Bayesian optimization has emerged at the forefront of expensive black-box optimization due to its data efficiency. Recent years have witnessed a proliferation of studies on the development of new Bayesian optimization algorithms and their applications. Hence, this paper attempts to provide a comprehensive and updated survey of recent advances in Bayesian optimization and identify interesting open problems. We categorize the existing work on Bayesian optimization into nine main groups according to the motivations and focus of the proposed algorithms. For each category, we present the main advances with respect to the construction of surrogate models and adaptation of the acquisition functions. Finally, we discuss the open questions and suggest promising future research directions, in particular with regard to heterogeneity, privacy preservation, and fairness in distributed and federated optimization systems.
With the ever increasing complexity of specifications, manual sizing for analog circuits recently became very challenging. Especially for innovative, large-scale circuits designs, with tens of design variables, operating conditions and conflicting objectives to be optimized, design engineers spend many weeks, running time-consuming simulations, in their attempt at finding the right configuration. Recent years brought machine learning and optimization techniques to the field of analog circuits design, with evolutionary algorithms and Bayesian models showing good results for circuit sizing. In this context, we introduce a design optimization method based on Generalized Differential Evolution 3 (GDE3) and Gaussian Processes (GPs). The proposed method is able to perform sizing for complex circuits with a large number of design variables and many conflicting objectives to be optimized. While state-of-the-art methods reduce multi-objective problems to single-objective optimization and potentially induce a prior bias, we search directly over the multi-objective space using Pareto dominance and ensure that diverse solutions are provided to the designers to choose from. To the best of our knowledge, the proposed method is the first to specifically address the diversity of the solutions, while also focusing on minimizing the number of simulations required to reach feasible configurations. We evaluate the introduced method on two voltage regulators showing different levels of complexity and we highlight that the proposed innovative candidate selection method and survival policy leads to obtaining feasible solutions, with a high degree of diversity, much faster than with GDE3 or Bayesian Optimization-based algorithms.
The tuning of hyperparameters becomes increasingly important as machine learning (ML) models have been extensively applied in data mining applications. Among various approaches, Bayesian optimization (BO) is a successful methodology to tune hyper-parameters automatically. While traditional methods optimize each tuning task in isolation, there has been recent interest in speeding up BO by transferring knowledge across previous tasks. In this work, we introduce an automatic method to design the BO search space with the aid of tuning history from past tasks. This simple yet effective approach can be used to endow many existing BO methods with transfer learning capabilities. In addition, it enjoys the three advantages: universality, generality, and safeness. The extensive experiments show that our approach considerably boosts BO by designing a promising and compact search space instead of using the entire space, and outperforms the state-of-the-arts on a wide range of benchmarks, including machine learning and deep learning tuning tasks, and neural architecture search.
This paper presents a new type of hybrid model for Bayesian optimization (BO) adept at managing mixed variables, encompassing both quantitative (continuous and integer) and qualitative (categorical) types. Our proposed new hybrid models (named hybridM) merge the Monte Carlo Tree Search structure (MCTS) for categorical variables with Gaussian Processes (GP) for continuous ones. hybridM leverages the upper confidence bound tree search (UCTS) for MCTS strategy, showcasing the tree architecture's integration into Bayesian optimization. Our innovations, including dynamic online kernel selection in the surrogate modeling phase and a unique UCTS search strategy, position our hybrid models as an advancement in mixed-variable surrogate models. Numerical experiments underscore the superiority of hybrid models, highlighting their potential in Bayesian optimization.
Fuels with high-knock resistance enable modern spark-ignition engines to achieve high efficiency and thus low CO2 emissions. Identification of molecules with desired autoignition properties indicated by a high research octane number and a high octane sensitivity is therefore of great practical relevance and can be supported by computer-aided molecular design (CAMD). Recent developments in the field of graph machine learning (graph-ML) provide novel, promising tools for CAMD. We propose a modular graph-ML CAMD framework that integrates generative graph-ML models with graph neural networks and optimization, enabling the design of molecules with desired ignition properties in a continuous molecular space. In particular, we explore the potential of Bayesian optimization and genetic algorithms in combination with generative graph-ML models. The graph-ML CAMD framework successfully identifies well-established high-octane components. It also suggests new candidates, one of which we experimentally investigate and use to illustrate the need for further auto-ignition training data.
