提出新方法缓解分子构象生成中的暴露偏差,提升生成精度与多样性。
Mitigating Exposure Bias in Score-Based Generation of Molecular Conformations
- 设计输入扰动(IP)算法补偿得分模型的暴露偏差
- 在GEOM-Drugs上达到新最好性能,多样性与精度双提升
- 适用于基于得分的分子构象生成,尤其适合Torsional Diffusion等模型
分子构象生成是计算化学中的关键挑战。近年来,扩散概率模型(DPMs)和基于得分的生成模型(SGMs)因其能生成远超传统物理方法的精确构象而被广泛应用。然而,训练与推理之间的不一致导致了严重的暴露偏差问题。尽管该问题在DPMs中已有研究,但其在SGMs中的存在及有效度量仍未解决,阻碍了补偿方法的应用。本文首次提出一种测量SGMs中暴露偏差的方法,证实其显著存在并量化其程度。我们设计了新的补偿算法输入扰动(IP),该方法源自仅用于DPMs的原始技术。实验表明,引入IP后,基于SGM的分子构象生成模型在准确性和多样性上均有显著提升。尤其使用IP增强的扭转扩散模型(Torsional Diffusion),在GEOM-Drugs数据集上达到新最佳表现,且在GEOM-QM9上表现相当。代码已公开:https://github.com/jia-975/torsionalDiff-ip。
原文摘要 · Abstract (English)
Molecular conformation generation poses a significant challenge in the field of computational chemistry. Recently, Diffusion Probabilistic Models (DPMs) and Score-Based Generative Models (SGMs) are effectively used due to their capacity for generating accurate conformations far beyond conventional physics-based approaches. However, the discrepancy between training and inference rises a critical problem known as the exposure bias. While this issue has been extensively investigated in DPMs, the existence of exposure bias in SGMs and its effective measurement remain unsolved, which hinders the use of compensation methods for SGMs, including ConfGF and Torsional Diffusion as the representatives. In this work, we first propose a method for measuring exposure bias in SGMs used for molecular conformation generation, which confirms the significant existence of exposure bias in these models and measures its value. We design a new compensation algorithm Input Perturbation (IP), which is adapted from a method originally designed for DPMs only. Experimental results show that by introducing IP, SGM-based molecular conformation models can significantly improve both the accuracy and diversity of the generated conformations. Especially by using the IP-enhanced Torsional Diffusion model, we achieve new state-of-the-art performance on the GEOM-Drugs dataset and are on par on GEOM-QM9. We provide the code publicly at https://github.com/jia-975/torsionalDiff-ip.
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