The practical use of Bayesian Optimization (BO) in engineering applications imposes special requirements: high sampling efficiency on the one hand and finding a robust solution on the other hand. We address the case of adversarial robustness, where all parameters are controllable during the optimization process, but a subset of them is uncontrollable or even adversely perturbed at the time of application. To this end, we develop an efficient information-based acquisition function that we call Robust Entropy Search (RES). We empirically demonstrate its benefits in experiments on synthetic and real-life data. The results showthat RES reliably finds robust optima, outperforming state-of-the-art algorithms.
This paper studies the challenging black-box adversarial attack that aims to generate adversarial examples against a black-box model by only using output feedback of the model to input queries. Some previous methods improve the query efficiency by incorporating the gradient of a surrogate white-box model into query-based attacks due to the adversarial transferability. However, the localized gradient is not informative enough, making these methods still query-intensive. In this paper, we propose a Prior-guided Bayesian Optimization (P-BO) algorithm that leverages the surrogate model as a global function prior in black-box adversarial attacks. As the surrogate model contains rich prior information of the black-box one, P-BO models the attack objective with a Gaussian process whose mean function is initialized as the surrogate model's loss. Our theoretical analysis on the regret bound indicates that the performance of P-BO may be affected by a bad prior. Therefore, we further propose an adaptive integration strategy to automatically adjust a coefficient on the function prior by minimizing the regret bound. Extensive experiments on image classifiers and large vision-language models demonstrate the superiority of the proposed algorithm in reducing queries and improving attack success rates compared with the state-of-the-art black-box attacks. Code is available at https://github.com/yibo-miao/PBO-Attack.
Generative modeling of crystal structures is significantly challenged by the complexity of input data, which constrains the ability of these models to explore and discover novel crystals. This complexity often confines de novo design methodologies to merely small perturbations of known crystals and hampers the effective application of advanced optimization techniques. One such optimization technique, Latent Space Bayesian Optimization (LSBO) has demonstrated promising results in uncovering novel objects across various domains, especially when combined with Variational Autoencoders (VAEs). Recognizing LSBO's potential and the critical need for innovative crystal discovery, we introduce Crystal-LSBO, a de novo design framework for crystals specifically tailored to enhance explorability within LSBO frameworks. Crystal-LSBO employs multiple VAEs, each dedicated to a distinct aspect of crystal structure: lattice, coordinates, and chemical elements, orchestrated by an integrative model that synthesizes these components into a cohesive output. This setup not only streamlines the learning process but also produces explorable latent spaces thanks to the decreased complexity of the learning task for each model, enabling LSBO approaches to operate. Our study pioneers the use of LSBO for de novo crystal design, demonstrating its efficacy through optimization tasks focused mainly on formation energy values. Our results highlight the effectiveness of our methodology, offering a new perspective for de novo crystal discovery.
This work addresses data-driven inverse optimization (IO), where the goal is to estimate unknown parameters in an optimization model from observed decisions that can be assumed to be optimal or near-optimal solutions to the optimization problem. The IO problem is commonly formulated as a large-scale bilevel program that is notoriously difficult to solve. Deviating from traditional exact solution methods, we propose a derivative-free optimization approach based on Bayesian optimization, which we call BO4IO, to solve general IO problems. We treat the IO loss function as a black box and approximate it with a Gaussian process model. Using the predicted posterior function, an acquisition function is minimized at each iteration to query new candidate solutions and sequentially converge to the optimal parameter estimates. The main advantages of using Bayesian optimization for IO are two-fold: (i) it circumvents the need of complex reformulations of the bilevel program or specialized algorithms and can hence enable computational tractability even when the underlying optimization problem is nonconvex or involves discrete variables, and (ii) it allows approximations of the profile likelihood, which provide uncertainty quantification on the IO parameter estimates. We apply the proposed method to three computational case studies, covering different classes of forward optimization problems ranging from convex nonlinear to nonconvex mixed-integer nonlinear programs. Our extensive computational results demonstrate the efficacy and robustness of BO4IO to accurately estimate unknown model parameters from small and noisy datasets. In addition, the proposed profile likelihood analysis has proven to be effective in providing good approximations of the confidence intervals on the parameter estimates and assessing the identifiability of the unknown parameters.
