├── .gitignore ├── Figure1.png ├── LICENSE ├── README.md ├── callbacks ├── __init__.py ├── __pycache__ │ ├── __init__.cpython-36.pyc │ ├── ensemble.cpython-36.pyc │ └── eval.cpython-36.pyc ├── ensemble.py └── eval.py ├── config.py ├── layers ├── __init__.py ├── __pycache__ │ ├── __init__.cpython-36.pyc │ └── aggregator.cpython-36.pyc └── aggregator.py ├── log ├── kegg_result.txt └── kgcn_performance.log ├── main.py ├── models ├── __init__.py ├── __pycache__ │ ├── __init__.cpython-36.pyc │ ├── base_model.cpython-36.pyc │ ├── kgcn.cpython-36.pyc │ └── kgcn_AVG.cpython-36.pyc ├── base_model.py └── kgcn.py ├── raw_data └── kegg │ ├── approved_example.txt │ ├── entity2id.txt │ ├── relation2id.txt │ └── train2id.txt ├── requirement.txt ├── run.py └── utils ├── __init__.py ├── __pycache__ ├── __init__.cpython-36.pyc ├── __init__.cpython-37.pyc ├── data_loader.cpython-36.pyc ├── data_loader.cpython-37.pyc ├── io.cpython-36.pyc └── io.cpython-37.pyc ├── data_loader.py └── io.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzenglab/KGNN/HEAD/.gitignore -------------------------------------------------------------------------------- /Figure1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzenglab/KGNN/HEAD/Figure1.png -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzenglab/KGNN/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzenglab/KGNN/HEAD/README.md -------------------------------------------------------------------------------- /callbacks/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzenglab/KGNN/HEAD/callbacks/__init__.py -------------------------------------------------------------------------------- /callbacks/__pycache__/__init__.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzenglab/KGNN/HEAD/callbacks/__pycache__/__init__.cpython-36.pyc -------------------------------------------------------------------------------- /callbacks/__pycache__/ensemble.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzenglab/KGNN/HEAD/callbacks/__pycache__/ensemble.cpython-36.pyc -------------------------------------------------------------------------------- /callbacks/__pycache__/eval.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzenglab/KGNN/HEAD/callbacks/__pycache__/eval.cpython-36.pyc -------------------------------------------------------------------------------- /callbacks/ensemble.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzenglab/KGNN/HEAD/callbacks/ensemble.py -------------------------------------------------------------------------------- /callbacks/eval.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzenglab/KGNN/HEAD/callbacks/eval.py -------------------------------------------------------------------------------- /config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzenglab/KGNN/HEAD/config.py -------------------------------------------------------------------------------- /layers/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzenglab/KGNN/HEAD/layers/__init__.py -------------------------------------------------------------------------------- /layers/__pycache__/__init__.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzenglab/KGNN/HEAD/layers/__pycache__/__init__.cpython-36.pyc -------------------------------------------------------------------------------- /layers/__pycache__/aggregator.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzenglab/KGNN/HEAD/layers/__pycache__/aggregator.cpython-36.pyc -------------------------------------------------------------------------------- /layers/aggregator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzenglab/KGNN/HEAD/layers/aggregator.py -------------------------------------------------------------------------------- /log/kegg_result.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzenglab/KGNN/HEAD/log/kegg_result.txt -------------------------------------------------------------------------------- /log/kgcn_performance.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzenglab/KGNN/HEAD/log/kgcn_performance.log -------------------------------------------------------------------------------- /main.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzenglab/KGNN/HEAD/main.py -------------------------------------------------------------------------------- /models/__init__.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | 3 | from .kgcn import KGCN -------------------------------------------------------------------------------- /models/__pycache__/__init__.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzenglab/KGNN/HEAD/models/__pycache__/__init__.cpython-36.pyc -------------------------------------------------------------------------------- /models/__pycache__/base_model.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzenglab/KGNN/HEAD/models/__pycache__/base_model.cpython-36.pyc -------------------------------------------------------------------------------- /models/__pycache__/kgcn.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzenglab/KGNN/HEAD/models/__pycache__/kgcn.cpython-36.pyc -------------------------------------------------------------------------------- /models/__pycache__/kgcn_AVG.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzenglab/KGNN/HEAD/models/__pycache__/kgcn_AVG.cpython-36.pyc -------------------------------------------------------------------------------- /models/base_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzenglab/KGNN/HEAD/models/base_model.py -------------------------------------------------------------------------------- /models/kgcn.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzenglab/KGNN/HEAD/models/kgcn.py -------------------------------------------------------------------------------- /raw_data/kegg/approved_example.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzenglab/KGNN/HEAD/raw_data/kegg/approved_example.txt -------------------------------------------------------------------------------- /raw_data/kegg/entity2id.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzenglab/KGNN/HEAD/raw_data/kegg/entity2id.txt -------------------------------------------------------------------------------- /raw_data/kegg/relation2id.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzenglab/KGNN/HEAD/raw_data/kegg/relation2id.txt -------------------------------------------------------------------------------- /raw_data/kegg/train2id.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzenglab/KGNN/HEAD/raw_data/kegg/train2id.txt -------------------------------------------------------------------------------- /requirement.txt: -------------------------------------------------------------------------------- 1 | keras==2.3.0 2 | tensorflow-gpu==1.13.1 3 | scikit-learn==0.22 4 | -------------------------------------------------------------------------------- /run.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzenglab/KGNN/HEAD/run.py -------------------------------------------------------------------------------- /utils/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzenglab/KGNN/HEAD/utils/__init__.py -------------------------------------------------------------------------------- /utils/__pycache__/__init__.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzenglab/KGNN/HEAD/utils/__pycache__/__init__.cpython-36.pyc -------------------------------------------------------------------------------- /utils/__pycache__/__init__.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzenglab/KGNN/HEAD/utils/__pycache__/__init__.cpython-37.pyc -------------------------------------------------------------------------------- /utils/__pycache__/data_loader.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzenglab/KGNN/HEAD/utils/__pycache__/data_loader.cpython-36.pyc -------------------------------------------------------------------------------- /utils/__pycache__/data_loader.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzenglab/KGNN/HEAD/utils/__pycache__/data_loader.cpython-37.pyc -------------------------------------------------------------------------------- /utils/__pycache__/io.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzenglab/KGNN/HEAD/utils/__pycache__/io.cpython-36.pyc -------------------------------------------------------------------------------- /utils/__pycache__/io.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzenglab/KGNN/HEAD/utils/__pycache__/io.cpython-37.pyc -------------------------------------------------------------------------------- /utils/data_loader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzenglab/KGNN/HEAD/utils/data_loader.py -------------------------------------------------------------------------------- /utils/io.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzenglab/KGNN/HEAD/utils/io.py --------------------------------------------------------------------------------