I have been working on implementing Deep Neural networks on BioInformatics field for past 6 months, I have helped many people finished their advanced mathematical modeling with the help of Python/TensorFlow/Keras/SciKit-Learn/TPOT/PyMD. I feel confident about my expertise on ML, and your task would be categorized under that.
Fixing your GPU issue can be done in less than a day. could you please let me know more about the execution environment? is it on Amazon? google cloud engine? your local data center?