Bayesian Optimization (BO) is an effective method for finding the global optimum of expensive black-box functions. However, it is well known that applying BO to high-dimensional optimization problems is challenging. To address this issue, a promising solution is to use a local search strategy that partitions the search domain into local regions with high likelihood of containing the global optimum, and then use BO to optimize the objective function within these regions. In this paper, we propose a novel technique for defining the local regions using the Covariance Matrix Adaptation (CMA) strategy. Specifically, we use CMA to learn a search distribution that can estimate the probabilities of data points being the global optimum of the objective function. Based on this search distribution, we then define the local regions consisting of data points with high probabilities of being the global optimum. Our approach serves as a meta-algorithm as it can incorporate existing black-box BO optimizers, such as BO, TuRBO, and BAxUS, to find the global optimum of the objective function within our derived local regions. We evaluate our proposed method on various benchmark synthetic and real-world problems. The results demonstrate that our method outperforms existing state-of-the-art techniques.
Manual parameter tuning of cyber-physical systems is a common practice, but it is labor-intensive. Bayesian Optimization (BO) offers an automated alternative, yet its black-box nature reduces trust and limits human-BO collaborative system tuning. Experts struggle to interpret BO recommendations due to the lack of explanations. This paper addresses the post-hoc BO explainability problem for cyber-physical systems. We introduce TNTRules (Tune-No-Tune Rules), a novel algorithm that provides both global and local explanations for BO recommendations. TNTRules generates actionable rules and visual graphs, identifying optimal solution bounds and ranges, as well as potential alternative solutions. Unlike existing explainable AI (XAI) methods, TNTRules is tailored specifically for BO, by encoding uncertainty via a variance pruning technique and hierarchical agglomerative clustering. A multi-objective optimization approach allows maximizing explanation quality. We evaluate TNTRules using established XAI metrics (Correctness, Completeness, and Compactness) and compare it against adapted baseline methods. The results demonstrate that TNTRules generates high-fidelity, compact, and complete explanations, significantly outperforming three baselines on 5 multi-objective testing functions and 2 hyperparameter tuning problems.
Bayesian Optimization (BO) is a powerful method for optimizing black-box functions by combining prior knowledge with ongoing function evaluations. BO constructs a probabilistic surrogate model of the objective function given the covariates, which is in turn used to inform the selection of future evaluation points through an acquisition function. For smooth continuous search spaces, Gaussian Processes (GPs) are commonly used as the surrogate model as they offer analytical access to posterior predictive distributions, thus facilitating the computation and optimization of acquisition functions. However, in complex scenarios involving optimization over categorical or mixed covariate spaces, GPs may not be ideal. This paper introduces Simulation Based Bayesian Optimization (SBBO) as a novel approach to optimizing acquisition functions that only requires sampling-based access to posterior predictive distributions. SBBO allows the use of surrogate probabilistic models tailored for combinatorial spaces with discrete variables. Any Bayesian model in which posterior inference is carried out through Markov chain Monte Carlo can be selected as the surrogate model in SBBO. We demonstrate empirically the effectiveness of SBBO using various choices of surrogate models in applications involving combinatorial optimization. choices of surrogate models.
Gaussian processes are a powerful framework for quantifying uncertainty and for sequential decision-making but are limited by the requirement of solving linear systems. In general, this has a cubic cost in dataset size and is sensitive to conditioning. We explore stochastic gradient algorithms as a computationally efficient method of approximately solving these linear systems: we develop low-variance optimization objectives for sampling from the posterior and extend these to inducing points. Counterintuitively, stochastic gradient descent often produces accurate predictions, even in cases where it does not converge quickly to the optimum. We explain this through a spectral characterization of the implicit bias from non-convergence. We show that stochastic gradient descent produces predictive distributions close to the true posterior both in regions with sufficient data coverage, and in regions sufficiently far away from the data. Experimentally, stochastic gradient descent achieves state-of-the-art performance on sufficiently large-scale or ill-conditioned regression tasks. Its uncertainty estimates match the performance of significantly more expensive baselines on a large-scale Bayesian optimization task.
