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Surabhivj / BRANEnet

Embedding Multilayer Networks for Omics Data Integration
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if use Random Walk in BRANEnet.py #2

Open 1830416002 opened 6 months ago

1830416002 commented 6 months ago

Hi, if I just use the command "python BRANEnet.py --multilayer_networkfile network_file.gml --T 3 --d 128 --type 'gml" to compute embedding, I think this python code does not use the Random Walk. I want to know if my thought is true.

1830416002 commented 6 months ago

It just use the SVD?

Surabhivj commented 6 months ago

Hi! Yes, command "python BRANEnet.py --multilayer_networkfile network_file.gml --T 3 --d 128 --type 'gml do compute random walk PPMI matrix. Please refer to functions.py to know all the functions used in BRANEnet.py

1830416002 commented 6 months ago

OK. Thanks. I also want to know why the PPMI matrix is called "random walk PPMI matrix". It seems that the "PPMI_matrix" function in function.py does not use random walk.

Surabhivj commented 6 months ago

The formula that is used to compute PPMI matrix is an approximation of random walks. In order to reduce the complexity of simulating explicit random walks in large networks, we have taken the approximation. If it is too complicate to understand, I recommend reading section 3.1 of this article -> https://academic.oup.com/bioinformatics/article/38/24/5383/6793849#387288686

1830416002 commented 6 months ago

OK. Thank you very much.