Zhenqian Shen

Zhenqian Shen, Mingyang Zhou, Yongqi Zhang et al.

Motivation: Emerging drug-drug interaction (DDI) prediction is crucial for new drugs but is hindered by distribution changes between known and new drugs in real-world scenarios. Current evaluation often neglects these changes, relying on unrealistic i.i.d. split due to the absence of drug approval data. Results: We propose DDI-Ben, a benchmarking framework for emerging DDI prediction under distribution changes. DDI-Ben introduces a distribution change simulation framework that leverages distribution changes between drug sets as a surrogate for real-world distribution changes of DDIs, and is compatible with various drug split strategies. Through extensive benchmarking on ten representative methods, we show that most existing approaches suffer substantial performance degradation under distribution changes. Our analysis further indicates that large language model (LLM) based methods and the integration of drug-related textual information offer promising robustness against such degradation. To support future research, we release the benchmark datasets with simulated distribution changes. Overall, DDI-Ben highlights the importance of explicitly addressing distribution changes and provides a foundation for developing more resilient methods for emerging DDI prediction. Availability and implementation: Our code and data are available at https://github.com/LARS-research/DDI-Bench.

Zhenqian Shen, Yongqi Zhang, Lanning Wei et al.

Machine learning (ML) methods have been developing rapidly, but configuring and selecting proper methods to achieve a desired performance is increasingly difficult and tedious. To address this challenge, automated machine learning (AutoML) has emerged, which aims to generate satisfactory ML configurations for given tasks in a data-driven way. In this paper, we provide a comprehensive survey on this topic. We begin with the formal definition of AutoML and then introduce its principles, including the bi-level learning objective, the learning strategy, and the theoretical interpretation. Then, we summarize the AutoML practices by setting up the taxonomy of existing works based on three main factors: the search space, the search algorithm, and the evaluation strategy. Each category is also explained with the representative methods. Then, we illustrate the principles and practices with exemplary applications from configuring ML pipeline, one-shot neural architecture search, and integration with foundation models. Finally, we highlight the emerging directions of AutoML and conclude the survey.