Xuezhong Zhou

Xinyan Wang, Ting Jia, Chongyu Wang et al. · tsinghua

Accurate identification of disease genes has consistently been one of the keys to decoding a disease's molecular mechanism. Most current approaches focus on constructing biological networks and utilizing machine learning, especially, deep learning to identify disease genes, but ignore the complex relations between entities in the biological knowledge graph. In this paper, we construct a biological knowledge graph centered on diseases and genes, and develop an end-to-end Knowledge graph completion model for Disease Gene Prediction using interactional tensor decomposition (called KDGene). KDGene introduces an interaction module between the embeddings of entities and relations to tensor decomposition, which can effectively enhance the information interaction in biological knowledge. Experimental results show that KDGene significantly outperforms state-of-the-art algorithms. Furthermore, the comprehensive biological analysis of the case of diabetes mellitus confirms KDGene's ability for identifying new and accurate candidate genes. This work proposes a scalable knowledge graph completion framework to identify disease candidate genes, from which the results are promising to provide valuable references for further wet experiments.

Rui Hua, Yu Wei, Zixin Shu et al.

Large language models (LLMs) are advancing rapidly in medical NLP, yet Traditional Chinese Medicine (TCM) with its distinctive ontology, terminology, and reasoning patterns requires domain-faithful evaluation. Existing TCM benchmarks are fragmented in coverage and scale and rely on non-unified or generation-heavy scoring that hinders fair comparison. We present the LingLanMiDian (LingLan) benchmark, a large-scale, expert-curated, multi-task suite that unifies evaluation across knowledge recall, multi-hop reasoning, information extraction, and real-world clinical decision-making. LingLan introduces a consistent metric design, a synonym-tolerant protocol for clinical labels, a per-dataset 400-item Hard subset, and a reframing of diagnosis and treatment recommendation into single-choice decision recognition. We conduct comprehensive, zero-shot evaluations on 14 leading open-source and proprietary LLMs, providing a unified perspective on their strengths and limitations in TCM commonsense knowledge understanding, reasoning, and clinical decision support; critically, the evaluation on Hard subset reveals a substantial gap between current models and human experts in TCM-specialized reasoning. By bridging fundamental knowledge and applied reasoning through standardized evaluation, LingLan establishes a unified, quantitative, and extensible foundation for advancing TCM LLMs and domain-specific medical AI research. All evaluation data and code are available at https://github.com/TCMAI-BJTU/LingLan and http://tcmnlp.com.

Kuo Yang, Zecong Yu, Xin Su et al. · tsinghua

Treatment planning for chronic diseases is a critical task in medical artificial intelligence, particularly in traditional Chinese medicine (TCM). However, generating optimized sequential treatment strategies for patients with chronic diseases in different clinical encounters remains a challenging issue that requires further exploration. In this study, we proposed a TCM herbal prescription planning framework based on deep reinforcement learning for chronic disease treatment (PrescDRL). PrescDRL is a sequential herbal prescription optimization model that focuses on long-term effectiveness rather than achieving maximum reward at every step, thereby ensuring better patient outcomes. We constructed a high-quality benchmark dataset for sequential diagnosis and treatment of diabetes and evaluated PrescDRL against this benchmark. Our results showed that PrescDRL achieved a higher curative effect, with the single-step reward improving by 117% and 153% compared to doctors. Furthermore, PrescDRL outperformed the benchmark in prescription prediction, with precision improving by 40.5% and recall improving by 63%. Overall, our study demonstrates the potential of using artificial intelligence to improve clinical intelligent diagnosis and treatment in TCM.

Kuan Xu, Kuo Yang, Hanyang Dong et al. · tsinghua

Knowledge graph completion (KGC) is one of the effective methods to identify new facts in knowledge graph. Except for a few methods based on graph network, most of KGC methods trend to be trained based on independent triples, while are difficult to take a full account of the information of global network connection contained in knowledge network. To address these issues, in this study, we propose a simple and effective Network-based Pre-training framework for knowledge graph completion (termed NetPeace), which takes into account the information of global network connection and local triple relationships in knowledge graph. Experiments show that in NetPeace framework, multiple KGC models yields consistent and significant improvements on benchmarks (e.g., 36.45% Hits@1 and 27.40% MRR improvements for TuckER on FB15k-237), especially dense knowledge graph. On the challenging low-resource task, NetPeace that benefits from the global features of KG achieves higher performance (104.03% MRR and 143.89% Hit@1 improvements at most) than original models.

