The repo is based on GraphGPS which is built using PyG and GraphGym from PyG2.
Data set downloads automatically, you can setup the downloading root in each config file. For example, in ./configs/GCN/peptides-func-GCN.yaml
the default root is dataset: dir: ./data
.
Dataset | Domain | Task | Node Feat. (dim) | Edge Feat. (dim) | Perf. Metric |
---|---|---|---|---|---|
PCQM-Contact | Quantum Chemistry | Link Prediction | Atom Encoder (9) | Bond Encoder (3) | Hits@K, MRR |
Peptides-func | Chemistry | Graph Classification | Atom Encoder (9) | Bond Encoder (3) | AP |
Peptides-struct | Chemistry | Graph Regression | Atom Encoder (9) | Bond Encoder (3) | MAE |
Dataset | # Graphs | # Nodes | μ Nodes | μ Deg. | # Edges | μ Edges | μ Short. Path | μ Diameter |
---|---|---|---|---|---|---|---|---|
PascalVOC-SP | 11,355 | 5,443,545 | 479.40 | 5.65 | 30,777,444 | 2,710.48 | 10.74±0.51 | 27.62±2.13 |
COCO-SP | 123,286 | 58,793,216 | 476.88 | 5.65 | 332,091,902 | 2,693.67 | 10.66±0.55 | 27.39±2.14 |
PCQM-Contact | 529,434 | 15,955,687 | 30.14 | 2.03 | 32,341,644 | 61.09 | 4.63±0.63 | 9.86±1.79 |
Peptides-func | 15,535 | 2,344,859 | 150.94 | 2.04 | 4,773,974 | 307.30 | 20.89±9.79 | 56.99±28.72 |
Peptides-struct | 15,535 | 2,344,859 | 150.94 | 2.04 | 4,773,974 | 307.30 | 20.89±9.79 | 56.99±28.72 |
conda create -n lrgb python=3.9
conda activate lrgb
conda install pytorch=1.9 torchvision torchaudio -c pytorch -c nvidia
conda install pyg=2.0.2 -c pyg -c conda-forge
conda install pandas scikit-learn
# RDKit is required for OGB-LSC PCQM4Mv2 and datasets derived from it.
conda install openbabel fsspec rdkit -c conda-forge
# Check https://www.dgl.ai/pages/start.html to install DGL based on your CUDA requirements
pip install dgl-cu111 dglgo -f https://data.dgl.ai/wheels/repo.html
pip install performer-pytorch
pip install torchmetrics==0.7.2
pip install ogb
pip install wandb
conda clean --all
Given GCN
as example, using Decremental (desc)
setting shown in Fig.4 and pool ratio is setted as 0.9
with random seed
as 0
, we have:
conda activate lrgb
cd 2D_Molecule
# Running GCN w/ Neural Atoms for Peptides-func.
python main.py --cfg ./configs/GCN/peptides-func-GCN.yaml seed 0