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Optimal inverter substation planning is solved by minimising the overall cost of power consumption and inverter investment for mass rapid transit power systems with immune algorithm (IA). The objective function and constraints are expressed as antigens, and all feasible solutions are expressed as antibodies in the IA simulation process. The diversity of antibodies is then enhanced by considering the proximity of antigens so that the global optimisation during the solution process can be obtained. It is found that energy regeneration, which results from the braking operation of train sets approaching the next station, can be restored effectively by the optimal planning of inverters using the proposed immune algorithm.