arXiv:2505.09630q-bio.QMcs.CV2025-05被引 6

用生成式扩散模型加速生物细胞模型模拟,20000步预测快22倍

Generative diffusion model surrogates for mechanistic agent-based biological models

  • 用去噪扩散模型构建细胞模型的生成式代理
  • 可提前20000时间步生成模拟结果,计算提速22倍
  • 适合需要快速仿真生物系统的研究人员

机制性多细胞代理模型常用于单细胞分辨率下研究组织、器官及生物体尺度的生物学问题。细胞-庞斯模型(CPM)是开发和探究此类模型的有力且流行框架。然而,在大空间和长时间尺度下,CPM计算成本高昂,使模型应用与研究变得困难。代理模型可实现对复杂生物系统CPM的加速评估。但这些模型的随机性导致同一组参数可能产生不同配置,增加了代理模型构建难度。本文利用去噪扩散概率模型训练了一个用于研究体外血管生成的CPM生成式代理。通过图像分类器学习二维参数空间中独特区域的特征,并用于辅助代理模型选择与验证。该代理模型可生成参考配置20000时间步后的模型配置,相比原代码执行计算时间减少约22倍。本工作为应用DDPM构建随机生物系统数字孪生迈出重要一步。

原文摘要 · Abstract (English)

Mechanistic, multicellular, agent-based models are commonly used to investigate tissue, organ, and organism-scale biology at single-cell resolution. The Cellular-Potts Model (CPM) is a powerful and popular framework for developing and interrogating these models. CPMs become computationally expensive at large space- and time- scales making application and investigation of developed models difficult. Surrogate models may allow for the accelerated evaluation of CPMs of complex biological systems. However, the stochastic nature of these models means each set of parameters may give rise to different model configurations, complicating surrogate model development. In this work, we leverage denoising diffusion probabilistic models to train a generative AI surrogate of a CPM used to investigate in vitro vasculogenesis. We describe the use of an image classifier to learn the characteristics that define unique areas of a 2-dimensional parameter space. We then apply this classifier to aid in surrogate model selection and verification. Our CPM model surrogate generates model configurations 20,000 timesteps ahead of a reference configuration and demonstrates approximately a 22x reduction in computational time as compared to native code execution. Our work represents a step towards the implementation of DDPMs to develop digital twins of stochastic biological systems.

生成模型生物模拟扩散模型数字孪生

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