Liver cancer knowledge graph construction based on dynamic entity replacement and masking strategies RoBERTa-wwm-large-BiLSTM-CRF model with clinical Chinese EMRs

Yichi Zhang¹Xiaojun Hu²Hailing Wang^1*Ke Liu³Yongbin Gao¹Xiaoyan Jiang¹Yingfang Fan^2*Zhijun Fang¹

• ¹Shanghai University of Engineering Sciences, Shanghai, China
• ²The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
• ³Beijing Anding Hospital Capital Medical University, Beijing, China

Introduction: Liver cancer is a leading cause of cancer-related mortality worldwide, necessitating advanced tools for diagnosis and management. Knowledge graphs (KGs) are crucial for advancing smart healthcare, but existing liver cancer-specific KGs are mostly derived from literature or public databases, lacking integration with real-world clinical data (e.g., Electronic Medical Records (EMRs)), creating a critical gap. Furthermore, there is currently no publicly available KGs specifically for liver cancer, creating a significant gap in structured clinical knowledge resources. Methods: This study proposes a novel framework to construct the first Chinese liver cancer KG from Real-World Liver Cancer Electronic Medical Records (RLC-EMRs). A new named entity recognition (NER) model, DERM-RoBERTa-wwm-large-BiLSTM-CRF was developed that uses a Dynamic Entity Replacement and Masking (DERM) strategy to address data scarcity. Knowledge fusion was performed using the TF-IDF algorithm to standardize and integrate entities from clinical records, the professional medical website XYWY.com, and the CCMT-2019 terminology standard. Results: The final constructed liver cancer KG contained 46,364 entities and 296,655 semantic relationships. The proposed NER model achieved a state-of-the-art F1 score of 68.84% on the public CMeEE-v2 dataset. On the proprietary RLC-EMRs dataset, the model demonstrated high effectiveness with a precision of 93.23%, recall of 94.69%, and an F1 score of 93.96%. In addition, a KG-based retrieval system was successfully developed to query for complications, medications, and other related information. Discussion: The findings demonstrated the effectiveness of the proposed framework in constructing a comprehensive and clinically relevant liver cancer KG. The novel DERM-based NER model significantly improved entity extraction from complex medical texts. By successfully integrating real-world clinical data, this study addresses a critical gap in existing liver cancer-specific KGs, which are mostly derived from literature or public databases and lack integration with real-world clinical information.