The ability to accelerate the design of biological sequences can have a substantial impact on the progress of the medical field. The problem can be framed as a global optimization problem where the objective is an expensive black-box function such that we can query large batches restricted with a limitation of a low number of rounds. Bayesian Optimization is a principled method for tackling this problem. However, the astronomically large state space of biological sequences renders brute-force iterating over all possible sequences infeasible. In this paper, we propose MetaRLBO where we train an autoregressive generative model via Meta-Reinforcement Learning to propose promising sequences for selection via Bayesian Optimization. We pose this problem as that of finding an optimal policy over a distribution of MDPs induced by sampling subsets of the data acquired in the previous rounds. Our in-silico experiments show that meta-learning over such ensembles provides robustness against reward misspecification and achieves competitive results compared to existing strong baselines.
Cyber-physical systems (CPSs) are often complex and safety-critical, making it both challenging and crucial to ensure that the system's specifications are met. Simulation-based falsification is a practical testing technique for increasing confidence in a CPS's correctness, as it only requires that the system be simulated. Reducing the number of computationally intensive simulations needed for falsification is a key concern. In this study, we investigate Bayesian optimization (BO), a sample-efficient approach that learns a surrogate model to capture the relationship between input signal parameterization and specification evaluation. We propose two enhancements to the basic BO for improving falsification: (1) leveraging local surrogate models, and (2) utilizing the user's prior knowledge. Additionally, we address the formulation of acquisition functions for falsification by proposing and evaluating various alternatives. Our benchmark evaluation demonstrates significant improvements when using local surrogate models in BO for falsifying challenging benchmark examples. Incorporating prior knowledge is found to be especially beneficial when the simulation budget is constrained. For some benchmark problems, the choice of acquisition function noticeably impacts the number of simulations required for successful falsification.
Bayesian Optimisation (BO) methods seek to find global optima of objective functions which are only available as a black-box or are expensive to evaluate. Such methods construct a surrogate model for the objective function, quantifying the uncertainty in that surrogate through Bayesian inference. Objective evaluations are sequentially determined by maximising an acquisition function at each step. However, this ancilliary optimisation problem can be highly non-trivial to solve, due to the non-convexity of the acquisition function, particularly in the case of batch Bayesian optimisation, where multiple points are selected in every step. In this work we reformulate batch BO as an optimisation problem over the space of probability measures. We construct a new acquisition function based on multipoint expected improvement which is convex over the space of probability measures. Practical schemes for solving this `inner' optimisation problem arise naturally as gradient flows of this objective function. We demonstrate the efficacy of this new method on different benchmark functions and compare with state-of-the-art batch BO methods.
Although beam emittance is critical for the performance of high-brightness accelerators, optimization is often time limited as emittance calculations, commonly done via quadrupole scans, are typically slow. Such calculations are a type of $\textit{multipoint query}$, i.e. each query requires multiple secondary measurements. Traditional black-box optimizers such as Bayesian optimization are slow and inefficient when dealing with such objectives as they must acquire the full series of measurements, but return only the emittance, with each query. We propose a new information-theoretic algorithm, Multipoint-BAX, for black-box optimization on multipoint queries, which queries and models individual beam-size measurements using techniques from Bayesian Algorithm Execution (BAX). Our method avoids the slow multipoint query on the accelerator by acquiring points through a $\textit{virtual objective}$, i.e. calculating the emittance objective from a fast learned model rather than directly from the accelerator. We use Multipoint-BAX to minimize emittance at the Linac Coherent Light Source (LCLS) and the Facility for Advanced Accelerator Experimental Tests II (FACET-II). In simulation, our method is 20$\times$ faster and more robust to noise compared to existing methods. In live tests, it matched the hand-tuned emittance at FACET-II and achieved a 24% lower emittance than hand-tuning at LCLS. Our method represents a conceptual shift for optimizing multipoint queries, and we anticipate that it can be readily adapted to similar problems in particle accelerators and other scientific instruments.
