G2T: Tissue Reconstruction from Gene Expression via Embedding-Distance Flow Matching

Single-cell RNA sequencing (scRNA-seq) profiles transcriptomes at high resolution but discards the spatial context of cells within a tissue—information that is essential for studying intercellular mechanisms and tissue architecture. Spatial transcriptomics (ST) retains coordinates but, depending on the assay, trades this off against gene-panel breadth, spatial resolution, or cost. We present G2T (Gene-to-Tissue), a generative deep learning model that reassembles a tissue from gene expression — its only observed input — by predicting the matrix of pairwise distances between cells in a learned embedding space. G2T uses an attention-based Transformer with an Euclidean-Distance-Matrix (EDM) output head and is trained with conditional flow matching: the network learns to denoise corrupted cell positions, conditioned on the slice’s gene expression, by predicting per-cell embeddings whose pairwise squared distances match the ground-truth distance matrix. At inference, a fast locally-optimal-block (LOBPCG) multidimensional scaling step turns the predicted distance matrix into 2-D coordinates. On a published MERFISH mouse primary motor cortex benchmark, G2T improves over the previous state-of-the-art method, LUNA, across all three standard metrics— Spearman correlation of pairwise-distance ranks, Contact F1, and per-cell-class Sum RSSD — and even larger relative gains on the mouse central-nervous-system scRNA-seq atlas, evaluated against an imputed spatial reference (STARmap PLUS-integrated locations, not measured coordinates). By predicting this geometry in a higher-dimensional embedding space rather than regressing 2-D coordinates, G2T relaxes the 2-D output parameterisation of prior diffusion-based methods and yields a compact, scalable building block for reconstructing tissue from dissociated cells, enabling downstream spatial niche and cell–cell communication analysis.