Shuhei Watanabe

Shuhei Watanabe

Recent scientific advances require complex experiment design, necessitating the meticulous tuning of many experiment parameters. Tree-structured Parzen estimator (TPE) is a widely used Bayesian optimization method in recent parameter tuning frameworks such as Hyperopt and Optuna. Despite its popularity, the roles of each control parameter in TPE and the algorithm intuition have not been discussed so far. The goal of this paper is to identify the roles of each control parameter and their impacts on parameter tuning based on the ablation studies using diverse benchmark datasets. The recommended setting concluded from the ablation studies is demonstrated to improve the performance of TPE. Our TPE implementation used in this paper is available at https://github.com/nabenabe0928/tpe/tree/single-opt.

Shuhei Watanabe, Archit Bansal, Frank Hutter

The recent rise in popularity of Hyperparameter Optimization (HPO) for deep learning has highlighted the role that good hyperparameter (HP) space design can play in training strong models. In turn, designing a good HP space is critically dependent on understanding the role of different HPs. This motivates research on HP Importance (HPI), e.g., with the popular method of functional ANOVA (f-ANOVA). However, the original f-ANOVA formulation is inapplicable to the subspaces most relevant to algorithm designers, such as those defined by top performance. To overcome this issue, we derive a novel formulation of f-ANOVA for arbitrary subspaces and propose an algorithm that uses Pearson divergence (PED) to enable a closed-form calculation of HPI. We demonstrate that this new algorithm, dubbed PED-ANOVA, is able to successfully identify important HPs in different subspaces while also being extremely computationally efficient.

Shuhei Watanabe, Frank Hutter

Hyperparameter optimization (HPO) is crucial for strong performance of deep learning algorithms and real-world applications often impose some constraints, such as memory usage, or latency on top of the performance requirement. In this work, we propose constrained TPE (c-TPE), an extension of the widely-used versatile Bayesian optimization method, tree-structured Parzen estimator (TPE), to handle these constraints. Our proposed extension goes beyond a simple combination of an existing acquisition function and the original TPE, and instead includes modifications that address issues that cause poor performance. We thoroughly analyze these modifications both empirically and theoretically, providing insights into how they effectively overcome these challenges. In the experiments, we demonstrate that c-TPE exhibits the best average rank performance among existing methods with statistical significance on 81 expensive HPO with inequality constraints. Due to the lack of baselines, we only discuss the applicability of our method to hard-constrained optimization in Appendix D.

Shuhei Watanabe, Noor Awad, Masaki Onishi et al.

Hyperparameter optimization (HPO) is a vital step in improving performance in deep learning (DL). Practitioners are often faced with the trade-off between multiple criteria, such as accuracy and latency. Given the high computational needs of DL and the growing demand for efficient HPO, the acceleration of multi-objective (MO) optimization becomes ever more important. Despite the significant body of work on meta-learning for HPO, existing methods are inapplicable to MO tree-structured Parzen estimator (MO-TPE), a simple yet powerful MO-HPO algorithm. In this paper, we extend TPE's acquisition function to the meta-learning setting using a task similarity defined by the overlap of top domains between tasks. We also theoretically analyze and address the limitations of our task similarity. In the experiments, we demonstrate that our method speeds up MO-TPE on tabular HPO benchmarks and attains state-of-the-art performance. Our method was also validated externally by winning the AutoML 2022 competition on "Multiobjective Hyperparameter Optimization for Transformers".

Kaito Baba, Yoshihiko Ozaki, Shuhei Watanabe

We propose conditional PED-ANOVA (condPED-ANOVA), a principled framework for estimating hyperparameter importance (HPI) in conditional search spaces, where the presence or domain of a hyperparameter can depend on other hyperparameters. Although the original PED-ANOVA provides a fast and efficient way to estimate HPI within the top-performing regions of the search space, it assumes a fixed, unconditional search space and therefore cannot properly handle conditional hyperparameters. To address this, we introduce a conditional HPI for top-performing regions and derive a closed-form estimator that accurately reflects conditional activation and domain changes. Experiments show that naive adaptations of existing HPI estimators yield misleading or uninterpretable importance estimates in conditional settings, whereas condPED-ANOVA consistently provides meaningful importances that reflect the underlying conditional structure.