Neural Architecture Search (NAS) methods are widely used in various industries to obtain high quality taskspecific solutions with minimal human intervention. Event Sequences find widespread use in various industrial applications including churn prediction customer segmentation fraud detection and fault diagnosis among others. Such data consist of categorical and real-valued components with irregular timestamps. Despite the usefulness of NAS methods previous approaches only have been applied to other domains images texts or time series. Our work addresses this limitation by introducing a novel NAS algorithm SeqNAS specifically designed for event sequence classification. We develop a simple yet expressive search space that leverages commonly used building blocks for event sequence classification including multihead self attention convolutions and recurrent cells. To perform the search we adopt sequential Bayesian Optimization and utilize previously trained models as an ensemble of teachers to augment knowledge distillation. As a result of our work we demonstrate that our method surpasses state of the art NAS methods and popular architectures suitable for sequence classification and holds great potential for various industrial applications.
Sample efficiency is crucial in optimization, particularly in black-box scenarios characterized by expensive evaluations and zeroth-order feedback. When computing resources are plentiful, Bayesian optimization is often favored over evolution strategies. In this paper, we introduce a full invariance oriented evolution strategies algorithm, derived from its corresponding framework, that effectively rivals the leading Bayesian optimization method in tasks with dimensions at the upper limit of Bayesian capability. Specifically, we first build the framework InvIGO that fully incorporates historical information while retaining the full invariant and computational complexity. We then exemplify InvIGO on multi-dimensional Gaussian, which gives an invariant and scalable optimizer SynCMA . The theoretical behavior and advantages of our algorithm over other Gaussian-based evolution strategies are further analyzed. Finally, We benchmark SynCMA against leading algorithms in Bayesian optimization and evolution strategies on various high dimension tasks, in cluding Mujoco locomotion tasks, rover planning task and synthetic functions. In all scenarios, SynCMA demonstrates great competence, if not dominance, over other algorithms in sample efficiency, showing the underdeveloped potential of property oriented evolution strategies.
Variational Autoencoder based Bayesian Optimization (VAE-BO) has demonstrated its excellent performance in addressing high-dimensional structured optimization problems. However, current mainstream methods overlook the potential of utilizing a pool of unlabeled data to construct the latent space, while only concentrating on designing sophisticated models to leverage the labeled data. Despite their effective usage of labeled data, these methods often require extra network structures, additional procedure, resulting in computational inefficiency. To address this issue, we propose a novel method to effectively utilize unlabeled data with the guidance of labeled data. Specifically, we tailor the pseudo-labeling technique from semi-supervised learning to explicitly reveal the relative magnitudes of optimization objective values hidden within the unlabeled data. Based on this technique, we assign appropriate training weights to unlabeled data to enhance the construction of a discriminative latent space. Furthermore, we treat the VAE encoder and the Gaussian Process (GP) in Bayesian optimization as a unified deep kernel learning process, allowing the direct utilization of labeled data, which we term as Gaussian Process guidance. This directly and effectively integrates the goal of improving GP accuracy into the VAE training, thereby guiding the construction of the latent space. The extensive experiments demonstrate that our proposed method outperforms existing VAE-BO algorithms in various optimization scenarios. Our code will be published at https://github.com/TaicaiChen/PG-LBO.
Transfer optimization enables data-efficient optimization of a target task by leveraging experiential priors from related source tasks. This is especially useful in multiobjective optimization settings where a set of trade-off solutions is sought under tight evaluation budgets. In this paper, we introduce a novel concept of \textit{inverse transfer} in multiobjective optimization. Inverse transfer stands out by employing Bayesian inverse Gaussian process models to map performance vectors in the objective space to population search distributions in task-specific decision space, facilitating knowledge transfer through objective space unification. Building upon this idea, we introduce the first Inverse Transfer Evolutionary Multiobjective Optimizer (invTrEMO). A key highlight of invTrEMO is its ability to harness the common objective functions prevalent in many application areas, even when decision spaces do not precisely align between tasks. This allows invTrEMO to uniquely and effectively utilize information from heterogeneous source tasks as well. Furthermore, invTrEMO yields high-precision inverse models as a significant byproduct, enabling the generation of tailored solutions on-demand based on user preferences. Empirical studies on multi- and many-objective benchmark problems, as well as a practical case study, showcase the faster convergence rate and modelling accuracy of the invTrEMO relative to state-of-the-art evolutionary and Bayesian optimization algorithms. The source code of the invTrEMO is made available at https://github.com/LiuJ-2023/invTrEMO.
