Running

[milesgep]

How do you run train.py for ppi? What file is needed for the argument "--problem-path" so I can run it?
Also for reddit because the h5 files are not working for running as well.

[bkj]

There are scripts for converting data here:
https://github.com/bkj/pytorch-graphsage/blob/master/utils/run-convert.sh
And invocations of train here:
https://github.com/bkj/pytorch-graphsage/blob/master/run.sh

You may find this repo helpful:
https://github.com/bkj/graphsage-age-prediction
That's a boiled down implementation of graphsage w/ instructions on running on a particular dataset.

~ Ben

[milesgep]

I am having an issue with running the run-convert.sh. I was having an assertion error with networkx so I updated it and the issue did not go away. I commented out the line causing the error and now I have this issue:

File "convert.py", line 165, in
feats = np.vstack([feats[id2idx[str(id)]] for id in G.nodes()])
KeyError: '0'

Is there certain versions of packages I need for this to operate correctly?

[bkj]

Yeah, likely you need an older version of pytorch. I can put a requirements.txt here later. If I don't do it in the next few days ping me here again to remind me

[milesgep]

I am making some progress now

Traceback (most recent call last):
File "convert.py", line 202, in
}, args.outpath)
File "convert.py", line 56, in save_problem
assert validate_problem(problem)
File "convert.py", line 48, in validate_problem
if not problem['sparse']:
KeyError: 'sparse'

I am getting this error, is this line wanting to check if sparse is in the dictionary? I see prior to this that the dictionary is made with no key "sparse" so I am trying to figure out what you want to do with the line of code.

[milesgep]

I am having another issue where the function to_numpy(x) recursively calls itself until my program crashes. I was not having this issue earlier so I am not 100% what is causing it.

[bkj]

That sounds like a pytorch version problem, I think this expectes 0.3.1, but I'll have to double check

[lannester666]

Hi，I have the same problem with you.(File "convert.py", line 48, in validate_problem
if not problem['sparse']:
KeyError: 'sparse')
Did you solve this?