├── .gitignore ├── Annotation ├── E_dict_0.json ├── E_dict_1.json ├── E_dict_2.json ├── E_dict_3.json ├── E_dict_4.json ├── E_dict_5.json └── get_E_dict.py ├── Dataset ├── _cancer5 │ ├── dev.csv │ ├── entity.csv │ ├── relation.csv │ ├── test.csv │ └── train.csv ├── _disease11 │ ├── dev.csv │ ├── entity.csv │ ├── relation.csv │ ├── test.csv │ └── train.csv ├── alzheimer_disease │ ├── dev.csv │ ├── entity.csv │ ├── relation.csv │ ├── test.csv │ └── train.csv ├── colon_cancer │ ├── dev.csv │ ├── entity.csv │ ├── relation.csv │ ├── test.csv │ └── train.csv ├── copd │ ├── dev.csv │ ├── entity.csv │ ├── relation.csv │ ├── test.csv │ └── train.csv ├── coronary_heart_disease │ ├── dev.csv │ ├── entity.csv │ ├── relation.csv │ ├── test.csv │ └── train.csv ├── diabetes │ ├── dev.csv │ ├── entity.csv │ ├── relation.csv │ ├── test.csv │ └── train.csv ├── gallbladder_cancer │ ├── dev.csv │ ├── entity.csv │ ├── relation.csv │ ├── test.csv │ └── train.csv ├── gastric_cancer │ ├── dev.csv │ ├── entity.csv │ ├── relation.csv │ ├── test.csv │ └── train.csv ├── heart_failure │ ├── dev.csv │ ├── entity.csv │ ├── relation.csv │ ├── test.csv │ └── train.csv ├── liver_cancer │ ├── dev.csv │ ├── entity.csv │ ├── relation.csv │ ├── test.csv │ └── train.csv ├── lung_cancer │ ├── dev.csv │ ├── entity.csv │ ├── relation.csv │ ├── test.csv │ └── train.csv └── rheumatoid_arthritis │ ├── dev.csv │ ├── entity.csv │ ├── relation.csv │ ├── test.csv │ └── train.csv ├── Model ├── C&D │ ├── C_dict.data │ ├── D_Table.py │ ├── E_index.json │ ├── Optimization.py │ ├── Run_D_Table.py │ ├── Tokenization.py │ └── get_C_dict.py ├── KGE.py ├── Models.py ├── Pretrained BioBERT │ └── vocab.txt └── Run_KGE.py ├── README.md └── Supplementary Table ├── Supplementary Table S1 (statistical analysis of entity prediction).xlsx ├── Supplementary Table S2 (drug-gene new inferred knowledge).xlsx ├── Supplementary Table S3 (gene-disease new inferred knowledge).xlsx ├── Supplementary Table S4 (disease-drug new inferred knowledge).xlsx └── Supplementary Table S5 (closed-triplets).xlsx /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/.gitignore -------------------------------------------------------------------------------- /Annotation/E_dict_0.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Annotation/E_dict_0.json -------------------------------------------------------------------------------- /Annotation/E_dict_1.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Annotation/E_dict_1.json -------------------------------------------------------------------------------- /Annotation/E_dict_2.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Annotation/E_dict_2.json -------------------------------------------------------------------------------- /Annotation/E_dict_3.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Annotation/E_dict_3.json -------------------------------------------------------------------------------- /Annotation/E_dict_4.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Annotation/E_dict_4.json -------------------------------------------------------------------------------- /Annotation/E_dict_5.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Annotation/E_dict_5.json -------------------------------------------------------------------------------- /Annotation/get_E_dict.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Annotation/get_E_dict.py -------------------------------------------------------------------------------- /Dataset/_cancer5/dev.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/_cancer5/dev.csv -------------------------------------------------------------------------------- /Dataset/_cancer5/entity.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/_cancer5/entity.csv -------------------------------------------------------------------------------- /Dataset/_cancer5/relation.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/_cancer5/relation.csv -------------------------------------------------------------------------------- /Dataset/_cancer5/test.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/_cancer5/test.csv -------------------------------------------------------------------------------- /Dataset/_cancer5/train.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/_cancer5/train.csv -------------------------------------------------------------------------------- /Dataset/_disease11/dev.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/_disease11/dev.csv -------------------------------------------------------------------------------- /Dataset/_disease11/entity.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/_disease11/entity.csv -------------------------------------------------------------------------------- /Dataset/_disease11/relation.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/_disease11/relation.csv -------------------------------------------------------------------------------- /Dataset/_disease11/test.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/_disease11/test.csv -------------------------------------------------------------------------------- /Dataset/_disease11/train.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/_disease11/train.csv -------------------------------------------------------------------------------- /Dataset/alzheimer_disease/dev.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/alzheimer_disease/dev.csv -------------------------------------------------------------------------------- /Dataset/alzheimer_disease/entity.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/alzheimer_disease/entity.csv -------------------------------------------------------------------------------- /Dataset/alzheimer_disease/relation.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/alzheimer_disease/relation.csv -------------------------------------------------------------------------------- /Dataset/alzheimer_disease/test.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/alzheimer_disease/test.csv -------------------------------------------------------------------------------- /Dataset/alzheimer_disease/train.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/alzheimer_disease/train.csv -------------------------------------------------------------------------------- /Dataset/colon_cancer/dev.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/colon_cancer/dev.csv -------------------------------------------------------------------------------- /Dataset/colon_cancer/entity.