In this paper, we propose a novel inverse parameter estimation approach called Bayesian optimized physics-informed neural network (BOPINN). In this study, a PINN solves the partial differential equation (PDE), whereas Bayesian optimization (BO) estimates its parameter. The proposed BOPINN estimates wave velocity associated with wave propagation PDE using a single snapshot observation. An objective function for BO is defined as the mean squared error (MSE) between the surrogate displacement field and snapshot observation. The inverse estimation capability of the proposed approach is tested in three different isotropic media with different wave velocities. From the obtained results, we have observed that BOPINN can accurately estimate wave velocities with lower MSE, even in the presence of noisy conditions. The proposed algorithm shows robust predictions in limited iterations across different runs.
Many crucial scientific problems involve designing novel molecules with desired properties, which can be formulated as a black-box optimization problem over the discrete chemical space. In practice, multiple conflicting objectives and costly evaluations (e.g., wet-lab experiments) make the diversity of candidates paramount. Computational methods have achieved initial success but still struggle with considering diversity in both objective and search space. To fill this gap, we propose a multi-objective Bayesian optimization (MOBO) algorithm leveraging the hypernetwork-based GFlowNets (HN-GFN) as an acquisition function optimizer, with the purpose of sampling a diverse batch of candidate molecular graphs from an approximate Pareto front. Using a single preference-conditioned hypernetwork, HN-GFN learns to explore various trade-offs between objectives. We further propose a hindsight-like off-policy strategy to share high-performing molecules among different preferences in order to speed up learning for HN-GFN. We empirically illustrate that HN-GFN has adequate capacity to generalize over preferences. Moreover, experiments in various real-world MOBO settings demonstrate that our framework predominantly outperforms existing methods in terms of candidate quality and sample efficiency. The code is available at https://github.com/violet-sto/HN-GFN.
Out-of-distribution (OOD) generalization has long been a challenging problem that remains largely unsolved. Gaussian processes (GP), as popular probabilistic model classes, especially in the small data regime, presume strong OOD generalization abilities. Surprisingly, their OOD generalization abilities have been under-explored before compared with other lines of GP research. In this paper, we identify that GP is not free from the problem and propose a domain invariant learning algorithm for Gaussian processes (DIL-GP) with a min-max optimization on the likelihood. DIL-GP discovers the heterogeneity in the data and forces invariance across partitioned subsets of data. We further extend the DIL-GP to improve Bayesian optimization's adaptability on changing environments. Numerical experiments demonstrate the superiority of DIL-GP for predictions on several synthetic and real-world datasets. We further demonstrate the effectiveness of the DIL-GP Bayesian optimization method on a PID parameters tuning experiment for a quadrotor. The full version and source code are available at: https://github.com/Billzxl/DIL-GP.
Deep reinforcement learning (RL) approaches have been broadly applied to a large number of robotics tasks, such as robot manipulation and autonomous driving. However, an open problem in deep RL is learning policies that are robust to variations in the environment, which is an important condition for such systems to be deployed into real-world, unstructured settings. Curriculum learning is one approach that has been applied to improve generalization performance in both supervised and reinforcement learning domains, but selecting the appropriate curriculum to achieve robustness can be a user-intensive process. In our work, we show that performing probabilistic inference of the underlying curriculum-reward function using Bayesian Optimization can be a promising technique for finding a robust curriculum. We demonstrate that a curriculum found with Bayesian optimization can outperform a vanilla deep RL agent and a hand-engineered curriculum in the domain of autonomous racing with obstacle avoidance. Our code is available at https://github.com/PRISHIta123/Curriculum_RL_for_Driving.