Kenshin Abe, Yunzhuo Wang, Shuhei Watanabe

Tree-structured Parzen estimator (TPE) is a versatile hyperparameter optimization (HPO) method supported by popular HPO tools. Since these HPO tools have been developed in line with the trend of deep learning (DL), the problem setups often used in the DL domain have been discussed for TPE such as multi-objective optimization and multi-fidelity optimization. However, the practical applications of HPO are not limited to DL, and black-box combinatorial optimization is actively utilized in some domains, e.g., chemistry and biology. As combinatorial optimization has been an untouched, yet very important, topic in TPE, we propose an efficient combinatorial optimization algorithm for TPE. In this paper, we first generalize the categorical kernel with the numerical kernel in TPE, enabling us to introduce a distance structure to the categorical kernel. Then we discuss modifications for the newly developed kernel to handle a large combinatorial search space. These modifications reduce the time complexity of the kernel calculation with respect to the size of a combinatorial search space. In the experiments using synthetic problems, we verified that our proposed method identifies better solutions with fewer evaluations than the original TPE. Our algorithm is available in Optuna, an open-source framework for HPO.

Shuhei Watanabe

Hyperparameter (HP) optimization of deep learning (DL) is essential for high performance. As DL often requires several hours to days for its training, HP optimization (HPO) of DL is often prohibitively expensive. This boosted the emergence of tabular or surrogate benchmarks, which enable querying the (predictive) performance of DL with a specific HP configuration in a fraction. However, since the actual runtime of a DL training is significantly different from its query response time, simulators of an asynchronous HPO, e.g. multi-fidelity optimization, must wait for the actual runtime at each iteration in a naïve implementation; otherwise, the evaluation order during simulation does not match with the real experiment. To ease this issue, we developed a Python wrapper and describe its usage. This wrapper forces each worker to wait so that we yield exactly the same evaluation order as in the real experiment with only $10^{-2}$ seconds of waiting instead of waiting several hours. Our implementation is available at https://github.com/nabenabe0928/mfhpo-simulator/.

Shuhei Watanabe

Hyperparameter optimization is crucial to achieving high performance in deep learning. On top of the performance, other criteria such as inference time or memory requirement often need to be optimized due to some practical reasons. This motivates research on multi-objective optimization (MOO). However, Pareto fronts of MOO methods are often shown without considering the variability caused by random seeds and this makes the performance stability evaluation difficult. Although there is a concept named empirical attainment surface to enable the visualization with uncertainty over multiple runs, there is no major Python package for empirical attainment surface. We, therefore, develop a Python package for this purpose and describe the usage. The package is available at https://github.com/nabenabe0928/empirical-attainment-func.

Shuhei Watanabe, Neeratyoy Mallik, Edward Bergman et al.

While deep learning has celebrated many successes, its results often hinge on the meticulous selection of hyperparameters (HPs). However, the time-consuming nature of deep learning training makes HP optimization (HPO) a costly endeavor, slowing down the development of efficient HPO tools. While zero-cost benchmarks, which provide performance and runtime without actual training, offer a solution for non-parallel setups, they fall short in parallel setups as each worker must communicate its queried runtime to return its evaluation in the exact order. This work addresses this challenge by introducing a user-friendly Python package that facilitates efficient parallel HPO with zero-cost benchmarks. Our approach calculates the exact return order based on the information stored in file system, eliminating the need for long waiting times and enabling much faster HPO evaluations. We first verify the correctness of our approach through extensive testing and the experiments with 6 popular HPO libraries show its applicability to diverse libraries and its ability to achieve over 1000x speedup compared to a traditional approach. Our package can be installed via pip install mfhpo-simulator.

Shuhei Watanabe

Gaussian process (GP) is arguably one of the most widely used machine learning algorithms in practice. One of its prominent applications is Bayesian optimization (BO). Although the vanilla GP itself is already a powerful tool for BO, it is often beneficial to be able to consider the dependencies of multiple outputs. To do so, Multi-task GP (MTGP) is formulated, but it is not trivial to fully understand the derivations of its formulations and their gradients from the previous literature. This paper serves friendly derivations of the MTGP formulations and their gradients.

