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Recently, the use of neural quantum states for describing the ground state of many- and few-body problems has been gaining popularity because of their high expressivity and ability to handle intractably large Hilbert spaces. In particular, methods based on variational Monte Carlo have proven to be successful in describing the physics of bosonic systems such as the Bose-Hubbard (BH) model. However, this technique has not been systematically tested on the parameter space of the BH model, particularly at the boundary between the Mott insulator and superfluid phases. In this work, we evaluate the capabilities of variational Monte Carlo with a trial wavefunction given by a Restricted Boltzmann Machine to reproduce the quantum ground state of the BH model on several points of its parameter space. To benchmark the technique, we compare its results to the ground state found through exact diagonalization for small one-dimensional chains. In general, we find that the learned ground state correctly estimates many observables, reproducing to a high degree the phase diagram for the first Mott lobe and part of the second one. However, we find that the technique is challenged whenever the system transitions between excitation manifolds, as the ground state is not learned correctly at these boundaries. We improve the quality of the results produced by the technique by proposing a method to discard noisy probabilities learned in the ground state.