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This repository contains the official code for the paper Graph as Point Set.

Environment

We use python 3.10 with pytorch 2.0.1, torchmetrics 1.0.3, ogb 1.3.6, and pyg 2.3.1

Reproduce our results

On ZINC:

cd zinc
python main.py --dataset zinc --repeat 10 --epochs 1200 --batch_size 96 --testbatch_size 96 --lr 0.0015 --warmstart 17 --conststep 1000 --cosstep 17 --lexp_layer 1 --decompnoise 1e-4  --gradclipnorm 1e-1 --wd 1e-1 --align_size 4

on ZINC-full:

cd zinc
mkdir mod

python main.py --dataset zinc-full --repeat 1 --epochs 360 --batch_size 128 --testbatch_size 128 --cosstep 40 --conststep 240 --warmstart 40 --num_layers 8 --decompnoise 0   --wd 1e-1 

qm9

cd qm9
target=1 # you can choose target from 0 to 11
python main.py --dataset qm9$target --repeat 1 --epochs 240 --batch_size 256 --testbatch_size 256 --warmstart 1  --cosstep 40 --conststep 199  --num_layers 8 --decompnoise 1e-5   --wd 1e-1 --use_y_scale

pascalvoc-sp

python main.py --dataset pascalvocsp --repeat 1 --epochs 40 --batch_size 6 --testbatch_size 6 --warmstart 5 --conststep 40 --cosstep 5 --num_layers 4 --decompnoise 1e-5   --wd 1e-1 --hiddim 96 --align_size 32

peptide-func

python main.py --dataset pepfunc --repeat 1 --epochs 80 --el_norm ln --batch_size 6 --testbatch_size 6 --lr 0.0003 --pool max --warmstart 8 --conststep 64 --cosstep 8 --noconv_tailact --nosv_tailact --novmean --novnorm --noelvmean --noelvnorm --align_size 32

peptide-struct

python main.py --dataset pepstruct --repeat 1 --epochs 80 --gsizenorm 1.9 --el_norm ln --batch_size 2 --testbatch_size 2 --lr 0.0008 --warmstart 80 --conststep 0 --cosstep 8 --num_layers 8 --l_layers 4 --decompnoise 1e-06 --beta 0.997 --noconv_tailact --nosv_tailact --novmean --novnorm --noelvmean --noelvnorm --align_size 32

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