The performance of a guidance, navigation and control (GNC) system of an autonomous underwater vehicle (AUV) heavily depends on the correct tuning of its parameters. Our objective is to automatically tune these parameters with respect to arbitrary high-level control objectives within different operational scenarios. In contrast to literature, an overall tuning is performed for the entire GNC system, which is new in the context of autonomous underwater vehicles. The main challenges in solving the optimization problem are computationally expensive objective function evaluations, crashing simulations due to infeasible parametrization and the numerous tunable parameters (in our case 13). These challenges are met by using constrained Bayesian optimization with crash constraints. The method is demonstrated in simulation on a GNC system of an underactuated miniature AUV designed within the TRIPLE-nanoAUV initiative for exploration of sub-glacial lakes. We quantify the substantial reduction in energy consumption achieved by tuning the overall system. Furthermore, different parametrizations are automatically generated for different power consumption functions, robustness, and accuracy requirements. E.g. energy consumption can be reduced by ~28%, if the maximum allowed deviation from the planned path is increased by ~65%. This shows the versatile practical applicability of the optimization-based tuning approach.
Modern advanced manufacturing and advanced materials design often require searches of relatively high-dimensional process control parameter spaces for settings that result in optimal structure, property, and performance parameters. The mapping from the former to the latter must be determined from noisy experiments or from expensive simulations. We abstract this problem to a mathematical framework in which an unknown function from a control space to a design space must be ascertained by means of expensive noisy measurements, which locate optimal control settings generating desired design features within specified tolerances, with quantified uncertainty. We describe targeted adaptive design (TAD), a new algorithm that performs this sampling task efficiently. TAD creates a Gaussian process surrogate model of the unknown mapping at each iterative stage, proposing a new batch of control settings to sample experimentally and optimizing the updated log-predictive likelihood of the target design. TAD either stops upon locating a solution with uncertainties that fit inside the tolerance box or uses a measure of expected future information to determine that the search space has been exhausted with no solution. TAD thus embodies the exploration-exploitation tension in a manner that recalls, but is essentially different from, Bayesian optimization and optimal experimental design.
Bayesian optimization (BO) has well-documented merits for optimizing black-box functions with an expensive evaluation cost. Such functions emerge in applications as diverse as hyperparameter tuning, drug discovery, and robotics. BO hinges on a Bayesian surrogate model to sequentially select query points so as to balance exploration with exploitation of the search space. Most existing works rely on a single Gaussian process (GP) based surrogate model, where the kernel function form is typically preselected using domain knowledge. To bypass such a design process, this paper leverages an ensemble (E) of GPs to adaptively select the surrogate model fit on-the-fly, yielding a GP mixture posterior with enhanced expressiveness for the sought function. Acquisition of the next evaluation input using this EGP-based function posterior is then enabled by Thompson sampling (TS) that requires no additional design parameters. To endow function sampling with scalability, random feature-based kernel approximation is leveraged per GP model. The novel EGP-TS readily accommodates parallel operation. To further establish convergence of the proposed EGP-TS to the global optimum, analysis is conducted based on the notion of Bayesian regret for both sequential and parallel settings. Tests on synthetic functions and real-world applications showcase the merits of the proposed method.
Transfer learning is a promising approach to creating predictive models that incorporate simulation and experimental data into a common framework. In this technique, a neural network is first trained on a large database of simulations, then partially retrained on sparse sets of experimental data to adjust predictions to be more consistent with reality. Previously, this technique has been used to create predictive models of Omega and NIF inertial confinement fusion (ICF) experiments that are more accurate than simulations alone. In this work, we conduct a transfer learning driven hypothetical ICF campaign in which the goal is to maximize experimental neutron yield via Bayesian optimization. The transfer learning model achieves yields within 5% of the maximum achievable yield in a modest-sized design space in fewer than 20 experiments. Furthermore, we demonstrate that this method is more efficient at optimizing designs than traditional model calibration techniques commonly employed in ICF design. Such an approach to ICF design could enable robust optimization of experimental performance under uncertainty.
We propose a framework for the configuration and operation of expensive-to-evaluate advanced manufacturing methods, based on Bayesian optimization. The framework unifies a tailored acquisition function, a parallel acquisition procedure, and the integration of process information providing context to the optimization procedure. \cmtb{The novel acquisition function is demonstrated, analyzed and compared on state-of-the-art benchmarking problems. We apply the optimization approach to atmospheric plasma spraying and fused deposition modeling.} Our results demonstrate that the proposed framework can efficiently find input parameters that produce the desired outcome and minimize the process cost.
