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TODO.md

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PDGrapher: TODO

This file summarizes things that still need to be done and some observations.

Bugs:

  • There is some CUDA memory leak, but it is only present when we train a lot of models in one go, as in train them with one python ... call. An example is examples/hyperparameter_tuning.py script, which crashed due to OOM error in CUDA after training >130 models for 1 epoch. I suspect it is related to lightning.Fabric, which handles moving tensort to and from GPU.

TODO:

  • data folder has no data currently, and the folder structure with 'raw' folders is not consistent with code in scripts folders. Maybe we can rename them to '2022-03-PPI', '2022-02-LINCS_Level3' and so on. There are two such PPI folders, so we need to be careful there.
  • main README.md needs some updating, like add authors, project description.