Bayesian optimization (BO) is a popular approach for optimizing expensive-to-evaluate black-box objective functions. An important challenge in BO is its application to high-dimensional search spaces due in large part to the curse of dimensionality. One way to overcome this challenge is to focus on local BO methods that aim to efficiently learn gradients, which have shown strong empirical performance on a variety of high-dimensional problems including policy search in reinforcement learning (RL). However, current local BO methods assume access to only a single high-fidelity information source whereas, in many engineering and control problems, one has access to multiple cheaper approximations of the objective. We propose a novel algorithm, Cost-Aware Gradient Entropy Search (CAGES), for local BO of multi-fidelity black-box functions. CAGES makes no assumption about the relationship between different information sources, making it more flexible than other multi-fidelity methods. It also employs a new type of information-theoretic acquisition function, which enables systematic identification of samples that maximize the information gain about the unknown gradient per cost of the evaluation. We demonstrate CAGES can achieve significant performance improvements compared to other state-of-the-art methods on a variety of synthetic and benchmark RL problems.
We introduce a Bayesian optimization approach to guide the sputter deposition of molybdenum thin films, aiming to achieve desired residual stress and sheet resistance while minimizing susceptibility to stochastic fluctuations during deposition. Thin films are pivotal in numerous technologies, including semiconductors and optical devices, where their properties are critical. Sputter deposition parameters, such as deposition power, vacuum chamber pressure, and working distance, influence physical properties like residual stress and resistance. Excessive stress and high resistance can impair device performance, necessitating the selection of optimal process parameters. Furthermore, these parameters should ensure the consistency and reliability of thin film properties, assisting in the reproducibility of the devices. However, exploring the multidimensional design space for process optimization is expensive. Bayesian optimization is ideal for optimizing inputs/parameters of general black-box functions without reliance on gradient information. We utilize Bayesian optimization to optimize deposition power and pressure using a custom-built objective function incorporating observed stress and resistance data. Additionally, we integrate prior knowledge of stress variation with pressure into the objective function to prioritize films least affected by stochastic variations. Our findings demonstrate that Bayesian optimization effectively explores the design space and identifies optimal parameter combinations meeting desired stress and resistance specifications.
Experimental design techniques such as active search and Bayesian optimization are widely used in the natural sciences for data collection and discovery. However, existing techniques tend to favor exploitation over exploration of the search space, which causes them to get stuck in local optima. This ``collapse" problem prevents experimental design algorithms from yielding diverse high-quality data. In this paper, we extend the Vendi scores -- a family of interpretable similarity-based diversity metrics -- to account for quality. We then leverage these quality-weighted Vendi scores to tackle experimental design problems across various applications, including drug discovery, materials discovery, and reinforcement learning. We found that quality-weighted Vendi scores allow us to construct policies for experimental design that flexibly balance quality and diversity, and ultimately assemble rich and diverse sets of high-performing data points. Our algorithms led to a 70%-170% increase in the number of effective discoveries compared to baselines.
State-of-the-art automated machine learning systems for tabular data often employ cross-validation; ensuring that measured performances generalize to unseen data, or that subsequent ensembling does not overfit. However, using k-fold cross-validation instead of holdout validation drastically increases the computational cost of validating a single configuration. While ensuring better generalization and, by extension, better performance, the additional cost is often prohibitive for effective model selection within a time budget. We aim to make model selection with cross-validation more effective. Therefore, we study early stopping the process of cross-validation during model selection. We investigate the impact of early stopping on random search for two algorithms, MLP and random forest, across 36 classification datasets. We further analyze the impact of the number of folds by considering 3-, 5-, and 10-folds. In addition, we investigate the impact of early stopping with Bayesian optimization instead of random search and also repeated cross-validation. Our exploratory study shows that even a simple-to-understand and easy-to-implement method consistently allows model selection to converge faster; in ~94% of all datasets, on average by ~214%. Moreover, stopping cross-validation enables model selection to explore the search space more exhaustively by considering +167% configurations on average within one hour, while also obtaining better overall performance.
