Knowledge-aware Attention Network for Protein-Protein Interaction Extraction
This work addresses the problem of extracting protein-protein interactions for precision medicine, offering an incremental improvement by incorporating knowledge bases to reduce feature engineering.
The paper tackled protein-protein interaction extraction from scientific literature by proposing a knowledge-aware attention network that fuses prior knowledge and context information, achieving new state-of-the-art performance on the BioCreative VI PPI dataset.
Protein-protein interaction (PPI) extraction from published scientific literature provides additional support for precision medicine efforts. However, many of the current PPI extraction methods need extensive feature engineering and cannot make full use of the prior knowledge in knowledge bases (KB). KBs contain huge amounts of structured information about entities and relationships, therefore plays a pivotal role in PPI extraction. This paper proposes a knowledge-aware attention network (KAN) to fuse prior knowledge about protein-protein pairs and context information for PPI extraction. The proposed model first adopts a diagonal-disabled multi-head attention mechanism to encode context sequence along with knowledge representations learned from KB. Then a novel multi-dimensional attention mechanism is used to select the features that can best describe the encoded context. Experiment results on the BioCreative VI PPI dataset show that the proposed approach could acquire knowledge-aware dependencies between different words in a sequence and lead to a new state-of-the-art performance.