In this paper, we describe our method for tackling the automated hyperparameter optimization challenge in QQ Browser 2021 AI Algorithm Competiton (ACM CIKM 2021 AnalyticCup Track 2). The competition organizers provide anonymized realistic industrial tasks and datasets for black-box optimization. Based on our open-sourced package OpenBox, we adopt the Bayesian optimization framework for configuration sampling and a heuristic early stopping strategy. We won first place in both the preliminary and final contests with the results of 0.938291 and 0.918753, respectively.
Decision making in uncertain scenarios is an ubiquitous challenge in real world systems. Tools to deal with this challenge include simulations to gather information and statistical emulation to quantify uncertainty. The machine learning community has developed a number of methods to facilitate decision making, but so far they are scattered in multiple different toolkits, and generally rely on a fixed backend. In this paper, we present Emukit, a highly adaptable Python toolkit for enriching decision making under uncertainty. Emukit allows users to: (i) use state of the art methods including Bayesian optimization, multi-fidelity emulation, experimental design, Bayesian quadrature and sensitivity analysis; (ii) easily prototype new decision making methods for new problems. Emukit is agnostic to the underlying modeling framework and enables users to use their own custom models. We show how Emukit can be used on three exemplary case studies.
This paper studies the problem of performing a sequence of optimal interventions in a causal dynamical system where both the target variable of interest and the inputs evolve over time. This problem arises in a variety of domains e.g. system biology and operational research. Dynamic Causal Bayesian Optimization (DCBO) brings together ideas from sequential decision making, causal inference and Gaussian process (GP) emulation. DCBO is useful in scenarios where all causal effects in a graph are changing over time. At every time step DCBO identifies a local optimal intervention by integrating both observational and past interventional data collected from the system. We give theoretical results detailing how one can transfer interventional information across time steps and define a dynamic causal GP model which can be used to quantify uncertainty and find optimal interventions in practice. We demonstrate how DCBO identifies optimal interventions faster than competing approaches in multiple settings and applications.
We consider the problem of black-box multi-objective optimization (MOO) using expensive function evaluations (also referred to as experiments), where the goal is to approximate the true Pareto set of solutions by minimizing the total resource cost of experiments. For example, in hardware design optimization, we need to find the designs that trade-off performance, energy, and area overhead using expensive computational simulations. The key challenge is to select the sequence of experiments to uncover high-quality solutions using minimal resources. In this paper, we propose a general framework for solving MOO problems based on the principle of output space entropy (OSE) search: select the experiment that maximizes the information gained per unit resource cost about the true Pareto front. We appropriately instantiate the principle of OSE search to derive efficient algorithms for the following four MOO problem settings: 1) The most basic em single-fidelity setting, where experiments are expensive and accurate; 2) Handling em black-box constraints} which cannot be evaluated without performing experiments; 3) The discrete multi-fidelity setting, where experiments can vary in the amount of resources consumed and their evaluation accuracy; and 4) The em continuous-fidelity setting, where continuous function approximations result in a huge space of experiments. Experiments on diverse synthetic and real-world benchmarks show that our OSE search based algorithms improve over state-of-the-art methods in terms of both computational-efficiency and accuracy of MOO solutions.
We propose a surrogate-assisted reference vector adaptation (SRVA) method to solve expensive multi- and many-objective optimization problems with various Pareto front shapes. SRVA is coupled with a multi-objective Bayesian optimization (MBO) algorithm using reference vectors for scalarization of objective functions. The Kriging surrogate models for MBO is used to estimate the Pareto front shape and generate adaptive reference vectors uniformly distributed on the estimated Pareto front. We combine SRVA with expected improvement of penalty-based boundary intersection as an infill criterion for MBO. The proposed algorithm is compared with two other MBO algorithms by applying them to benchmark problems with various Pareto front shapes. Experimental results show that the proposed algorithm outperforms the other two in the problems whose objective functions are reasonably approximated by the Kriging models. SRVA improves diversity of non-dominated solutions for these problems with continuous, discontinuous, and degenerated Pareto fronts. Besides, the proposed algorithm obtains much better solutions from early stages of optimization especially in many-objective problems.