Agents based on large language models have shown great potential in accelerating scientific discovery by leveraging their rich background knowledge and reasoning capabilities. In this paper, we introduce BioDiscoveryAgent, an agent that designs new experiments, reasons about their outcomes, and efficiently navigates the hypothesis space to reach desired solutions. We demonstrate our agent on the problem of designing genetic perturbation experiments, where the aim is to find a small subset out of many possible genes that, when perturbed, result in a specific phenotype (e.g., cell growth). Utilizing its biological knowledge, BioDiscoveryAgent can uniquely design new experiments without the need to train a machine learning model or explicitly design an acquisition function as in Bayesian optimization. Moreover, BioDiscoveryAgent, using Claude 3.5 Sonnet, achieves an average of 21% improvement in predicting relevant genetic perturbations across six datasets, and a 46% improvement in the harder task of non-essential gene perturbation, compared to existing Bayesian optimization baselines specifically trained for this task. Our evaluation includes one dataset that is unpublished, ensuring it is not part of the language model's training data. Additionally, BioDiscoveryAgent predicts gene combinations to perturb more than twice as accurately as a random baseline, a task so far not explored in the context of closed-loop experiment design. The agent also has access to tools for searching the biomedical literature, executing code to analyze biological datasets, and prompting another agent to critically evaluate its predictions. Overall, BioDiscoveryAgent is interpretable at every stage, representing an accessible new paradigm in the computational design of biological experiments with the potential to augment scientists' efficacy.
In this paper, we address the problem of cost-sensitive multi-fidelity Bayesian Optimization (BO) for efficient hyperparameter optimization (HPO). Specifically, we assume a scenario where users want to early-stop the BO when the performance improvement is not satisfactory with respect to the required computational cost. Motivated by this scenario, we introduce utility, which is a function predefined by each user and describes the trade-off between cost and performance of BO. This utility function, combined with our novel acquisition function and stopping criterion, allows us to dynamically choose for each BO step the best configuration that we expect to maximally improve the utility in future, and also automatically stop the BO around the maximum utility. Further, we improve the sample efficiency of existing learning curve (LC) extrapolation methods with transfer learning, while successfully capturing the correlations between different configurations to develop a sensible surrogate function for multi-fidelity BO. We validate our algorithm on various LC datasets and found it outperform all the previous multi-fidelity BO and transfer-BO baselines we consider, achieving significantly better trade-off between cost and performance of BO.
Training machine learning models inherently involves a resource-intensive and noisy iterative learning procedure that allows epoch-wise monitoring of the model performance. However, the insights gained from the iterative learning procedure typically remain underutilized in multi-objective hyperparameter optimization scenarios. Despite the limited research in this area, existing methods commonly identify the trade-offs only at the end of model training, overlooking the fact that trade-offs can emerge at earlier epochs in cases such as overfitting. To bridge this gap, we propose an enhanced multi-objective hyperparameter optimization problem that treats the number of training epochs as a decision variable, rather than merely an auxiliary parameter, to account for trade-offs at an earlier training stage. To solve this problem and accommodate its iterative learning, we then present a trajectory-based multi-objective Bayesian optimization algorithm characterized by two features: 1) a novel acquisition function that captures the improvement along the predictive trajectory of model performances over epochs for any hyperparameter setting and 2) a multi-objective early stopping mechanism that determines when to terminate the training to maximize epoch efficiency. Experiments on synthetic simulations and hyperparameter tuning benchmarks demonstrate that our algorithm can effectively identify the desirable trade-offs while improving tuning efficiency.
