Molecular property optimization (MPO) problems are inherently challenging since they are formulated over discrete, unstructured spaces and the labeling process involves expensive simulations or experiments, which fundamentally limits the amount of available data. Bayesian optimization (BO) is a powerful and popular framework for efficient optimization of noisy, black-box objective functions (e.g., measured property values), thus is a potentially attractive framework for MPO. To apply BO to MPO problems, one must select a structured molecular representation that enables construction of a probabilistic surrogate model. Many molecular representations have been developed, however, they are all high-dimensional, which introduces important challenges in the BO process -- mainly because the curse of dimensionality makes it difficult to define and perform inference over a suitable class of surrogate models. This challenge has been recently addressed by learning a lower-dimensional encoding of a SMILE or graph representation of a molecule in an unsupervised manner and then performing BO in the encoded space. In this work, we show that such methods have a tendency to "get stuck," which we hypothesize occurs since the mapping from the encoded space to property values is not necessarily well-modeled by a Gaussian process. We argue for an alternative approach that combines numerical molecular descriptors with a sparse axis-aligned Gaussian process model, which is capable of rapidly identifying sparse subspaces that are most relevant to modeling the unknown property function. We demonstrate that our proposed method substantially outperforms existing MPO methods on a variety of benchmark and real-world problems. Specifically, we show that our method can routinely find near-optimal molecules out of a set of more than $>100$k alternatives within 100 or fewer expensive queries.
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.
Fault-tolerant deep learning accelerator is the basis for highly reliable deep learning processing and critical to deploy deep learning in safety-critical applications such as avionics and robotics. Since deep learning is known to be computing- and memory-intensive, traditional fault-tolerant approaches based on redundant computing will incur substantial overhead including power consumption and chip area. To this end, we propose to characterize deep learning vulnerability difference across both neurons and bits of each neuron, and leverage the vulnerability difference to enable selective protection of the deep learning processing components from the perspective of architecture layer and circuit layer respectively. At the same time, we observe the correlation between model quantization and bit protection overhead of the underlying processing elements of deep learning accelerators, and propose to reduce the bit protection overhead by adding additional quantization constrain without compromising the model accuracy. Finally, we employ Bayesian optimization strategy to co-optimize the correlated cross-layer design parameters at algorithm layer, architecture layer, and circuit layer to minimize the hardware resource consumption while fulfilling multiple user constraints including reliability, accuracy, and performance of the deep learning processing at the same time.
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.
Azure Cognitive Search (ACS) has emerged as a major contender in "Search as a Service" cloud products in recent years. However, one of the major challenges for ACS users is to improve the relevance of the search results for their specific usecases. In this paper, we propose a novel method to find the optimal ACS configuration that maximizes search relevance for a specific usecase (product search, document search...) The proposed solution improves key online marketplace metrics such as click through rates (CTR) by formulating the search relevance problem as hyperparameter tuning. We have observed significant improvements in real-world search call to action (CTA) rate in multiple marketplaces by introducing optimized weights generated from the proposed approach.
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 adoption of high-fidelity models for many-query optimization problems is majorly limited by the significant computational cost required for their evaluation at every query. Multifidelity Bayesian methods (MFBO) allow to include costly high-fidelity responses for a sub-selection of queries only, and use fast lower-fidelity models to accelerate the optimization process. State-of-the-art methods rely on a purely data-driven search and do not include explicit information about the physical context. This paper acknowledges that prior knowledge about the physical domains of engineering problems can be leveraged to accelerate these data-driven searches, and proposes a generalized formulation for MFBO to embed a form of domain awareness during the optimization procedure. In particular, we formalize a bias as a multifidelity acquisition function that captures the physical structure of the domain. This permits to partially alleviate the data-driven search from learning the domain properties on-the-fly, and sensitively enhances the management of multiple sources of information. The method allows to efficiently include high-fidelity simulations to guide the optimization search while containing the overall computational expense. Our physics-aware multifidelity Bayesian optimization is presented and illustrated for two classes of optimization problems frequently met in science and engineering, namely design optimization and health monitoring problems.
In software engineering, the meticulous configuration of software tools is crucial in ensuring optimal performance within intricate systems. However, the complexity inherent in selecting optimal configurations is exacerbated by the high-dimensional search spaces presented in modern applications. Conventional trial-and-error or intuition-driven methods are both inefficient and error-prone, impeding scalability and reproducibility. In this study, we embark on an exploration of leveraging Large-Language Models (LLMs) to streamline the software configuration process. We identify that the task of hyperparameter configuration for machine learning components within intelligent applications is particularly challenging due to the extensive search space and performance-critical nature. Existing methods, including Bayesian optimization, have limitations regarding initial setup, computational cost, and convergence efficiency. Our work presents a novel approach that employs LLMs, such as Chat-GPT, to identify starting conditions and narrow down the search space, improving configuration efficiency. We conducted a series of experiments to investigate the variability of LLM-generated responses, uncovering intriguing findings such as potential response caching and consistent behavior based on domain-specific keywords. Furthermore, our results from hyperparameter optimization experiments reveal the potential of LLMs in expediting initialization processes and optimizing configurations. While our initial insights are promising, they also indicate the need for further in-depth investigations and experiments in this domain.
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.
This paper explores the use of foundational large language models (LLMs) in hyperparameter optimization (HPO). Hyperparameters are critical in determining the effectiveness of machine learning models, yet their optimization often relies on manual approaches in limited-budget settings. By prompting LLMs with dataset and model descriptions, we develop a methodology where LLMs suggest hyperparameter configurations, which are iteratively refined based on model performance. Our empirical evaluations on standard benchmarks reveal that within constrained search budgets, LLMs can match or outperform traditional HPO methods like Bayesian optimization across different models on standard benchmarks. Furthermore, we propose to treat the code specifying our model as a hyperparameter, which the LLM outputs and affords greater flexibility than existing HPO approaches.