用类别扩散模型一次性生成化学逆合成路径,性能超越现有方法。
DiffER: Categorical Diffusion for Chemical Retrosynthesis
- 采用类别扩散机制并行生成完整反应物SMILES序列,摆脱传统自回归限制。
- 在无模板方法中达到最高1次命中率,3/5/10次命中率也表现优异。
- 适合需要高精度逆合成规划的研究者,尤其关注生成质量与置信度。
自动化学逆合成方法近年来得益于自然语言处理中常用的Transformer神经网络取得显著进展,这些模型能有效在产物与反应物的SMILES编码间进行转换,但受限于其自回归特性。本文提出DiffER,一种基于类别扩散的无模板逆合成预测新方法,可一次性并行预测整个SMILES序列。通过构建包含新颖长度预测组件(带方差)的扩散模型集成,该方法在无模板方法中实现最优的top-1准确率,并在top-3、top-5和top-10准确率上表现竞争力。实验证明,准确预测SMILES序列长度是提升类别扩散模型性能的关键。该方法能近似采样反应物的后验分布,生成具有高置信度和似然性的结果,展现出作为新一代无模板模型强基准的潜力。
原文摘要 · Abstract (English)
Methods for automatic chemical retrosynthesis have found recent success through the application of models traditionally built for natural language processing, primarily through transformer neural networks. These models have demonstrated significant ability to translate between the SMILES encodings of chemical products and reactants, but are constrained as a result of their autoregressive nature. We propose DiffER, an alternative template-free method for retrosynthesis prediction in the form of categorical diffusion, which allows the entire output SMILES sequence to be predicted in unison. We construct an ensemble of diffusion models which achieves state-of-the-art performance for top-1 accuracy and competitive performance for top-3, top-5, and top-10 accuracy among template-free methods. We prove that DiffER is a strong baseline for a new class of template-free model, capable of learning a variety of synthetic techniques used in laboratory settings and outperforming a variety of other template-free methods on top-k accuracy metrics. By constructing an ensemble of categorical diffusion models with a novel length prediction component with variance, our method is able to approximately sample from the posterior distribution of reactants, producing results with strong metrics of confidence and likelihood. Furthermore, our analyses demonstrate that accurate prediction of the SMILES sequence length is key to further boosting the performance of categorical diffusion models.
Thank you to arXiv for use of its open access interoperability. PaperDance 不是 arXiv 官方产品;中文卡片由大模型生成,请以原文为准。