Field experiments and computer simulations are effective but time-consuming methods of measuring the quality of engineered systems at different settings. To reduce the total time required, experimenters may employ Bayesian optimization, which is parsimonious with measurements, and take measurements of multiple settings simultaneously, in a batch. In practice, experimenters use very few batches, thus, it is imperative that each batch be as informative as possible. Typically, the initial batch in a Batch Bayesian Optimization (BBO) is constructed from a quasi-random sample of settings values. We propose a batch-design acquisition function, Minimal Terminal Variance (MTV), that designs a batch by optimization rather than random sampling. MTV adapts a design criterion function from Design of Experiments, called I-Optimality, which minimizes the variance of the post-evaluation estimates of quality, integrated over the entire space of settings. MTV weights the integral by the probability that a setting is optimal, making it able to design not only an initial batch but all subsequent batches, as well. Applicability to both initialization and subsequent batches is novel among acquisition functions. Numerical experiments on test functions and simulators show that MTV compares favorably to other BBO methods.
To optimize efficiently over discrete data and with only few available target observations is a challenge in Bayesian optimization. We propose a continuous relaxation of the objective function and show that inference and optimization can be computationally tractable. We consider in particular the optimization domain where very few observations and strict budgets exist; motivated by optimizing protein sequences for expensive to evaluate bio-chemical properties. The advantages of our approach are two-fold: the problem is treated in the continuous setting, and available prior knowledge over sequences can be incorporated directly. More specifically, we utilize available and learned distributions over the problem domain for a weighting of the Hellinger distance which yields a covariance function. We show that the resulting acquisition function can be optimized with both continuous or discrete optimization algorithms and empirically assess our method on two bio-chemical sequence optimization tasks.
Many real-world optimization scenarios involve expensive evaluation with unknown and heterogeneous costs. Cost-aware Bayesian optimization stands out as a prominent solution in addressing these challenges. To approach the global optimum within a limited budget in a cost-efficient manner, the design of cost-aware acquisition functions (AFs) becomes a crucial step. However, traditional manual design paradigm typically requires extensive domain knowledge and involves a labor-intensive trial-and-error process. This paper introduces EvolCAF, a novel framework that integrates large language models (LLMs) with evolutionary computation (EC) to automatically design cost-aware AFs. Leveraging the crossover and mutation in the algorithmic space, EvolCAF offers a novel design paradigm, significantly reduces the reliance on domain expertise and model training. The designed cost-aware AF maximizes the utilization of available information from historical data, surrogate models and budget details. It introduces novel ideas not previously explored in the existing literature on acquisition function design, allowing for clear interpretations to provide insights into its behavior and decision-making process. In comparison to the well-known EIpu and EI-cool methods designed by human experts, our approach showcases remarkable efficiency and generalization across various tasks, including 12 synthetic problems and 3 real-world hyperparameter tuning test sets.
With the increasing computational costs associated with deep learning, automated hyperparameter optimization methods, strongly relying on black-box Bayesian optimization (BO), face limitations. Freeze-thaw BO offers a promising grey-box alternative, strategically allocating scarce resources incrementally to different configurations. However, the frequent surrogate model updates inherent to this approach pose challenges for existing methods, requiring retraining or fine-tuning their neural network surrogates online, introducing overhead, instability, and hyper-hyperparameters. In this work, we propose FT-PFN, a novel surrogate for Freeze-thaw style BO. FT-PFN is a prior-data fitted network (PFN) that leverages the transformers' in-context learning ability to efficiently and reliably do Bayesian learning curve extrapolation in a single forward pass. Our empirical analysis across three benchmark suites shows that the predictions made by FT-PFN are more accurate and 10-100 times faster than those of the deep Gaussian process and deep ensemble surrogates used in previous work. Furthermore, we show that, when combined with our novel acquisition mechanism (MFPI-random), the resulting in-context freeze-thaw BO method (ifBO), yields new state-of-the-art performance in the same three families of deep learning HPO benchmarks considered in prior work.
