PEER_Benchmark
PEER Benchmark, appear at NeurIPS 2022 Dataset and Benchmark Track (https://arxiv.org/abs/2206.02096)
파일 탐색기
최종 버전 다운로드 (.zip)- benchmark.png
- aav_contact_BERT.yaml
- aav_fold_BERT.yaml
- aav_ss_BERT.yaml
- beta_contact_BERT.yaml
- beta_fold_BERT.yaml
- beta_ss_BERT.yaml
- bindingdb_contact_BERT.yaml
- bindingdb_fold_BERT.yaml
- bindingdb_ss_BERT.yaml
- binloc_contact_BERT.yaml
- binloc_fold_BERT.yaml
- binloc_ss_BERT.yaml
- contact_fold_BERT.yaml
- contact_ss_BERT.yaml
- fluorescence_contact_BERT.yaml
- fluorescence_fold_BERT.yaml
- fluorescence_ss_BERT.yaml
- fold_contact_BERT.yaml
- fold_ss_BERT.yaml
- gb1_contact_BERT.yaml
- gb1_fold_BERT.yaml
- gb1_ss_BERT.yaml
- human_contact_BERT.yaml
- human_fold_BERT.yaml
- human_ss_BERT.yaml
- pdbbind_contact_BERT.yaml
- pdbbind_fold_BERT.yaml
- pdbbind_ss_BERT.yaml
- ppi_affinity_contact_BERT.yaml
- ppi_affinity_fold_BERT.yaml
- ppi_affinity_ss_BERT.yaml
- solubility_contact_BERT.yaml
- solubility_fold_BERT.yaml
- solubility_ss_BERT.yaml
- ss_contact_BERT.yaml
- ss_fold_BERT.yaml
- stability_contact_BERT.yaml
- stability_fold_BERT.yaml
- stability_ss_BERT.yaml
- subloc_contact_BERT.yaml
- subloc_fold_BERT.yaml
- subloc_ss_BERT.yaml
- thermo_contact_BERT.yaml
- thermo_fold_BERT.yaml
- thermo_ss_BERT.yaml
- yeast_contact_BERT.yaml
- yeast_fold_BERT.yaml
- yeast_ss_BERT.yaml
- aav_contact_CNN.yaml
- aav_fold_CNN.yaml
- aav_ss_CNN.yaml
- beta_contact_CNN.yaml
- beta_fold_CNN.yaml
- beta_ss_CNN.yaml
- bindingdb_contact_CNN.yaml
- bindingdb_fold_CNN.yaml
- bindingdb_ss_CNN.yaml
- binloc_contact_CNN.yaml
- binloc_fold_CNN.yaml
- binloc_ss_CNN.yaml
- contact_fold_CNN.yaml
- contact_ss_CNN.yaml
- fluorescence_contact_CNN.yaml
- fluorescence_fold_CNN.yaml
- fluorescence_ss_CNN.yaml
- fold_contact_CNN.yaml
- fold_ss_CNN.yaml
- gb1_contact_CNN.yaml
- gb1_fold_CNN.yaml
- gb1_ss_CNN.yaml
- human_contact_CNN.yaml
- human_fold_CNN.yaml
- human_ss_CNN.yaml
- pdbbind_contact_CNN.yaml
- pdbbind_fold_CNN.yaml
- pdbbind_ss_CNN.yaml
- ppi_affinity_contact_CNN.yaml
- ppi_affinity_fold_CNN.yaml
- ppi_affinity_ss_CNN.yaml
- solubility_contact_CNN.yaml
- solubility_fold_CNN.yaml
- solubility_ss_CNN.yaml
- ss_contact_CNN.yaml
- ss_fold_CNN.yaml
- stability_contact_CNN.yaml
- stability_fold_CNN.yaml
- stability_ss_CNN.yaml
- subloc_contact_CNN.yaml
- subloc_fold_CNN.yaml
- subloc_ss_CNN.yaml
- thermo_contact_CNN.yaml
- thermo_fold_CNN.yaml
- thermo_ss_CNN.yaml
- yeast_contact_CNN.yaml
- yeast_fold_CNN.yaml
- yeast_ss_CNN.yaml
- aav_contact_ESM.yaml
- aav_fold_ESM.yaml
- aav_ss_ESM.yaml
- beta_contact_ESM.yaml
- beta_fold_ESM.yaml
- beta_ss_ESM.yaml
- bindingdb_contact_ESM.yaml
- bindingdb_fold_ESM.yaml
- bindingdb_ss_ESM.yaml
- binloc_contact_ESM.yaml
- binloc_fold_ESM.yaml
- binloc_ss_ESM.yaml
- contact_fold_ESM.yaml
- contact_ss_ESM.yaml
