LYNX: a deep generative model for linking spatial dynamics and cell interactions in multimodal spatial data

Tissues are spatially organized systems in which cell states, functions and interactions vary across spatial coordinates, forming compartments or gradients shaped by local microenvironments. Understanding how molecular features and cell–cell interactions change across space and time is central to studying development, homeostasis and disease. Addressing these questions increasingly requires the integration of multi-modal spatial data, which provides complementary views of cellular and structural organization. However, existing computational approaches typically combine modalities by weighting them equally, overlooking domain-specific technical artifacts, differences in spatial resolution and non-overlapping feature spaces. In addition, methods for spatial cell–cell communication analysis are largely developed for single-modality settings and do not model how interactions vary across the tissue. To address these gaps, we introduce LYNX, a deep generative framework that learns a shared latent representation of spatial dynamics from joint-measured modalities in the 2D or 3D domain, to provide a unified coordinate system for modeling how cell–cell interactions, phenotypes, and molecular programs vary along continuous spatial gradients. LYNX identifies spatial programs difficult to resolve with existing approaches, including metabolically coupled porto-central interaction remodeling in liver, recovery of degraded proteomic signals along the cortico-medullary axis in thymus, and branching trajectories towards DCIS and invasive niches marked by distinct stromal activation-states and immune-tumor crosstalk in breast tumor microenvironment. We demonstrate that LYNX robustly infers spatially resolved gradients, maps functional compartments and cell-cell interactions along spatial axes and is compatible across diverse spatial profiling technologies, modalities, and resolution disparities. LYNX provides a foundational and scalable framework to advance our understanding of healthy tissue physiology and to decode temporal evolution of complex diseases.