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Monte-Carlo Tree Search (MCTS) is a powerful tool for many non-differentiable search related problems such as adversarial games. However, the performance of such approach highly depends on the order of the nodes that are considered at each branching of the tree. If the first branches are not discriminative enough, i.e. they cannot distinguish between promising and deceiving configurations for the final task, the efficiency of the search is exponentially reduced. While in some cases the order of the branching is given as part of the problem (e.g. in chess the sequential order of the moves is defined by the game), in others, such as Neural Architecture Search (NAS), the visiting order of the tree is not important, and only the final architecture matters. In this paper, we study the application of MCTS to NAS for the task of image classification. We analyze several sampling methods and branching alternatives for MCTS and propose to learn the branching by hierarchical clustering of architectures based on their similarity. The similarity is measured by the pairwise distance of output vectors of architectures. Extensive experiments on two challenging benchmarks on CIFAR10 and ImageNet show that MCTS, if provided with a good branching hierarchy, can yield promising solutions more efficiently than other approaches for NAS problems.