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Principal Neighbourhood Aggregation for Graph Nets (PNA)

Dataset

The ZINC dataset from the ZINC database and the Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules paper, containing about 250,000 molecular graphs with up to 38 heavy atoms. Our experiments only load a subset of the dataset (12,000 molecular graphs), following the Benchmarking Graph Neural Networks paper.

Results from the Paper

Task Dataset Model Metric Name Metric Value
Graph Regression ZINC PNA MAE 0.188±0.004

Our Results

TL_BACKEND="paddle" python pna_trainer.py --batch_size 128 --lr 0.001 --n_epoch 400
TL_BACKEND="torch" python pna_trainer.py --batch_size 128 --lr 0.001 --n_epoch 400
TL_BACKEND="tensorflow" python pna_trainer.py --batch_size 128 --lr 0.001 --n_epoch 400
Dataset Our(pd) Our(torch) Our(tf)
ZINC OOM 0.186 0.195(±0.006)