diff --git a/examples/pytorch/cluster_gcn/run_reddit.sh b/examples/pytorch/cluster_gcn/run_reddit.sh index efa15aabac8d..17e7e3847747 100644 --- a/examples/pytorch/cluster_gcn/run_reddit.sh +++ b/examples/pytorch/cluster_gcn/run_reddit.sh @@ -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 diff --git a/examples/pytorch/dgmg/README.md b/examples/pytorch/dgmg/README.md index 3d57b0029c5f..305c7a399dd7 100644 --- a/examples/pytorch/dgmg/README.md +++ b/examples/pytorch/dgmg/README.md @@ -1,7 +1,10 @@ # Learning Deep Generative Models of Graphs 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. +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 diff --git a/examples/pytorch/model_zoo/chem/README.md b/examples/pytorch/model_zoo/chem/README.md index 5a32cdf0feec..1f7e545123c5 100644 --- a/examples/pytorch/model_zoo/chem/README.md +++ b/examples/pytorch/model_zoo/chem/README.md @@ -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