arXiv:2502.12186cs.LGcs.AI2025-02被引 1

用图神经网络与Transformer结合,精准预测大麻素受体配体活性并解释关键分子结构。

E2CB2former: Effecitve and Explainable Transformer for CB2 Receptor Ligand Activity Prediction

  • 融合GCN与Transformer,利用注意力机制捕捉分子结构特征。
  • 在多个数据集上达到R²=0.685、RMSE=0.675、AUC=0.940的优异性能。
  • 可识别影响受体活性的关键分子片段,助力药物设计优化。

准确预测CB2受体配体活性对靶向该受体的药物研发至关重要,该受体与炎症、镇痛及神经退行性疾病相关。尽管传统机器学习和深度学习方法已展现潜力,但其可解释性不足仍是理性药物设计的主要障碍。本文提出CB2former,将图卷积网络(GCN)与Transformer架构结合,用于预测CB2受体配体活性。通过Transformer的自注意力机制与GCN的结构学习能力协同,不仅提升预测性能,还揭示了影响受体活性的分子特征。我们在多种基线模型(包括随机森林、支持向量机、K近邻、梯度提升、极端梯度提升、多层感知机、卷积神经网络和循环神经网络)上进行对比,结果显示CB2former表现最优,取得R²=0.685、RMSE=0.675、AUC=0.940的指标。此外,注意力权重分析识别出影响CB2受体活性的关键分子亚结构,表明该模型具有可解释性,可应用于虚拟筛选、先导化合物优化与治疗开发加速。整体表明,以CB2former为代表的先进AI方法在提供高精度预测的同时,还能输出可操作的分子洞见,推动跨学科协作与药物发现创新。

原文摘要 · Abstract (English)

Accurate prediction of CB2 receptor ligand activity is pivotal for advancing drug discovery targeting this receptor, which is implicated in inflammation, pain management, and neurodegenerative conditions. Although conventional machine learning and deep learning techniques have shown promise, their limited interpretability remains a significant barrier to rational drug design. In this work, we introduce CB2former, a framework that combines a Graph Convolutional Network with a Transformer architecture to predict CB2 receptor ligand activity. By leveraging the Transformer's self attention mechanism alongside the GCN's structural learning capability, CB2former not only enhances predictive performance but also offers insights into the molecular features underlying receptor activity. We benchmark CB2former against diverse baseline models including Random Forest, Support Vector Machine, K Nearest Neighbors, Gradient Boosting, Extreme Gradient Boosting, Multilayer Perceptron, Convolutional Neural Network, and Recurrent Neural Network and demonstrate its superior performance with an R squared of 0.685, an RMSE of 0.675, and an AUC of 0.940. Moreover, attention weight analysis reveals key molecular substructures influencing CB2 receptor activity, underscoring the model's potential as an interpretable AI tool for drug discovery. This ability to pinpoint critical molecular motifs can streamline virtual screening, guide lead optimization, and expedite therapeutic development. Overall, our results showcase the transformative potential of advanced AI approaches exemplified by CB2former in delivering both accurate predictions and actionable molecular insights, thus fostering interdisciplinary collaboration and innovation in drug discovery.

药物发现图神经网络可解释性AI受体预测

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