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基于动态推理方法的小分子生成OA

Dynamic inference-guided small molecule generation

中文摘要英文摘要

小分子生成在药物设计、新材料开发等科学领域具有重要应用前景.近年来,扩散模型因其卓越的生成能力而被广泛用于分子结构生成任务.然而,现有的扩散生成方法多将分子性质视为静态条件输入,未能充分捕捉结构与性质之间的动态关系,难以实现对目标性质的精准控制.为解决这一问题,本文提出了一种基于动态推理的小分子条件生成模型,该模型结合了边缘引导的离散扩散机制与分子性质预测模块,从而实现了分子图结构与性质在生成过程中的联合建模与动态协同优化.该方法引入图神经网络对扩散中间状态的分子图进行性质估计,并在去噪过程中将估计结果与目标性质共同纳入损失函数中,提升模型对结构-性质一致性的建模能力.实验结果表明,本文方法在多个性质控制范围内均显著优于现有基线模型,在精确目标性质控制任务中,所提方法将HOMO和μ的MAE分别降低了21%和18%;在随机条件生成任务中,对应MAE指标分别下降约33.3%和31.7%,验证了动态推理机制在提升性质可控性与生成质量方面的有效性.

Small molecule generation plays an increasingly vital role in scientific fields such as drug design and new materials development.In recent years,diffusion models have been widely employed for molecular structure generation tasks owing to their exceptional generative capabilities.However,existing diffusion-based methods often treat molecular properties as static conditions,failing to adequately capture the dynamic relationship between structure and properties,thus hindering the precise control of target properties.To ad-dress this challenge,we propose a dynamic inference-based conditional molecular generation model that inte-grates an edge-guided discrete diffusion mechanism with a molecular property prediction module.This ap-proach facilitates the joint modeling and dynamic co-optimization of molecular graph structures and their corre-sponding properties during the generation process.Specifically,we employed a graph neural network to esti-mate the properties of intermediate molecular graphs at each diffusion step.During the denoising phase,these estimations were jointly incorporated into the loss function along with the target properties,thereby enhancing the model′s ability to enforce structure-property consistency.Experimental results demonstrate that our method significantly outperforms existing baselines across various property control tasks.In the targeted prop-erty control setting,the proposed method reduced the Mean Absolute Error(MAE)of HOMO and μ by 21%and 18%,respectively.Furthermore,in the random conditional generation tasks,the MAE for these properties were reduced by approximately 33.3%and 31.7%,respectively.These results validate the effec-tiveness of the dynamic inference mechanism in improving property controllability and the quality of the gener-ated molecules.

王乾旭;刘祥根;张文博;李文杰;蔡玥

四川大学计算机学院/软件学院/智能科学与技术学院,成都 610065四川大学计算机学院/软件学院/智能科学与技术学院,成都 610065西安电子科技大学计算机科学与技术学院,西安 710126中国核动力研究设计院,成都 610005四川大学华西医院,成都 610041

信息技术与安全科学

小分子生成动态推理扩散模型分子性质预测图神经网络

molecular generationdynamic inferencediffusion modelproperty predictiongraph neural net-works

《四川大学学报(自然科学版)》 2026 (1)

111-120,10

中国核动力研究设计院先进核能技术全国重点实验室稳定支持科研项目(STSW-0224-0202-08)

10.19907/j.0490-6756.250139

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