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phanein / deepwalk

DeepWalk - Deep Learning for Graphs
http://www.perozzi.net/projects/deepwalk/
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TypeError in running deepwalk #9

Closed Jessilee closed 9 years ago

Jessilee commented 9 years ago

Hi, I'm tying to run the deepwalk with Blogcatalog dataset on Fedora20 sys. Here's the error I've got: [HH@localhost deepwalk-master]$ deepwalk --input example_graphs/blogcatalog.mat --output blogcatalog.embeddings --format mat /usr/lib/python2.7/site-packages/pkg_resources.py:979: UserWarning: /home/HH/.python-eggs is writable by group/others and vulnerable to attack when used with get_resource_filename. Consider a more secure location (set with .set_extraction_path or the PYTHON_EGG_CACHE environment variable). warnings.warn(msg, UserWarning) Number of nodes: 10312 Number of walks: 618720 Data size (walks_length): 18561600 Data size 18561600 is larger than limit (max-memory-data-size: 10). Dumping walks to disk. Walking... Counting vertex frequency... Training... Traceback (most recent call last): File "/usr/bin/deepwalk", line 9, in load_entry_point('deepwalk==1.0.1', 'console_scripts', 'deepwalk')() File "/usr/lib/python2.7/site-packages/deepwalk-1.0.1-py2.7.egg/deepwalk/main.py", line 160, in main process(args) File "/usr/lib/python2.7/site-packages/deepwalk-1.0.1-py2.7.egg/deepwalk/main.py", line 94, in process window=args.window_size, mincount=0, workers=args.workers) File "/usr/lib/python2.7/site-packages/deepwalk-1.0.1-py2.7.egg/deepwalk/skipgram.py", line 27, in init super(Skipgram, self).init(*kwargs) File "/usr/lib/python2.7/site-packages/gensim-0.11.1_1-py2.7-linux-i686.egg/gensim/models/word2vec.py", line 314, in init raise TypeError("You can't pass a generator as the sentences argument. Try an iterator.") TypeError: You can't pass a generator as the sentences argument. Try an iterator.

phanein commented 9 years ago

It looks like you're using a newer version of gensim. I would try the following:

  1. pip uninstall gensim
  2. pip uninstall deepwalk
  3. pip install gensim==0.10.2
  4. pip install deepwalk==v1.0.2
Jessilee commented 9 years ago

Thanks a lot, phanein.

joelkuiper commented 8 years ago

Hmm also running into this, but downgrading gensim is not really an option. What would the proper fix be for this?

phanein commented 8 years ago

@joelkuiper The quick fix would be to dump the walks to disk using argument --max-memory-data-size 0 - This will use another codepath, and will probably just work.

The proper fix is probably to create a virtual environment for deepwalk and use older library dependencies.

joelkuiper commented 8 years ago

Ended up rewriting it, https://github.com/vortext/DeepOntology I need it for a slightly different purpose anyway!