The ogbg-molhiv and ogbg-molpcba datasets are two molecular property prediction datasets of different sizes: ogbg-molhiv (small) and ogbg-molpcba (medium). The task is to predict the target molecular properties as accurately as possible, where the molecular properties are cast as binary labels, e.g, whether a molecule inhibits HIV virus replication or not. Note that some datasets (e.g., ogbg-molpcba) can have multiple tasks, and can contain nan that indicates the corresponding label is not assigned to the molecule. The challenge leaderboard can be checked at: https://ogb.stanford.edu/docs/leader_graphprop/. We apply Heterogeneous interpolation to solve this challenge and this repo contains our code submission. The techniqual report can be checked at ./report/.

Install base packages: bash Python>=3.7 Pytorch>=1.9.0 tensorflow>=2.0.0 pytorch_geometric>=1.6.0 ogb>=1.3.2 dgl>=0.5.3 numpy==1.20.3 pandas==1.2.5 scikit-learn==0.24.2 deep_gcns_torch LibAUC

Running the default code 10 times, here we present our results on the ogbg-molhiv and ogbg-molpcba dataset. For ogbg-molhiv, as the dataset is relatively small, we use DeepGCN as our backbone.

For ogbg-molpcba, we use Graphormer as our backbone.

The training process has three steps:

1. Preparation: Extract fingerprints and train Random Forest by following PaddleHelix

python extract_fingerprint.py
python random_forest.py

2. Pretrain: Jointly Train a DeepGCN model with FingerPrints Model.

python main.py --use_gpu --conv_encode_edge --num_layers 14 --block res+ --gcn_aggr softmax --t 1.0 --learn_t --dropout 0.2 \
            --dataset ogbg-molhiv \
            --loss auroc \
            --optimizer pesg \
            --batch_size 512 \
            --lr 0.1 \
            --gamma 500 \
            --margin 1.0 \
            --weight_decay 1e-5 \
            --random_seed 0 \
            --epochs 300

python finetune.py --use_gpu --conv_encode_edge --num_layers 14 --block res+ --gcn_aggr softmax --t 1.0 --learn_t --dropout 0.2 \
            --dataset ogbg-molhiv \
            --loss auroc \
            --optimizer pesg \
            --batch_size 512 \
            --lr 0.01 \
            --gamma 300 \
            --margin 1.0 \
            --weight_decay 1e-5 \
            --random_seed 0 \
            --epochs 100

3. Finetune: Finetune the pretrain model got in Step 2 using NodeDrop Augmentation. We offer a pretrain model in ./saved_models/FT.

python finetune_dropnode.py --use_gpu --conv_encode_edge --num_layers 14 --block res+ --gcn_aggr softmax --t 1.0 --learn_t --dropout 0 \
            --dataset ogbg-molhiv \
            --loss auroc \
            --optimizer pesg \
            --batch_size 512 \
            --lr 0.01 \
            --gamma 300 \
            --margin 1.0 \
            --weight_decay 1e-5 \
            --random_seed 0 \
            --epochs 100

We offer one sample log file: log_ft_molhiv_20211202.txt.

##Training Process for ogbg-molpcba

The training process has three steps:

cd ./Graphormer_with_HIG

1. Pretrain: Pretrain a Graphormer model on dataset PCQM4M.

sh ./examples/ogb-lsc/lsc-pcba.sh

2. Finetune: Finetune the pretrain model got in Step 1 using NodeDrop Augmentation and KL divergence constraint. We offer a pretrain model in ./exps/tmp.

sh ./examples/ogb/finetune_dropnode.sh

sh ./examples/ogb/finetune_kl.sh

• https://libauc.org/
• https://github.com/Optimization-AI/LibAUC
• https://github.com/PaddlePaddle/PaddleHelix/tree/dev/competition/ogbg_molhiv
• https://github.com/lightaime/deep_gcns_torch/
• https://github.com/yzhuoning/DeepAUC_OGB_Challenge
• https://github.com/microsoft/Graphormer
• https://ogb.stanford.edu/