Bayesian optimization (BO) is a sample-efficient method and has been widely used for optimizing expensive black-box functions. Recently, there has been a considerable interest in BO literature in optimizing functions that are affected by context variable in the environment, which is uncontrollable by decision makers. In this paper, we focus on the optimization of functions' expectations over continuous context variable, subject to an unknown distribution. To address this problem, we propose two algorithms that employ kernel density estimation to learn the probability density function (PDF) of continuous context variable online. The first algorithm is simpler, which directly optimizes the expectation under the estimated PDF. Considering that the estimated PDF may have high estimation error when the true distribution is complicated, we further propose the second algorithm that optimizes the distributionally robust objective. Theoretical results demonstrate that both algorithms have sub-linear Bayesian cumulative regret on the expectation objective. Furthermore, we conduct numerical experiments to empirically demonstrate the effectiveness of our algorithms.
The identification of the Purkinje conduction system in the heart is a challenging task, yet essential for a correct definition of cardiac digital twins for precision cardiology. Here, we propose a probabilistic approach for identifying the Purkinje network from non-invasive clinical data such as the standard electrocardiogram (ECG). We use cardiac imaging to build an anatomically accurate model of the ventricles; we algorithmically generate a rule-based Purkinje network tailored to the anatomy; we simulate physiological electrocardiograms with a fast model; we identify the geometrical and electrical parameters of the Purkinje-ECG model with Bayesian optimization and approximate Bayesian computation. The proposed approach is inherently probabilistic and generates a population of plausible Purkinje networks, all fitting the ECG within a given tolerance. In this way, we can estimate the uncertainty of the parameters, thus providing reliable predictions. We test our methodology in physiological and pathological scenarios, showing that we are able to accurately recover the ECG with our model. We propagate the uncertainty in the Purkinje network parameters in a simulation of conduction system pacing therapy. Our methodology is a step forward in creation of digital twins from non-invasive data in precision medicine. An open source implementation can be found at http://github.com/fsahli/purkinje-learning
In today's data-driven landscape, time series forecasting is pivotal in decision-making across various sectors. Yet, the proliferation of more diverse time series data, coupled with the expanding landscape of available forecasting methods, poses significant challenges for forecasters. To meet the growing demand for efficient forecasting, we introduce auto-sktime, a novel framework for automated time series forecasting. The proposed framework uses the power of automated machine learning (AutoML) techniques to automate the creation of the entire forecasting pipeline. The framework employs Bayesian optimization, to automatically construct pipelines from statistical, machine learning (ML) and deep neural network (DNN) models. Furthermore, we propose three essential improvements to adapt AutoML to time series data. First, pipeline templates to account for the different supported forecasting models. Second, a novel warm-starting technique to start the optimization from prior optimization runs. Third, we adapt multi-fidelity optimizations to make them applicable to a search space containing statistical, ML and DNN models. Experimental results on 64 diverse real-world time series datasets demonstrate the effectiveness and efficiency of the framework, outperforming traditional methods while requiring minimal human involvement.
Bayesian optimization (BO) has proven to be a powerful tool for automatically tuning control parameters without requiring knowledge of the underlying system dynamics. Safe BO methods, in addition, guarantee safety during the optimization process, assuming that the underlying objective function does not change. However, in real-world scenarios, time-variations frequently occur, for example, due to wear in the system or changes in operation. Utilizing standard safe BO strategies that do not address time-variations can result in failure as previous safe decisions may become unsafe over time, which we demonstrate herein. To address this, we introduce a new algorithm, Event-Triggered SafeOpt (ETSO), which adapts to changes online solely relying on the observed costs. At its core, ETSO uses an event trigger to detect significant deviations between observations and the current surrogate of the objective function. When such change is detected, the algorithm reverts to a safe backup controller, and exploration is restarted. In this way, safety is recovered and maintained across changes. We evaluate ETSO on quadcopter controller tuning, both in simulation and hardware experiments. ETSO outperforms state-of-the-art safe BO, achieving superior control performance over time while maintaining safety.
