scholarly journals Challenges and solutions in drug-target interaction prediction

2018 ◽  
Author(s):  
◽  
Ali Ezzat
Keyword(s):  
Drug Target ◽  
Target Interaction ◽  
Interaction Prediction

Drug-Target Interaction Prediction with Graph Regularized Matrix Factorization

2017 ◽  
Vol 14 (3) ◽  
pp. 646-656 ◽  
Author(s):  
Ali Ezzat ◽  
Peilin Zhao ◽  
Min Wu ◽  
Xiao-Li Li ◽  
Chee-Keong Kwoh
Keyword(s):  
Matrix Factorization ◽  
Drug Target ◽  
Target Interaction ◽  
Interaction Prediction

scholarly journals Autoencoders for Drug-Target Interaction Prediction

2020 ◽  
Author(s):  
Ming Chen ◽  
Xiuze Zhou
Keyword(s):  
Network Architecture ◽  
Drug Target ◽  
Real Data ◽  
Data Sets ◽  
Nonlinear Method ◽  
Target Interaction ◽  
Interaction Prediction ◽  
Biological Studies ◽  
Latent Features ◽  
Full Interaction

Abstract Background: Because it is so laborious and expensive to experimentally identify Drug-Target Interactions (DTIs), only a few DTIs have been verified. Computational methods are useful for identifying DTIs in biological studies of drug discovery and development. Results: For drug-target interaction prediction, we propose a novel neural network architecture, DAEi, extended from Denoising AutoEncoder (DAE). We assume that a set of verified DTIs is a corrupted version of the full interaction set. We use DAEi to learn latent features from corrupted DTIs to reconstruct the full input. Also, to better predict DTIs, we add some similarities to DAEi and adopt a new nonlinear method for calculation. Similarity information is very effective at improving the prediction of DTIs. Conclusion: Results of the extensive experiments we conducted on four real data sets show that our proposed methods are superior to other baseline approaches.Availability: All codes in this paper are open-sourced, and our projects are available at: https://github.com/XiuzeZhou/DAEi.

scholarly journals DrugE-Rank: improving drug–target interaction prediction of new candidate drugs or targets by ensemble learning to rank

2016 ◽  
Vol 32 (12) ◽  
pp. i18-i27 ◽  
Author(s):  
Qingjun Yuan ◽  
Junning Gao ◽  
Dongliang Wu ◽  
Shihua Zhang ◽  
Hiroshi Mamitsuka ◽  
...  
Keyword(s):  
Ensemble Learning ◽  
Drug Target ◽  
Learning To Rank ◽  
Target Interaction ◽  
Interaction Prediction

scholarly journals DeepPurpose: a deep learning library for drug–target interaction prediction

2020 ◽  
Author(s):  
Kexin Huang ◽  
Tianfan Fu ◽  
Lucas M Glass ◽  
Marinka Zitnik ◽  
Cao Xiao ◽  
...  
Keyword(s):  
Deep Learning ◽  
Drug Target ◽  
Prediction Models ◽  
State Of The Art ◽  
Supplementary Information ◽  
Target Interaction ◽  
Interaction Prediction ◽  
Computer Scientists ◽  
Benchmark Datasets ◽  
Biomedical Field

Abstract Summary Accurate prediction of drug–target interactions (DTI) is crucial for drug discovery. Recently, deep learning (DL) models for show promising performance for DTI prediction. However, these models can be difficult to use for both computer scientists entering the biomedical field and bioinformaticians with limited DL experience. We present DeepPurpose, a comprehensive and easy-to-use DL library for DTI prediction. DeepPurpose supports training of customized DTI prediction models by implementing 15 compound and protein encoders and over 50 neural architectures, along with providing many other useful features. We demonstrate state-of-the-art performance of DeepPurpose on several benchmark datasets. Availability and implementation https://github.com/kexinhuang12345/DeepPurpose. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

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