Since you are asking about deep learning, I assume that you are more interested in end-to-end systems, rather than object design. Neural networks that can process variable data inputs:
1) Convolutional neural networks with pools. They are commonly used in the context of pattern recognition, but recently they have also been applied to modeling offers. (I think they should also be good at classifying stars).
2) Recursive neural networks. (Good for sequential data, such as time series, sequence marking tasks are also good for machine translation).
3) Tree-based auto-encoders (also called recursive auto-encoders) for data located in tree structures (can be applied to sentence parsing trees)
Many articles describing sample applications can be easily found with googling.
For unusual tasks, you can choose one of them based on the structure of your data or you can develop some options and combinations of these systems.
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