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cannin / graph_neural_network_drug_response

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Running DrugCell on binder occurs OOM probably. #15

Open inoue0426 opened 2 years ago

inoue0426 commented 2 years ago

When running DrugCell on the binder, will happen kernel restarting. This seems like OOM or something happens. DrugCell uses PyTorch and this is a huge library, so it can happen. Not sure how to resolve rn, but need to check what happens and then solve this.

inoue0426 commented 2 years ago

Using rcellminer data with original feature data, we can run DrugCell on Binder. https://mybinder.org/v2/gh/cannin/graph_neural_network_drug_response/6b109d5c31c760237d51dfb4bd5cbd1a44db5aae Definitely our data is huge and it's impossible to run on Binder. So if you want to use huge data, you must use your own machine.

cannin commented 2 years ago

Maybe switch to Google Colab?

inoue0426 commented 2 years ago

I just created the Colab version. https://colab.research.google.com/github/cannin/graph_neural_network_drug_response/blob/main/notebook/Run_DrugCell_Model_for_CellMinerCDB_Data.ipynb