Variational inference (VI) is a specific type of approximate Bayesian inference that approximates an intractable posterior distribution with a tractable one. VI casts the inference problem as an optimization problem, more specifically, the goal is to maximize a lower bound of the logarithm of the marginal likelihood with respect to the parameters of the approximate posterior. Reinforcement learning (RL) on the other hand deals with autonomous agents and how to make them act optimally such as to maximize some notion of expected future cumulative reward. In the non-sequential setting where agents' actions do not have an impact on future states of the environment, RL is covered by contextual bandits and Bayesian optimization. In a proper sequential scenario, however, where agents' actions affect future states, instantaneous rewards need to be carefully traded off against potential long-term rewards. This manuscript shows how the apparently different subjects of VI and RL are linked in two fundamental ways. First, the optimization objective of RL to maximize future cumulative rewards can be recovered via a VI objective under a soft policy constraint in both the non-sequential and the sequential setting. This policy constraint is not just merely artificial but has proven as a useful regularizer in many RL tasks yielding significant improvements in agent performance. And second, in model-based RL where agents aim to learn about the environment they are operating in, the model-learning part can be naturally phrased as an inference problem over the process that governs environment dynamics. We are going to distinguish between two scenarios for the latter: VI when environment states are fully observable by the agent and VI when they are only partially observable through an observation distribution.
Bayesian optimization is a popular formalism for global optimization, but its computational costs limit it to expensive-to-evaluate functions. A competing, computationally more efficient, global optimization framework is optimistic optimization, which exploits prior knowledge about the geometry of the search space in form of a dissimilarity function. We investigate to which degree the conceptual advantages of Bayesian Optimization can be combined with the computational efficiency of optimistic optimization. By mapping the kernel to a dissimilarity, we obtain an optimistic optimization algorithm for the Bayesian Optimization setting with a run-time of up to $\mathcal{O}(N \log N)$. As a high-level take-away we find that, when using stationary kernels on objectives of relatively low evaluation cost, optimistic optimization can be strongly preferable over Bayesian optimization, while for strongly coupled and parametric models, good implementations of Bayesian optimization can perform much better, even at low evaluation cost. We argue that there is a new research domain between geometric and probabilistic search, i.e. methods that run drastically faster than traditional Bayesian optimization, while retaining some of the crucial functionality of Bayesian optimization.
Biofilms pose significant problems for engineers in diverse fields, such as marine science, bioenergy, and biomedicine, where effective biofilm control is a long-term goal. The adhesion and surface mechanics of biofilms play crucial roles in generating and removing biofilm. Designing customized nano-surfaces with different surface topologies can alter the adhesive properties to remove biofilms more easily and greatly improve long-term biofilm control. To rapidly design such topologies, we employ individual-based modeling and Bayesian optimization to automate the design process and generate different active surfaces for effective biofilm removal. Our framework successfully generated ideal nano-surfaces for biofilm removal through applied shear and vibration. Densely distributed short pillar topography is the optimal geometry to prevent biofilm formation. Under fluidic shearing, the optimal topography is to sparsely distribute tall, slim, pillar-like structures. When subjected to either vertical or lateral vibrations, thick trapezoidal cones are found to be optimal. Optimizing the vibrational loading indicates a small vibration magnitude with relatively low frequencies is more efficient in removing biofilm. Our results provide insights into various engineering fields that require surface-mediated biofilm control. Our framework can also be applied to more general materials design and optimization.
We study the combinatorial assignment domain, which includes combinatorial auctions and course allocation. The main challenge in this domain is that the bundle space grows exponentially in the number of items. To address this, several papers have recently proposed machine learning-based preference elicitation algorithms that aim to elicit only the most important information from agents. However, the main shortcoming of this prior work is that it does not model a mechanism's uncertainty over values for not yet elicited bundles. In this paper, we address this shortcoming by presenting a Bayesian optimization-based combinatorial assignment (BOCA) mechanism. Our key technical contribution is to integrate a method for capturing model uncertainty into an iterative combinatorial auction mechanism. Concretely, we design a new method for estimating an upper uncertainty bound that can be used to define an acquisition function to determine the next query to the agents. This enables the mechanism to properly explore (and not just exploit) the bundle space during its preference elicitation phase. We run computational experiments in several spectrum auction domains to evaluate BOCA's performance. Our results show that BOCA achieves higher allocative efficiency than state-of-the-art approaches.
