Structure-based virtual screening is an important tool in early stage drug discovery that scores the interactions between a target protein and candidate ligands. As virtual libraries continue to grow (in excess of $10^8$ molecules), so too do the resources necessary to conduct exhaustive virtual screening campaigns on these libraries. However, Bayesian optimization techniques can aid in their exploration: a surrogate structure-property relationship model trained on the predicted affinities of a subset of the library can be applied to the remaining library members, allowing the least promising compounds to be excluded from evaluation. In this study, we assess various surrogate model architectures, acquisition functions, and acquisition batch sizes as applied to several protein-ligand docking datasets and observe significant reductions in computational costs, even when using a greedy acquisition strategy; for example, 87.9% of the top-50000 ligands can be found after testing only 2.4% of a 100M member library. Such model-guided searches mitigate the increasing computational costs of screening increasingly large virtual libraries and can accelerate high-throughput virtual screening campaigns with applications beyond docking.
Hyperparameter optimization (HPO), formulated as black-box optimization (BBO), is recognized as essential for automation and high performance of machine learning approaches. The CMA-ES is a promising BBO approach with a high degree of parallelism, and has been applied to HPO tasks, often under parallel implementation, and shown superior performance to other approaches including Bayesian optimization (BO). However, if the budget of hyperparameter evaluations is severely limited, which is often the case for end users who do not deserve parallel computing, the CMA-ES exhausts the budget without improving the performance due to its long adaptation phase, resulting in being outperformed by BO approaches. To address this issue, we propose to transfer prior knowledge on similar HPO tasks through the initialization of the CMA-ES, leading to significantly shortening the adaptation time. The knowledge transfer is designed based on the novel definition of task similarity, with which the correlation of the performance of the proposed approach is confirmed on synthetic problems. The proposed warm starting CMA-ES, called WS-CMA-ES, is applied to different HPO tasks where some prior knowledge is available, showing its superior performance over the original CMA-ES as well as BO approaches with or without using the prior knowledge.
Bayesian optimization (BO) is an efficient framework for solving black-box optimization problems with expensive function evaluations. This paper addresses the BO problem setting for combinatorial spaces (e.g., sequences and graphs) that occurs naturally in science and engineering applications. A prototypical example is molecular optimization guided by expensive experiments. The key challenge is to balance the complexity of statistical models and tractability of search to select combinatorial structures for evaluation. In this paper, we propose an efficient approach referred as Mercer Features for Combinatorial Bayesian Optimization (MerCBO). The key idea behind MerCBO is to provide explicit feature maps for diffusion kernels over discrete objects by exploiting the structure of their combinatorial graph representation. These Mercer features combined with Thompson sampling as the acquisition function allows us to employ tractable solvers to find next structures for evaluation. Experiments on diverse real-world benchmarks demonstrate that MerCBO performs similarly or better than prior methods. The source code is available at https://github.com/aryandeshwal/MerCBO .
Neural architecture search (NAS) methods rely on a search strategy for deciding which architectures to evaluate next and a performance estimation strategy for assessing their performance (e.g., using full evaluations, multi-fidelity evaluations, or the one-shot model). In this paper, we focus on the search strategy. We introduce the simple yet powerful evolutionary algorithm of differential evolution to the NAS community. Using the simplest performance evaluation strategy of full evaluations, we comprehensively compare this search strategy to regularized evolution and Bayesian optimization and demonstrate that it yields improved and more robust results for 13 tabular NAS benchmarks based on NAS-Bench-101, NAS-Bench-1Shot1, NAS-Bench-201 and NAS-HPO bench.
In this paper, we propose a surrogate-assisted evolutionary algorithm (EA) for hyperparameter optimization of machine learning (ML) models. The proposed STEADE model initially estimates the objective function landscape using RadialBasis Function interpolation, and then transfers the knowledge to an EA technique called Differential Evolution that is used to evolve new solutions guided by a Bayesian optimization framework. We empirically evaluate our model on the hyperparameter optimization problems as a part of the black box optimization challenge at NeurIPS 2020 and demonstrate the improvement brought about by STEADE over the vanilla EA.
The Combined Algorithm Selection and Hyperparameter optimization (CASH) is one of the most fundamental problems in Automatic Machine Learning (AutoML). The existing Bayesian optimization (BO) based solutions turn the CASH problem into a Hyperparameter Optimization (HPO) problem by combining the hyperparameters of all machine learning (ML) algorithms, and use BO methods to solve it. As a result, these methods suffer from the low-efficiency problem due to the huge hyperparameter space in CASH. To alleviate this issue, we propose the alternating optimization framework, where the HPO problem for each ML algorithm and the algorithm selection problem are optimized alternately. In this framework, the BO methods are used to solve the HPO problem for each ML algorithm separately, incorporating a much smaller hyperparameter space for BO methods. Furthermore, we introduce Rising Bandits, a CASH-oriented Multi-Armed Bandits (MAB) variant, to model the algorithm selection in CASH. This framework can take the advantages of both BO in solving the HPO problem with a relatively small hyperparameter space and the MABs in accelerating the algorithm selection. Moreover, we further develop an efficient online algorithm to solve the Rising Bandits with provably theoretical guarantees. The extensive experiments on 30 OpenML datasets demonstrate the superiority of the proposed approach over the competitive baselines.
