We present a system for the high-level analysis of beat-synchronous drum patterns to be used as part of a comprehensive rhythmic understanding system. We use a multilayer neural network, which is greedily pre-trained layer-by-layer using restriced Boltzmann machines (RBMs), in order to model the contextual time-sequence information of a drum pattern. For the input layer of the network, we use a conditional RBM, which has been shown to be an effective generative model of multi-dimensional sequences. Subsequent layers of the neural network can be pre-trained as conditional or standard RBMs in order to learn higherlevel rhythmic features. We show that this model can be fine-tuned in a discriminative manner to make accurate predictions about beat-measure alignment. The model generalizes well to multiple rhythmic styles due to the distributed state-space of the multi-layer neural network. In addition, the outputs of the discriminative network can serve as posterior probabilities over beat-alignment labels. These posterior probabilities can be used for Viterbi decoding in a hidden Markov model in order to maintain temporal continuity of the predicted information.