Local Bayesian optimization is a promising practical approach to solve the high dimensional black-box function optimization problem. Among them is the approximated gradient class of methods, which implements a strategy similar to gradient descent. These methods have achieved good experimental results and theoretical guarantees. However, given the distributional properties of the Gaussian processes applied on these methods, there may be potential to further exploit the information of the Gaussian processes to facilitate the BO search. In this work, we develop the relationship between the steps of the gradient descent method and one that minimizes the Upper Confidence Bound (UCB), and show that the latter can be a better strategy than direct gradient descent when a Gaussian process is applied as a surrogate. Through this insight, we propose a new local Bayesian optimization algorithm, MinUCB, which replaces the gradient descent step with minimizing UCB in GIBO. We further show that MinUCB maintains a similar convergence rate with GIBO. We then improve the acquisition function of MinUCB further through a look ahead strategy, and obtain a more efficient algorithm LA-MinUCB. We apply our algorithms on different synthetic and real-world functions, and the results show the effectiveness of our method. Our algorithms also illustrate improvements on local search strategies from an upper bound perspective in Bayesian optimization, and provides a new direction for future algorithm design.
We address the problem of optimizing over functions defined on node subsets in a graph. The optimization of such functions is often a non-trivial task given their combinatorial, black-box and expensive-to-evaluate nature. Although various algorithms have been introduced in the literature, most are either task-specific or computationally inefficient and only utilize information about the graph structure without considering the characteristics of the function. To address these limitations, we utilize Bayesian Optimization (BO), a sample-efficient black-box solver, and propose a novel framework for combinatorial optimization on graphs. More specifically, we map each $k$-node subset in the original graph to a node in a new combinatorial graph and adopt a local modeling approach to efficiently traverse the latter graph by progressively sampling its subgraphs using a recursive algorithm. Extensive experiments under both synthetic and real-world setups demonstrate the effectiveness of the proposed BO framework on various types of graphs and optimization tasks, where its behavior is analyzed in detail with ablation studies.
This paper investigates the potential of Bayesian optimization (BO) to optimize the atr multiplier and atr period -the parameters of the Supertrend indicator for maximizing trading profits across diverse stock datasets. By employing BO, the thesis aims to automate the identification of optimal parameter settings, leading to a more data-driven and potentially more profitable trading strategy compared to relying on manually chosen parameters. The effectiveness of the BO-optimized Supertrend strategy will be evaluated through backtesting on a variety of stock datasets.
Preferential Bayesian optimization (PBO) is a sample-efficient framework for learning human preferences between candidate designs. PBO classically relies on homoscedastic noise models to represent human aleatoric uncertainty. Yet, such noise fails to accurately capture the varying levels of human aleatoric uncertainty, particularly when the user possesses partial knowledge among different pairs of candidates. For instance, a chemist with solid expertise in glucose-related molecules may easily compare two compounds from that family while struggling to compare alcohol-related molecules. Currently, PBO overlooks this uncertainty during the search for a new candidate through the maximization of the acquisition function, consequently underestimating the risk associated with human uncertainty. To address this issue, we propose a heteroscedastic noise model to capture human aleatoric uncertainty. This model adaptively assigns noise levels based on the distance of a specific input to a predefined set of reliable inputs known as anchors provided by the human. Anchors encapsulate partial knowledge and offer insight into the comparative difficulty of evaluating different candidate pairs. Such a model can be seamlessly integrated into the acquisition function, thus leading to candidate design pairs that elegantly trade informativeness and ease of comparison for the human expert. We perform an extensive empirical evaluation of the proposed approach, demonstrating a consistent improvement over homoscedastic PBO.
Bayesian Optimization (BO) has proven to be very successful at optimizing a static, noisy, costly-to-evaluate black-box function $f : \mathcal{S} \to \mathbb{R}$. However, optimizing a black-box which is also a function of time (i.e., a dynamic function) $f : \mathcal{S} \times \mathcal{T} \to \mathbb{R}$ remains a challenge, since a dynamic Bayesian Optimization (DBO) algorithm has to keep track of the optimum over time. This changes the nature of the optimization problem in at least three aspects: (i) querying an arbitrary point in $\mathcal{S} \times \mathcal{T}$ is impossible, (ii) past observations become less and less relevant for keeping track of the optimum as time goes by and (iii) the DBO algorithm must have a high sampling frequency so it can collect enough relevant observations to keep track of the optimum through time. In this paper, we design a Wasserstein distance-based criterion able to quantify the relevancy of an observation with respect to future predictions. Then, we leverage this criterion to build W-DBO, a DBO algorithm able to remove irrelevant observations from its dataset on the fly, thus maintaining simultaneously a good predictive performance and a high sampling frequency, even in continuous-time optimization tasks with unknown horizon. Numerical experiments establish the superiority of W-DBO, which outperforms state-of-the-art methods by a comfortable margin.
