Lida Zhu

Shuoying Wei, Xinlong Wen, Lida Zhu et al.

Obtaining accurate and valid information for drug molecules is a crucial and challenging task. However, chemical knowledge and information have been accumulated over the past 100 years from various regions, laboratories, and experimental purposes. Little has been explored in terms of the out-of-distribution (OOD) problem with noise and inconsistency, which may lead to weak robustness and unsatisfied performance. This study proposes a novel benchmark ADMEOOD, a systematic OOD dataset curator and benchmark specifically designed for drug property prediction. ADMEOOD obtained 27 ADME (Absorption, Distribution, Metabolism, Excretion) drug properties from Chembl and relevant literature. Additionally, it includes two kinds of OOD data shifts: Noise Shift and Concept Conflict Drift (CCD). Noise Shift responds to the noise level by categorizing the environment into different confidence levels. On the other hand, CCD describes the data which has inconsistent label among the original data. Finally, it tested on a variety of domain generalization models, and the experimental results demonstrate the effectiveness of the proposed partition method in ADMEOOD: ADMEOOD demonstrates a significant difference performance between in-distribution and out-of-distribution data. Moreover, ERM (Empirical Risk Minimization) and other models exhibit distinct trends in performance across different domains and measurement types.

Zhengyi Li, Menglu Li, Lida Zhu et al.

Protein post-translational modification (PTM) site prediction is a fundamental task in bioinformatics. Several computational methods have been developed to predict PTM sites. However, existing methods ignore the structure information and merely utilize protein sequences. Furthermore, designing a more fine-grained structure representation learning method is urgently needed as PTM is a biological event that occurs at the atom granularity. In this paper, we propose a PTM site prediction method by Coupling of Multi-Granularity structure and Multi-Scale sequence representation, PTM-CMGMS for brevity. Specifically, multigranularity structure-aware representation learning is designed to learn neighborhood structure representations at the amino acid, atom, and whole protein granularity from AlphaFold predicted structures, followed by utilizing contrastive learning to optimize the structure representations.Additionally, multi-scale sequence representation learning is used to extract context sequence information, and motif generated by aligning all context sequences of PTM sites assists the prediction. Extensive experiments on three datasets show that PTM-CMGMS outperforms the state-of-the-art methods.