Shuhei Watanabe

Expected Improvement (EI) is arguably the most widely used acquisition function in Bayesian optimization. However, it is often challenging to enhance the performance with EI due to its sensitivity to numerical precision. Previously, Hutter et al. (2009) tackled this problem by using Gaussian process trained on the log-transformed objective function and it was reported that this trick improves the predictive accuracy of GP, leading to substantially better performance. Although Hutter et al. (2009) offered the closed form of their EI, its intermediate derivation has not been provided so far. In this paper, we give a friendly derivation of their proposition.

Shuhei Watanabe

Hypervolume (HV)-based Bayesian optimization (BO) is one of the standard approaches for multi-objective decision-making. However, the computational cost of optimizing the acquisition function remains a significant bottleneck, primarily due to the expense of HV improvement calculations. While HV box-decomposition offers an efficient way to cope with the frequent exact improvement calculations, it suffers from super-polynomial memory complexity $O(MN^{\lfloor \frac{M + 1}{2} \rfloor})$ in the worst case as proposed by Lacour et al. (2017). To tackle this problem, Couckuyt et al. (2012) employed an approximation algorithm. However, a rigorous algorithmic description is currently absent from the literature. This paper bridges this gap by providing comprehensive mathematical and algorithmic details of this approximation algorithm.

Kaichi Irie, Shuhei Watanabe, Masaki Onishi

Bayesian optimization (BO) efficiently finds high-performing parameters by maximizing an acquisition function, which models the promise of parameters. A major computational bottleneck arises in acquisition function optimization, where multi-start optimization (MSO) with quasi-Newton (QN) methods is required due to the non-convexity of the acquisition function. BoTorch, a widely used BO library, currently optimizes the summed acquisition function over multiple points, leading to the speedup of MSO owing to PyTorch batching. Nevertheless, this paper empirically demonstrates the suboptimality of this approach in terms of off-diagonal approximation errors in the inverse Hessian of a QN method, slowing down its convergence. To address this problem, we propose to decouple QN updates using a coroutine while batching the acquisition function calls. Our approach not only yields the theoretically identical convergence to the sequential MSO but also drastically reduces the wall-clock time compared to the previous approaches. Our approach is available in GPSampler in Optuna, effectively reducing its computational overhead.

Yoshihiko Ozaki, Shuhei Watanabe, Toshihiko Yanase

Black-box optimization (BBO) drives advances in domains such as AutoML and Materials Informatics, yet research efforts often remain fragmented across domains. We introduce OptunaHub (https://hub.optuna.org/), a community platform that centralizes BBO methods and benchmarks. OptunaHub provides unified Python APIs, a contributor package registry, and a web interface to promote searchability and cross-domain research. OptunaHub aims to foster a virtuous cycle of contributions and applications. The source code is publicly available in the optunahub, optunahub-registry, and optunahub-web repositories under the Optuna organization on GitHub (https://github.com/optuna/).

Chisa Mori, Shuhei Watanabe, Masaki Onishi et al.

Parallel coordinate plots (PCPs) are a prevalent method to interpret the relationship between the control parameters and metrics. PCPs deliver such an interpretation by color gradation based on a single metric. However, it is challenging to provide such a gradation when multiple metrics are present. Although a naive approach involves calculating a single metric by linearly weighting each metric, such weighting is unclear for users. To address this problem, we first propose a principled formulation for calculating the optimal weight based on a specific preferred metric combination. Although users can simply select their preference from a two-dimensional (2D) plane for bi-metric problems, multi-metric problems require intuitive visualization to allow them to select their preference. We achieved this using various radar charts to visualize the metric trade-offs on the 2D plane reduced by UMAP. In the analysis using pedestrian flow guidance planning, our method identified unique patterns of control parameter importance for each user preference, highlighting the effectiveness of our method.

Masahiro Nomura, Shuhei Watanabe, Youhei Akimoto et al.

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.