arXiv:2501.08995cs.LG2025-01被引 4

用生成模型解决药物研发数据少的问题,提升小样本数据建模效果

VECT-GAN: A variationally encoded generative model for overcoming data scarcity in pharmaceutical science

  • 设计新型生成模型VECT-GAN,专为小而杂的药物数据增强
  • 在6个真实药物数据集上显著提升回归模型性能
  • 可直接用于小分子药物开发,支持实验验证和开源使用

药物研究中的数据稀缺导致依赖耗时的试错法,而非数据驱动方法。尽管机器学习提供了解决方案,但现有数据集普遍规模小且噪声大,限制了其应用。为此,我们提出一种变分编码的条件表格生成对抗网络(VECT-GAN),专门用于增强小规模、含噪数据集。构建了一个先生成再建模的流程,在六个药物数据集上均显著优于当前最优的表格生成模型。通过该流程成功设计并实验表征了具有理想黏膜粘附特性的新聚合物。此外,模型在包含药物样分子的ChEMBL数据库上预训练,并通过知识蒸馏提升泛化能力,使其可直接应用于常见小分子药物任务。结果表明,合成数据能有效正则化小表格数据,有望成为药物建模的标准实践。我们已将VECT-GAN及在ChEMBL上预训练的版本发布为pip包。

原文摘要 · Abstract (English)

Data scarcity in pharmaceutical research has led to reliance on labour-intensive trial-and-error approaches for development rather than data-driven methods. While Machine Learning offers a solution, existing datasets are often small and noisy, limiting their utility. To address this, we developed a Variationally Encoded Conditional Tabular Generative Adversarial Network (VECT-GAN), a novel generative model specifically designed for augmenting small, noisy datasets. We introduce a pipeline where data is augmented before regression model development and demonstrate that this consistently and significantly improves performance over other state-of-the-art tabular generative models. We apply this pipeline across six pharmaceutical datasets, and highlight its real-world applicability by developing novel polymers with medically desirable mucoadhesive properties, which we made and experimentally characterised. Additionally, we pre-train the model on the ChEMBL database of drug-like molecules, leveraging knowledge distillation to enhance its generalisability, making it readily available for use on pharmaceutical datasets containing small molecules, an extremely common pharmaceutical task. We demonstrate the power of synthetic data for regularising small tabular datasets, highlighting its potential to become standard practice in pharmaceutical model development, and make our method, including VECT-GAN pre-trained on ChEMBL available as a pip package.

生成模型药物研发数据增强小样本学习

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