- python 3.8.16
- cuda 11.3
- pytorch 1.12.1
- dgl 1.1.1
- numpy 1.24.3
- sklearn 1.2.2
- python
main.py
Options are:--num_channels: the number of channels, default: 4
--num_layers: the maximum length of the learned meta-paths, default: 3
--alpha: hyperparameter in loss function, default: 0.4
-t: select experimental data, default: 'o'
data
Folder. This folder contains the DTINet dataset.
drug.txt
: list of drug names.protein.txt
: list of protein names.disease.txt
: list of disease names.se.txt
: list of side effect names.drug_dict_map.txt
: a complete ID mapping between drug names and DrugBank ID.protein_dict_map.txt
: a complete ID mapping between protein names and UniProt ID.drug_se.npy
: Drug-SideEffect association matrix.protein_protein.npy
: Protein-Protein interaction matrix.drug_drug.npy
: Drug-Drug interaction matrix.protein_disease.npy
: Protein-Disease association matrix.drug_disease.npy
: Drug-Disease association matrix.protein_drug.npy
: Protein-Drug interaction matrix.drug_protein.npy
: Drug-Protein interaction matrix.drug_protein.npy
: Drug-Protein interaction matrix.drug_protein_indepent.npy
: the cross-validation set.drug_structure.pt
: drug structure features.protein_structure.pt
: protein sequence features.mat_drug_protein_homo_protein_drug.txt
: Drug-Protein interaction matrix, in which DTIs with similar drugs (i.e., drug chemical structure similarities > 0.6) or similar proteins (i.e., protein sequence similarities > 40%) were removed (see the paper).mat_drug_protein_drug.txt
: Drug-Protein interaction matrix, in which DTIs with drugs sharing similar drug interactions (i.e., Jaccard similarities > 0.6) were removed (see the paper).mat_drug_protein_sideeffect.txt
: Drug-Protein interaction matrix, in which DTIs with drugs sharing similar side effects (i.e., Jaccard similarities > 0.6) were removed (see the paper).mat_drug_protein_disease.txt
: Drug-Protein interaction matrix, in which DTIs with drugs or proteins sharing similar diseases (i.e., Jaccard similarities > 0.6) were removed (see the paper).mat_drug_protein_unique.txt
: Drug-Protein interaction matrix, in which known unique and non-unique DTIs were labelled as 3 and 1, respectively, the corresponding unknown ones were labelled as 2 and 0 (see the paper for the definition of unique).
drug_protein_feature
Folder
Run main.py
to learn drug structure features and protein sequence features.
These files: drug.txt, protein.txt, disease.txt, se.txt, drug_dict_map, protein_dict_map, mat_drug_se.txt, mat_protein_protein.txt, mat_drug_drug.txt, mat_protein_disease.txt, mat_drug_disease.txt, mat_protein_drug.txt, mat_drug_protein.txt, Similarity_Matrix_Proteins.txt, are extracted from https://github.com/luoyunan/DTINet.
These files: mat_drug_protein_homo_protein_drug.txt, mat_drug_protein_drug.txt, mat_drug_protein_sideeffect.txt, mat_drug_protein_disease.txt, mat_drug_protein_unique.txt are extracted from https://github.com/FangpingWan/NeoDTI