Needle-in-a-Haystack problems exist across a wide range of applications including rare disease prediction, ecological resource management, fraud detection, and material property optimization. A Needle-in-a-Haystack problem arises when there is an extreme imbalance of optimum conditions relative to the size of the dataset. For example, only $0.82\%$ out of $146$k total materials in the open-access Materials Project database have a negative Poisson's ratio. However, current state-of-the-art optimization algorithms are not designed with the capabilities to find solutions to these challenging multidimensional Needle-in-a-Haystack problems, resulting in slow convergence to a global optimum or pigeonholing into a local minimum. In this paper, we present a Zooming Memory-Based Initialization algorithm, entitled ZoMBI. ZoMBI actively extracts knowledge from the previously best-performing evaluated experiments to iteratively zoom in the sampling search bounds towards the global optimum "needle" and then prunes the memory of low-performing historical experiments to accelerate compute times by reducing the algorithm time complexity from $O(n^3)$ to $O(\phi^3)$ for $\phi$ forward experiments per activation, which trends to a constant $O(1)$ over several activations. Additionally, ZoMBI implements two custom adaptive acquisition functions to further guide the sampling of new experiments toward the global optimum. We validate the algorithm's optimization performance on three real-world datasets exhibiting Needle-in-a-Haystack and further stress-test the algorithm's performance on an additional 174 analytical datasets. The ZoMBI algorithm demonstrates compute time speed-ups of 400x compared to traditional Bayesian optimization as well as efficiently discovering optima in under 100 experiments that are up to 3x more highly optimized than those discovered by similar methods MiP-EGO, TuRBO, and HEBO.
In this paper, a new methodology is proposed that allows for the low-complexity development of neural network (NN) based equalizers for the mitigation of impairments in high-speed coherent optical transmission systems. In this work, we provide a comprehensive description and comparison of various deep model compression approaches that have been applied to feed-forward and recurrent NN designs. Additionally, we evaluate the influence these strategies have on the performance of each NN equalizer. Quantization, weight clustering, pruning, and other cutting-edge strategies for model compression are taken into consideration. In this work, we propose and evaluate a Bayesian optimization-assisted compression, in which the hyperparameters of the compression are chosen to simultaneously reduce complexity and improve performance. In conclusion, the trade-off between the complexity of each compression approach and its performance is evaluated by utilizing both simulated and experimental data in order to complete the analysis. By utilizing optimal compression approaches, we show that it is possible to design an NN-based equalizer that is simpler to implement and has better performance than the conventional digital back-propagation (DBP) equalizer with only one step per span. This is accomplished by reducing the number of multipliers used in the NN equalizer after applying the weighted clustering and pruning algorithms. Furthermore, we demonstrate that an equalizer based on NN can also achieve superior performance while still maintaining the same degree of complexity as the full electronic chromatic dispersion compensation block. We conclude our analysis by highlighting open questions and existing challenges, as well as possible future research directions.
Hyperparameter optimization in machine learning is often achieved using naive techniques that only lead to an approximate set of hyperparameters. Although techniques such as Bayesian optimization perform an intelligent search on a given domain of hyperparameters, it does not guarantee an optimal solution. A major drawback of most of these approaches is an exponential increase of their search domain with number of hyperparameters, increasing the computational cost and making the approaches slow. The hyperparameter optimization problem is inherently a bilevel optimization task, and some studies have attempted bilevel solution methodologies for solving this problem. However, these studies assume a unique set of model weights that minimize the training loss, which is generally violated by deep learning architectures. This paper discusses a gradient-based bilevel method addressing these drawbacks for solving the hyperparameter optimization problem. The proposed method can handle continuous hyperparameters for which we have chosen the regularization hyperparameter in our experiments. The method guarantees convergence to the set of optimal hyperparameters that this study has theoretically proven. The idea is based on approximating the lower-level optimal value function using Gaussian process regression. As a result, the bilevel problem is reduced to a single level constrained optimization task that is solved using the augmented Lagrangian method. We have performed an extensive computational study on the MNIST and CIFAR-10 datasets on multi-layer perceptron and LeNet architectures that confirms the efficiency of the proposed method. A comparative study against grid search, random search, Bayesian optimization, and HyberBand method on various hyperparameter problems shows that the proposed algorithm converges with lower computation and leads to models that generalize better on the testing set.
