arXiv:2507.02902cs.LGcs.CE2025-07ICLR被引 1

用可控扩散模型生成生物多通道空间数据,支持任意缺失通道补全。

Controllable diffusion-based generation for multi-channel biological data

  • 分层特征注入实现多分辨率空间条件建模
  • 潜空间与输出空间注意力捕捉通道间依赖关系
  • 随机掩码训练使模型泛化至未见条件组合

生物学中的空间分析技术(如成像质谱流式细胞术IMC和空间转录组ST)产生具有强空间对齐性和复杂通道间关系的高维多通道数据。生成建模需同时捕捉通道内与通道间结构,并能对任意观测/缺失通道组合进行泛化。现有扩散模型通常假设低维输入(如RGB图像),依赖简单条件机制,破坏空间对应性且忽略通道依赖。本文提出统一的可控扩散框架,用于结构化空间生物数据生成。模型包含两项创新:(1) 分层特征注入机制,实现对空间对齐通道的多分辨率条件建模;(2) 潜空间与输出空间的通道注意力联合设计,以捕获通道间关系。通过随机掩码策略训练,模型可从任意输入组合重建缺失通道。在IMC蛋白补全及单细胞基因到蛋白预测等任务中表现优于现有方法,并展现出对未见条件配置的强大泛化能力。

原文摘要 · Abstract (English)

Spatial profiling technologies in biology, such as imaging mass cytometry (IMC) and spatial transcriptomics (ST), generate high-dimensional, multi-channel data with strong spatial alignment and complex inter-channel relationships. Generative modeling of such data requires jointly capturing intra- and inter-channel structure, while also generalizing across arbitrary combinations of observed and missing channels for practical application. Existing diffusion-based models generally assume low-dimensional inputs (e.g., RGB images) and rely on simple conditioning mechanisms that break spatial correspondence and ignore inter-channel dependencies. This work proposes a unified diffusion framework for controllable generation over structured and spatial biological data. Our model contains two key innovations: (1) a hierarchical feature injection mechanism that enables multi-resolution conditioning on spatially aligned channels, and (2) a combination of latent-space and output-space channel-wise attention to capture inter-channel relationships. To support flexible conditioning and generalization to arbitrary subsets of observed channels, we train the model using a random masking strategy, enabling it to reconstruct missing channels from any combination of inputs. We demonstrate state-of-the-art performance across both spatial and non-spatial prediction tasks, including protein imputation in IMC and gene-to-protein prediction in single-cell datasets, and show strong generalization to unseen conditional configurations.

扩散模型生物数据多通道生成空间建模

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