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idrugLab / MMSyn

Code for "Multimodal data fusion-driven prediction of synergistic drug combinations with MMSyn"

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File not found #1

Open jonesse3 opened 5 months ago

jonesse3 commented 5 months ago

When trying to run _cellautoencoder.py, I got an error saying that a file was not found.

How can I get the following files in order to reproduce the model:

cell_index_file = 'data/cell/cell_30_ge_cn_id.csv'
cell_ge_file = 'data/cell/ONeil_31_cell_47838_dim_genex.csv'
cell_cn_file = 'data/cell/ONeil_31_cell_23316_dim_CNV.csv'
cell_ge_ae = "data\cell\ONeil_30cell_ge_512dim.pt"
cell_cn_ae = "data\cell\ONeil_30cell_cn_512dim.pt"

yuupang commented 4 months ago

These files were processed. Original file can be downloaded by CCLE. The files can be generated by the paper.

jonesse3 commented 4 months ago

Can I get the processed files so I can reproduce the results from the paper? Otherwise I can't run the code per the instructions in the README.

I went to the links provided, but it's unclear what files and their versions I should download from depmap. Once these are identified, do I run preprocess.py to process these files and generate the autoencoders (also missing from the data/cell folder)?