In this work, we construct a primal-dual forward-backward (PDFB) splitting method for computing a class of cross-diffusion systems that can be formulated as gradient flows under transport distances induced by matrix mobilities. By leveraging their gradient flow structure, we use minimizing movements as the variational formulation and compute these cross-diffusion systems by solving the minimizing movements as optimization problems at the fully discrete level. Our strategy to solve the optimization problems is the PDFB splitting method outlined in our previous work \cite{PDFB2024}. The efficiency of the proposed PDFB splitting method is demonstrated on several challenging cross-diffusion equations from the literature.

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