论文标题

Chemicalx:一个用于药物对的深度学习库

ChemicalX: A Deep Learning Library for Drug Pair Scoring

论文作者

Rozemberczki, Benedek, Hoyt, Charles Tapley, Gogleva, Anna, Grabowski, Piotr, Karis, Klas, Lamov, Andrej, Nikolov, Andriy, Nilsson, Sebastian, Ughetto, Michael, Wang, Yu, Derr, Tyler, Gyori, Benjamin M

论文摘要

在本文中,我们介绍了Chemicalx,这是一个基于Pytorch的深度学习库,旨在提供一系列最先进的模型来解决药物对得分任务。该图书馆的主要目的是在简化的框架中使机器学习研究人员和从业人员可以访问深度药物对评分模型。Chemicalx的设计现有的高水平模型培训公用事业,几何深度学习以及Pytorch生态系统的深层化学层。我们的系统为最终用户提供神经网络层,自定义对评分架构,数据加载程序和批次迭代器。我们通过示例代码片段和案例研究展示了这些功能,以突出化学特征。关于现实世界的药物相互作用,多药副作用和组合协同预测任务的一系列实验表明,ChemicalX中可用的模型可有效解决配对评分任务。最后,我们表明ChemicalX可用于在大型药物对数据集上训练和评分机器学习模型,其中数十万种商品硬件。

In this paper, we introduce ChemicalX, a PyTorch-based deep learning library designed for providing a range of state of the art models to solve the drug pair scoring task. The primary objective of the library is to make deep drug pair scoring models accessible to machine learning researchers and practitioners in a streamlined framework.The design of ChemicalX reuses existing high level model training utilities, geometric deep learning, and deep chemistry layers from the PyTorch ecosystem. Our system provides neural network layers, custom pair scoring architectures, data loaders, and batch iterators for end users. We showcase these features with example code snippets and case studies to highlight the characteristics of ChemicalX. A range of experiments on real world drug-drug interaction, polypharmacy side effect, and combination synergy prediction tasks demonstrate that the models available in ChemicalX are effective at solving the pair scoring task. Finally, we show that ChemicalX could be used to train and score machine learning models on large drug pair datasets with hundreds of thousands of compounds on commodity hardware.

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