arXiv:2603.26114cs.LGcs.AI2026-03

用图注意力模型预测抗癌药活性,准确率高且结果可解释。

DPD-Cancer: Explainable Graph-Based Deep Learning for Small Molecule Anti-Cancer Activity Prediction

  • 基于图注意力网络建模分子结构与癌细胞系关系
  • 测试集AUROC达0.87,对73种癌细胞系的预测相关系数中位数为0.64
  • 提供可解释性分析和在线免费使用工具,适合药物研发人员

DPD-Cancer是一种基于图注意力的深度学习框架,用于预测小分子在NCI-60癌细胞系面板中的抗癌活性,采用严格的化学感知数据划分策略进行训练与评估。在独立测试集上,分类器的受试者工作特征曲线下面积(AUROC)为0.87(95%置信区间[0.86, 0.88]),精确率-召回率曲线下面积(AUPRC)为0.73(95%置信区间[0.70, 0.76]);针对73种细胞系的回归模型,pGI50值预测的中位皮尔逊相关系数(Pearson's R)为0.64,中位均方根误差(RMSE)为0.67。在相同数据条件下对比pdCSM-Cancer、MLASM和ACLPred,DPD-Cancer consistently取得更高的马修斯相关系数(MCC)。基于遮蔽的归因分析表明模型解释与分类决策高度一致,适用域分析刻画了化学距离与预测可靠性之间的关系。为促进广泛应用,DPD-Cancer已开放为免费、易用的在线服务器,地址为https://biosig.lab.uq.edu.au/dpd_cancer/。

原文摘要 · Abstract (English)

DPD-Cancer is a graph-attention deep learning framework for predicting small-molecule DPD-Cancer is a graph-attention deep learning framework for predicting small-molecule anti-cancer activity across the NCI-60 panel, trained and evaluated under a strict chemistry-aware data-partitioning scheme. On the hold-out test set, the classifier achieved an Area Under the Receiver Operating Characteristic Curve (AUROC) of 0.87 (95% CI [0.86, 0.88]) and Area Under the Precision-Recall Curve (AUPRC) of 0.73 (95% CI [0.70, 0.76]); per-cell-line regression models for 73 cell lines produced a median Pearson's Correlation Coefficient (Pearson's R) of 0.64 and median Root Mean Squared Error (RMSE) of 0.67 for pGI50-value prediction. Benchmarks against pdCSM-Cancer, MLASM, and ACLPred under matched data conditions yielded consistently higher Matthew's Correlation Coefficient (MCC) scores, an occlusion-based attribution analysis confirmed that model explanations were quantitatively faithful to classifier decisions, and an applicability-domain analysis characterised reliability as a function of chemical distance. To facilitate widespread adoption, DPD-Cancer is available as a free, user-friendly web server for unrestricted use at https://biosig.lab.uq.edu.au/dpd_cancer/.

抗癌药物图神经网络可解释性药物发现

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