ProtGO: Function-Guided Protein Modeling for Unified Representation Learning

Protein representation learning is indispensable for various downstream applications of artificial intelligence for bio-medicine research, such as drug design and function prediction. However, achieving effective representation learning for proteins poses challenges due to the diversity of data modalities involved, including sequence, structure, and function annotations. Despite the impressive capabilities of large language models in biomedical text modelling, there remains a pressing need for a framework that seamlessly integrates these diverse modalities, particularly focusing on the three critical aspects of protein information: sequence, structure, and function. Moreover, addressing the inherent data scale differences among these modalities is essential. To tackle these challenges, we introduce ProtGO, a unified model that harnesses a teacher network equipped with a customized graph neural network (GNN) and a Gene Ontology (GO) encoder to learn hybrid embeddings. Notably, our approach eliminates the need for additional functions as input for the student network, which shares the same GNN module. Importantly, we utilize a domain adaptation method to facilitate distribution approximation for guiding the training of the teacher-student framework. This approach leverages distributions learned from latent representations to avoid the alignment of individual samples. Benchmark experiments highlight that ProtGO significantly outperforms state-of-the-art baselines, clearly demonstrating the advantages of the proposed unified framework.