We consider the problem of optimizing a robot morphology to achieve the best performance for a target task, under computational resource limitations. The evaluation process for each morphological design involves learning a controller for the design, which can consume substantial time and computational resources. To address the challenge of expensive robot morphology evaluation, we present a continuous multi-fidelity Bayesian Optimization framework that efficiently utilizes computational resources via low-fidelity evaluations. We identify the problem of non-stationarity over fidelity space. Our proposed fidelity warping mechanism can learn representations of learning epochs and tasks to model non-stationary covariances between continuous fidelity evaluations which prove challenging for off-the-shelf stationary kernels. Various experiments demonstrate that our method can utilize the low-fidelity evaluations to efficiently search for the optimal robot morphology, outperforming state-of-the-art methods.
This article explores search strategies for the design of parameterized quantum circuits. We propose several optimization approaches including random search plus survival of the fittest, reinforcement learning both with classical and hybrid quantum classical controllers and Bayesian optimization as decision makers to design a quantum circuit in an automated way for a specific task such as multi-labeled classification over a dataset. We introduce nontrivial circuit architectures that are arduous to be hand-designed and efficient in terms of trainability. In addition, we introduce reuploading of initial data into quantum circuits as an option to find more general designs. We numerically show that some of the suggested architectures for the Iris dataset accomplish better results compared to the established parameterized quantum circuit designs in the literature. In addition, we investigate the trainability of these structures on the unseen dataset Glass. We report meaningful advantages over the benchmarks for the classification of the Glass dataset which supports the fact that the suggested designs are inherently more trainable.
Glioblastoma is profoundly heterogeneous in microstructure and vasculature, which may lead to tumor regional diversity and distinct treatment response. Although successful in tumor sub-region segmentation and survival prediction, radiomics based on machine learning algorithms, is challenged by its robustness, due to the vague intermediate process and track changes. Also, the weak interpretability of the model poses challenges to clinical application. Here we proposed a machine learning framework to semi-automatically fine-tune the clustering algorithms and quantitatively identify stable sub-regions for reliable clinical survival prediction. Hyper-parameters are automatically determined by the global minimum of the trained Gaussian Process (GP) surrogate model through Bayesian optimization(BO) to alleviate the difficulty of tuning parameters for clinical researchers. To enhance the interpretability of the survival prediction model, we incorporated the prior knowledge of intra-tumoral heterogeneity, by segmenting tumor sub-regions and extracting sub-regional features. The results demonstrated that the global minimum of the trained GP surrogate can be used as sub-optimal hyper-parameter solutions for efficient. The sub-regions segmented based on physiological MRI can be applied to predict patient survival, which could enhance the clinical interpretability for the machine learning model.
In the machine learning algorithms, the choice of the hyperparameter is often an art more than a science, requiring labor-intensive search with expert experience. Therefore, automation on hyperparameter optimization to exclude human intervention is a great appeal, especially for the black-box functions. Recently, there have been increasing demands of solving such concealed tasks for better generalization, though the task-dependent issue is not easy to solve. The Black-Box Optimization challenge (NeurIPS 2020) required competitors to build a robust black-box optimizer across different domains of standard machine learning problems. This paper describes the approach of team KAIST OSI in a step-wise manner, which outperforms the baseline algorithms by up to +20.39%. We first strengthen the local Bayesian search under the concept of region reliability. Then, we design a combinatorial kernel for a Gaussian process kernel. In a similar vein, we combine the methodology of Bayesian and multi-armed bandit,(MAB) approach to select the values with the consideration of the variable types; the real and integer variables are with Bayesian, while the boolean and categorical variables are with MAB. Empirical evaluations demonstrate that our method outperforms the existing methods across different tasks.