Drop-on-demand (DOD) inkjet printing has been considered as one of promising technologies for the fabrication of advanced functional materials. For a DOD printer, high-precision dispensing techniques for achieving satellite-free smaller droplets, have long been desired for patterning thin-film structures. The present study considers the inlet velocity of a liquid chamber located upstream of a dispensing nozzle as a control variable and aims to optimize its waveform using a sample-efficient Bayesian optimization algorithm. Firstly, the droplet dispensing dynamics are numerically reproduced by using an open-source OpenFOAM solver, interFoam, and the results are passed on to another code based on pyFoam. Then, the parameters characterizing the actuation waveform driving a DOD printer are determined by the Bayesian optimization (BO) algorithm so as to maximize a prescribed multi-objective function expressed as the sum of two factors, i.e., the size of a primary droplet and the presence of satellite droplets. The results show that the present BO algorithm can successfully find high-precision dispensing waveforms within 150 simulations. Specifically, satellite droplets can be effectively eliminated and the droplet diameter can be significantly reduced to 24.9% of the nozzle diameter by applying the optimal waveform.
We study the problem of globally optimizing the causal effect on a target variable of an unknown causal graph in which interventions can be performed. This problem arises in many areas of science including biology, operations research and healthcare. We propose Causal Entropy Optimization (CEO), a framework that generalizes Causal Bayesian Optimization (CBO) to account for all sources of uncertainty, including the one arising from the causal graph structure. CEO incorporates the causal structure uncertainty both in the surrogate models for the causal effects and in the mechanism used to select interventions via an information-theoretic acquisition function. The resulting algorithm automatically trades-off structure learning and causal effect optimization, while naturally accounting for observation noise. For various synthetic and real-world structural causal models, CEO achieves faster convergence to the global optimum compared with CBO while also learning the graph. Furthermore, our joint approach to structure learning and causal optimization improves upon sequential, structure-learning-first approaches.
We consider the problem of sequentially optimizing a time-varying objective function using time-varying Bayesian optimization (TVBO). To cope with stale data arising from time variations, current approaches to TVBO require prior knowledge of a constant rate of change. However, in practice, the rate of change is usually unknown. We propose an event-triggered algorithm, ET-GP-UCB, that treats the optimization problem as static until it detects changes in the objective function and then resets the dataset. This allows the algorithm to adapt online to realized temporal changes without the need for exact prior knowledge. The event trigger is based on probabilistic uniform error bounds used in Gaussian process regression. We derive regret bounds of adaptive resets without exact prior knowledge on the temporal changes, and show in numerical experiments that ET-GP-UCB outperforms state-of-the-art algorithms on both synthetic and real-world data. The results demonstrate that ET-GP-UCB is readily applicable to various settings without extensive hyperparameter tuning.
Bayesian optimization (BO) is a well-established method to optimize black-box functions whose direct evaluations are costly. In this paper, we tackle the problem of incorporating expert knowledge into BO, with the goal of further accelerating the optimization, which has received very little attention so far. We design a multi-task learning architecture for this task, with the goal of jointly eliciting the expert knowledge and minimizing the objective function. In particular, this allows for the expert knowledge to be transferred into the BO task. We introduce a specific architecture based on Siamese neural networks to handle the knowledge elicitation from pairwise queries. Experiments on various benchmark functions with both simulated and actual human experts show that the proposed method significantly speeds up BO even when the expert knowledge is biased compared to the objective function.
Density functional theory (DFT) is a powerful computational method used to obtain physical and chemical properties of materials. In the materials discovery framework, it is often necessary to virtually screen a large and high-dimensional chemical space to find materials with desired properties. However, grid searching a large chemical space with DFT is inefficient due to its high computational cost. We propose an approach utilizing Bayesian optimization (BO) with an artificial neural network kernel to enable smart search. This method leverages the BO algorithm, where the neural network, trained on a limited number of DFT results, determines the most promising regions of the chemical space to explore in subsequent iterations. This approach aims to discover materials with target properties while minimizing the number of DFT calculations required. To demonstrate the effectiveness of this method, we investigated 63 doped graphene quantum dots (GQDs) with sizes ranging from 1 to 2 nm to find the structure with the highest light absorbance. Using time-dependent DFT (TDDFT) only 12 times, we achieved a significant reduction in computational cost, approximately 20% of what would be required for a full grid search, by employing the BO algorithm with a neural network kernel. Considering that TDDFT calculations for a single GQD require about half a day of wall time on high-performance computing nodes, this reduction is substantial. Our approach can be generalized to the discovery of new drugs, chemicals, crystals, and alloys with high-dimensional and large chemical spaces, offering a scalable solution for various applications in materials science.