The integration of cyber-physical systems (CPS) into everyday life raises the critical necessity of ensuring their safety and reliability. An important step in this direction is requirement mining, i.e. inferring formally specified system properties from observed behaviors, in order to discover knowledge about the system. Signal Temporal Logic (STL) offers a concise yet expressive language for specifying requirements, particularly suited for CPS, where behaviors are typically represented as time series data. This work addresses the task of learning STL requirements from observed behaviors in a data-driven manner, focusing on binary classification, i.e. on inferring properties of the system which are able to discriminate between regular and anomalous behaviour, and that can be used both as classifiers and as monitors of the compliance of the CPS to desirable specifications. We present a novel framework that combines Bayesian Optimization (BO) and Information Retrieval (IR) techniques to simultaneously learn both the structure and the parameters of STL formulae, without restrictions on the STL grammar. Specifically, we propose a framework that leverages a dense vector database containing semantic-preserving continuous representations of millions of formulae, queried for facilitating the mining of requirements inside a BO loop. We demonstrate the effectiveness of our approach in several signal classification applications, showing its ability to extract interpretable insights from system executions and advance the state-of-the-art in requirement mining for CPS.
In this paper, we develop a novel power control solution for subnetworks-enabled distributed control systems in factory settings. We propose a channel-independent control-aware (CICA) policy based on the logistic model and learn the parameters using Bayesian optimization with a multi-objective tree-structured Parzen estimator. The objective is to minimize the control cost of the plants, measured as a finite horizon linear quadratic regulator cost. The proposed policy can be executed in a fully distributed manner and does not require cumbersome measurement of channel gain information, hence it is scalable for large-scale deployment of subnetworks for distributed control applications. With extensive numerical simulation and considering different densities of subnetworks, we show that the proposed method can achieve competitive stability performance and high availability for large-scale distributed control plants with limited radio resources.
In recent years, the researches about solving partial differential equations (PDEs) based on artificial neural network have attracted considerable attention. In these researches, the neural network models are usually designed depend on human experience or trial and error. Despite the emergence of several model searching methods, these methods primarily concentrate on optimizing the hyperparameters of fully connected neural network model based on the framework of physics-informed neural networks (PINNs), and the corresponding search spaces are relatively restricted, thereby limiting the exploration of superior models. This article proposes an evolutionary computation method aimed at discovering the PINNs model with higher approximation accuracy and faster convergence rate. In addition to searching the numbers of layers and neurons per hidden layer, this method concurrently explores the optimal shortcut connections between the layers and the novel parametric activation functions expressed by the binary trees. In evolution, the strategy about dynamic population size and training epochs (DPSTE) is adopted, which significantly increases the number of models to be explored and facilitates the discovery of models with fast convergence rate. In experiments, the performance of different models that are searched through Bayesian optimization, random search and evolution is compared in solving Klein-Gordon, Burgers, and Lam\'e equations. The experimental results affirm that the models discovered by the proposed evolutionary computation method generally exhibit superior approximation accuracy and convergence rate, and these models also show commendable generalization performance with respect to the source term, initial and boundary conditions, equation coefficient and computational domain. The corresponding code is available at https://github.com/MathBon/Discover-PINNs-Model.
Unconstrained optimization problems are typically solved using iterative methods, which often depend on line search techniques to determine optimal step lengths in each iteration. This paper introduces a novel line search approach. Traditional line search methods, aimed at determining optimal step lengths, often discard valuable data from the search process and focus on refining step length intervals. This paper proposes a more efficient method using Bayesian optimization, which utilizes all available data points, i.e., function values and gradients, to guide the search towards a potential global minimum. This new approach more effectively explores the search space, leading to better solution quality. It is also easy to implement and integrate into existing frameworks. Tested on the challenging CUTEst test set, it demonstrates superior performance compared to existing state-of-the-art methods, solving more problems to optimality with equivalent resource usage.
