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Spatial transcriptomics data analysis integrates gene expression profiles with their corresponding spatial locations to identify spatial domains, infer cell‐type dynamics, and detect gene expression patterns within tissues. However, the current spatial transcriptomics analysis neglects the multiscale cell–cell interactions that are crucial in biology. To fill this gap, multiscale cell–cell interactive spatial transcriptomics (MCIST) analysis is proposed. MCIST combines the advantages of an ensemble of multiscale topological representations of cell–cell interactions in the gene expression space with those of cutting edge spatial deep learning techniques. MCIST is validated by a comparison of 14 cutting‐edge methods on a huge collection of 37 benchmark spatial transcriptomics datasets. It is demonstrated that MCIST yields superior performance in spatial domain detection. It achieves the best clustering score on 23/37 datasets and is among the top three methods on 33/37 datasets, while the second best method scored only 6/37 and 17/37 on these measures, respectively. In terms of overall performance with respect to a quantitative metric, MCIST offers more than an 11% improvement to the previous state‐of‐the‐art in spatial domain detection. In addition, MCIST offers multiscale insights with respect to trajectory inference, differentially expressed gene detection, and signaling pathway enrichment analysis. This MCIST sheds valuable light on the multiscale perspective in spatial transcriptomics.
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1 Department of Mathematics, Michigan State University, East Lansing, MI, USA, Department of Computational Mathematics, Science, and Engineering, Michigan State University, East Lansing, MI, USA
2 Department of Mathematics, Michigan State University, East Lansing, MI, USA, Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI, USA, Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA