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deepnf's Issues

RWR and PPMI

The input of code is PPMI matrix. How to get PPMI matrix? Can you provide the code about RWR and PPMI?

How do you preserve the node order in the final embedding file?

I have 2 networks. when I check list(G.nodes) for both networks, the order of nodes is different.

I want to print embeddings in following way:
Node1 feature1 feature2.......featuren
Node2 feature1 feature2.......featuren
Node3 feature1 feature2.......featuren
.
.
.
.
.
Nodem feature1 feature2.......featuren

but i am not sure of the order of nodes to be considered.

thanks in advance

Run the code in 2023

Dear author of deepNF, I'm pretty interested in this paper.

Is it possible to add the environment requirement? Also, the link to the data in README has expired, could it still be available?

Model files not found

First of all, thanks for making this available!
I tried running python main.py example_params.txt after downloading the annotations, but I get an error saying the models file yeast_MDA_arch_2_final_res.h5 is not found (see below). If I change the mark parameter to --all it seems to run just fine.

Also, a little more description about what each parameter does (specifically mark) would definitely be helpful.

python main.py example_params.txt 
Using TensorFlow backend.
mark=--no
org=yeast
valid_type=th
model_type=mda
select_arch=[2]
ofile_keywords=final_res
epochs=10
batch_size=128
n_trials=10
K=3
alpha=0.98
models_path=models/
results_path=results/
###############################################################


### [1] Loading network...
### [2] Loading network...
### [3] Loading network...
### [4] Loading network...
### [5] Loading network...
### [6] Loading network...
### [Model] Running for architecture:  [12000, 600, 12000]
### Running for: yeast_MDA_arch_2_final_res.h5
Traceback (most recent call last):
  File "main.py", line 202, in <module>
    mid_model = load_model(models_path + model_name)
  File "/home/jeffl/git-workspace/from-lit/deepNF/venv/local/lib/python2.7/site-packages/keras/models.py", line 234, in load_model
    with h5py.File(filepath, mode='r') as f:
  File "/home/jeffl/git-workspace/from-lit/deepNF/venv/local/lib/python2.7/site-packages/h5py/_hl/files.py", line 269, in __init__
    fid = make_fid(name, mode, userblock_size, fapl, swmr=swmr)
  File "/home/jeffl/git-workspace/from-lit/deepNF/venv/local/lib/python2.7/site-packages/h5py/_hl/files.py", line 99, in make_fid
    fid = h5f.open(name, flags, fapl=fapl)
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "h5py/h5f.pyx", line 78, in h5py.h5f.open
IOError: Unable to open file (unable to open file: name = 'models/yeast_MDA_arch_2_final_res.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

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