In this paper we introduce GP+, an open-source library for kernel-based learning via Gaussian processes (GPs) which are powerful statistical models that are completely characterized by their parametric covariance and mean functions. GP+ is built on PyTorch and provides a user-friendly and object-oriented tool for probabilistic learning and inference. As we demonstrate with a host of examples, GP+ has a few unique advantages over other GP modeling libraries. We achieve these advantages primarily by integrating nonlinear manifold learning techniques with GPs' covariance and mean functions. As part of introducing GP+, in this paper we also make methodological contributions that (1) enable probabilistic data fusion and inverse parameter estimation, and (2) equip GPs with parsimonious parametric mean functions which span mixed feature spaces that have both categorical and quantitative variables. We demonstrate the impact of these contributions in the context of Bayesian optimization, multi-fidelity modeling, sensitivity analysis, and calibration of computer models.
Bayesian optimization has emerged as a highly effective tool for the safe online optimization of systems, due to its high sample efficiency and noise robustness. To further enhance its efficiency, reduced physical models of the system can be incorporated into the optimization process, accelerating it. These models are able to offer an approximation of the actual system, and evaluating them is significantly cheaper. The similarity between the model and reality is represented by additional hyperparameters, which are learned within the optimization process. Safety is a crucial criterion for online optimization methods such as Bayesian optimization, which has been addressed by recent works that provide safety guarantees under the assumption of known hyperparameters. In practice, however, this does not apply. Therefore, we extend the robust Gaussian process uniform error bounds to meet the multi-task setting, which involves the calculation of a confidence region from the hyperparameter posterior distribution utilizing Markov chain Monte Carlo methods. Subsequently, the robust safety bounds are employed to facilitate the safe optimization of the system, while incorporating measurements of the models. Simulation results indicate that the optimization can be significantly accelerated for expensive to evaluate functions in comparison to other state-of-the-art safe Bayesian optimization methods, contingent on the fidelity of the models.
A popular approach to protein design is to combine a generative model with a discriminative model for conditional sampling. The generative model samples plausible sequences while the discriminative model guides a search for sequences with high fitness. Given its broad success in conditional sampling, classifier-guided diffusion modeling is a promising foundation for protein design, leading many to develop guided diffusion models for structure with inverse folding to recover sequences. In this work, we propose diffusioN Optimized Sampling (NOS), a guidance method for discrete diffusion models that follows gradients in the hidden states of the denoising network. NOS makes it possible to perform design directly in sequence space, circumventing significant limitations of structure-based methods, including scarce data and challenging inverse design. Moreover, we use NOS to generalize LaMBO, a Bayesian optimization procedure for sequence design that facilitates multiple objectives and edit-based constraints. The resulting method, LaMBO-2, enables discrete diffusions and stronger performance with limited edits through a novel application of saliency maps. We apply LaMBO-2 to a real-world protein design task, optimizing antibodies for higher expression yield and binding affinity to several therapeutic targets under locality and developability constraints, attaining a 99% expression rate and 40% binding rate in exploratory in vitro experiments.
The discovery of neural architectures from simple building blocks is a long-standing goal of Neural Architecture Search (NAS). Hierarchical search spaces are a promising step towards this goal but lack a unifying search space design framework and typically only search over some limited aspect of architectures. In this work, we introduce a unifying search space design framework based on context-free grammars that can naturally and compactly generate expressive hierarchical search spaces that are 100s of orders of magnitude larger than common spaces from the literature. By enhancing and using their properties, we effectively enable search over the complete architecture and can foster regularity. Further, we propose an efficient hierarchical kernel design for a Bayesian Optimization search strategy to efficiently search over such huge spaces. We demonstrate the versatility of our search space design framework and show that our search strategy can be superior to existing NAS approaches. Code is available at https://github.com/automl/hierarchical_nas_construction.