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We consider load balancing in large-scale heterogeneous server systems in the presence of data locality that imposes constraints on which tasks can be assigned to which servers. The constraints are naturally captured by a bipartite graph between the servers and the dispatchers handling assignments of various arrival flows. When a task arrives, the corresponding dispatcher assigns it to a server with the shortest queue among $d\geq 2$ randomly selected servers obeying the above constraints. Server processing speeds are heterogeneous and they depend on the server-type. For a broad class of bipartite graphs, we characterize the limit of the appropriately scaled occupancy process, both on the process-level and in steady state, as the system size becomes large. Using such a characterization, we show that data locality constraints can be used to significantly improve the performance of heterogeneous systems. This is in stark contrast to either heterogeneous servers in a full flexible system or data locality constraints in systems with homogeneous servers, both of which have been observed to degrade the system performance. Extensive numerical experiments corroborate the theoretical results.