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OpenDAS
dgl
Commits
c23a61bd
"vscode:/vscode.git/clone" did not exist on "c18941b01ad0ea6b07d020f353d81153c632a374"
Unverified
Commit
c23a61bd
authored
Mar 04, 2020
by
Jinjing Zhou
Committed by
GitHub
Mar 04, 2020
Browse files
fix s3 link (#1310)
parent
349a48bd
Changes
24
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20 changed files
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51 additions
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51 deletions
+51
-51
apps/kg/README.md
apps/kg/README.md
+5
-5
apps/kg/dataloader/KGDataset.py
apps/kg/dataloader/KGDataset.py
+2
-2
docker/README.md
docker/README.md
+2
-2
examples/pytorch/graphwriter/README.md
examples/pytorch/graphwriter/README.md
+2
-2
examples/pytorch/graphwriter/prepare_data.sh
examples/pytorch/graphwriter/prepare_data.sh
+1
-1
examples/pytorch/metapath2vec/download.py
examples/pytorch/metapath2vec/download.py
+1
-1
examples/pytorch/model_zoo/chem/generative_models/dgmg/README.md
...s/pytorch/model_zoo/chem/generative_models/dgmg/README.md
+2
-2
examples/pytorch/model_zoo/chem/property_prediction/README.md
...ples/pytorch/model_zoo/chem/property_prediction/README.md
+2
-2
examples/pytorch/pointcloud/main.py
examples/pytorch/pointcloud/main.py
+1
-1
examples/pytorch/recommendation/README.md
examples/pytorch/recommendation/README.md
+1
-1
examples/pytorch/rrn/sudoku_data.py
examples/pytorch/rrn/sudoku_data.py
+1
-1
examples/pytorch/rrn/sudoku_solver.py
examples/pytorch/rrn/sudoku_solver.py
+1
-1
examples/pytorch/transformer/dataset/utils.py
examples/pytorch/transformer/dataset/utils.py
+2
-2
python/dgl/contrib/sampling/sampler.py
python/dgl/contrib/sampling/sampler.py
+1
-1
python/dgl/nodeflow.py
python/dgl/nodeflow.py
+1
-1
tutorials/basics/1_first.py
tutorials/basics/1_first.py
+4
-4
tutorials/basics/4_batch.py
tutorials/basics/4_batch.py
+6
-6
tutorials/basics/5_hetero.py
tutorials/basics/5_hetero.py
+4
-4
tutorials/models/1_gnn/8_sse_mx.py
tutorials/models/1_gnn/8_sse_mx.py
+3
-3
tutorials/models/1_gnn/9_gat.py
tutorials/models/1_gnn/9_gat.py
+9
-9
No files found.
apps/kg/README.md
View file @
c23a61bd
...
...
@@ -48,11 +48,11 @@ DGL-KE provides five knowledge graphs:
| Dataset | #nodes | #edges | #relations |
|---------|--------|--------|------------|
|
[
FB15k
](
https://
s3.us-east-2.amazonaws.com/
dgl.ai/dataset/FB15k.zip
)
| 14951 | 592213 | 1345 |
|
[
FB15k-237
](
https://
s3.us-east-2.amazonaws.com/
dgl.ai/dataset/FB15k-237.zip
)
| 14541 | 310116 | 237 |
|
[
wn18
](
https://
s3.us-east-2.amazonaws.com/
dgl.ai/dataset/wn18.zip
)
| 40943 | 151442 | 18 |
|
[
wn18rr
](
https://
s3.us-east-2.amazonaws.com/
dgl.ai/dataset/wn18rr.zip
)
| 40943 | 93003 | 11 |
|
[
Freebase
](
https://
s3.us-east-2.amazonaws.com/
dgl.ai/dataset/Freebase.zip
)
| 86054151 | 338586276 | 14824 |
|
[
FB15k
](
https://
data.
dgl.ai/dataset/FB15k.zip
)
| 14951 | 592213 | 1345 |
|
[
FB15k-237
](
https://
data.
dgl.ai/dataset/FB15k-237.zip
)
| 14541 | 310116 | 237 |
|
[
wn18
](
https://
data.
dgl.ai/dataset/wn18.zip
)
| 40943 | 151442 | 18 |
|
[
wn18rr
](
https://
data.
dgl.ai/dataset/wn18rr.zip
)
| 40943 | 93003 | 11 |
|
[
Freebase
](
https://
data.
dgl.ai/dataset/Freebase.zip
)
| 86054151 | 338586276 | 14824 |
Users can specify one of the datasets with
`--dataset`
in
`train.py`
and
`eval.py`
.
...
...
apps/kg/dataloader/KGDataset.py
View file @
c23a61bd
...
...
@@ -38,7 +38,7 @@ class KGDataset1:
The triples are stored as 'head_name
\t
relation_name
\t
tail_name'.
'''
def
__init__
(
self
,
path
,
name
,
read_triple
=
True
,
only_train
=
False
):
url
=
'https://
s3.us-east-2.amazonaws.com/
dgl.ai/dataset/{}.zip'
.
format
(
name
)
url
=
'https://
data.
dgl.ai/dataset/{}.zip'
.
format
(
name
)
if
not
os
.
path
.
exists
(
os
.
path
.
join
(
path
,
name
)):
print
(
'File not found. Downloading from'
,
url
)
...
...
@@ -105,7 +105,7 @@ class KGDataset2:
The triples are stored as 'head_nid
\t
relation_id
\t
tail_nid'.
'''
def
__init__
(
self
,
path
,
name
,
read_triple
=
True
,
only_train
=
False
):
url
=
'https://
s3.us-east-2.amazonaws.com/
dgl.ai/dataset/{}.zip'
.
format
(
name
)
url
=
'https://
data.
dgl.ai/dataset/{}.zip'
.
format
(
name
)
if
not
os
.
path
.
exists
(
os
.
path
.
join
(
path
,
name
)):
print
(
'File not found. Downloading from'
,
url
)
...
...
docker/README.md
View file @
c23a61bd
...
...
@@ -17,12 +17,12 @@ docker build -t dgl-lint -f Dockerfile.ci_lint .
### CPU image for kg
```
bash
wget https://
s3.us-east-2.amazonaws.com/
dgl.ai/dataset/FB15k.zip
-P
install
/
wget https://
data.
dgl.ai/dataset/FB15k.zip
-P
install
/
docker build
-t
dgl-cpu:torch-1.2.0
-f
Dockerfile.ci_cpu_torch_1.2.0 .
```
### GPU image for kg
```
bash
wget https://
s3.us-east-2.amazonaws.com/
dgl.ai/dataset/FB15k.zip
-P
install
/
wget https://
data.
dgl.ai/dataset/FB15k.zip
-P
install
/
docker build
-t
dgl-gpu:torch-1.2.0
-f
Dockerfile.ci_gpu_torch_1.2.0 .
```
examples/pytorch/graphwriter/README.md
View file @
c23a61bd
...
...
@@ -39,6 +39,6 @@ We repeat the experiment five times.
### Examples
We also provide the output of our implementation on test set together with the reference text.
-
[
GraphWriter's output
](
https://
s3.us-east-2.amazonaws.com/
dgl.ai/models/graphwriter/tmp_pred.txt
)
-
[
Reference text
](
https://
s3.us-east-2.amazonaws.com/
dgl.ai/models/graphwriter/tmp_gold.txt
)
-
[
GraphWriter's output
](
https://
data.
dgl.ai/models/graphwriter/tmp_pred.txt
)
-
[
Reference text
](
https://
data.
dgl.ai/models/graphwriter/tmp_gold.txt
)
examples/pytorch/graphwriter/prepare_data.sh
View file @
c23a61bd
wget https://
s3.us-east-2.amazonaws.com/
dgl.ai/dataset/AGENDA.tar.gz
wget https://
data.
dgl.ai/dataset/AGENDA.tar.gz
mkdir
data
tar
-C
data/
-xvzf
AGENDA.tar.gz
examples/pytorch/metapath2vec/download.py
View file @
c23a61bd
...
...
@@ -24,7 +24,7 @@ class AminerDataset(object):
"""
def
__init__
(
self
,
path
):
self
.
url
=
'https://
s3.us-east-2.amazonaws.com/
dgl.ai/dataset/aminer.zip'
self
.
url
=
'https://
data.
dgl.ai/dataset/aminer.zip'
if
not
os
.
path
.
exists
(
os
.
path
.
join
(
path
,
'aminer.txt'
)):
print
(
'File not found. Downloading from'
,
self
.
url
)
...
...
examples/pytorch/model_zoo/chem/generative_models/dgmg/README.md
View file @
c23a61bd
...
...
@@ -124,11 +124,11 @@ directory, with three statistics logged in `generation_stats.txt` under `eval_re
We also provide a jupyter notebook where you can visualize the generated molecules


and compare their property distributions against the training molecule property distributions


You can download the notebook with
`wget https://data.dgl.ai/dgllife/dgmg/eval_jupyter.ipynb`
.
...
...
examples/pytorch/model_zoo/chem/property_prediction/README.md
View file @
c23a61bd
...
...
@@ -111,9 +111,9 @@ on the training and validation set for reference.
[8] visualizes the weights of atoms in readout for possible interpretations like the figure below.
We provide a jupyter notebook for performing the visualization and you can download it with
`wget https://
s3.us-east-2.amazonaws.com/
dgl.ai/model_zoo/drug_discovery/AttentiveFP/atom_weight_visualization.ipynb`
.
`wget https://
data.
dgl.ai/model_zoo/drug_discovery/AttentiveFP/atom_weight_visualization.ipynb`
.


## Dataset Customization
...
...
examples/pytorch/pointcloud/main.py
View file @
c23a61bd
...
...
@@ -28,7 +28,7 @@ data_filename = 'modelnet40-sampled-2048.h5'
local_path
=
args
.
dataset_path
or
os
.
path
.
join
(
get_download_dir
(),
data_filename
)
if
not
os
.
path
.
exists
(
local_path
):
download
(
'https://
s3.us-east-2.amazonaws.com/
dgl.ai/dataset/modelnet40-sampled-2048.h5'
,
local_path
)
download
(
'https://
data.
dgl.ai/dataset/modelnet40-sampled-2048.h5'
,
local_path
)
CustomDataLoader
=
partial
(
DataLoader
,
...
...
examples/pytorch/recommendation/README.md
View file @
c23a61bd
...
...
@@ -4,7 +4,7 @@ NOTE: this version is not using NodeFlow yet.
This example only work with Python 3.6+
First, download and extract from https://dgl.ai
.s3.us-east-2.amazonaws.com
/dataset/ml-1m.tar.gz
First, download and extract from https://d
ata.d
gl.ai/dataset/ml-1m.tar.gz
One can then run the following to train PinSage on MovieLens-1M:
...
...
examples/pytorch/rrn/sudoku_data.py
View file @
c23a61bd
...
...
@@ -56,7 +56,7 @@ class ListDataset(Dataset):
def
_get_sudoku_dataset
(
segment
=
'train'
):
assert
segment
in
[
'train'
,
'valid'
,
'test'
]
url
=
"https://
s3.us-east-2.amazonaws.com/
dgl.ai/dataset/sudoku-hard.zip"
url
=
"https://
data.
dgl.ai/dataset/sudoku-hard.zip"
zip_fname
=
"/tmp/sudoku-hard.zip"
dest_dir
=
'/tmp/sudoku-hard/'
...
...
examples/pytorch/rrn/sudoku_solver.py
View file @
c23a61bd
...
...
@@ -20,7 +20,7 @@ def solve_sudoku(puzzle):
model_filename
=
os
.
path
.
join
(
model_path
,
'rrn-sudoku.pkl'
)
if
not
os
.
path
.
exists
(
model_filename
):
print
(
'Downloading model...'
)
url
=
'https://
s3.us-east-2.amazonaws.com/
dgl.ai/models/rrn-sudoku.pkl'
url
=
'https://
data.
dgl.ai/models/rrn-sudoku.pkl'
urllib
.
request
.
urlretrieve
(
url
,
model_filename
)
model
=
torch
.
load
(
model_filename
,
map_location
=
'cpu'
)
...
...
examples/pytorch/transformer/dataset/utils.py
View file @
c23a61bd
...
...
@@ -4,8 +4,8 @@ import os
from
dgl.data.utils
import
*
_urls
=
{
'wmt'
:
'https://
s3.us-east-2.amazonaws.com/
dgl.ai/dataset/wmt14bpe_de_en.zip'
,
'scripts'
:
'https://
s3.us-east-2.amazonaws.com/
dgl.ai/dataset/transformer_scripts.zip'
,
'wmt'
:
'https://
data.
dgl.ai/dataset/wmt14bpe_de_en.zip'
,
'scripts'
:
'https://
data.
dgl.ai/dataset/transformer_scripts.zip'
,
}
def
prepare_dataset
(
dataset_name
):
...
...
python/dgl/contrib/sampling/sampler.py
View file @
c23a61bd
...
...
@@ -224,7 +224,7 @@ class NeighborSampler(NodeFlowSampler):
layer :math:`i+1` are in layer :math:`i`. All the edges are from nodes
in layer :math:`i` to layer :math:`i+1`.
.. image:: https://
s3.us-east-2.amazonaws.com/
dgl.ai/tutorial/sampling/NodeFlow.png
.. image:: https://
data.
dgl.ai/tutorial/sampling/NodeFlow.png
As an analogy to mini-batch training, the ``batch_size`` here is equal to the number
of the initial seed nodes (number of nodes in the last layer).
...
...
python/dgl/nodeflow.py
View file @
c23a61bd
...
...
@@ -82,7 +82,7 @@ class NodeFlow(DGLBaseGraph):
We store extra information, such as the node and edge mapping from
the NodeFlow graph to the parent graph.
.. image:: https://
s3.us-east-2.amazonaws.com/
dgl.ai/api/sampling.nodeflow.png
.. image:: https://
data.
dgl.ai/api/sampling.nodeflow.png
DO NOT create NodeFlow object directly. Use sampling method to
generate NodeFlow instead.
...
...
tutorials/basics/1_first.py
View file @
c23a61bd
...
...
@@ -32,7 +32,7 @@ At the end of this tutorial, we hope you get a brief feeling of how DGL works.
# 33). The network is visualized as follows with the color indicating the
# community:
#
# .. image:: https://
s3.us-east-2.amazonaws.com/
dgl.ai/tutorial/img/karate-club.png
# .. image:: https://
data.
dgl.ai/tutorial/img/karate-club.png
# :align: center
#
# The task is to predict which side (0 or 33) each member tends to join given
...
...
@@ -135,7 +135,7 @@ print(G.nodes[[10, 11]].data['feat'])
# node will update its own feature with information sent from neighboring
# nodes. A graphical demonstration is displayed below.
#
# .. image:: https://
s3.us-east-2.amazonaws.com/
dgl.ai/tutorial/1_first/mailbox.png
# .. image:: https://
data.
dgl.ai/tutorial/1_first/mailbox.png
# :alt: mailbox
# :align: center
#
...
...
@@ -266,7 +266,7 @@ draw(0) # draw the prediction of the first epoch
plt
.
close
()
###############################################################################
# .. image:: https://
s3.us-east-2.amazonaws.com/
dgl.ai/tutorial/1_first/karate0.png
# .. image:: https://
data.
dgl.ai/tutorial/1_first/karate0.png
# :height: 300px
# :width: 400px
# :align: center
...
...
@@ -278,7 +278,7 @@ plt.close()
ani
=
animation
.
FuncAnimation
(
fig
,
draw
,
frames
=
len
(
all_logits
),
interval
=
200
)
###############################################################################
# .. image:: https://
s3.us-east-2.amazonaws.com/
dgl.ai/tutorial/1_first/karate.gif
# .. image:: https://
data.
dgl.ai/tutorial/1_first/karate.gif
# :height: 300px
# :width: 400px
# :align: center
...
...
tutorials/basics/4_batch.py
View file @
c23a61bd
...
...
@@ -30,7 +30,7 @@ networks to this problem has been a popular approach recently. This can be seen
# In this tutorial, you learn how to perform batched graph classification
# with DGL. The example task objective is to classify eight types of topologies shown here.
#
# .. image:: https://
s3.us-east-2.amazonaws.com/
dgl.ai/tutorial/batch/dataset_overview.png
# .. image:: https://
data.
dgl.ai/tutorial/batch/dataset_overview.png
# :align: center
#
# Implement a synthetic dataset :class:`data.MiniGCDataset` in DGL. The dataset has eight
...
...
@@ -64,7 +64,7 @@ plt.show()
# a batch of graphs can be viewed as a large graph that has many disjointed
# connected components. Below is a visualization that gives the general idea.
#
# .. image:: https://
s3.us-east-2.amazonaws.com/
dgl.ai/tutorial/batch/batch.png
# .. image:: https://
data.
dgl.ai/tutorial/batch/batch.png
# :width: 400pt
# :align: center
#
...
