Bayesian optimization (BO) has emerged as a powerful tool for navigating complex search spaces, showcasing practical applications in the fields of science and engineering.However, since it typically relies on a surrogate model to approximate the objective function, BO grapples with heightened computational costs that tend to escalate as the number of parameters and experiments grows. Several methods such as parallelization, surrogate model approximations, and memory pruning have been proposed to cut down computing time, but they all fall short of resolving the core issue behind BO's curse of dimensionality. In this paper, a 1D reparametrization trick is proposed to break this curse and sustain linear time complexity for BO in high-dimensional landscapes. This fast and scalable approach named SCORE can successfully find the global minimum of needle-in-a-haystack optimization functions and fit real-world data without the high-performance computing resources typically required by state-of-the-art techniques.
We consider the problem of multi-objective optimization (MOO) of expensive black-box functions with the goal of discovering high-quality and diverse Pareto fronts where we are allowed to evaluate a batch of inputs. This problem arises in many real-world applications including penicillin production where diversity of solutions is critical. We solve this problem in the framework of Bayesian optimization (BO) and propose a novel approach referred to as Pareto front-Diverse Batch Multi-Objective BO (PDBO). PDBO tackles two important challenges: 1) How to automatically select the best acquisition function in each BO iteration, and 2) How to select a diverse batch of inputs by considering multiple objectives. We propose principled solutions to address these two challenges. First, PDBO employs a multi-armed bandit approach to select one acquisition function from a given library. We solve a cheap MOO problem by assigning the selected acquisition function for each expensive objective function to obtain a candidate set of inputs for evaluation. Second, it utilizes Determinantal Point Processes (DPPs) to choose a Pareto-front-diverse batch of inputs for evaluation from the candidate set obtained from the first step. The key parameters for the methods behind these two steps are updated after each round of function evaluations. Experiments on multiple MOO benchmarks demonstrate that PDBO outperforms prior methods in terms of both the quality and diversity of Pareto solutions.
Bayesian optimization (BO) is a principled approach to molecular design tasks. In this paper we explain three pitfalls of BO which can cause poor empirical performance: an incorrect prior width, over-smoothing, and inadequate acquisition function maximization. We show that with these issues addressed, even a basic BO setup is able to achieve the highest overall performance on the PMO benchmark for molecule design (Gao et al 2022). These results suggest that BO may benefit from more attention in the machine learning for molecules community.
Bayesian optimization (BO) is an integral part of automated scientific discovery -- the so-called self-driving lab -- where human inputs are ideally minimal or at least non-blocking. However, scientists often have strong intuition, and thus human feedback is still useful. Nevertheless, prior works in enhancing BO with expert feedback, such as by incorporating it in an offline or online but blocking (arrives at each BO iteration) manner, are incompatible with the spirit of self-driving labs. In this work, we study whether a small amount of randomly arriving expert feedback that is being incorporated in a non-blocking manner can improve a BO campaign. To this end, we run an additional, independent computing thread on top of the BO loop to handle the feedback-gathering process. The gathered feedback is used to learn a Bayesian preference model that can readily be incorporated into the BO thread, to steer its exploration-exploitation process. Experiments on toy and chemistry datasets suggest that even just a few intermittent, asynchronous expert feedback can be useful for improving or constraining BO. This can especially be useful for its implication in improving self-driving labs, e.g. making them more data-efficient and less costly.
In this paper, we propose a novel and powerful method to harness Bayesian optimization for Variational Quantum Eigensolvers (VQEs) -- a hybrid quantum-classical protocol used to approximate the ground state of a quantum Hamiltonian. Specifically, we derive a VQE-kernel which incorporates important prior information about quantum circuits: the kernel feature map of the VQE-kernel exactly matches the known functional form of the VQE's objective function and thereby significantly reduces the posterior uncertainty. Moreover, we propose a novel acquisition function for Bayesian optimization called Expected Maximum Improvement over Confident Regions (EMICoRe) which can actively exploit the inductive bias of the VQE-kernel by treating regions with low predictive uncertainty as indirectly ``observed''. As a result, observations at as few as three points in the search domain are sufficient to determine the complete objective function along an entire one-dimensional subspace of the optimization landscape. Our numerical experiments demonstrate that our approach improves over state-of-the-art baselines.