Perovskite photovoltaics (PV) have achieved rapid development in the past decade in terms of power conversion efficiency of small-area lab-scale devices; however, successful commercialization still requires further development of low-cost, scalable, and high-throughput manufacturing techniques. One of the critical challenges of developing a new fabrication technique is the high-dimensional parameter space for optimization, but machine learning (ML) can readily be used to accelerate perovskite PV scaling. Herein, we present an ML-guided framework of sequential learning for manufacturing process optimization. We apply our methodology to the Rapid Spray Plasma Processing (RSPP) technique for perovskite thin films in ambient conditions. With a limited experimental budget of screening 100 process conditions, we demonstrated an efficiency improvement to 18.5% as the best-in-our-lab device fabricated by RSPP, and we also experimentally found 10 unique process conditions to produce the top-performing devices of more than 17% efficiency, which is 5 times higher rate of success than the control experiments with pseudo-random Latin hypercube sampling. Our model is enabled by three innovations: (a) flexible knowledge transfer between experimental processes by incorporating data from prior experimental data as a probabilistic constraint; (b) incorporation of both subjective human observations and ML insights when selecting next experiments; (c) adaptive strategy of locating the region of interest using Bayesian optimization first, and then conducting local exploration for high-efficiency devices. Furthermore, in virtual benchmarking, our framework achieves faster improvements with limited experimental budgets than traditional design-of-experiments methods (e.g., one-variable-at-a-time sampling).
Recently, there is great interest to investigate the application of deep learning models for the prediction of clinical events using electronic health records (EHR) data. In EHR data, a patient's history is often represented as a sequence of visits, and each visit contains multiple events. As a result, deep learning models developed for sequence modeling, like recurrent neural networks (RNNs) are common architecture for EHR-based clinical events predictive models. While a large variety of RNN models were proposed in the literature, it is unclear if complex architecture innovations will offer superior predictive performance. In order to move this field forward, a rigorous evaluation of various methods is needed. In this study, we conducted a thorough benchmark of RNN architectures in modeling EHR data. We used two prediction tasks: the risk for developing heart failure and the risk of early readmission for inpatient hospitalization. We found that simple gated RNN models, including GRUs and LSTMs, often offer competitive results when properly tuned with Bayesian Optimization, which is in line with similar to findings in the natural language processing (NLP) domain. For reproducibility, Our codebase is shared at https://github.com/ZhiGroup/pytorch_ehr.
Pruning is an effective technique for convolutional neural networks (CNNs) model compression, but it is difficult to find the optimal pruning policy due to the large design space. To improve the usability of pruning, many auto pruning methods have been developed. Recently, Bayesian optimization (BO) has been considered to be a competitive algorithm for auto pruning due to its solid theoretical foundation and high sampling efficiency. However, BO suffers from the curse of dimensionality. The performance of BO deteriorates when pruning deep CNNs, since the dimension of the design spaces increase. We propose a novel clustering algorithm that reduces the dimension of the design space to speed up the searching process. Subsequently, a rollback algorithm is proposed to recover the high-dimensional design space so that higher pruning accuracy can be obtained. We validate our proposed method on ResNet, MobileNetV1, and MobileNetV2 models. Experiments show that the proposed method significantly improves the convergence rate of BO when pruning deep CNNs with no increase in running time. The source code is available at https://github.com/fanhanwei/BOCR.
Algorithm parameters, in particular hyperparameters of machine learning algorithms, can substantially impact their performance. To support users in determining well-performing hyperparameter configurations for their algorithms, datasets and applications at hand, SMAC3 offers a robust and flexible framework for Bayesian Optimization, which can improve performance within a few evaluations. It offers several facades and pre-sets for typical use cases, such as optimizing hyperparameters, solving low dimensional continuous (artificial) global optimization problems and configuring algorithms to perform well across multiple problem instances. The SMAC3 package is available under a permissive BSD-license at https://github.com/automl/SMAC3.
Bayesian Optimization (BO) is a method for globally optimizing black-box functions. While BO has been successfully applied to many scenarios, developing effective BO algorithms that scale to functions with high-dimensional domains is still a challenge. Optimizing such functions by vanilla BO is extremely time-consuming. Alternative strategies for high-dimensional BO that are based on the idea of embedding the high-dimensional space to the one with low dimension are sensitive to the choice of the embedding dimension, which needs to be pre-specified. We develop a new computationally efficient high-dimensional BO method that exploits variable selection. Our method is able to automatically learn axis-aligned sub-spaces, i.e. spaces containing selected variables, without the demand of any pre-specified hyperparameters. We theoretically analyze the computational complexity of our algorithm and derive the regret bound. We empirically show the efficacy of our method on several synthetic and real problems.