Hyperparameter optimization (HPO) is a fundamental problem in automatic machine learning (AutoML). However, due to the expensive evaluation cost of models (e.g., training deep learning models or training models on large datasets), vanilla Bayesian optimization (BO) is typically computationally infeasible. To alleviate this issue, Hyperband (HB) utilizes the early stopping mechanism to speed up configuration evaluations by terminating those badly-performing configurations in advance. This leads to two kinds of quality measurements: (1) many low-fidelity measurements for configurations that get early-stopped, and (2) few high-fidelity measurements for configurations that are evaluated without being early stopped. The state-of-the-art HB-style method, BOHB, aims to combine the benefits of both BO and HB. Instead of sampling configurations randomly in HB, BOHB samples configurations based on a BO surrogate model, which is constructed with the high-fidelity measurements only. However, the scarcity of high-fidelity measurements greatly hampers the efficiency of BO to guide the configuration search. In this paper, we present MFES-HB, an efficient Hyperband method that is capable of utilizing both the high-fidelity and low-fidelity measurements to accelerate the convergence of HPO tasks. Designing MFES-HB is not trivial as the low-fidelity measurements can be biased yet informative to guide the configuration search. Thus we propose to build a Multi- Fidelity Ensemble Surrogate (MFES) based on the generalized Product of Experts framework, which can integrate useful information from multi-fidelity measurements effectively. The empirical studies on the real-world AutoML tasks demonstrate that MFES-HB can achieve 3.3-8.9x speedups over the state-of-the-art approach - BOHB.
This paper presents an automated, model-free, data-driven method for the safe tuning of PID cascade controller gains based on Bayesian optimization. The optimization objective is composed of data-driven performance metrics and modeled using Gaussian processes. We further introduce a data-driven constraint that captures the stability requirements from system data. Numerical evaluation shows that the proposed approach outperforms relay feedback autotuning and quickly converges to the global optimum, thanks to a tailored stopping criterion. We demonstrate the performance of the method in simulations and experiments. For experimental implementation, in addition to the introduced safety constraint, we integrate a method for automatic detection of the critical gains and extend the optimization objective with a penalty depending on the proximity of the current candidate points to the critical gains. The resulting automated tuning method optimizes system performance while ensuring stability and standardization
Wireless cellular networks have many parameters that are normally tuned upon deployment and re-tuned as the network changes. Many operational parameters affect reference signal received power (RSRP), reference signal received quality (RSRQ), signal-to-interference-plus-noise-ratio (SINR), and, ultimately, throughput. In this paper, we develop and compare two approaches for maximizing coverage and minimizing interference by jointly optimizing the transmit power and downtilt (elevation tilt) settings across sectors. To evaluate different parameter configurations offline, we construct a realistic simulation model that captures geographic correlations. Using this model, we evaluate two optimization methods: deep deterministic policy gradient (DDPG), a reinforcement learning (RL) algorithm, and multi-objective Bayesian optimization (BO). Our simulations show that both approaches significantly outperform random search and converge to comparable Pareto frontiers, but that BO converges with two orders of magnitude fewer evaluations than DDPG. Our results suggest that data-driven techniques can effectively self-optimize coverage and capacity in cellular networks.
In a world of aging infrastructure, structural health monitoring (SHM) emerges as a major step towards resilient and sustainable societies. The current advancements in machine learning and sensor technology have made SHM a more promising damage detection method than the traditional non-destructive testing methods. SHM using unsupervised learning methods offers an attractive alternative to the more commonly used supervised learning since it only requires data of the structure in normal conditions for the training process. The density-based novelty detection method provides a statistical element to the damage detection process but it relies heavily on the accuracy of the estimated probability density function (PDF). In this study, a novel unsupervised learning approach for SHM is proposed. It is based on the Kernel Density Maximum Entropy method by leveraging Bayesian optimization for hyperparameter tuning and also by extending the method into the multivariate space by the use of independent components analysis. The proposed approach is evaluated on a numerically simulated three-story reinforced concrete moment frame, where 94% of accuracy is achieved in structural damage detection.
Cancer pathology is unique to a given individual, and developing personalized diagnostic and treatment protocols are a primary concern. Mathematical modeling and simulation is a promising approach to personalized cancer medicine. Yet, the complexity, heterogeneity and multiscale nature of cancer present severe challenges. One of the major barriers to use mathematical models to predict the outcome of therapeutic regimens in a particular patient lies in their initialization and parameterization in order to reflect individual cancer characteristics accurately. Here we present a study where we used multitype measurements acquired routinely on a single breast tumor, including histopathology, magnetic resonance imaging (MRI), and molecular profiling, to personalize a multiscale hybrid cellular automaton model of breast cancer treated with chemotherapeutic and antiangiogenic agents. We model drug pharmacokinetics and pharmacodynamics at the tumor tissue level but with cellular and subcellular resolution. We simulate those spatio-temporal dynamics in 2D cross-sections of tumor portions over 12-week therapy regimes, resulting in complex and computationally intensive simulations. For such computationally demanding systems, formal statistical inference methods to estimate individual parameters from data have not been feasible in practice to until most recently, after the emergence of machine learning techniques applied to likelihood-free inference methods. Here we use the inference advances provided by Bayesian optimization to fit our model to simulated data of individual patients. In this way, we investigate if some key parameters can be estimated from a series of measurements of cell density in the tumor tissue, as well as how often the measurements need to be taken to allow reliable predictions.
