A popular testbed for deep learning has been multimodal recognition of human activity or gesture involving diverse inputs such as video, audio, skeletal pose and depth images. Deep learning architectures have excelled on such problems due to their ability to combine modality representations at different levels of nonlinear feature extraction. However, designing an optimal architecture in which to fuse such learned representations has largely been a non-trivial human engineering effort. We treat fusion structure optimization as a hyper-parameter search and cast it as a discrete optimization problem under the Bayesian optimization framework. We propose a novel graph-induced kernel to compute structural similarities in the search space of tree-structured multimodal architectures and demonstrate its effectiveness using two challenging multimodal human activity recognition datasets.