...
@@ -91,7 +91,7 @@ def collate(samples):
# ----------------
# Graph classification proceeds as follows.
#
# .. image:: https://
s3.us-east-2.amazonaws.com/
dgl.ai/tutorial/batch/graph_classifier.png
# .. image:: https://
data.
dgl.ai/tutorial/batch/graph_classifier.png
#
# From a batch of graphs, perform message passing and graph convolution
# for nodes to communicate with others. After message passing, compute a
...
...
@@ -254,16 +254,16 @@ print('Accuracy of argmax predictions on the test set: {:4f}%'.format(
###############################################################################
# The animation here plots the probability that a trained model predicts the correct graph type.
#
# .. image:: https://
s3.us-east-2.amazonaws.com/
dgl.ai/tutorial/batch/test_eval4.gif
# .. image:: https://
data.
dgl.ai/tutorial/batch/test_eval4.gif
#
# To understand the node and graph representations that a trained model learned,
# we use `t-SNE, <https://lvdmaaten.github.io/tsne/>`_ for dimensionality reduction
# and visualization.
#
# .. image:: https://
s3.us-east-2.amazonaws.com/
dgl.ai/tutorial/batch/tsne_node2.png
# .. image:: https://
data.
dgl.ai/tutorial/batch/tsne_node2.png
# :align: center
#
# .. image:: https://
s3.us-east-2.amazonaws.com/
dgl.ai/tutorial/batch/tsne_graph2.png
# .. image:: https://
data.
dgl.ai/tutorial/batch/tsne_graph2.png
# :align: center
#
# The two small figures on the top separately visualize node representations after one and two
...
...
tutorials/basics/5_hetero.py
View file @
c23a61bd
...
...
@@ -46,7 +46,7 @@ using the heterograph class and its associated API.
# The following diagram shows several entities in the ACM dataset and the relationships among them
# (taken from `Shi et al., 2015 <https://arxiv.org/pdf/1511.04854.pdf>`_).
#
# .. figure:: https://
s3.us-east-2.amazonaws.com/
dgl.ai/tutorial/hetero/acm-example.png#
# .. figure:: https://
data.
dgl.ai/tutorial/hetero/acm-example.png#
#
# This graph has three types of entities that correspond to papers, authors, and publication venues.
# It also contains three types of edges that connect the following:
...
...
@@ -70,7 +70,7 @@ using the heterograph class and its associated API.
# marked with a rating, then each rating value could correspond to a different edge type.
# The following diagram shows an example of user-item interactions as a heterograph.
#
# .. figure:: https://
s3.us-east-2.amazonaws.com/
dgl.ai/tutorial/hetero/recsys-example.png
# .. figure:: https://
data.
dgl.ai/tutorial/hetero/recsys-example.png
#
#
# Knowledge graph
...
...
@@ -81,7 +81,7 @@ using the heterograph class and its associated API.
# occupation (item P106) is politician (item Q82955). The relationships are shown in the following.
# diagram.
#
# .. figure:: https://
s3.us-east-2.amazonaws.com/
dgl.ai/tutorial/hetero/kg-example.png
# .. figure:: https://
data.
dgl.ai/tutorial/hetero/kg-example.png
#
###############################################################################
...
...
@@ -144,7 +144,7 @@ ratings = dgl.heterograph(
import
scipy.io
import
urllib.request
data_url
=
'https://
s3.us-east-2.amazonaws.com/
dgl.ai/dataset/ACM.mat'
data_url
=
'https://
data.
dgl.ai/dataset/ACM.mat'
data_file_path
=
'/tmp/ACM.mat'
urllib
.
request
.
urlretrieve
(
data_url
,
data_file_path
)
...
...
tutorials/models/1_gnn/8_sse_mx.py
View file @
c23a61bd
...
...
@@ -567,6 +567,6 @@ for i in range(n_epochs):
#
# For full examples, see `Benchmark SSE on multi-GPUs <https://github.com/dmlc/dgl/tree/master/examples/mxnet/sse>`_ on Github.
