Li Zhen, Huang Juyuan, Liu Xinxin, Xu Peng, Shen Xinwen, Pan Chu, Zhang Wei, Liu Wenbin, Han Henry
Institute of Computational Science and Technology, Guangzhou University, Guangzhou, Guangdong, 510006, China; School of Computer Science of Information Technology, Qiannan Normal University for Nationalities, Duyun, Guizhou, 558000, China.
Department of Gynecology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430071, China.
Methods. 2025 Aug;240:137-144. doi: 10.1016/j.ymeth.2025.04.009. Epub 2025 Apr 24.
Predicting drug-target interactions (DTIs) accurately is essential in the field of drug discovery. Recently, artificial intelligence (AI) technologies, especially graph convolutional networks (GCNs), have been developed to tackle this challenge. However, as the number of GCN layers increases, models may lose critical information due to excessive smoothing. Moreover, these methods often lack interpretability and are dependent on specific datasets, which limits their generalizability. Consequently, this study introduces a novel method, KRN-DTI, which employs interpretable GCN technology to predict DTIs based on a drug-target heterogeneous network. The method uses GCN technology to identify potential DTIs by leveraging known interactions and dynamically adjusting the weights, thereby enhancing the model's interpretability. Additionally, residual connection technology is employed to integrate GNN outputs, mitigating the over-smoothing issue. Furthermore, the model's interpretability is enhanced by adaptively adjusting weights using Kolmogorov-Arnold Networks (KAN) and attention mechanisms. Experimental results show that KRN-DTI outperforms several advanced computational methods on the benchmark dataset. Case studies further highlight the effectiveness of KRN-DTI in predicting potential DTIs, showcasing its potential for real-world applications in drug discovery. Our code and data are publicly accessible at: https://github.com/lizhen5000/KRN-DTI.git.
准确预测药物-靶点相互作用(DTIs)在药物发现领域至关重要。最近,人工智能(AI)技术,尤其是图卷积网络(GCNs),已被开发用于应对这一挑战。然而,随着GCN层数的增加,模型可能会因过度平滑而丢失关键信息。此外,这些方法通常缺乏可解释性,并且依赖于特定的数据集,这限制了它们的通用性。因此,本研究引入了一种新方法KRN-DTI,该方法采用可解释的GCN技术基于药物-靶点异质网络预测DTIs。该方法利用已知的相互作用并动态调整权重,使用GCN技术识别潜在的DTIs,从而增强模型的可解释性。此外,采用残差连接技术整合GNN输出,减轻过度平滑问题。此外,通过使用柯尔莫哥洛夫-阿诺德网络(KAN)和注意力机制自适应调整权重,增强了模型的可解释性。实验结果表明,KRN-DTI在基准数据集上优于几种先进的计算方法。案例研究进一步突出了KRN-DTI在预测潜在DTIs方面的有效性,展示了其在药物发现实际应用中的潜力。我们的代码和数据可在以下网址公开获取:https://github.com/lizhen5000/KRN-DTI.git。