Adapting Differential Molecular Representation with Hierarchical Prompts for Multi-label Property Prediction

Accurate prediction of molecular properties is critical in the field of drug discovery. However, existing methods do not fully consider the fact that molecules in the real world usually possess multiple property labels, and complex high-order relationships may exist among these labels. Therefore, molecular representation learning models should generate differential molecular representations that consider multi-granularity correlation information among tasks. To this end, our research introduces a Hierarchical Prompted Molecular Representation Learning Framework (HiPM), which enhances the differential expression of tasks in molecular representations through task-aware prompts, and utilizes shared information among labels to mitigate negative transfer between different tasks. HiPM primarily consists of two core components: the Molecular Representation Encoder (MRE) and the Task-Aware Prompter (TAP). The MRE employs a hierarchical message-passing network architecture to capture molecular features at both the atomic and motif levels, while the TAP uses agglomerative hierarchical clustering to build a prompt tree that reflects the affinity and distinctiveness of tasks, enabling the model to effectively handle the complexity of multi-label property predictions. Extensive experiments demonstrate that HiPM achieves state-of-the-art performance across various multi-label datasets, offering a new perspective on multi-label molecular representation learning.