#
# .. |image0| image:: https://
s3.us-east-2.amazonaws.com/
dgl.ai/tutorial/img/floodfill-paths.gif
# .. |image1| image:: https://
s3.us-east-2.amazonaws.com/
dgl.ai/tutorial/img/neighbor-sampling.gif
# .. |image2| image:: https://
s3.us-east-2.amazonaws.com/
dgl.ai/tutorial/img/sse.gif
# .. |image0| image:: https://
data.
dgl.ai/tutorial/img/floodfill-paths.gif
# .. |image1| image:: https://
data.
dgl.ai/tutorial/img/neighbor-sampling.gif
# .. |image2| image:: https://
data.
dgl.ai/tutorial/img/sse.gif
tutorials/models/1_gnn/9_gat.py
View file @
c23a61bd
...
...
@@ -55,7 +55,7 @@ structure-free normalization, in the style of attention.
# embedding :math:`h_i^{(l+1)}` of layer :math:`l+1` from the embeddings of
# layer :math:`l`.
#
# .. image:: https://
s3.us-east-2.amazonaws.com/
dgl.ai/tutorial/gat/gat.png
# .. image:: https://
data.
dgl.ai/tutorial/gat/gat.png
# :width: 450px
# :align: center
#
...
...
@@ -355,7 +355,7 @@ for epoch in range(30):
# to their labels, whereas the edges are colored according to the magnitude of
# the attention weights, which can be referred with the colorbar on the right.
#
# .. image:: https://
s3.us-east-2.amazonaws.com/
dgl.ai/tutorial/gat/cora-attention.png
# .. image:: https://
data.
dgl.ai/tutorial/gat/cora-attention.png
# :width: 600px
# :align: center
#
...
...
@@ -383,7 +383,7 @@ for epoch in range(30):
#
# As a reference, here is the histogram if all the nodes have uniform attention weight distribution.
#
# .. image:: https://
s3.us-east-2.amazonaws.com/
dgl.ai/tutorial/gat/cora-attention-uniform-hist.png
# .. image:: https://
data.
dgl.ai/tutorial/gat/cora-attention-uniform-hist.png
# :width: 250px
# :align: center
#
...
...
@@ -453,7 +453,7 @@ for epoch in range(30):
# learning curves of GAT and GCN are presented below; what is evident is the
# dramatic performance adavantage of GAT over GCN.
#
# .. image:: https://
s3.us-east-2.amazonaws.com/
dgl.ai/tutorial/gat/ppi-curve.png
# .. image:: https://
data.
dgl.ai/tutorial/gat/ppi-curve.png
# :width: 300px
# :align: center
#
...
...
@@ -475,7 +475,7 @@ for epoch in range(30):
#
# Again, comparing with uniform distribution:
#
# .. image:: https://
s3.us-east-2.amazonaws.com/
dgl.ai/tutorial/gat/ppi-uniform-hist.png
# .. image:: https://
data.
dgl.ai/tutorial/gat/ppi-uniform-hist.png
# :width: 250px
# :align: center
#
...
...
@@ -502,7 +502,7 @@ for epoch in range(30):
# * See the optimized `full example <https://github.com/dmlc/dgl/blob/master/examples/pytorch/gat/gat.py>`_.
# * The next tutorial describes how to speedup GAT models by parallelizing multiple attention heads and SPMV optimization.
#
# .. |image2| image:: https://
s3.us-east-2.amazonaws.com/
dgl.ai/tutorial/gat/cora-attention-hist.png
# .. |image5| image:: https://
s3.us-east-2.amazonaws.com/
dgl.ai/tutorial/gat/ppi-first-layer-hist.png
# .. |image6| image:: https://
s3.us-east-2.amazonaws.com/
dgl.ai/tutorial/gat/ppi-second-layer-hist.png
# .. |image7| image:: https://
s3.us-east-2.amazonaws.com/
dgl.ai/tutorial/gat/ppi-final-layer-hist.png
# .. |image2| image:: https://
data.
dgl.ai/tutorial/gat/cora-attention-hist.png
# .. |image5| image:: https://
data.
dgl.ai/tutorial/gat/ppi-first-layer-hist.png
# .. |image6| image:: https://
data.
dgl.ai/tutorial/gat/ppi-second-layer-hist.png
# .. |image7| image:: https://
data.
dgl.ai/tutorial/gat/ppi-final-layer-hist.png
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