finally, based on experimental results using synthetic and real datasets, we provide recommendations for the practitioners.
Bayesian Optimization (BO) has shown significant success in tackling expensive low-dimensional black-box optimization problems. Many optimization problems of interest are high-dimensional, and scaling BO to such settings remains an important challenge. In this paper, we consider generalized additive models in which low-dimensional functions with overlapping subsets of variables are composed to model a high-dimensional target function. Our goal is to lower the computational resources required and facilitate faster model learning by reducing the model complexity while retaining the sample-efficiency of existing methods. Specifically, we constrain the underlying dependency graphs to tree structures in order to facilitate both the structure learning and optimization of the acquisition function. For the former, we propose a hybrid graph learning algorithm based on Gibbs sampling and mutation. In addition, we propose a novel zooming-based algorithm that permits generalized additive models to be employed more efficiently in the case of continuous domains. We demonstrate and discuss the efficacy of our approach via a range of experiments on synthetic functions and real-world datasets.
This paper presents an information-theoretic framework for unifying active learning problems: level set estimation (LSE), Bayesian optimization (BO), and their generalized variant. We first introduce a novel active learning criterion that subsumes an existing LSE algorithm and achieves state-of-the-art performance in LSE problems with a continuous input domain. Then, by exploiting the relationship between LSE and BO, we design a competitive information-theoretic acquisition function for BO that has interesting connections to upper confidence bound and max-value entropy search (MES). The latter connection reveals a drawback of MES which has important implications on not only MES but also on other MES-based acquisition functions. Finally, our unifying information-theoretic framework can be applied to solve a generalized problem of LSE and BO involving multiple level sets in a data-efficient manner. We empirically evaluate the performance of our proposed algorithms using synthetic benchmark functions, a real-world dataset, and in hyperparameter tuning of machine learning models.
This paper presents a novel approach to top-$k$ ranking Bayesian optimization (top-$k$ ranking BO) which is a practical and significant generalization of preferential BO to handle top-$k$ ranking and tie/indifference observations. We first design a surrogate model that is not only capable of catering to the above observations, but is also supported by a classic random utility model. Another equally important contribution is the introduction of the first information-theoretic acquisition function in BO with preferential observation called multinomial predictive entropy search (MPES) which is flexible in handling these observations and optimized for all inputs of a query jointly. MPES possesses superior performance compared with existing acquisition functions that select the inputs of a query one at a time greedily. We empirically evaluate the performance of MPES using several synthetic benchmark functions, CIFAR-$10$ dataset, and SUSHI preference dataset.
Black-box optimization is one of the vital tasks in machine learning, since it approximates real-world conditions, in that we do not always know all the properties of a given system, up to knowing almost nothing but the results. This paper describes our approach to solving the black-box optimization challenge at NeurIPS 2020 through learning search space partition for local Bayesian optimization. We describe the task of the challenge as well as our algorithm for low budget optimization that we named \texttt{SPBOpt}. We optimize the hyper-parameters of our algorithm for the competition finals using multi-task Bayesian optimization on results from the first two evaluation settings. Our approach has ranked third in the competition finals.
In this report, we survey Bayesian Optimization methods focussed on the Multi-Armed Bandit Problem. We take the help of the paper "Portfolio Allocation for Bayesian Optimization". We report a small literature survey on the acquisition functions and the types of portfolio strategies used in papers discussing Bayesian Optimization. We also replicate the experiments and report our findings and compare them to the results in the paper. Code link: https://colab.research.google.com/drive/1GZ14klEDoe3dcBeZKo5l8qqrKf_GmBDn?usp=sharing#scrollTo=XgIBau3O45_V.
Structure-based virtual screening is an important tool in early stage drug discovery that scores the interactions between a target protein and candidate ligands. As virtual libraries continue to grow (in excess of $10^8$ molecules), so too do the resources necessary to conduct exhaustive virtual screening campaigns on these libraries. However, Bayesian optimization techniques can aid in their exploration: a surrogate structure-property relationship model trained on the predicted affinities of a subset of the library can be applied to the remaining library members, allowing the least promising compounds to be excluded from evaluation. In this study, we assess various surrogate model architectures, acquisition functions, and acquisition batch sizes as applied to several protein-ligand docking datasets and observe significant reductions in computational costs, even when using a greedy acquisition strategy; for example, 87.9% of the top-50000 ligands can be found after testing only 2.4% of a 100M member library. Such model-guided searches mitigate the increasing computational costs of screening increasingly large virtual libraries and can accelerate high-throughput virtual screening campaigns with applications beyond docking.
Hyperparameter optimization (HPO), formulated as black-box optimization (BBO), is recognized as essential for automation and high performance of machine learning approaches. The CMA-ES is a promising BBO approach with a high degree of parallelism, and has been applied to HPO tasks, often under parallel implementation, and shown superior performance to other approaches including Bayesian optimization (BO). However, if the budget of hyperparameter evaluations is severely limited, which is often the case for end users who do not deserve parallel computing, the CMA-ES exhausts the budget without improving the performance due to its long adaptation phase, resulting in being outperformed by BO approaches. To address this issue, we propose to transfer prior knowledge on similar HPO tasks through the initialization of the CMA-ES, leading to significantly shortening the adaptation time. The knowledge transfer is designed based on the novel definition of task similarity, with which the correlation of the performance of the proposed approach is confirmed on synthetic problems. The proposed warm starting CMA-ES, called WS-CMA-ES, is applied to different HPO tasks where some prior knowledge is available, showing its superior performance over the original CMA-ES as well as BO approaches with or without using the prior knowledge.