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OpenDAS
dgl
Commits
86cf154b
Unverified
Commit
86cf154b
authored
Oct 29, 2019
by
Mufei Li
Committed by
GitHub
Oct 29, 2019
Browse files
[Misc] Update README(s) (#962)
* Update * Update
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examples/pytorch/cluster_gcn/run_reddit.sh
examples/pytorch/cluster_gcn/run_reddit.sh
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examples/pytorch/dgmg/README.md
examples/pytorch/dgmg/README.md
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examples/pytorch/model_zoo/chem/README.md
examples/pytorch/model_zoo/chem/README.md
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examples/pytorch/cluster_gcn/run_reddit.sh
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@@ -2,5 +2,5 @@
python cluster_gcn.py
--gpu
0
--dataset
reddit-self-loop
--lr
1e-2
--weight-decay
0.0
--psize
1500
--batch-size
20
\
--n-epochs
30
--n-hidden
128
--n-layers
0
--log-every
100
--use-pp
--self-loop
\
--n-epochs
30
--n-hidden
128
--n-layers
1
--log-every
100
--use-pp
--self-loop
\
--note
self-loop-reddit-non-sym-ly3-pp-cluster-2-2-wd-5e-4
--dropout
0.2
--use-val
--normalize
examples/pytorch/dgmg/README.md
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@@ -3,6 +3,9 @@
This is an implementation of
[
Learning Deep Generative Models of Graphs
](
https://arxiv.org/pdf/1803.03324.pdf
)
by
Yujia Li, Oriol Vinyals, Chris Dyer, Razvan Pascanu, Peter Battaglia.
For molecule generation, see
[
our model zoo for Chemistry
](
https://github.com/dmlc/dgl/tree/master/examples/pytorch/model_zoo/chem/generative_models/dgmg
)
.
## Dependencies
-
Python 3.5.2
-
[
Pytorch 0.4.1
](
https://pytorch.org/
)
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examples/pytorch/model_zoo/chem/README.md
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@@ -21,6 +21,16 @@ Before you proceed, make sure you have installed the dependencies below:
The rest dependencies can be installed with
`pip install -r requirements.txt`
.
## Speed Reference
Below we provide some reference numbers to show how DGL improves the speed of training models per epoch in seconds.
| Model | Original Implementation | DGL Implementation | Improvement |
| -------------------------- | ----------------------- | ------------------ | ----------- |
| GCN on Tox21 | 5.5 (DeepChem) | 1.0 | 5.5x |
| AttentiveFP on Aromaticity | 6.0 | 1.2 | 5x |
| JTNN on ZINC | 1826 | 743 | 2.5x |
## Property Prediction
To evaluate molecules for drug candidates, we need to know their properties and activities. In practice, this is
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