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arXiv 2109.10469cs.LG
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用于分子优化的可微支架树

Differentiable Scaffolding Tree for Molecular Optimization

Amplitude(Amplitude公司);Massachusetts Institute of Technology(麻省理工学院);University of Illinois at Urbana-Champaign(伊利诺伊大学厄巴纳-香槟分校);Georgia Institute of Technology(佐治亚理工学院)

Tianfan Fu, Wenhao Gao, Cao Xiao, Jacob Yasonik, Connor W. Coley, Jimeng Sun

摘要:

功能分子的结构设计,也称为分子优化,是一项重要的化学科学和工程任务,具有重要的应用,如药物发现。深度生成模型和组合优化方法取得了初步成功,但仍然难以直接建模离散化学结构,并且通常严重依赖蛮力枚举。挑战来自分子结构的离散和不可微性质。为了解决这个问题,我们提出了可微支架树(DST),利用学习的知识网络将离散的化学结构转换为局部可微的。DST通过将来自目标性质的导数反向传播通过图神经网络(GNN)来实现对化学图结构的基于梯度的优化。我们的实验研究表明,基于梯度的分子优化是有效的和样本效率。此外,学习的图参数还可以提供解释,帮助领域专家理解模型输出。

英文摘要:

The structural design of functional molecules, also called molecular optimization, is an essential chemical science and engineering task with important applications, such as drug discovery. Deep generative models and combinatorial optimization methods achieve initial success but still struggle with directly modeling discrete chemical structures and often heavily rely on brute-force enumeration. The challenge comes from the discrete and non-differentiable nature of molecule structures. To address this, we propose differentiable scaffolding tree (DST) that utilizes a learned knowledge network to convert discrete chemical structures to locally differentiable ones. DST enables a gradient-based optimization on a chemical graph structure by back-propagating the derivatives from the target properties through a graph neural network (GNN). Our empirical studies show the gradient-based molecular optimizations are both effective and sample efficient. Furthermore, the learned graph parameters can also provide an explanation that helps domain experts understand the model output.

机构、总结、中文摘要均由AI分析而来,可能存在错误,请以论文正文为准。

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