Bayesian optimization (BO) has become a popular strategy for global optimization of expensive real-world functions. Contrary to a common expectation that BO is suited to optimizing black-box functions, it actually requires domain knowledge about those functions to deploy BO successfully. Such domain knowledge often manifests in Gaussian process (GP) priors that specify initial beliefs on functions. However, even with expert knowledge, it is non-trivial to quantitatively define a prior. This is especially true for hyperparameter tuning problems on complex machine learning models, where landscapes of tuning objectives are often difficult to comprehend. We seek an alternative practice for setting these functional priors. In particular, we consider the scenario where we have data from similar functions that allow us to pre-train a tighter distribution a priori. We detail what pre-training entails for GPs using a KL divergence based loss function, and propose a new pre-training based BO framework named HyperBO. Theoretically, we show bounded posterior predictions and near-zero regrets for HyperBO without assuming the "ground truth" GP prior is known. To verify our approach in realistic setups, we collect a large multi-task hyperparameter tuning dataset by training tens of thousands of configurations of near-state-of-the-art deep learning models on popular image and text datasets, as well as a protein sequence dataset. Our results show that on average, HyperBO is able to locate good hyperparameters at least 3 times more efficiently than the best competing methods on both our new tuning dataset and existing multi-task BO benchmarks.
Building surrogate models is one common approach when we attempt to learn unknown black-box functions. Bayesian optimization provides a framework which allows us to build surrogate models based on sequential samples drawn from the function and find the optimum. Tuning algorithmic parameters to optimize the performance of large, complicated "black-box" application codes is a specific important application, which aims at finding the optima of black-box functions. Within the Bayesian optimization framework, the Gaussian process model produces smooth or continuous sample paths. However, the black-box function in the tuning problem is often non-smooth. This difficult tuning problem is worsened by the fact that we usually have limited sequential samples from the black-box function. Motivated by these issues encountered in tuning, we propose a novel additive Gaussian process model called clustered Gaussian process (cGP), where the additive components are induced by clustering. In the examples we studied, the performance can be improved by as much as 90% among repetitive experiments. By using this surrogate model, we want to capture the non-smoothness of the black-box function. In addition to an algorithm for constructing this model, we also apply the model to several artificial and real applications to evaluate it.
This paper considers the open challenge of identifying complete, concise, and explainable quantitative microstructure representations for disordered heterogeneous material systems. Completeness and conciseness have been achieved through existing data-driven methods, e.g., deep generative models, which, however, do not provide mathematically explainable latent representations. This study investigates representations composed of three-point correlation functions, which are a special type of spatial convolutions. We show that a variety of microstructures can be characterized by a concise subset of three-point correlations, and the identification of such subsets can be achieved by Bayesian optimization. Lastly, we show that the proposed representation can directly be used to compute material properties based on the effective medium theory.
Data augmentation aims to enrich training samples for alleviating the overfitting issue in low-resource or class-imbalanced situations. Traditional methods first devise task-specific operations such as Synonym Substitute, then preset the corresponding parameters such as the substitution rate artificially, which require a lot of prior knowledge and are prone to fall into the sub-optimum. Besides, the number of editing operations is limited in the previous methods, which decreases the diversity of the augmented data and thus restricts the performance gain. To overcome the above limitations, we propose a framework named Text AutoAugment (TAA) to establish a compositional and learnable paradigm for data augmentation. We regard a combination of various operations as an augmentation policy and utilize an efficient Bayesian Optimization algorithm to automatically search for the best policy, which substantially improves the generalization capability of models. Experiments on six benchmark datasets show that TAA boosts classification accuracy in low-resource and class-imbalanced regimes by an average of 8.8% and 9.7%, respectively, outperforming strong baselines.
There is a wave of interest in using unsupervised neural networks for solving differential equations. The existing methods are based on feed-forward networks, {while} recurrent neural network differential equation solvers have not yet been reported. We introduce an unsupervised reservoir computing (RC), an echo-state recurrent neural network capable of discovering approximate solutions that satisfy ordinary differential equations (ODEs). We suggest an approach to calculate time derivatives of recurrent neural network outputs without using backpropagation. The internal weights of an RC are fixed, while only a linear output layer is trained, yielding efficient training. However, RC performance strongly depends on finding the optimal hyper-parameters, which is a computationally expensive process. We use Bayesian optimization to efficiently discover optimal sets in a high-dimensional hyper-parameter space and numerically show that one set is robust and can be used to solve an ODE for different initial conditions and time ranges. A closed-form formula for the optimal output weights is derived to solve first order linear equations in a backpropagation-free learning process. We extend the RC approach by solving nonlinear system of ODEs using a hybrid optimization method consisting of gradient descent and Bayesian optimization. Evaluation of linear and nonlinear systems of equations demonstrates the efficiency of the RC ODE solver.
