arXiv subjects

Xuezhong Zhou

Publications and source records attributed to Xuezhong Zhou.

9 recordsLinked to original sources

arXiv2026

LingShu: A Large-Scale Symptom-Centric Contextualized Knowledge Graph Bridging Traditional Chinese Medicine and Modern Biomedicine

Biomedical knowledge graphs (KGs) are pivotal for knowledge organization, yet traditional binary relations often struggle to represent the conditional nature of biomedical knowledge. Symptoms provide a shared phenotypic layer for linking Traditional Chinese Medicine (TCM), which relies on symptom patterns for syndrome differentiation and treatment selection, with modern biomedicine, which connects clinical manifestations to diseases and molecular mechanisms. We present LingShu, a large-scale symptom-centric contextualized knowledge graph designed to bridge TCM and modern biomedicine. The exported version of LingShu analyzed in this study comprises 17.33 million atom-level entity records and 39.47 million relation records, including 17.19 million semantic triples and 22.29 million contextualized quadruples. LingShu integrates multi-source data, including clinical electronic medical records, authoritative TCM texts, biomedical ontologies, and curated knowledge bases, through a pipeline combining natural language processing, terminology normalization, and human-in-the-loop verification. A key innovation of LingShu is its hybrid data model: it maintains 64 typed triple relation patterns to ensure broad connectivity, while incorporating 35 contextual quadruple relation patterns to capture conditional medical associations. This dual-structure approach explicitly encodes conditional knowledge, providing a granular representation of the contexts associated with medical relations. These contextualized relations cover syndrome-dependent herb efficacy, disease-contextualized drug effects, population-specific clinical associations, and mechanism-related therapeutic responses. Furthermore, we developed a web platform (http://www.tcmkg.com/) that integrates graph visualization, graph-based reasoning, and an evidence-grounded knowledge question-answering agent.

cs.CL↗

arXiv2026

LingLanMiDian: Systematic Evaluation of LLMs on TCM Knowledge and Clinical Reasoning

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.

cs.AI↗

arXiv2025

OEMA: Ontology-Enhanced Multi-Agent Collaboration Framework for Zero-Shot Clinical Named Entity Recognition

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.

cs.CL↗

arXiv2024

TCM-FTP: Fine-Tuning Large Language Models for Herbal Prescription Prediction

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.

cs.CL↗

arXiv2024

ISPO: An Integrated Ontology of Symptom Phenotypes for Semantic Integration of Traditional Chinese Medical Data

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.

cs.CL↗

arXiv2023

A optimization framework for herbal prescription planning based on deep reinforcement learning

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.

cs.AI↗

arXiv2023

A Pre-training Framework for Knowledge Graph Completion

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.

cs.AI↗

arXiv2023

Knowledge Graph Completion based on Tensor Decomposition for Disease Gene Prediction

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.

cs.AI↗

arXiv2022

Network medicine framework reveals generic herb-symptom effectiveness of Traditional Chinese Medicine

Traditional Chinese medicine (TCM) relies on natural medical products to treat symptoms and diseases. While clinical data have demonstrated the effectiveness of selected TCM-based treatments, the mechanistic root of how TCM herbs treat diseases remains largely unknown. More importantly, current approaches focus on single herbs or prescriptions, missing the high-level general principles of TCM. To uncover the mechanistic nature of TCM on a system level, in this work we establish a generic network medicine framework for TCM from the human protein interactome. Applying our framework reveals a network pattern between symptoms (diseases) and herbs in TCM. We first observe that genes associated with a symptom are not distributed randomly in the interactome, but cluster into localized modules; furthermore, a short network distance between two symptom modules is indicative of the symptoms' co-occurrence and similarity. Next, we show that the network proximity of a herb's targets to a symptom module is predictive of the herb's effectiveness in treating the symptom. We validate our framework with real-world hospital patient data by showing that (1) shorter network distance between symptoms of inpatients correlates with higher relative risk (co-occurrence), and (2) herb-symptom network proximity is indicative of patients' symptom recovery rate after herbal treatment. Finally, we identified novel herb-symptom pairs in which the herb's effectiveness in treating the symptom is predicted by network and confirmed in hospital data, but previously unknown to the TCM community. These predictions highlight our framework's potential in creating herb discovery or repurposing opportunities. In conclusion, network medicine offers a powerful novel platform to understand the mechanism of traditional medicine and to predict novel herbal treatment against diseases.

q-bio.MN↗