Vibration-based condition monitoring techniques are commonly used to detect and diagnose failures of rolling bearings. Accuracy and delay in detecting and diagnosing different types of failures are the main performance measures in condition monitoring. Achieving high accuracy with low delay improves system reliability and prevents catastrophic equipment failure. Further, delay is crucial to remote condition monitoring and time-sensitive industrial applications. While most of the proposed methods focus on accuracy, slight attention has been paid to addressing the delay introduced in the condition monitoring process. In this paper, we attempt to bridge this gap and propose a hybrid method for vibration-based condition monitoring and fault diagnosis of rolling bearings that outperforms previous methods in terms of accuracy and delay. Specifically, we address the overall delay in vibration-based condition monitoring systems and introduce the concept of system delay to assess it. Then, we present the proposed method for condition monitoring. It uses Wavelet Packet Transform (WPT) and Fourier analysis to decompose short-duration input segments of the vibration signal into elementary waveforms and obtain their spectral contents. Accordingly, energy concentration in the spectral components-caused by defect induced transient vibrations-is utilized to extract a small number of features with high discriminative capabilities. Consequently, Bayesian optimization-based Random Forest (RF) algorithm is used to classify healthy and faulty operating conditions under varying motor speeds. The experimental results show that the proposed method can achieve high accuracy with low system delay.
Optimizing management practices and selecting the best cultivar for planting play a significant role in increasing agricultural food production and decreasing environmental footprint. In this study, we develop optimization frameworks under uncertainty using conditional value-at-risk in the stochastic programming objective function. We integrate the crop model, APSIM, and a parallel Bayesian optimization algorithm to optimize the management practices and select the best cultivar at different levels of risk aversion. This approach integrates the power of optimization in determining the best decisions and crop model in simulating nature's output corresponding to various decisions. As a case study, we set up the crop model for 25 locations across the US Corn Belt. We optimized the management options (planting date, N fertilizer amount, fertilizing date, and plant density in the farm) and cultivar options (cultivars with different maturity days) three times: a) before, b) at planting and c) after a growing season with known weather. Results indicated that the proposed model produced meaningful connections between weather and optima decisions. Also, we found risk-tolerance farmers get more expected yield than risk-averse ones in wet and non-wet weathers.
We approach the problem of designing an automated trading strategy that can consistently profit by adapting to changing market conditions. This challenge can be framed as a Nonstationary Continuum-Armed Bandit (NCAB) problem. To solve the NCAB problem, we propose PRBO, a novel trading algorithm that uses Bayesian optimization and a ``bandit-over-bandit'' framework to dynamically adjust strategy parameters in response to market conditions. We use Bristol Stock Exchange (BSE) to simulate financial markets containing heterogeneous populations of automated trading agents and compare PRBO with PRSH, a reference trading strategy that adapts strategy parameters through stochastic hill-climbing. Results show that PRBO generates significantly more profit than PRSH, despite having fewer hyperparameters to tune. The code for PRBO and performing experiments is available online open-source (https://github.com/HarmoniaLeo/PRZI-Bayesian-Optimisation).
Bayesian optimization is a methodology for global optimization of unknown and expensive objectives. It combines a surrogate Bayesian regression model with an acquisition function to decide where to evaluate the objective. Typical regression models are given by Gaussian processes with stationary covariance functions. However, these functions are unable to express prior input-dependent information, including possible locations of the optimum. The ubiquity of stationary models has led to the common practice of exploiting prior information via informative mean functions. In this paper, we highlight that these models can perform poorly, especially in high dimensions. We propose novel informative covariance functions for optimization, leveraging nonstationarity to encode preferences for certain regions of the search space and adaptively promote local exploration during optimization. We demonstrate that the proposed functions can increase the sample efficiency of Bayesian optimization in high dimensions, even under weak prior information.