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This paper presents new algorithms for throughput optimization in mobile backbone networks. This hierarchical sensing approach combines mobile backbone nodes, which have superior mobility and communication capability, with regular nodes, which are constrained in mobility and communication capability but which can sense the environment. An important quantity of interest in mobile backbone networks is the number of regular nodes that can be successfully assigned to mobile backbone nodes at a given throughput level. This paper develops a novel technique for optimizing this quantity using mixed-integer linear programming (MILP). The MILP- based algorithm provides a significant reduction in computation time compared to existing methods and is computationally tractable for problems of moderate size. An approximation algorithm is also developed that is appropriate for large- scale problems. This approximation algorithm has a theoretical performance guarantee and is demonstrated to perform well in practice.