In this paper, we propose an approach to address the problems with ambiguity in tuning the process and observation noises for a discrete-time linear Kalman filter. Conventional approaches to tuning (e.g. using normalized estimation error squared and covariance minimization) compute empirical measures of filter performance and the parameter are selected manually or selected using some kind of optimization algorithm to maximize these measures of performance. However, there are two challenges with this approach. First, in theory, many of these measures do not guarantee a unique solution due to observability issues. Second, in practice, empirically computed statistical quantities can be very noisy due to a finite number of samples. We propose a method to overcome these limitations. Our method has two main parts to it. The first is to ensure that the tuning problem has a single unique solution. We achieve this by simultaneously tuning the filter over multiple different prediction intervals. Although this yields a unique solution, practical issues (such as sampling noise) mean that it cannot be directly applied. Therefore, we use Bayesian Optimization. This technique handles noisy data and the local minima that it introduces.
Predicting clinical outcomes from medical images using quantitative features (``radiomics'') requires many method design choices, Currently, in new clinical applications, finding the optimal radiomics method out of the wide range of methods relies on a manual, heuristic trial-and-error process. We introduce a novel automated framework that optimizes radiomics workflow construction per application by standardizing the radiomics workflow in modular components, including a large collection of algorithms for each component, and formulating a combined algorithm selection and hyperparameter optimization problem. To solve it, we employ automated machine learning through two strategies (random search and Bayesian optimization) and three ensembling approaches. Results show that a medium-sized random search and straight-forward ensembling perform similar to more advanced methods while being more efficient. Validated across twelve clinical applications, our approach outperforms both a radiomics baseline and human experts. Concluding, our framework improves and streamlines radiomics research by fully automatically optimizing radiomics workflow construction. To facilitate reproducibility, we publicly release six datasets, software of the method, and code to reproduce this study.
Information-based Bayesian optimization (BO) algorithms have achieved state-of-the-art performance in optimizing a black-box objective function. However, they usually require several approximations or simplifying assumptions (without clearly understanding their effects on the BO performance) and/or their generalization to batch BO is computationally unwieldy, especially with an increasing batch size. To alleviate these issues, this paper presents a novel trusted-maximizers entropy search (TES) acquisition function: It measures how much an input query contributes to the information gain on the maximizer over a finite set of trusted maximizers, i.e., inputs optimizing functions that are sampled from the Gaussian process posterior belief of the objective function. Evaluating TES requires either only a stochastic approximation with sampling or a deterministic approximation with expectation propagation, both of which are investigated and empirically evaluated using synthetic benchmark objective functions and real-world optimization problems, e.g., hyperparameter tuning of a convolutional neural network and synthesizing 'physically realizable' faces to fool a black-box face recognition system. Though TES can naturally be generalized to a batch variant with either approximation, the latter is amenable to be scaled to a much larger batch size in our experiments.
A solution that is only reliable under favourable conditions is hardly a safe solution. Min Max Optimization is an approach that returns optima that are robust against worst case conditions. We propose algorithms that perform Min Max Optimization in a setting where the function that should be optimized is not known a priori and hence has to be learned by experiments. Therefore we extend the Bayesian Optimization setting, which is tailored to maximization problems, to Min Max Optimization problems. While related work extends the two acquisition functions Expected Improvement and Gaussian Process Upper Confidence Bound; we extend the two acquisition functions Entropy Search and Knowledge Gradient. These acquisition functions are able to gain knowledge about the optimum instead of just looking for points that are supposed to be optimal. In our evaluation we show that these acquisition functions allow for better solutions - converging faster to the optimum than the benchmark settings.
Bayesian optimization (BO) is an approach to globally optimizing black-box objective functions that are expensive to evaluate. BO-powered experimental design has found wide application in materials science, chemistry, experimental physics, drug development, etc. This work aims to bring attention to the benefits of applying BO in designing experiments and to provide a BO manual, covering both methodology and software, for the convenience of anyone who wants to apply or learn BO. In particular, we briefly explain the BO technique, review all the applications of BO in additive manufacturing, compare and exemplify the features of different open BO libraries, unlock new potential applications of BO to other types of data (e.g., preferential output). This article is aimed at readers with some understanding of Bayesian methods, but not necessarily with knowledge of additive manufacturing; the software performance overview and implementation instructions are instrumental for any experimental-design practitioner. Moreover, our review in the field of additive manufacturing highlights the current knowledge and technological trends of BO. This article has a supplementary material online.