PRAGA: Prototype-aware Graph Adaptive Aggregation for Spatial Multi-modal Omics Analysis

TL;DR

PRAGA introduces a dynamic, prototype-aware graph neural network framework that enhances spatial multi-modal omics analysis by capturing latent semantic relations and denoising data perturbations, outperforming existing methods.

Contribution

The paper proposes PRAGA, a novel framework that constructs a dynamic graph and employs prototype contrastive learning to improve spatial multi-modal omics analysis.

Findings

PRAGA outperforms 7 competing methods on simulated and real datasets.

The dynamic graph captures latent semantic relations more effectively.

Prototype contrastive learning enhances representation quality.

Abstract

Spatial multi-modal omics technology, highlighted by Nature Methods as an advanced biological technique in 2023, plays a critical role in resolving biological regulatory processes with spatial context. Recently, graph neural networks based on K-nearest neighbor (KNN) graphs have gained prominence in spatial multi-modal omics methods due to their ability to model semantic relations between sequencing spots. However, the fixed KNN graph fails to capture the latent semantic relations hidden by the inevitable data perturbations during the biological sequencing process, resulting in the loss of semantic information. In addition, the common lack of spot annotation and class number priors in practice further hinders the optimization of spatial multi-modal omics models. Here, we propose a novel spatial multi-modal omics resolved framework, termed PRototype-Aware Graph Adaptative Aggregation for Spatial Multi-modal Omics Analysis (PRAGA). PRAGA constructs a dynamic graph to capture latent semantic relations and comprehensively integrate spatial information and feature semantics. The learnable graph structure can also denoise perturbations by learning cross-modal knowledge. Moreover, a dynamic prototype contrastive learning is proposed based on the dynamic adaptability of Bayesian Gaussian Mixture Models to optimize the multi-modal omics representations for unknown biological priors. Quantitative and qualitative experiments on simulated and real datasets with 7 competing methods demonstrate the superior performance of PRAGA. Code is available at https://github.com/Xubin-s-Lab/PRAGA.