arXiv:2410.09280cs.LG2024-10ICML

用图神经网络同时预测多种药物效应,解决数据不平衡难题。

Predicting Drug Effects from High-Dimensional, Asymmetric Drug Datasets by Using Graph Neural Networks: A Comprehensive Analysis of Multitarget Drug Effect Prediction

  • 构建混合图神经网络,统一处理连续与分类目标
  • 提出新采样方法,显著改善标签稀疏与不对称问题
  • 在多个数据集上超越传统模型,适合多靶点药物研发

图神经网络(GNN)已成为从药物分子图中预测药物效应的有效机器学习技术。然而,在高维、标签不对称且存在复杂相关性的多靶点药物效应数据集上,现有GNN模型性能受限。为解决此问题,我们开发了标准与混合型GNN,分别执行多回归(连续值)与多标签分类(类别值)任务。由于多标签分类使目标数据更稀疏并引入标签共现不对称性,模型训练难度大,严重影响性能。为此,我们提出一种新型数据采样技术,在保持数据完整性前提下降低药物效应的数据不平衡比。最终评估表明,该方法优化后的数据集上,最佳混合GNN模型在精确率、召回率与F1分数等指标上显著优于其他机器学习模型,包括在原始数据或采用经典MLSMOTE技术采样后训练的GNN模型。

原文摘要 · Abstract (English)

Graph neural networks (GNNs) have emerged as one of the most effective ML techniques for drug effect prediction from drug molecular graphs. Despite having immense potential, GNN models lack performance when using datasets that contain high-dimensional, asymmetrically co-occurrent drug effects as targets with complex correlations between them. Training individual learning models for each drug effect and incorporating every prediction result for a wide spectrum of drug effects are impractical. Therefore, an opportunity exists to address this challenge as multitarget prediction problems and predict all drug effects at a time. We developed standard and hybrid GNNs to perform two separate tasks: multiregression for continuous values and multilabel classification for categorical values contained in our datasets. Because multilabel classification makes the target data even more sparse and introduces asymmetric label co-occurrence, learning these models becomes difficult and heavily impacts the GNN's performance. To address these challenges, we propose a new data oversampling technique to improve multilabel classification performances on all the given imbalanced molecular graph datasets. Using the technique, we improve the data imbalance ratio of the drug effects while protecting the datasets' integrity. Finally, we evaluate the multilabel classification performance of the best-performing hybrid GNN model on all the oversampled datasets obtained from the proposed oversampling technique. In all the evaluation metrics (i.e., precision, recall, and F1 score), this model significantly outperforms other ML models, including GNN models when they are trained on the original datasets or oversampled datasets with MLSMOTE, which is a well-known oversampling technique.

药物效应预测图神经网络多标签分类数据采样

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