README.md

Customized Subgraph Selection and Encoding for Drug-drug Interaction Prediction

---

Requirements

torch==1.13.0
dgl-cu111==0.6.1
optuna==3.2.0

Run

Unpack Dataset

unzip datasets.zip

Supernet Training

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 --ss_search_algorithm snas

Sub-Supernet Training

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 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 snas

Subgraph Selection and Encoding Function Searching

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 --weight_sharing --ss_search_algorithm snas --arch_search_mode ng

Citation

Readers are welcomed to follow our work. Please kindly cite our paper:

@inproceedings{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},
    booktitle={The Thirty-eighth Annual Conference on Neural Information Processing Systems},
    year={2024}
}

Contact

If you have any questions, feel free to contact me at duhaotong@mail.nwpu.edu.cn.

Acknowledgement

The codes of this paper are partially based on the codes of SEAL_dgl, PS2, and Interstellar. We thank the authors of above work.