In this paper, we consider the problem of learning prediction models for spatiotemporal physical processes driven by unknown partial differential equations (PDEs). We propose a deep learning framework that learns the underlying dynamics and predicts its evolution using sparsely distributed data sites. Deep learning has shown promising results in modeling physical dynamics in recent years. However, most of the existing deep learning methods for modeling physical dynamics either focus on solving known PDEs or require data in a dense grid when the governing PDEs are unknown. In contrast, our method focuses on learning prediction models for unknown PDE-driven dynamics only from sparsely observed data. The proposed method is spatial dimension-independent and geometrically flexible. We demonstrate our method in the forecasting task for the two-dimensional wave equation and the Burgers-Fisher equation in multiple geometries with different boundary conditions, and the ten-dimensional heat equation.