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One of possible levels of computer protection may consist in splitting computer networks into logical chunks that are known as virtual computer networks or virtual subnets. The paper considers a novel approach to determine virtual subnets that is based on the given matrix of logic connectivity of computers. The paper shows that the problem considered is related to one of the forms of Boolean Matrix Factorization. It formulates the virtual subnet design task and proposes genetic algorithms as a means to solve it. Basic improvements proposed in the paper are using trivial solutions to generate an initial population, taking into account in the fitness function the criterion of minimum number of virtual subnets, and using columns of the connectivity matrix as genes of chromosomes. Experimental results show the proposed genetic algorithm has high effectiveness.