Xingzhi Zhou, Xin Dong, Chunhao Li et al.

Traditional Chinese medicine (TCM) has relied on specific combinations of herbs in prescriptions to treat various symptoms and signs for thousands of years. Predicting TCM prescriptions poses a fascinating technical challenge with significant practical implications. However, this task faces limitations due to the scarcity of high-quality clinical datasets and the complex relationship between symptoms and herbs. To address these issues, we introduce \textit{DigestDS}, a novel dataset comprising practical medical records from experienced experts in digestive system diseases. We also propose a method, TCM-FTP (TCM Fine-Tuning Pre-trained), to leverage pre-trained large language models (LLMs) via supervised fine-tuning on \textit{DigestDS}. Additionally, we enhance computational efficiency using a low-rank adaptation technique. Moreover, TCM-FTP incorporates data augmentation by permuting herbs within prescriptions, exploiting their order-agnostic nature. Impressively, TCM-FTP achieves an F1-score of 0.8031, significantly outperforming previous methods. Furthermore, it demonstrates remarkable accuracy in dosage prediction, achieving a normalized mean square error of 0.0604. In contrast, LLMs without fine-tuning exhibit poor performance. Although LLMs have demonstrated wide-ranging capabilities, our work underscores the necessity of fine-tuning for TCM prescription prediction and presents an effective way to accomplish this.

Zixin Shu, Rui Hua, Dengying Yan et al.

Symptom phenotypes are one of the key types of manifestations for diagnosis and treatment of various disease conditions. However, the diversity of symptom terminologies is one of the major obstacles hindering the analysis and knowledge sharing of various types of symptom-related medical data particularly in the fields of Traditional Chinese Medicine (TCM). Objective: This study aimed to construct an Integrated Ontology of symptom phenotypes (ISPO) to support the data mining of Chinese EMRs and real-world study in TCM field. Methods: To construct an integrated ontology of symptom phenotypes (ISPO), we manually annotated classical TCM textbooks and large-scale Chinese electronic medical records (EMRs) to collect symptom terms with support from a medical text annotation system. Furthermore, to facilitate the semantic interoperability between different terminologies, we incorporated public available biomedical vocabularies by manual mapping between Chinese terms and English terms with cross-references to source vocabularies. In addition, we evaluated the ISPO using independent clinical EMRs to provide a high-usable medical ontology for clinical data analysis. Results: By integrating 78,696 inpatient cases of EMRs, 5 biomedical vocabularies, 21 TCM books and dictionaries, ISPO provides 3,147 concepts, 23,475 terms, and 55,552 definition or contextual texts. Adhering to the taxonomical structure of the related anatomical systems of symptom phenotypes, ISPO provides 12 top-level categories and 79 middle-level sub-categories. The validation of data analysis showed the ISPO has a coverage rate of 95.35%, 98.53% and 92.66% for symptom terms with occurrence rates of 0.5% in additional three independent curated clinical datasets, which can demonstrate the significant value of ISPO in mapping clinical terms to ontologies.

Xinli Tao, Xin Dong, Xuezhong Zhou

With the rapid expansion of unstructured clinical texts in electronic health records (EHRs), clinical named entity recognition (NER) has become a crucial technique for extracting medical information. However, traditional supervised models such as CRF and BioClinicalBERT suffer from high annotation costs. Although zero-shot NER based on large language models (LLMs) reduces the dependency on labeled data, challenges remain in aligning example selection with task granularity and effectively integrating prompt design with self-improvement frameworks. To address these limitations, we propose OEMA, a novel zero-shot clinical NER framework based on multi-agent collaboration. OEMA consists of three core components: (1) a self-annotator that autonomously generates candidate examples; (2) a discriminator that leverages SNOMED CT to filter token-level examples by clinical relevance; and (3) a predictor that incorporates entity-type descriptions to enhance inference accuracy. Experimental results on two benchmark datasets, MTSamples and VAERS, demonstrate that OEMA achieves state-of-the-art performance under exact-match evaluation. Moreover, under related-match criteria, OEMA performs comparably to the supervised BioClinicalBERT model while significantly outperforming the traditional CRF method. OEMA improves zero-shot clinical NER, achieving near-supervised performance under related-match criteria. Future work will focus on continual learning and open-domain adaptation to expand its applicability in clinical NLP.