There has been significant recent interest in the mechanics community to design structures that can either violate reciprocity, or exhibit elastic asymmetry or odd elasticity. While these properties are highly desirable to enable mechanical metamaterials to exhibit novel wave propagation phenomena, it remains an open question as to how to design passive structures that exhibit both significant non-reciprocity and elastic asymmetry. In this paper, we first define several design spaces for chiral metamaterials leveraging specific design parameters, including the ligament contact angles, the ligament shape, and circle radius. Having defined the design spaces, we then leverage machine learning approaches, and specifically Bayesian optimization, to determine optimally performing designs within each design space satisfying maximal non-reciprocity or stiffness asymmetry. Finally, we perform multi-objective optimization by determining the Pareto optimum and find chiral metamaterials that simultaneously exhibit high non-reciprocity and stiffness asymmetry. Our analysis of the underlying mechanisms reveals that chiral metamaterials that can display multiple different contact states under loading in different directions are able to simultaneously exhibit both high non-reciprocity and stiffness asymmetry. Overall, this work demonstrates the effectiveness of employing ML to bring insights to a novel domain with limited prior information, and more generally will pave the way for metamaterials with unique properties and functionality in directing and guiding mechanical wave energy.
The rise of electron microscopy has expanded our ability to acquire nanometer and atomically resolved images of complex materials. The resulting vast datasets are typically analyzed by human operators, an intrinsically challenging process due to the multiple possible analysis steps and the corresponding need to build and optimize complex analysis workflows. We present a methodology based on the concept of a Reward Function coupled with Bayesian Optimization, to optimize image analysis workflows dynamically. The Reward Function is engineered to closely align with the experimental objectives and broader context and is quantifiable upon completion of the analysis. Here, cross-section, high-angle annular dark field (HAADF) images of ion-irradiated $(Y, Dy)Ba_2Cu_3O_{7-\delta}$ thin-films were used as a model system. The reward functions were formed based on the expected materials density and atomic spacings and used to drive multi-objective optimization of the classical Laplacian-of-Gaussian (LoG) method. These results can be benchmarked against the DCNN segmentation. This optimized LoG* compares favorably against DCNN in the presence of the additional noise. We further extend the reward function approach towards the identification of partially-disordered regions, creating a physics-driven reward function and action space of high-dimensional clustering. We pose that with correct definition, the reward function approach allows real-time optimization of complex analysis workflows at much higher speeds and lower computational costs than classical DCNN-based inference, ensuring the attainment of results that are both precise and aligned with the human-defined objectives.
High-performance catalysts are crucial for sustainable energy conversion and human health. However, the discovery of catalysts faces challenges due to the absence of efficient approaches to navigating vast and high-dimensional structure and composition spaces. In this study, we propose a high-throughput computational catalyst screening approach integrating density functional theory (DFT) and Bayesian Optimization (BO). Within the BO framework, we propose an uncertainty-aware atomistic machine learning model, UPNet, which enables automated representation learning directly from high-dimensional catalyst structures and achieves principled uncertainty quantification. Utilizing a constrained expected improvement acquisition function, our BO framework simultaneously considers multiple evaluation criteria. Using the proposed methods, we explore catalyst discovery for the CO2 reduction reaction. The results demonstrate that our approach achieves high prediction accuracy, facilitates interpretable feature extraction, and enables multicriteria design optimization, leading to significant reduction of computing power and time (10x reduction of required DFT calculations) in high-performance catalyst discovery.
Parallelisation in Bayesian optimisation is a common strategy but faces several challenges: the need for flexibility in acquisition functions and kernel choices, flexibility dealing with discrete and continuous variables simultaneously, model misspecification, and lastly fast massive parallelisation. To address these challenges, we introduce a versatile and modular framework for batch Bayesian optimisation via probabilistic lifting with kernel quadrature, called SOBER, which we present as a Python library based on GPyTorch/BoTorch. Our framework offers the following unique benefits: (1) Versatility in downstream tasks under a unified approach. (2) A gradient-free sampler, which does not require the gradient of acquisition functions, offering domain-agnostic sampling (e.g., discrete and mixed variables, non-Euclidean space). (3) Flexibility in domain prior distribution. (4) Adaptive batch size (autonomous determination of the optimal batch size). (5) Robustness against a misspecified reproducing kernel Hilbert space. (6) Natural stopping criterion.
