Deep learning

Najmeddine Dhieb

Aznaur Aliev

M.S. Student

Drug Repositioning through the Development of Diverse Computational Methods using Machine Learning, Deep Learning, and Graph Mining

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KAUST

In this dissertation, we combined artificial intelligence and machine/deep learning with chemical and biological properties to develop several computational methods to solve biomedical domain problems, specifically drug repositioning, and demonstrated their efficiencies and capabilities. We developed three network-based DTI prediction methods using machine learning, graph embedding, and graph mining. These methods significantly improved prediction performance, and the best-performing method even reduces the error rate by more than 33% across all datasets compared to the best state-of-the-art method. As it is more insightful to predict continuous values that indicate how tightly the drug binds to a specific target, we conducted a comparison study of current regression-based methods that predict drug-target binding affinities (DTBA). Our methods demonstrated their efficiency and capability by achieving high prediction performance and identifying therapeutic targets for several cancer types. We further conducted a lung cancer case study of findings that support the novel predicted targets.

Our work on developing deep learning method for binding affinity prediction accepted by Bioinformatics (Sequence2Vec)

1 min read ·
Congratulates Ramzan, Hiro, and Yu on their work on developing a novel method that combines the strength of probabilistic graphical models, Hilbert space embedding, and deep learning to model binding affinity of transcription factors which was accepted by Bioinformatics.

Yu Li

Ph.D. Student, Computer Science
Research Interests Yu Li is a Ph.D. student at KAUST, majoring in Computer Science. His advisor is Prof. Xin Gao. His research interests are Deep Learning, Machine Learning, and Bioinformatics. He got his Master degree in Computer Science at KAUST in December 2016. Before that, he got his Bachelor degree in Biosciences at the University of Science and Technology of China (USTC). Scientific and Professional Membership Association for the Advancement of Artificial Intelligence(AAAI) Member International Society for Computational Biology (ISCB) Member Education Profile Ph.D student, Computer

Xuefeng Cui

Postdoctoral Research Fellow, Structural and Functional Bioinformatics
Xuefeng Cui worked as a Postdoctoral research fellow at Prof. Xin Gao's Structural and Functional Bioinformatics Group (SFB) at King Abdullah University of Science and Technology (KAUST) during 2014-2016. Currently, Xuefenga is a Professor at Shandong University, China. Education Profile Ph.D. degree, University of Waterloo, Canada, Jan 2007 - April 2014 (except May-Aug, 2012 and May-Aug, 2013). Master's degree, University of Waterloo, Canada, Sep 2004 - Dec 2006. Bachelor's degree, University of Waterloo, Canada, Sep 2000 - Apr 2004. Columbia International College, Canada, Sep 1999 - Aug 2000

Ramzan Umarov

Ph.D. Student, Computer Science
Ramzan is a PhD candidate, working on solving biological problems by using applied machine learning with focus on deep learning. He has developed deep learning based methods to solve bioinformatics problems achieving state-of-the-art performance, focusing on various aspects of gene regulation. Umarov obtained his Master degree from Imperial College London, Advanced Computing course. Research Interests The main research interest of Ramzan Umarov is applied machine learning especially Deep Learning. Professional Profile 2011-2012, Programmer, Softberry, Mount Kisko, NY, USA 2013-2014, Programmer

Maha Thafar

Ph.D. Student, Computer Science
Research Interests I am a computer scientist focusing on developing novel computational methods using artificial intelligence, machine learning, deep learning, and graph mining techniques to solve biomedical problems. I am developing these methods to be applied to large-scale chemical and biomedical data. Currently, I'm working on compound-protein interactions prediction and binding affinity prediction projects. My objective is to empower women in my country with a flourishing academic background that enables building better careers for themselves. Additionally, to create a research culture

Lizhong Ding

Postdoctoral Research Fellow, Structural and Functional Bioinformatics
Lizhong Ding worked as a Postdoctoral research fellow at Prof. Xin Gao's Structural and Functional Bioinformatics Group (SFB) at King Abdullah University of Science and Technology (KAUST) during 2016-2018. Currently, Lizhong is a research scientist at the Inception Institute of Artificial Intelligence. Research Interests Machine learning theory Impact of approximation on learning algorithms, especially discrepancy bounds between approximate and accurate learning, for kernel learning and deep learning Large scale machine learning Large scale matrix analysis/approximation Scalable model

Juexiao Zhou

Ph.D. Student, Computer Science
Juexiao Zhou is a Ph.D. candidate in the KAUST Structural and Functional Bioinformatics research group under the supervision of Professor Xin Gao. Before joining KAUST, Juexiao majored in Bioinformatics and graduated from the Southern University of Science and Technology (SUSTech), located in Shenzhen, Guangdong, China. Research Interests IngIntelligent Healthcare: develop machine learning (ML) / deep learning (DL) techniques for healthcare, including disease detection, risk assessment, etc. Bioinformatics: develop new methods for bioinformatics tasks, including gene regulation understanding