DTI-HCA

Requirements

• python 3.8.16
• cuda 11.3
• pytorch 1.12.1
• dgl 1.1.1
• numpy 1.24.3
• sklearn 1.2.2

Quick start

1. python main.py Options are:
   1. --num_channels: the number of channels, default: 4
   2. --num_layers: the maximum length of the learned meta-paths, default: 3
   3. --alpha: hyperparameter in loss function, default: 0.4
   4. -t: select experimental data, default: 'o'

Data description

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