Efficient parameter identification of electrochemical models is crucial for accurate monitoring and control of lithium-ion cells. This process becomes challenging when applied to complex models that rely on a considerable number of interdependent parameters that affect the output response. Gradient-based and metaheuristic optimization techniques, although previously employed for this task, are limited by their lack of robustness, high computational costs, and susceptibility to local minima. In this study, Bayesian Optimization is used for tuning the dynamic parameters of an electrochemical equivalent circuit battery model (E-ECM) for a nickel-manganese-cobalt (NMC)-graphite cell. The performance of the Bayesian Optimization is compared with baseline methods based on gradient-based and metaheuristic approaches. The robustness of the parameter optimization method is tested by performing verification using an experimental drive cycle. The results indicate that Bayesian Optimization outperforms Gradient Descent and PSO optimization techniques, achieving reductions on average testing loss by 28.8% and 5.8%, respectively. Moreover, Bayesian optimization significantly reduces the variance in testing loss by 95.8% and 72.7%, respectively.
In recent years, large language models (LLMs) have driven advances in natural language processing. Still, their growing scale has increased the computational burden, necessitating a balance between efficiency and performance. Low-rank compression, a promising technique, reduces non-essential parameters by decomposing weight matrices into products of two low-rank matrices. Yet, its application in LLMs has not been extensively studied. The key to low-rank compression lies in low-rank factorization and low-rank dimensions allocation. To address the challenges of low-rank compression in LLMs, we conduct empirical research on the low-rank characteristics of large models. We propose a low-rank compression method suitable for LLMs. This approach involves precise estimation of feature distributions through pooled covariance matrices and a Bayesian optimization strategy for allocating low-rank dimensions. Experiments on the LLaMA-2 models demonstrate that our method outperforms existing strong structured pruning and low-rank compression techniques in maintaining model performance at the same compression ratio.
In several real-world applications in medical and control engineering, there are unsafe solutions whose evaluations involve inherent risk. This optimization setting is known as safe optimization and formulated as a specialized type of constrained optimization problem with constraints for safety functions. Safe optimization requires performing efficient optimization without evaluating unsafe solutions. A few studies have proposed the optimization methods for safe optimization based on Bayesian optimization and the evolutionary algorithm. However, Bayesian optimization-based methods often struggle to achieve superior solutions, and the evolutionary algorithm-based method fails to effectively reduce unsafe evaluations. This study focuses on CMA-ES as an efficient evolutionary algorithm and proposes an optimization method termed safe CMA-ES. The safe CMA-ES is designed to achieve both safety and efficiency in safe optimization. The safe CMA-ES estimates the Lipschitz constants of safety functions transformed with the distribution parameters using the maximum norm of the gradient in Gaussian process regression. Subsequently, the safe CMA-ES projects the samples to the nearest point in the safe region constructed with the estimated Lipschitz constants. The numerical simulation using the benchmark functions shows that the safe CMA-ES successfully performs optimization, suppressing the unsafe evaluations, while the existing methods struggle to significantly reduce the unsafe evaluations.
Black-box optimization problems often require simultaneously optimizing different types of variables, such as continuous, integer, and categorical variables. Unlike integer variables, categorical variables do not necessarily have a meaningful order, and the discretization approach of continuous variables does not work well. Although several Bayesian optimization methods can deal with mixed-category black-box optimization (MC-BBO), they suffer from a lack of scalability to high-dimensional problems and internal computational cost. This paper proposes CatCMA, a stochastic optimization method for MC-BBO problems, which employs the joint probability distribution of multivariate Gaussian and categorical distributions as the search distribution. CatCMA updates the parameters of the joint probability distribution in the natural gradient direction. CatCMA also incorporates the acceleration techniques used in the covariance matrix adaptation evolution strategy (CMA-ES) and the stochastic natural gradient method, such as step-size adaptation and learning rate adaptation. In addition, we restrict the ranges of the categorical distribution parameters by margin to prevent premature convergence and analytically derive a promising margin setting. Numerical experiments show that the performance of CatCMA is superior and more robust to problem dimensions compared to state-of-the-art Bayesian optimization algorithms.