Directed evolution is a versatile technique in protein engineering that mimics the process of natural selection by iteratively alternating between mutagenesis and screening in order to search for sequences that optimize a given property of interest, such as catalytic activity and binding affinity to a specified target. However, the space of possible proteins is too large to search exhaustively in the laboratory, and functional proteins are scarce in the vast sequence space. Machine learning (ML) approaches can accelerate directed evolution by learning to map protein sequences to functions without building a detailed model of the underlying physics, chemistry and biological pathways. Despite the great potentials held by these ML methods, they encounter severe challenges in identifying the most suitable sequences for a targeted function. These failures can be attributed to the common practice of adopting a high-dimensional feature representation for protein sequences and inefficient search methods. To address these issues, we propose an efficient, experimental design-oriented closed-loop optimization framework for protein directed evolution, termed ODBO, which employs a combination of novel low-dimensional protein encoding strategy and Bayesian optimization enhanced with search space prescreening via outlier detection. We further design an initial sample selection strategy to minimize the number of experimental samples for training ML models. We conduct and report four protein directed evolution experiments that substantiate the capability of the proposed framework for finding of the variants with properties of interest. We expect the ODBO framework to greatly reduce the experimental cost and time cost of directed evolution, and can be further generalized as a powerful tool for adaptive experimental design in a broader context.
There is a consensus that focusing only on accuracy in searching for optimal machine learning models amplifies biases contained in the data, leading to unfair predictions and decision supports. Recently, multi-objective hyperparameter optimization has been proposed to search for machine learning models which offer equally Pareto-efficient trade-offs between accuracy and fairness. Although these approaches proved to be more versatile than fairness-aware machine learning algorithms -- which optimize accuracy constrained to some threshold on fairness -- they could drastically increase the energy consumption in the case of large datasets. In this paper we propose FanG-HPO, a Fair and Green Hyperparameter Optimization (HPO) approach based on both multi-objective and multiple information source Bayesian optimization. FanG-HPO uses subsets of the large dataset (aka information sources) to obtain cheap approximations of both accuracy and fairness, and multi-objective Bayesian Optimization to efficiently identify Pareto-efficient machine learning models. Experiments consider two benchmark (fairness) datasets and two machine learning algorithms (XGBoost and Multi-Layer Perceptron), and provide an assessment of FanG-HPO against both fairness-aware machine learning algorithms and hyperparameter optimization via a multi-objective single-source optimization algorithm in BoTorch, a state-of-the-art platform for Bayesian Optimization.
Since the deep learning model is highly dependent on hyperparameters, hyperparameter optimization is essential in developing deep learning model-based applications, even if it takes a long time. As service development using deep learning models has gradually become competitive, many developers highly demand rapid hyperparameter optimization algorithms. In order to keep pace with the needs of faster hyperparameter optimization algorithms, researchers are focusing on improving the speed of hyperparameter optimization algorithm. However, the huge time consumption of hyperparameter optimization due to the high computational cost of the deep learning model itself has not been dealt with in-depth. Like using surrogate model in Bayesian optimization, to solve this problem, it is necessary to consider proxy model for a neural network (N_B) to be used for hyperparameter optimization. Inspired by the main goal of neural network pruning, i.e., high computational cost reduction and performance preservation, we presumed that the neural network (N_P) obtained through neural network pruning would be a good proxy model of N_B. In order to verify our idea, we performed extensive experiments by using CIFAR10, CFIAR100, and TinyImageNet datasets and three generally-used neural networks and three representative hyperparameter optmization methods. Through these experiments, we verified that N_P can be a good proxy model of N_B for rapid hyperparameter optimization. The proposed hyperparameter optimization framework can reduce the amount of time up to 37%.
Motivated by applications to online learning in sparse estimation and Bayesian optimization, we consider the problem of online unconstrained nonsubmodular minimization with delayed costs in both full information and bandit feedback settings. In contrast to previous works on online unconstrained submodular minimization, we focus on a class of nonsubmodular functions with special structure, and prove regret guarantees for several variants of the online and approximate online bandit gradient descent algorithms in static and delayed scenarios. We derive bounds for the agent's regret in the full information and bandit feedback setting, even if the delay between choosing a decision and receiving the incurred cost is unbounded. Key to our approach is the notion of $(\alpha, \beta)$-regret and the extension of the generic convex relaxation model from~\citet{El-2020-Optimal}, the analysis of which is of independent interest. We conduct and showcase several simulation studies to demonstrate the efficacy of our algorithms.
Bayesian optimization (BO) has been widely used in machine learning and simulation optimization. With the increase in computational resources and storage capacities in these fields, high-dimensional and large-scale problems are becoming increasingly common. In this study, we propose a model aggregation method in the Bayesian optimization (MamBO) algorithm for efficiently solving high-dimensional large-scale optimization problems. MamBO uses a combination of subsampling and subspace embeddings to collectively address high dimensionality and large-scale issues; in addition, a model aggregation method is employed to address the surrogate model uncertainty issue that arises when embedding is applied. This surrogate model uncertainty issue is largely ignored in the embedding literature and practice, and it is exacerbated when the problem is high-dimensional and data are limited. Our proposed model aggregation method reduces these lower-dimensional surrogate model risks and improves the robustness of the BO algorithm. We derive an asymptotic bound for the proposed aggregated surrogate model and prove the convergence of MamBO. Benchmark numerical experiments indicate that our algorithm achieves superior or comparable performance to other commonly used high-dimensional BO algorithms. Moreover, we apply MamBO to a cascade classifier of a machine learning algorithm for face detection, and the results reveal that MamBO finds settings that achieve higher classification accuracy than the benchmark settings and is computationally faster than other high-dimensional BO algorithms.
