用可解释性方法筛选药物活性数据,提升模型预测精度。
AssayMatch: Learning to Select Data for Molecular Activity Models
- 基于实验描述的语义与兼容性,动态筛选训练数据
- 在9/12任务中超越完整数据集训练模型性能
- 适用于未知标签的药物发现场景,适合新药研发者
药物发现中机器学习模型的表现高度依赖训练数据的质量与一致性。由于数据集规模有限,许多模型通过整合来自不同来源(如ChEMBL)的生物活性数据进行训练,但实验协议差异常引入显著噪声。我们提出AssayMatch框架,通过构建更小、更同质的训练集来匹配目标测试集。该框架利用数据归因方法量化每个实验对模型性能的贡献,进而微调文本描述的语言嵌入,不仅捕捉语义相似性,还体现实验间的兼容性。不同于传统方法,本方案可在测试集标签未知时实现数据筛选,贴合真实药物发现流程。测试时,使用微调后的嵌入对所有可用训练数据进行排序。实验证明,由AssayMatch选出的数据训练的模型性能优于全数据集训练模型,有效过滤有害或噪声实验。在两种主流架构上,9/12模型-靶点对均优于仅使用语言特征的强基线。AssayMatch提供了一种数据驱动的高质量数据集构建方式,减少不兼容实验带来的噪声,提升模型预测能力与数据效率。代码已开源:https://github.com/Ozymandias314/AssayMatch。
原文摘要 · Abstract (English)
The performance of machine learning models in drug discovery is highly dependent on the quality and consistency of the underlying training data. Due to limitations in dataset sizes, many models are trained by aggregating bioactivity data from diverse sources, including public databases such as ChEMBL. However, this approach often introduces significant noise due to variability in experimental protocols. We introduce AssayMatch, a framework for data selection that builds smaller, more homogenous training sets attuned to the test set of interest. AssayMatch leverages data attribution methods to quantify the contribution of each training assay to model performance. These attribution scores are used to finetune language embeddings of text-based assay descriptions to capture not just semantic similarity, but also the compatibility between assays. Unlike existing data attribution methods, our approach enables data selection for a test set with unknown labels, mirroring real-world drug discovery campaigns where the activities of candidate molecules are not known in advance. At test time, embeddings finetuned with AssayMatch are used to rank all available training data. We demonstrate that models trained on data selected by AssayMatch are able to surpass the performance of the model trained on the complete dataset, highlighting its ability to effectively filter out harmful or noisy experiments. We perform experiments on two common machine learning architectures and see increased prediction capability over a strong language-only baseline for 9/12 model-target pairs. AssayMatch provides a data-driven mechanism to curate higher-quality datasets, reducing noise from incompatible experiments and improving the predictive power and data efficiency of models for drug discovery. AssayMatch is available at https://github.com/Ozymandias314/AssayMatch.
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