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NeuralAtom 2D

The repo is based on GraphGPS which is built using PyG and GraphGym from PyG2.

Overview of Datasets

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

Statistics of Datasets

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

Python environment setup with Conda

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

Running NeuralAtom

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