NaNa and MiGu: Semantic Data Augmentation Techniques to Enhance Protein Classification in Graph Neural Networks

Protein classification tasks are essential in drug discovery. Real-world protein structures are dynamic, which will determine the properties of proteins. However, the existing machine learning methods, like ProNet (Wang et al., 2022a), only access limited conformational characteristics and protein side-chain features, leading to impractical protein structure and inaccuracy of protein classes in their predictions. In this paper, we propose novel semantic data augmentation methods, Novel Augmentation of New Node Attributes (NaNa), and Molecular Interactions and Geometric Upgrading (MiGu) to incorporate backbone chemical and side-chain biophysical information into protein classification tasks and a co-embedding residual learning framework. Specifically, we leverage molecular biophysical, secondary structure, chemical bonds, and ionic features of proteins to facilitate protein classification tasks. Furthermore, our semantic augmentation methods and the co-embedding residual learning framework can improve the performance of GIN (Xu et al., 2019) on EC and Fold datasets (Bairoch, 2000; Andreeva et al., 2007) by 16.41% and 11.33% respectively. Our code is available at https://github.com/r08b46009/Code_for_MIGU_NANA/tree/main.