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This correspondence develops a methodology to synthesize supervisors for a special class of Petri nets that can well model many flexible manufacturing systems. In our previous work, siphons in a Petri net are divided into elementary and dependent ones on the condition that all emptiable minimal siphons are computed. In this research, a mixed integer programming (MlP)-based deadlock detection technique is used to find some, in general not all, minimal siphons in a plant model without complete siphon enumeration. For each siphon found, depending on its noncontrollability, a monitor is added such that it is invariant-controlled. Our siphon control method guarantees that no emptiable control-induced siphon is generated due to the addition of the monitors. The siphon control process proceeds iteratively until there is no unmarked siphon in the supervisor of a plant model. Compared with the existing approaches, the novel deadlock prevention policy can usually lead to a structurally simple liveness-enforcing supervisor by adding only a small number of monitors and arcs. More importantly, complete siphon enumeration is avoided. A practical flexible manufacturing system (FMS) example is utilized to illustrate the proposed methods.