mims-harvard / ohmnet

OhmNet: Representation learning in multi-layer graphs

Home Page:http://snap.stanford.edu/ohmnet

Geek Repo:Geek Repo

Github PK Tool:Github PK Tool

Hierarchy error in full tissue network

davidfstein opened this issue · comments

I am attempting to run ohmnet on the full tissue ppi network from http://snap.stanford.edu/ohmnet/. There appears to be an error with the provided hierarchy file. The following error is produced.

Traceback (most recent call last):
  File "main.py", line 66, in <module>
    main(args)
  File "main.py", line 62, in main
    on.embed_multilayer()
  File "/local/david/ohmnet/ohmnet/ohmnet.py", line 212, in embed_multilayer
    all_nodes, leaf_vectors, internal_vectors)
  File "/local/david/ohmnet/ohmnet/ohmnet.py", line 91, in update_internal_vectors
    assert len(parents) == 1, 'Problem'
AssertionError: Problem

I am running ohmnet as follows python2.7 main.py --input data/tissues.list --outdir . --hierarchy bio-tissue-hierarchy/tissue.hierarchy

When run on the example brain network provided the code executes properly. I can see that the brain hierarchy seems to follow a different format than the provided tissue hierarchy. Do you have a working tissue hierarchy file or can you guide me on how to construct one?

Thanks!