We propose a performance-based autotuning method for cascade control systems, where the parameters of a linear axis drive motion controller from two control loops are tuned jointly. Using Bayesian optimization as all parameters are tuned simultaneously, the method is guaranteed to converge asymptotically to the global optimum of the cost. The data-efficiency and performance of the method are studied numerically for several training configurations and compared numerically to those achieved with classical tuning methods and to the exhaustive evaluation of the cost. On the real system, the tracking performance and robustness against disturbances are compared experimentally to nominal tuning. The numerical study and the experimental data both demonstrate that the proposed automated tuning method is efficient in terms of required tuning iterations, robust to disturbances, and results in improved tracking.
Cascaded controller tuning is a multi-step iterative procedure that needs to be performed routinely upon maintenance and modification of mechanical systems. An automated data-driven method for cascaded controller tuning based on Bayesian optimization is proposed. The method is tested on a linear axis drive, modeled using a combination of first principles model and system identification. A custom cost function based on performance indicators derived from system data at different candidate configurations of controller parameters is modeled by a Gaussian process. It is further optimized by minimization of an acquisition function which serves as a sampling criterion to determine the subsequent candidate configuration for experimental trial and improvement of the cost model iteratively, until a minimum according to a termination criterion is found. This results in a data-efficient procedure that can be easily adapted to varying loads or mechanical modifications of the system. The method is further compared to several classical methods for auto-tuning, and demonstrates higher performance according to the defined data-driven performance indicators. The influence of the training data on a cost prior on the number of iterations required to reach optimum is studied, demonstrating the efficiency of the Bayesian optimization tuning method.
How to generate testing scenario libraries for connected and automated vehicles (CAVs) is a major challenge faced by the industry. In previous studies, to evaluate maneuver challenge of a scenario, surrogate models (SMs) are often used without explicit knowledge of the CAV under test. However, performance dissimilarities between the SM and the CAV under test usually exist, and it can lead to the generation of suboptimal scenario libraries. In this paper, an adaptive testing scenario library generation (ATSLG) method is proposed to solve this problem. A customized testing scenario library for a specific CAV model is generated through an adaptive process. To compensate the performance dissimilarities and leverage each test of the CAV, Bayesian optimization techniques are applied with classification-based Gaussian Process Regression and a new-designed acquisition function. Comparing with a pre-determined library, a CAV can be tested and evaluated in a more efficient manner with the customized library. To validate the proposed method, a cut-in case study was performed and the results demonstrate that the proposed method can further accelerate the evaluation process by a few orders of magnitude.
Many state estimation algorithms must be tuned given the state space process and observation models, the process and observation noise parameters must be chosen. Conventional tuning approaches rely on heuristic hand-tuning or gradient-based optimization techniques to minimize a performance cost function. However, the relationship between tuned noise values and estimator performance is highly nonlinear and stochastic. Therefore, the tuning solutions can easily get trapped in local minima, which can lead to poor choices of noise parameters and suboptimal estimator performance. This paper describes how Bayesian Optimization (BO) can overcome these issues. BO poses optimization as a Bayesian search problem for a stochastic ``black box'' cost function, where the goal is to search the solution space to maximize the probability of improving the current best solution. As such, BO offers a principled approach to optimization-based estimator tuning in the presence of local minima and performance stochasticity. While extended Kalman filters (EKFs) are the main focus of this work, BO can be similarly used to tune other related state space filters. The method presented here uses performance metrics derived from normalized innovation squared (NIS) filter residuals obtained via sensor data, which renders knowledge of ground-truth states unnecessary. The robustness, accuracy, and reliability of BO-based tuning is illustrated on practical nonlinear state estimation problems,losed-loop aero-robotic control.
We present a data-driven optimization framework that aims to address online adaptation of the flight path shape for an airborne wind energy system (AWE) that follows a repetitive path to generate power. Specifically, Bayesian optimization, which is a data-driven algorithm for finding the optimum of an unknown objective function, is utilized to solve the waypoint adaptation. To form a computationally efficient optimization framework, we describe each figure-$8$ flight via a compact set of parameters, termed as basis parameters. We model the underlying objective function by a Gaussian Process (GP). Bayesian optimization utilizes the predictive uncertainty information from the GP to determine the best subsequent basis parameters. Once a path is generated using Bayesian optimization, a path following mechanism is used to track the generated figure-$8$ flight. The proposed framework is validated on a simplified $2$-dimensional model that mimics the key behaviors of a $3$-dimensional AWE system. We demonstrate the capability of the proposed framework in a simulation environment for a simplified $2$-dimensional AWE system model.