DTI-CNN:

This repo is moved to 23AIBox

A learning-based method for drug-targetinteraction prediction based on feature representation learning and deep neural network

Quick start

We provide an example script to run experiments on our dataset:

• Run ./python/run_model.py: predict drug-target interactions, and evaluate the results with ten cross-validation.

All process

1. -Run compute_similarity.m

2. -Run run_joint.m

3. -Run run_DAE.py

4. -Run run_model.py

Code and data

matlab/ directory

• compute_similarity.m: compute Jaccard similarity based on interaction/association network
• joint.m: splicing the network of drugs and proteins
• diffusionRWR.m: network diffusion algorithm (random walk with restart)
• run_joint.m: implement the joint and RWR above.

python/ directory

• au_class.py: implement the autoencoder
• DAE.py: implement the denoising autoencoder
• run_DAE: use the dataset to run denoising autoencoder
• run_model.py: predict drug-target interactions, and evaluate the results with ten cross-validation

data/ directory

• 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
• mat_drug_se.txt : Drug-SideEffect association matrix
• mat_protein_protein.txt : Protein-Protein interaction matrix
• mat_protein_drug.txt : Protein-Drug interaction matrix
• mat_drug_protein.txt : Drug_Protein interaction matrix (transpose of the above matrix)
• mat_drug_protein_remove_homo.txt: Drug_Protein interaction matrix, in which homologous proteins with identity score >40% were excluded (see the paper).
• mat_drug_drug.txt : Drug-Drug interaction matrix
• mat_protein_disease.txt : Protein-Disease association matrix
• mat_drug_disease.txt : Drug-Disease association matrix
• Similarity_Matrix_Drugs.txt : Drug similarity scores based on chemical structures of drugs
• Similarity_Matrix_Proteins.txt : Protein similarity scores based on primary sequences of proteins

Note: drugs, proteins, diseases and side-effects are organized in the same order across all files, including name lists, ID mappings and interaction/association matrices.