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/colon_cancer/entity.csv -------------------------------------------------------------------------------- /Dataset/colon_cancer/relation.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/colon_cancer/relation.csv -------------------------------------------------------------------------------- /Dataset/colon_cancer/test.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/colon_cancer/test.csv -------------------------------------------------------------------------------- /Dataset/colon_cancer/train.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/colon_cancer/train.csv -------------------------------------------------------------------------------- /Dataset/copd/dev.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/copd/dev.csv -------------------------------------------------------------------------------- /Dataset/copd/entity.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/copd/entity.csv -------------------------------------------------------------------------------- /Dataset/copd/relation.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/copd/relation.csv -------------------------------------------------------------------------------- /Dataset/copd/test.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/copd/test.csv -------------------------------------------------------------------------------- /Dataset/copd/train.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/copd/train.csv -------------------------------------------------------------------------------- /Dataset/coronary_heart_disease/dev.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/coronary_heart_disease/dev.csv -------------------------------------------------------------------------------- /Dataset/coronary_heart_disease/entity.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/coronary_heart_disease/entity.csv -------------------------------------------------------------------------------- /Dataset/coronary_heart_disease/relation.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/coronary_heart_disease/relation.csv -------------------------------------------------------------------------------- /Dataset/coronary_heart_disease/test.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/coronary_heart_disease/test.csv -------------------------------------------------------------------------------- /Dataset/coronary_heart_disease/train.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/coronary_heart_disease/train.csv -------------------------------------------------------------------------------- /Dataset/diabetes/dev.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/diabetes/dev.csv -------------------------------------------------------------------------------- /Dataset/diabetes/entity.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/diabetes/entity.csv -------------------------------------------------------------------------------- /Dataset/diabetes/relation.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/diabetes/relation.csv -------------------------------------------------------------------------------- /Dataset/diabetes/test.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/diabetes/test.csv -------------------------------------------------------------------------------- /Dataset/diabetes/train.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/diabetes/train.csv -------------------------------------------------------------------------------- /Dataset/gallbladder_cancer/dev.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/gallbladder_cancer/dev.csv -------------------------------------------------------------------------------- /Dataset/gallbladder_cancer/entity.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/gallbladder_cancer/entity.csv -------------------------------------------------------------------------------- /Dataset/gallbladder_cancer/relation.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/gallbladder_cancer/relation.csv -------------------------------------------------------------------------------- /Dataset/gallbladder_cancer/test.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/gallbladder_cancer/test.csv -------------------------------------------------------------------------------- /Dataset/gallbladder_cancer/train.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/gallbladder_cancer/train.csv -------------------------------------------------------------------------------- /Dataset/gastric_cancer/dev.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/gastric_cancer/dev.csv -------------------------------------------------------------------------------- /Dataset/gastric_cancer/entity.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/gastric_cancer/entity.csv -------------------------------------------------------------------------------- /Dataset/gastric_cancer/relation.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/gastric_cancer/relation.csv -------------------------------------------------------------------------------- /Dataset/gastric_cancer/test.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/gastric_cancer/test.csv -------------------------------------------------------------------------------- /Dataset/gastric_cancer/train.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/gastric_cancer/train.csv -------------------------------------------------------------------------------- /Dataset/heart_failure/dev.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/heart_failure/dev.csv -------------------------------------------------------------------------------- /Dataset/heart_failure/entity.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/heart_failure/entity.csv -------------------------------------------------------------------------------- /Dataset/heart_failure/relation.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/heart_failure/relation.csv -------------------------------------------------------------------------------- /Dataset/heart_failure/test.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/heart_failure/test.csv -------------------------------------------------------------------------------- /Dataset/heart_failure/train.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/heart_failure/train.csv -------------------------------------------------------------------------------- /Dataset/liver_cancer/dev.