Spatio-relational inductive biases in spatial cell-type deconvolution

Ramon Viñas, Paul Scherer, Nikola Simidjievski, Mateja Jamnik, Pietro Liò
bioRxiv (2023)


Spatial transcriptomic technologies profile gene expression in-situ, facilitating the spatial characterisation of molecular phenomena within tissues, yet often at multi-cellular resolution. Computational approaches have been developed to infer fine-grained cell-type compositions across locations, but they frequently treat neighbouring spots independently of each other. Here we present GNN-C2L, a flexible deconvolution approach that leverages proximal inductive biases to propagate information along adjacent spots. In performance comparison on simulated and semisimulated datasets, GNN-C2L achieves increased deconvolution performance over spatial-agnostic variants. We believe that accounting for spatial inductive biases can yield improved characterisation of cell-type heterogeneity in tissues.