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Communication-based train control (CBTC) is an automated control system for railways using data communications. CBTC systems have stringent communication latency requirements. For rail transit systems, wireless local area network (WLAN)-based CBTC is a popular approach due to the wide availability of commercial-off-the-shelf WLAN equipment. However, WLANs were not originally designed for high-speed environments with frequent handoffs, which may result in communication interrupt and long latency. In this paper, we propose a handoff scheme in CBTC systems based on WLANs with multiple-input-multiple-output (MIMO) technologies to improve the handoff latency performance. In particular, we consider channel estimation errors and the tradeoff between MIMO multiplexing gain and diversity gain in making handoff decisions. The handoff problem is formulated as a partially observable Markov decision process (POMDP), and the optimal handoff policy can be derived to minimize the handoff latency. Simulations results based on real field channel measurements are presented to show the effectiveness of the proposed scheme.