We consider physics-informed neural networks (PINNs) [Raissi et al., J.~Comput. Phys. 278 (2019) 686-707] for forward physical problems. In order to find optimal PINNs configuration, we introduce a hyper-parameter optimization (HPO) procedure via Gaussian processes-based Bayesian optimization. We apply the HPO to Helmholtz equation for bounded domains and conduct a thorough study, focusing on: (i) performance, (ii) the collocation points density $r$ and (iii) the frequency $\kappa$, confirming the applicability and necessity of the method. Numerical experiments are performed in two and three dimensions, including comparison to finite element methods.
Recent years have witnessed tremendously improved efficiency of Automated Machine Learning (AutoML), especially Automated Deep Learning (AutoDL) systems, but recent work focuses on tabular, image, or NLP tasks. So far, little attention has been paid to general AutoDL frameworks for time series forecasting, despite the enormous success in applying different novel architectures to such tasks. In this paper, we propose an efficient approach for the joint optimization of neural architecture and hyperparameters of the entire data processing pipeline for time series forecasting. In contrast to common NAS search spaces, we designed a novel neural architecture search space covering various state-of-the-art architectures, allowing for an efficient macro-search over different DL approaches. To efficiently search in such a large configuration space, we use Bayesian optimization with multi-fidelity optimization. We empirically study several different budget types enabling efficient multi-fidelity optimization on different forecasting datasets. Furthermore, we compared our resulting system, dubbed \system, against several established baselines and show that it significantly outperforms all of them across several datasets.
Hypervolume improvement (HVI) is commonly employed in multi-objective Bayesian optimization algorithms to define acquisition functions due to its Pareto-compliant property. Rather than focusing on specific statistical moments of HVI, this work aims to provide the exact expression of HVI's probability distribution for bi-objective problems. Considering a bi-variate Gaussian random variable resulting from Gaussian process (GP) modeling, we derive the probability distribution of its hypervolume improvement via a cell partition-based method. Our exact expression is superior in numerical accuracy and computation efficiency compared to the Monte Carlo approximation of HVI's distribution. Utilizing this distribution, we propose a novel acquisition function - $\varepsilon$-probability of hypervolume improvement ($\varepsilon$-PoHVI). Experimentally, we show that on many widely-applied bi-objective test problems, $\varepsilon$-PoHVI significantly outperforms other related acquisition functions, e.g., $\varepsilon$-PoI, and expected hypervolume improvement, when the GP model exhibits a large the prediction uncertainty.
The expected improvement (EI) is one of the most popular acquisition functions for Bayesian optimization (BO) and has demonstrated good empirical performances in many applications for the minimization of simple regret. However, under the evaluation metric of cumulative regret, the performance of EI may not be competitive, and its existing theoretical regret upper bound still has room for improvement. To adapt the EI for better performance under cumulative regret, we introduce a novel quantity called the evaluation cost which is compared against the acquisition function, and with this, develop the expected improvement-cost (EIC) algorithm. In each iteration of EIC, a new point with the largest acquisition function value is sampled, only if that value exceeds its evaluation cost. If none meets this criteria, the current best point is resampled. This evaluation cost quantifies the potential downside of sampling a point, which is important under the cumulative regret metric as the objective function value in every iteration affects the performance measure. We establish in theory a high-probability regret upper bound of EIC based on the maximum information gain, which is tighter than the bound of existing EI-based algorithms. It is also comparable to the regret bound of other popular BO algorithms such as Thompson sampling (GP-TS) and upper confidence bound (GP-UCB). We further perform experiments to illustrate the improvement of EIC over several popular BO algorithms.
Many scientific and technological problems are related to optimization. Among them, black-box optimization in high-dimensional space is particularly challenging. Recent neural network-based black-box optimization studies have shown noteworthy achievements. However, their capability in high-dimensional search space is still limited. This study proposes a black-box optimization method based on the evolution strategy (ES) and the generative neural network (GNN) model. We designed the algorithm so that the ES and the GNN model work cooperatively. This hybrid model enables reliable training of surrogate networks; it optimizes multi-objective, high-dimensional, and stochastic black-box functions. Our method outperforms baseline optimization methods in this experiment, including ES, and Bayesian optimization.