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By employing latent Gaussian process ordinary differential equations, our model infers both independent dynamics and their interactions with reliable uncertainty estimates. In our formulation, each object is represented as a graph node and interactions are modeled by accumulating the messages coming from neighboring objects. We show that efficient inference of such a complex network of variables is possible with modern variational sparse Gaussian process inference techniques. We empirically demonstrate that our model improves the reliability of long-term predictions over neural network based alternatives and it successfully handles missing dynamic or static information. 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