graph mining

Novel Computational Methods to Predict Drug–target Interactions Using Graph Mining and Machine Learning Approaches

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B3 L5 R5220

Abstract Computational drug repurposing aims at finding new medical uses for existing drugs. The identification of novel drug-target interactions (DTIs) can be a useful part of such a task. Finding computationally DTIs is a convenient strategy to identify potentially new DTIs at low cost with reasonable accuracy. However, the current DTI prediction methods suffer a high false positive prediction rate. Here, we present a comprehensive review of the recent progress in the field of DTI prediction from data-centric and algorithmic-centric perspectives that can help in constructing novel reliable

Novel Computational Methods that Facilitate Development of Cyanofactories for Free Fatty Acid Production by Olaa Motwalli

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B3 L5 R5209

Abstract Finding a source from which high-energy-density biofuels can be derived at an industrial scale has become an urgent challenge for renewable energy production. Some microorganisms can produce free fatty acids (FFA) as precursors towards such high-energy-density biofuels. In particular, photosynthetic cyanobacteria are capable of directly converting carbon dioxide into FFA. However, current engineered strains need several rounds of engineering to reach the level of FFA production for it to be commercially viable. Thus, new chassis strains that require less engineering are needed

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.

Student life: studying and working at the Computational Bioscience Research Center (KAUST)

1 min read ·
For Ph.D. students Arturo Magana Mora, Haitham Ashoor and Olaa Motwalli, April 2017 was a particularly nerve-wracking month. After years of hard work and sleepless nights, they finally defended their thesis, bringing them one step closer to graduation.

Rawan Olayan

Rawan Olayan obtained both, her MS Degree and PhD Degree from Computer Science at KAUST in 2013 and 2018 respectively. Her master thesis and PhD thesis supervisor was Vladimir Bajic. Under the supervision of her advisor Professor Vladimir Bajic, she completed her thesis on developing novel computational methods to predict drug-target interactions and their functional effects using data integration, graph mining and machine learning approaches. Currently, Rawan is working as a postdoctoral associate in the Carter Lab at the Jackson Laboratory for Genomic Medicine in Farmington, Connecticut. In

Olaa A. Motwalli

Research Interests Olaa Motwalli is a Ph.D. student in Computational Science and a member of the Computational Bioscience Research Center (CBRC) at KAUST. She obtained her Bachelor's degree in Computer Science at King Abdul Aziz University in Jeddah and obtained her Master's degree in Computer and Software Engineering at Widener University in the USA. Her research interests are mainly the development and computational support for the design of sustainable biofuel production via microbial cell factories through machine learning, graph mining, and algorithm development, genome-scale metabolic

Karim Awara

Karim Awara obtained his Master's Degree in Computer Science under the supervision of Professor Panagiotis Kalnis from King Abdullah University of Science and Technology. Research Interests Karim's research interests included the Database and High-Performance Computing field. Awards and Distinctions Awarded, internationally, as one of the best 5 teams in SIGMOD 2010 contest for developing high multi-query optimization techniques. And presented the work at SIGMOD conference, June 2010 in Indianapolis, IN, USA. Rewarded as one of the top four teams in Egypt in a software Engineering competition