torch==1.13.0
dgl-cu111==0.6.1
optuna==3.2.0
unzip datasets.zippython run.py --encoder searchgcn --score_func mlp --combine_type concat --n_layer 3 --epoch 400 \
--batch 512 --seed 0 --search_mode joint_search --search_algorithm spos_train_supernet_ps2 --input_type allgraph \
--loss_type ce --dataset drugbank --ss_search_algorithm snaspython run.py --encoder searchgcn --score_func mlp --combine_type concat --n_layer 3 --epoch 400 \
--batch 512 --seed 0 --search_mode joint_search --search_algorithm spos_train_supernet_ps2 --input_type allgraph \
--loss_type ce --dataset drugbank --exp_note spfs --few_shot_op rotate --weight_sharing --ss_search_algorithm snas
python run.py --encoder searchgcn --score_func mlp --combine_type concat --n_layer 3 --epoch 400 \
--batch 512 --seed 0 --search_mode joint_search --search_algorithm spos_train_supernet_ps2 --input_type allgraph \
--loss_type ce --dataset drugbank --exp_note spfs --few_shot_op ccorr --weight_sharing --ss_search_algorithm snas
python run.py --encoder searchgcn --score_func mlp --combine_type concat --n_layer 3 --epoch 400 \
--batch 512 --seed 0 --search_mode joint_search --search_algorithm spos_train_supernet_ps2 --input_type allgraph \
--loss_type ce --dataset drugbank --exp_note spfs --few_shot_op mult --weight_sharing --ss_search_algorithm snas
python run.py --encoder searchgcn --score_func mlp --combine_type concat --n_layer 3 --epoch 400 \
--batch 512 --seed 0 --search_mode joint_search --search_algorithm spos_train_supernet_ps2 --input_type allgraph \
--loss_type ce --dataset drugbank --exp_note spfs --few_shot_op sub --weight_sharing --ss_search_algorithm snaspython run.py --encoder searchgcn --score_func mlp --combine_type concat --n_layer 3 --epoch 400 \
--batch 512 --seed 0 --search_mode joint_search --search_algorithm spos_arch_search_ps2 --input_type allgraph \
--loss_type ce --dataset drugbank --exp_note spfs --weight_sharing --ss_search_algorithm snas --arch_search_mode ngpython run.py --encoder searchgcn --score_func mlp --combine_type concat --n_layer 3 --epoch 400 \
--batch 512 --seed 0 --train_mode spos_tune --search_mode joint_search --input_type allgraph \
--loss_type ce --dataset drugbank --exp_note spfs --weight_sharing --ss_search_algorithm snasReaders are welcomed to follow our work. Please kindly cite our paper:
@article{du2024customized,
title={Customized subgraph selection and encoding for drug-drug interaction prediction},
author={Du, Haotong and Yao, Quanming and Zhang, Juzheng and Liu, Yang and Wang, Zhen},
journal={Advances in Neural Information Processing Systems},
volume={37},
pages={109582--109608},
year={2024}
}If you have any questions, feel free to contact me at [email protected].
The codes of this paper are partially based on the codes of SEAL_dgl, PS2, and Interstellar. We thank the authors of above work.
