基于异构蛋白质网络随机游走的中药重定位模型
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国家重点研发计划(2023YFC3402800); 国家自然科学基金(82441029, 62171230, 62101365, 92159301, 62301263, 62301265, 62302228, 82302291, 82302352, 62401272); 江苏省教育强省建设专项资金(1523142501042); 2024年江苏省高等教育内涵建设与发展专项(1311632401002); 江苏省科技厅前沿引领技术基础研究重大项目 (BK2023200)


Traditional Chinese Medicine Repurposing Models Based on Random Walk of Heterogeneous Protein Networks
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    摘要:

    中药是治疗疾病的重要药物资源, 历经数千年的临床实践与应用. 为推动中药现代化并发掘其在新适应症上的应用潜力, 本文借鉴西药领域药物重定位的研究经验, 结合近年来新兴的网络医学理论, 提出两种基于随机游走的中药-症状潜在治疗关系预测模型: M-RW与GO-DREAMwalk. 两种模型分别引入了中药与症状的路径信息和功能信息, 并以此指导随机游走过程, 生成节点序列后输入到异构Skip-gram模型, 学习节点的嵌入向量表示. 随后, 结合中药-症状关联标签与嵌入向量训练XGBoost分类器, 最终在肝硬化临床数据上对模型进行测试与评估. 在临床有效任务中, 两种模型的高排名预测准确率分别达到了0.0798和0.0684, 相较于机制驱动方法Proximity分别提升了145%与110%, 相较于数据驱动方法node2vec和edge2vec, 分别提升了40%、20%, 以及53%、31%. 此外, 通过Rank Aggregation方法聚合两种模型的预测结果, 准确率分别提升了75%和105%, 进一步增强了模型的预测能力. 两种模型在真实临床数据上的预测结果均具备良好的预测性能, 充分展现了其在中药重定位中的应用潜力, 有望推动中药在新适应症上的有效应用.

    Abstract:

    As an important therapeutic resource, traditional Chinese medicine (TCM) has undergone thousands of years of clinical practice and application. To promote the modernization of TCM and explore its application potential in new indications, this study draws on research experience from drug repurposing in Western medicine and combines emerging network medicine theories to propose two random walk-based models for predicting potential therapeutic associations between TCM and symptoms: M-RW and GO-DREAMwalk. The two models incorporate path-based and functional information between TCM and symptoms to guide the random walk process. The resulting node sequences are input into a heterogeneous Skip-gram model to learn the embedded vector representations of nodes. Subsequently, an XGBoost classifier is trained by adopting TCM-symptom association labels and the learned embedded vectors. Finally, the models are tested and evaluated by employing clinical data on liver cirrhosis. In the clinically effective prediction task, the top-ranking prediction precision of the two models reaches 0.0798 and 0.0684 respectively, improvements of 145% and 110% over the mechanism-based Proximity, 40% and 20% over the data-driven method node2vec, and 53% and 31% over the data-driven method edge2vec respectively. Furthermore, applying the Rank Aggregation method to integrate the prediction results of both models leads to precision improvements of 75% and 105%, further enhancing the predictive ability of the models. The prediction results on real-world clinical data of the two models demonstrate sound prediction performance, highlighting their potential to promote the effective application of TCM in novel indications.

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李政昊,徐军,陆俊滟,甘晓.基于异构蛋白质网络随机游走的中药重定位模型.计算机系统应用,,():1-14

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  • 收稿日期:2025-07-07
  • 最后修改日期:2025-08-01
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  • 在线发布日期: 2025-11-17
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