Analog layout synthesis faces significant challenges due to its dependence on manual processes, considerable time requirements, and performance instability. Current Bayesian Optimization (BO)-based techniques for analog layout synthesis, despite their potential for automation, suffer from slow convergence and extensive data needs, limiting their practical application. This paper presents the \texttt{LLANA} framework, a novel approach that leverages Large Language Models (LLMs) to enhance BO by exploiting the few-shot learning abilities of LLMs for more efficient generation of analog design-dependent parameter constraints. Experimental results demonstrate that \texttt{LLANA} not only achieves performance comparable to state-of-the-art (SOTA) BO methods but also enables a more effective exploration of the analog circuit design space, thanks to LLM's superior contextual understanding and learning efficiency. The code is available at https://github.com/dekura/LLANA.
Optimizing discrete black-box functions is key in several domains, e.g. protein engineering and drug design. Due to the lack of gradient information and the need for sample efficiency, Bayesian optimization is an ideal candidate for these tasks. Several methods for high-dimensional continuous and categorical Bayesian optimization have been proposed recently. However, our survey of the field reveals highly heterogeneous experimental set-ups across methods and technical barriers for the replicability and application of published algorithms to real-world tasks. To address these issues, we develop a unified framework to test a vast array of high-dimensional Bayesian optimization methods and a collection of standardized black-box functions representing real-world application domains in chemistry and biology. These two components of the benchmark are each supported by flexible, scalable, and easily extendable software libraries (poli and poli-baselines), allowing practitioners to readily incorporate new optimization objectives or discrete optimizers. Project website: https://machinelearninglifescience.github.io/hdbo_benchmark
A typical process of learning to play a piece on a piano consists of a progression through a series of practice units that focus on individual dimensions of the skill, the so-called practice modes. Practice modes in learning to play music comprise a particularly large set of possibilities, such as hand coordination, posture, articulation, ability to read a music score, correct timing or pitch, etc. Self-guided practice is known to be suboptimal, and a model that schedules optimal practice to maximize a learner's progress still does not exist. Because we each learn differently and there are many choices for possible piano practice tasks and methods, the set of practice modes should be dynamically adapted to the human learner, a process typically guided by a teacher. However, having a human teacher guide individual practice is not always feasible since it is time-consuming, expensive, and often unavailable. In this work, we present a modeling framework to guide the human learner through the learning process by choosing the practice modes generated by a policy model. To this end, we present a computational architecture building on a Gaussian process that incorporates 1) the learner state, 2) a policy that selects a suitable practice mode, 3) performance evaluation, and 4) expert knowledge. The proposed policy model is trained to approximate the expert-learner interaction during a practice session. In our future work, we will test different Bayesian optimization techniques, e.g., different acquisition functions, and evaluate their effect on the learning progress.
Variational logistic regression is a popular method for approximate Bayesian inference seeing wide-spread use in many areas of machine learning including: Bayesian optimization, reinforcement learning and multi-instance learning to name a few. However, due to the intractability of the Evidence Lower Bound, authors have turned to the use of Monte Carlo, quadrature or bounds to perform inference, methods which are costly or give poor approximations to the true posterior. In this paper we introduce a new bound for the expectation of softplus function and subsequently show how this can be applied to variational logistic regression and Gaussian process classification. Unlike other bounds, our proposal does not rely on extending the variational family, or introducing additional parameters to ensure the bound is tight. In fact, we show that this bound is tighter than the state-of-the-art, and that the resulting variational posterior achieves state-of-the-art performance, whilst being significantly faster to compute than Monte-Carlo methods.
We consider the problem of optimizing initial conditions and termination time in dynamical systems governed by unknown ordinary differential equations (ODEs), where evaluating different initial conditions is costly and the state's value can not be measured in real-time but only with a delay while the measuring device processes the sample. To identify the optimal conditions in limited trials, we introduce a few-shot Bayesian Optimization (BO) framework based on the system's prior information. At the core of our approach is the System-Aware Neural ODE Processes (SANODEP), an extension of Neural ODE Processes (NODEP) designed to meta-learn ODE systems from multiple trajectories using a novel context embedding block. We further develop a two-stage BO framework to effectively incorporate search space constraints, enabling efficient optimization of both initial conditions and observation timings. We conduct extensive experiments showcasing SANODEP's potential for few-shot BO within dynamical systems. We also explore SANODEP's adaptability to varying levels of prior information, highlighting the trade-off between prior flexibility and model fitting accuracy.
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.
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.
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.
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.
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.