- fluorescence_contact_ESM.yaml
- fluorescence_fold_ESM.yaml
- fluorescence_ss_ESM.yaml
- fold_contact_ESM.yaml
- fold_ss_ESM.yaml
- gb1_contact_ESM.yaml
- gb1_fold_ESM.yaml
- gb1_ss_ESM.yaml
- human_contact_ESM.yaml
- human_fold_ESM.yaml
- human_ss_ESM.yaml
- pdbbind_contact_ESM.yaml
- pdbbind_fold_ESM.yaml
- pdbbind_ss_ESM.yaml
- ppi_affinity_contact_ESM.yaml
- ppi_affinity_fold_ESM.yaml
- ppi_affinity_ss_ESM.yaml
- solubility_contact_ESM.yaml
- solubility_fold_ESM.yaml
- solubility_ss_ESM.yaml
- ss_contact_ESM.yaml
- ss_fold_ESM.yaml
- stability_contact_ESM.yaml
- stability_fold_ESM.yaml
- stability_ss_ESM.yaml
- subloc_contact_ESM.yaml
- subloc_fold_ESM.yaml
- subloc_ss_ESM.yaml
- thermo_contact_ESM.yaml
- thermo_fold_ESM.yaml
- thermo_ss_ESM.yaml
- yeast_contact_ESM.yaml
- yeast_fold_ESM.yaml
- yeast_ss_ESM.yaml
- aav_BERT.yaml
- beta_BERT.yaml
- bindingdb_BERT.yaml
- binloc_BERT.yaml
- contact_BERT.yaml
- fluorescence_BERT.yaml
- fold_BERT.yaml
- gb1_BERT.yaml
- human_BERT.yaml
- pdbbind_BERT.yaml
- ppi_affinity_BERT.yaml
- solubility_BERT.yaml
- ss_BERT.yaml
- stability_BERT.yaml
- subloc_BERT.yaml
- thermo_BERT.yaml
- yeast_BERT.yaml
- aav_CNN.yaml
- beta_CNN.yaml
- bindingdb_CNN.yaml
- binloc_CNN.yaml
- contact_CNN.yaml
- fluorescence_CNN.yaml
- fold_CNN.yaml
- gb1_CNN.yaml
- human_CNN.yaml
- pdbbind_CNN.yaml
- ppi_affinity_CNN.yaml
- solubility_CNN.yaml
- ss_CNN.yaml
- stability_CNN.yaml
- subloc_CNN.yaml
- thermo_CNN.yaml
- yeast_CNN.yaml
- aav_DDE.yaml
- beta_DDE.yaml
- binloc_DDE.yaml
- fluorescence_DDE.yaml
- fold_DDE.yaml
- gb1_DDE.yaml
- human_DDE.yaml
- ppi_affinity_DDE.yaml
- solubility_DDE.yaml
- stability_DDE.yaml
- subloc_DDE.yaml
- thermo_DDE.yaml
- yeast_DDE.yaml
- aav_ESM.yaml
- aav_ESM_fix.yaml
- beta_ESM.yaml
- beta_ESM_fix.yaml
- bindingdb_ESM.yaml
- bindingdb_ESM_fix.yaml
- binloc_ESM.yaml
- binloc_ESM_fix.yaml
- contact_ESM.yaml
- contact_ESM_fix.yaml
- fluorescence_ESM.yaml
- fluorescence_ESM_fix.yaml
- fold_ESM.yaml
- fold_ESM_fix.yaml
- gb1_ESM.yaml
- gb1_ESM_fix.yaml
- human_ESM.yaml
- human_ESM_fix.yaml
- pdbbind_ESM.yaml
- pdbbind_ESM_fix.yaml
- ppi_affinity_ESM.yaml
- ppi_affinity_ESM_fix.yaml
- solubility_ESM.yaml
- solubility_ESM_fix.yaml
- ss_ESM.yaml
- ss_ESM_fix.yaml
- stability_ESM.yaml
- stability_ESM_fix.yaml
- subloc_ESM.yaml
- subloc_ESM_fix.yaml
- thermo_ESM.yaml
- thermo_ESM_fix.yaml
- yeast_ESM.yaml
- yeast_ESM_fix.yaml
- aav_LSTM.yaml
- beta_LSTM.yaml
- bindingdb_LSTM.yaml
- binloc_LSTM.yaml
- contact_LSTM.yaml
- fluorescence_LSTM.yaml
- fold_LSTM.yaml
- gb1_LSTM.yaml
- human_LSTM.yaml
- pdbbind_LSTM.yaml
- ppi_affinity_LSTM.yaml
- solubility_LSTM.yaml
- ss_LSTM.yaml
- stability_LSTM.yaml
- subloc_LSTM.yaml
- thermo_LSTM.yaml
- yeast_LSTM.yaml
- aav_Moran.yaml
- beta_Moran.yaml
- binloc_Moran.yaml
- fluorescence_Moran.yaml
