HampDTI

This is the implementation of A heterogeneous graph automatic meta-path learning method for drug-target interaction prediction

Requirements

• Pytorch 1.7.0
• Numpy 1.19.2
• Rdkit 2021.09.2
• pyG 2.0.2

Quick start

To reproduce our results: please run 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 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: a complete ID mapping between drug names and DrugBank ID.
• protein_dict_map: 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_indepent.npy : the cross-validation set.
• indepent_one_index.npy and indepent_zero_index.npy : the independent test set.
• drug_structure.pt : drug structure features.
• protein_structure.pt : protein sequence features.
• 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: 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.

• smlies.txt : drug smlies for all drugs in DTINet datasets.
• proteinSquence.txt : protein squences for all proteins in DTINet datasets.

Contacts

If you have any questions or comments, please feel free to email [email protected] or [email protected]