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Deep Network Fusion (deepNF)
Could you please update the data to the github?
The input of code is PPMI matrix. How to get PPMI matrix? Can you provide the code about RWR and PPMI?
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
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?
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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