cherisezhu / gil Goto Github PK

Solved! thanks

Hi, when I try to run your code, several problems rise due to the environment.

1. the package sage, if installed by pip, will only has a version sage==0.0.0. is that the right package to use?
2. if working with geoopt==0.0.1, there is no module 'geoopt.manifolds.poincare.math', only geoopt==0.1.x has the module, however, it does not support torch==1.1.0
3. could you please share other version of the packages, such as torch-sparse and torch-cluster?

Thanks very much!

Hey @CheriseZhu, do you also have a variant implemented for Graph classification. I am looking to use this code for the same, and it will be of great help if you can let me know?

No module named 'geoopt.manifolds.poincare'

Thanks for the beautiful work.
But I run into 'tensor size'/'out of bound' error for link prediction task on all datasets, while all is okay with node classification.
This message showed under your example input (say, the disease_lp one):

Traceback (most recent call last):
File "train.py", line 163, in
train(args)
File "train.py", line 96, in train
embeddings = model.encode(data['features'], data['adj_train_norm'])
File "/home/server/code/embedding_methods/GIL/GIL/models/base_models.py", line 34, in encode
h = self.encoder.encode(x, adj)
File "/home/server/code/embedding_methods/GIL/GIL/models/encoders.py", line 341, in encode
return super(GIL, self).encode((x_hyp, x), adj)
File "/home/server/code/embedding_methods/GIL/GIL/models/encoders.py", line 22, in encode
output, _ = self.layers.forward(input)
File "/home/server/miniconda3/envs/hy-torch/lib/python3.6/site-packages/torch/nn/modules/container.py", line 139, in forward
input = module(input)
File "/home/server/miniconda3/envs/hy-torch/lib/python3.6/site-packages/torch/nn/modules/module.py", line 1051, in _call_impl
return forward_call(*input, **kwargs)
File "/home/server/code/embedding_methods/GIL/GIL/layers/hyp_layers.py", line 217, in forward
x = self.conv(input_h)
File "/home/server/miniconda3/envs/hy-torch/lib/python3.6/site-packages/torch/nn/modules/module.py", line 1051, in _call_impl
return forward_call(*input, **kwargs)
File "/home/server/code/embedding_methods/GIL/GIL/layers/hyp_layers.py", line 286, in forward
out = self.propagate(edge_index, x=log_x, num_nodes=x.size(0), original_x=x)
File "/home/server/miniconda3/envs/hy-torch/lib/python3.6/site-packages/torch_geometric/nn/conv/message_passing.py", line 262, in propagate
kwargs)
File "/home/server/miniconda3/envs/hy-torch/lib/python3.6/site-packages/torch_geometric/nn/conv/message_passing.py", line 170, in collect
self.set_size(size, dim, data)
File "/home/server/miniconda3/envs/hy-torch/lib/python3.6/site-packages/torch_geometric/nn/conv/message_passing.py", line 135, in set_size
(f'Encountered tensor with size {src.size(self.node_dim)} in '
ValueError: Encountered tensor with size 8 in dimension -2, but expected size 2665.

When it's the airport dataset for lp, the error is

RuntimeError: INDICES element is out of DATA bounds, id=1975 axis_dim=8

Do you have any idea what's the problem?
Many thanks!