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/liver_cancer/dev.csv -------------------------------------------------------------------------------- /Dataset/liver_cancer/entity.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/liver_cancer/entity.csv -------------------------------------------------------------------------------- /Dataset/liver_cancer/relation.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/liver_cancer/relation.csv -------------------------------------------------------------------------------- /Dataset/liver_cancer/test.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/liver_cancer/test.csv -------------------------------------------------------------------------------- /Dataset/liver_cancer/train.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/liver_cancer/train.csv -------------------------------------------------------------------------------- /Dataset/lung_cancer/dev.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/lung_cancer/dev.csv -------------------------------------------------------------------------------- /Dataset/lung_cancer/entity.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/lung_cancer/entity.csv -------------------------------------------------------------------------------- /Dataset/lung_cancer/relation.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/lung_cancer/relation.csv -------------------------------------------------------------------------------- /Dataset/lung_cancer/test.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/lung_cancer/test.csv -------------------------------------------------------------------------------- /Dataset/lung_cancer/train.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/lung_cancer/train.csv -------------------------------------------------------------------------------- /Dataset/rheumatoid_arthritis/dev.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/rheumatoid_arthritis/dev.csv -------------------------------------------------------------------------------- /Dataset/rheumatoid_arthritis/entity.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/rheumatoid_arthritis/entity.csv -------------------------------------------------------------------------------- /Dataset/rheumatoid_arthritis/relation.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/rheumatoid_arthritis/relation.csv -------------------------------------------------------------------------------- /Dataset/rheumatoid_arthritis/test.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/rheumatoid_arthritis/test.csv -------------------------------------------------------------------------------- /Dataset/rheumatoid_arthritis/train.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Dataset/rheumatoid_arthritis/train.csv -------------------------------------------------------------------------------- /Model/C&D/C_dict.data: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Model/C&D/C_dict.data -------------------------------------------------------------------------------- /Model/C&D/D_Table.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Model/C&D/D_Table.py -------------------------------------------------------------------------------- /Model/C&D/E_index.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Model/C&D/E_index.json -------------------------------------------------------------------------------- /Model/C&D/Optimization.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Model/C&D/Optimization.py -------------------------------------------------------------------------------- /Model/C&D/Run_D_Table.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Model/C&D/Run_D_Table.py -------------------------------------------------------------------------------- /Model/C&D/Tokenization.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Model/C&D/Tokenization.py -------------------------------------------------------------------------------- /Model/C&D/get_C_dict.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Model/C&D/get_C_dict.py -------------------------------------------------------------------------------- /Model/KGE.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Model/KGE.py -------------------------------------------------------------------------------- /Model/Models.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Model/Models.py -------------------------------------------------------------------------------- /Model/Pretrained BioBERT/vocab.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Model/Pretrained BioBERT/vocab.txt -------------------------------------------------------------------------------- /Model/Run_KGE.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Model/Run_KGE.py -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/README.md -------------------------------------------------------------------------------- /Supplementary Table/Supplementary Table S1 (statistical analysis of entity prediction).xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Supplementary Table/Supplementary Table S1 (statistical analysis of entity prediction).xlsx -------------------------------------------------------------------------------- /Supplementary Table/Supplementary Table S2 (drug-gene new inferred knowledge).xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Supplementary Table/Supplementary Table S2 (drug-gene new inferred knowledge).xlsx -------------------------------------------------------------------------------- /Supplementary Table/Supplementary Table S3 (gene-disease new inferred knowledge).xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Supplementary Table/Supplementary Table S3 (gene-disease new inferred knowledge).xlsx -------------------------------------------------------------------------------- /Supplementary Table/Supplementary Table S4 (disease-drug new inferred knowledge).xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Supplementary Table/Supplementary Table S4 (disease-drug new inferred knowledge).xlsx -------------------------------------------------------------------------------- /Supplementary Table/Supplementary Table S5 (closed-triplets).xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZhuChaoY/SDKG-11/HEAD/Supplementary Table/Supplementary Table S5 (closed-triplets).xlsx --------------------------------------------------------------------------------