Bayesian optimization (BO) algorithm is very popular for solving low-dimensional expensive optimization problems. Extending Bayesian optimization to high dimension is a meaningful but challenging task. One of the major challenges is that it is difficult to find good infill solutions as the acquisition functions are also high-dimensional. In this work, we propose the expected coordinate improvement (ECI) criterion for high-dimensional Bayesian optimization. The proposed ECI criterion measures the potential improvement we can get by moving the current best solution along one coordinate. The proposed approach selects the coordinate with the highest ECI value to refine in each iteration and covers all the coordinates gradually by iterating over the coordinates. The greatest advantage of the proposed ECI-BO (expected coordinate improvement based Bayesian optimization) algorithm over the standard BO algorithm is that the infill selection problem of the proposed algorithm is always a one-dimensional problem thus can be easily solved. Numerical experiments show that the proposed algorithm can achieve significantly better results than the standard BO algorithm and competitive results when compared with five state-of-the-art high-dimensional BOs. This work provides a simple but efficient approach for high-dimensional Bayesian optimization.
Bayesian optimization has been successfully applied throughout Chemical Engineering for the optimization of functions that are expensive-to-evaluate, or where gradients are not easily obtainable. However, domain experts often possess valuable physical insights that are overlooked in fully automated decision-making approaches, necessitating the inclusion of human input. In this article we re-introduce the human back into the data-driven decision making loop by outlining an approach for collaborative Bayesian optimization. Our methodology exploits the hypothesis that humans are more efficient at making discrete choices rather than continuous ones and enables experts to influence critical early decisions. We apply high-throughput (batch) Bayesian optimization alongside discrete decision theory to enable domain experts to influence the selection of experiments. At every iteration we apply a multi-objective approach that results in a set of alternate solutions that have both high utility and are reasonably distinct. The expert then selects the desired solution for evaluation from this set, allowing for the inclusion of expert knowledge and improving accountability, whilst maintaining the advantages of Bayesian optimization. We demonstrate our approach across a number of applied and numerical case studies including bioprocess optimization and reactor geometry design, demonstrating that even in the case of an uninformed practitioner our algorithm recovers the regret of standard Bayesian optimization. Through the inclusion of continuous expert opinion, our approach enables faster convergence, and improved accountability for Bayesian optimization in engineering systems.
Vector data management systems (VDMSs) have become an indispensable cornerstone in large-scale information retrieval and machine learning systems like large language models. To enhance the efficiency and flexibility of similarity search, VDMS exposes many tunable index parameters and system parameters for users to specify. However, due to the inherent characteristics of VDMS, automatic performance tuning for VDMS faces several critical challenges, which cannot be well addressed by the existing auto-tuning methods. In this paper, we introduce VDTuner, a learning-based automatic performance tuning framework for VDMS, leveraging multi-objective Bayesian optimization. VDTuner overcomes the challenges associated with VDMS by efficiently exploring a complex multi-dimensional parameter space without requiring any prior knowledge. Moreover, it is able to achieve a good balance between search speed and recall rate, delivering an optimal configuration. Extensive evaluations demonstrate that VDTuner can markedly improve VDMS performance (14.12% in search speed and 186.38% in recall rate) compared with default setting, and is more efficient compared with state-of-the-art baselines (up to 3.57 times faster in terms of tuning time). In addition, VDTuner is scalable to specific user preference and cost-aware optimization objective. VDTuner is available online at https://github.com/tiannuo-yang/VDTuner.
