DOI: 10.5281/zenodo.5500305
title: A unified DTI prediction framework based on knowledge graph and recommendation system

description: ## A unified DTI prediction framework based on knowledge graph and recommendation system # Code and data description ## Scripts - `kge_nfm.py`: the complement of the KGE_NFM & NFM methods. - `kge_rf.py`: the complement of the KGE_RF & RF methods. - `deepdit.py`: the complement of the MPNN_CNN & DeepDTI methods. - the complement of DTINet and DTiGEMS is tested based on their source packages (more in Prerequisites) <br> ## `data/` directory #### `yamanishi_08/` directory - `data_folds/`: 10 folds training set and test set in the three scenarios - `warm_start_1_1/` - `warm_start_1_10/` - `drug_coldstart/` - `protein_coldstart/` - `kg_data/`: supporting knowledge graph data - `dt_all_08.csv`: whole DTI dataset - `791drug_struc.csv`: drugbank id and smiles of drugs - `989proseq.csv`: kegg id and sequences of proteins - `morganfp.txt`: list of drug morgan fingerprints - `pro_ctd.txt`: list of protein descriptors #### `BioKG/` directory - `data_folds/`: 10 folds training set and test set in the three scenarios - `warm_start_1_10/` - `drug_coldstart/` - `protein_coldstart/` - `kg.csv`: supporting knowledge graph data - `dti.csv`: whole DTI dataset - `comp_struc.csv`: drugbank id and smiles of drugs - `pro_seq.csv`: sequences of proteins - `fp_df.csv`: list of drug morgan fingerprints - `prodes_df.csv`: list of protein descriptors #### `hetionet/` directory - `data_folds/`: 10 folds training set and test set in the three scenarios - `warm_start_1_10/` - `drug_coldstart/` - `protein_coldstart/` - `kg.csv`: supporting knowledge graph data - `dti.csv`: whole DTI dataset - `map_drugs_df`: drugbank id and smiles of drugs - `pro_seq.csv`: sequences of proteins - `fp_df.csv`: list of drug morgan fingerprints - `prodes_df.csv`: list of protein descriptors #### `luo's_dataset/` directory - `data_folds/`: 10 folds training set and test set in the three scenarios - `warm_start_1_1/` - `warm_start_1_10/` - `drug_coldstart/` - `protein_coldstart/` - `mapping/`: related mappings and similarity matrix (https://github.com/luoyunan/DTINet) - `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 - `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 - `feature/`: related features used in methods - `drug_smiles.csv`: drugbank id and smiles - `seq.txt`: list of protein sequences - `morganfp.txt`: list of drug morgan fingerprints - `pro_ctd.txt`: list of protein descriptors #### `eg_model/` directory We provided a pre-trained kge model for example. - `dismult_400_warm_1_10.pkl` <br> # Prerequisites #### Operating system: Linux #### Programing language: python #### KGE_NFM & NFM dependencies ``` - python 3.6 - pandas '1.1.5' - numpy '1.18.4' - scikit-learn '0.24.1' - tensorflow '1.15.0' - ampligraph '1.3.2' - deepctr '0.8.4' ``` #### baseline dependencies - RF & KGE_RF (included in KGE_NFM&NFM dependencies) - MPNN_CNN & DeepDTI: - source: https://github.com/kexinhuang12345/DeepPurpose ``` - deeppurpose '0.0.9' - torch '1.6.0+cu101' ``` - DTINet: - source: https://github.com/luoyunan/DTINet - note: in this work, we run the DTINet in a python environment, which need Linux system and python2. Importantly, this method requires the [Inductive Matrix Completion](http://bigdata.ices.utexas.edu/software/inductive-matrix-completion/) (IMC) library. More detailed information about the installation of this method could be found in the source code of the DTINet. - DTiGEMS: - source: https://github.com/MahaThafar/DTiGEMSplus - TriModel: - source: http://drugtargets.insight-centre.org/ <br> <br> # Example (kge_nfm.py) #### A brief presentation of the results: - return average loss when training kge model ``` Average Loss: 0.475181: 2%|###3 | 1/50 [01:10&lt;57:31, 70.44s/epoch] ``` - return performance(mrr) on training set of DTI for early stopping (kge_model in `eg_model/`) ``` In [35]: roc = roc_auc(test_label,test_score) ...: pr = pr_auc(test_label,test_score) ...: print(roc) ...: print(pr) 0.8731770833333332 0.44079654835037246 ``` - nfm training process (`patience=10`) ``` In [45]: roc_nfm,pr_nfm,pred_y = train_nfm(feature_columns,train_model_input,train_label,test_model_input,test_label,patience) Train on 44851 samples Epoch 1/2000 44851/44851 - 2s - loss: 0.5332 - precision: 0.0976 Epoch 2/2000 44851/44851 - 1s - loss: 0.4143 - precision: 0.0000e+00 Epoch 3/2000 44851/44851 - 1s - loss: 0.3456 - precision: 0.0000e+00 Epoch 4/2000 44851/44851 - 1s - loss: 0.3443 - precision: 0.0000e+00 Epoch 5/2000 44851/44851 - 1s - loss: 0.3470 - precision: 0.0000e+00 Epoch 6/2000 44851/44851 - 1s - loss: 0.3382 - precision: 0.0000e+00 ...... Epoch 279/2000 44851/44851 - 1s - loss: 0.0758 - precision: 0.9248 Epoch 280/2000 44851/44851 - 1s - loss: 0.0753 - precision: 0.9327 Epoch 281/2000 44851/44851 - 1s - loss: 0.0796 - precision: 0.9155 Epoch 282/2000 44851/44851 - 1s - loss: 0.0764 - precision: 0.9276 Epoch 283/2000 44851/44851 - 1s - loss: 0.0739 - precision: 0.9127 ``` - reutrn results as type of roc_auc & pr_auc ``` 0.9812476679104477 0.8803416284646345 ```