- fold_Moran.yaml
- gb1_Moran.yaml
- human_Moran.yaml
- ppi_affinity_Moran.yaml
- solubility_Moran.yaml
- stability_Moran.yaml
- subloc_Moran.yaml
- thermo_Moran.yaml
- yeast_Moran.yaml
- aav_ProtBert.yaml
- aav_ProtBert_fix.yaml
- beta_ProtBert.yaml
- beta_ProtBert_fix.yaml
- bindingdb_ProtBert.yaml
- bindingdb_ProtBert_fix.yaml
- binloc_ProtBert.yaml
- binloc_ProtBert_fix.yaml
- contact_ProtBert.yaml
- contact_ProtBert_fix.yaml
- fluorescence_ProtBert.yaml
- fluorescence_ProtBert_fix.yaml
- fold_ProtBert.yaml
- fold_ProtBert_fix.yaml
- gb1_ProtBert.yaml
- gb1_ProtBert_fix.yaml
- human_ProtBert.yaml
- human_ProtBert_fix.yaml
- pdbbind_ProtBert.yaml
- pdbbind_ProtBert_fix.yaml
- ppi_affinity_ProtBert.yaml
- ppi_affinity_ProtBert_fix.yaml
- solubility_ProtBert.yaml
- solubility_ProtBert_fix.yaml
- ss_ProtBert.yaml
- ss_ProtBert_fix.yaml
- stability_ProtBert.yaml
- stability_ProtBert_fix.yaml
- subloc_ProtBert.yaml
- subloc_ProtBert_fix.yaml
- thermo_ProtBert.yaml
- thermo_ProtBert_fix.yaml
- yeast_ProtBert.yaml
- yeast_ProtBert_fix.yaml
- aav_ResNet.yaml
- beta_ResNet.yaml
- bindingdb_ResNet.yaml
- binloc_ResNet.yaml
- contact_ResNet.yaml
- fluorescence_ResNet.yaml
- fold_ResNet.yaml
- gb1_ResNet.yaml
- human_ResNet.yaml
- pdbbind_ResNet.yaml
- ppi_affinity_ResNet.yaml
- solubility_ResNet.yaml
- ss_ResNet.yaml
- stability_ResNet.yaml
- subloc_ResNet.yaml
- thermo_ResNet.yaml
- yeast_ResNet.yaml
- __init__.py
- engine.py
- flip.py
- protbert.py
- util.py
- run_multi.py
- run_single.py
- .gitignore
- LICENSE
- README.md
- requirements.txt
# 설치 가이드
1. 코드 내려받기
git clone https://github.com/DeepGraphLearning/PEER_Benchmark
깃허브에서 프로젝트 코드 전체를 내 컴퓨터로 내려받습니다.
cd PEER_Benchmark
방금 내려받은 프로젝트 폴더 안으로 이동합니다.
2. 공식 설치 스크립트
쉬움 추천사전 준비물
- Python 3 pip 명령어를 쓰려면 Python이 필요합니다.
pip install fair-esm transformers easydict pyyaml lmdb
PyPI에 배포된 패키지를 바로 설치합니다. 소스 클론이 필요 없습니다.
설치 후 새 터미널을 열고, 프로그램의 버전 확인 명령(예: --version)으로 정상 설치됐는지 확인하세요.
이 레포의 README에 적힌 실제 명령어를 그대로 가져왔습니다.
3. Python
쉬움사전 준비물
pip install fair-esm transformers easydict pyyaml lmdb
PyPI에 배포된 패키지를 바로 설치합니다. 소스 클론이 필요 없습니다.
python -m pip install git+https://github.com/DeepGraphLearning/torchdrug/
requirements.txt 등에 명시된 파이썬 라이브러리를 설치합니다.
python -m torch.distributed.launch --nproc_per_node=4 script/run_single.py -c config/single_task/$model/$yaml_config --seed 0
파이썬 스크립트(또는 모듈)를 실행합니다.
python -m torch.distributed.launch --nproc_per_node=4 script/run_multi.py -c config/multi_task/$model/$yaml_config --seed 0
파이썬 스크립트(또는 모듈)를 실행합니다.
python -m torch.distributed.launch --nnodes=2 --nproc_per_node=4 script/run_single.py -c config/single_task/$model/$yaml_config --seed 0
파이썬 스크립트(또는 모듈)를 실행합니다.
에러 메시지 없이 실행되고 터미널에 안내 문구가 출력되면 정상입니다.
이 레포의 README에 적힌 실제 명령어를 그대로 가져왔습니다.
// repository documentation
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