AutoMPC is a Python package that automates and optimizes data-driven model predictive control. However, it can be computationally expensive and unstable when exploring large search spaces using pure Bayesian Optimization (BO). To address these issues, this paper proposes to employ a meta-learning approach called Portfolio that improves AutoMPC's efficiency and stability by warmstarting BO. Portfolio optimizes initial designs for BO using a diverse set of configurations from previous tasks and stabilizes the tuning process by fixing initial configurations instead of selecting them randomly. Experimental results demonstrate that Portfolio outperforms the pure BO in finding desirable solutions for AutoMPC within limited computational resources on 11 nonlinear control simulation benchmarks and 1 physical underwater soft robot dataset.
Influence maximization (IM) is the problem of identifying a limited number of initial influential users within a social network to maximize the number of influenced users. However, previous research has mostly focused on individual information propagation, neglecting the simultaneous and interactive dissemination of multiple information items. In reality, when users encounter a piece of information, such as a smartphone product, they often associate it with related products in their minds, such as earphones or computers from the same brand. Additionally, information platforms frequently recommend related content to users, amplifying this cascading effect and leading to multiplex influence diffusion. This paper first formulates the Multiplex Influence Maximization (Multi-IM) problem using multiplex diffusion models with an information association mechanism. In this problem, the seed set is a combination of influential users and information. To effectively manage the combinatorial complexity, we propose Graph Bayesian Optimization for Multi-IM (GBIM). The multiplex diffusion process is thoroughly investigated using a highly effective global kernelized attention message-passing module. This module, in conjunction with Bayesian linear regression (BLR), produces a scalable surrogate model. A data acquisition module incorporating the exploration-exploitation trade-off is developed to optimize the seed set further. Extensive experiments on synthetic and real-world datasets have proven our proposed framework effective. The code is available at https://github.com/zirui-yuan/GBIM.
Due to the significance of its various applications, source localization has garnered considerable attention as one of the most important means to confront diffusion hazards. Multi-source localization from a single-snapshot observation is especially relevant due to its prevalence. However, the inherent complexities of this problem, such as limited information, interactions among sources, and dependence on diffusion models, pose challenges to resolution. Current methods typically utilize heuristics and greedy selection, and they are usually bonded with one diffusion model. Consequently, their effectiveness is constrained. To address these limitations, we propose a simulation-based method termed BOSouL. Bayesian optimization (BO) is adopted to approximate the results for its sample efficiency. A surrogate function models uncertainty from the limited information. It takes sets of nodes as the input instead of individual nodes. BOSouL can incorporate any diffusion model in the data acquisition process through simulations. Empirical studies demonstrate that its performance is robust across graph structures and diffusion models. The code is available at https://github.com/XGraph-Team/BOSouL.
Turning pass-through network architectures into iterative ones, which use their own output as input, is a well-known approach for boosting performance. In this paper, we argue that such architectures offer an additional benefit: The convergence rate of their successive outputs is highly correlated with the accuracy of the value to which they converge. Thus, we can use the convergence rate as a useful proxy for uncertainty. This results in an approach to uncertainty estimation that provides state-of-the-art estimates at a much lower computational cost than techniques like Ensembles, and without requiring any modifications to the original iterative model. We demonstrate its practical value by embedding it in two application domains: road detection in aerial images and the estimation of aerodynamic properties of 2D and 3D shapes.
Black-box optimization problems, which are common in many real-world applications, require optimization through input-output interactions without access to internal workings. This often leads to significant computational resources being consumed for simulations. Bayesian Optimization (BO) and Surrogate-Assisted Evolutionary Algorithm (SAEA) are two widely used gradient-free optimization techniques employed to address such challenges. Both approaches follow a similar iterative procedure that relies on surrogate models to guide the search process. This paper aims to elucidate the similarities and differences in the utilization of model uncertainty between these two methods, as well as the impact of model inaccuracies on algorithmic performance. A novel model-assisted strategy is introduced, which utilizes unevaluated solutions to generate offspring, leveraging the population-based search capabilities of evolutionary algorithm to enhance the effectiveness of model-assisted optimization. Experimental results demonstrate that the proposed approach outperforms mainstream Bayesian optimization algorithms in terms of accuracy and efficiency.