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Deep Learning Predicts Drug-Drug and Drug-Food Interactions
A Korean research team from KAIST developed a computational framework, DeepDDI, that accurately predicts and generates 86 types of drug-drug and drug-food interactions as outputs of human-readable sentences, which allows in-depth understanding of the drug-drug and drug-food interactions.
Drug interactions, including drug-drug interactions (DDIs) and drug-food constituent interactions (DFIs), can trigger unexpected pharmacological effects, including adverse drug events (ADEs), with causal mechanisms often unknown. However, current prediction methods do not provide sufficient details beyond the chance of DDI occurrence, or require detailed drug information often unavailable for DDI prediction.
To tackle this problem, Dr. Jae Yong Ryu, Assistant Professor Hyun Uk Kim and Distinguished Professor Sang Yup Lee, all from the Department of Chemical and Biomolecular Engineering at Korea Advanced Institute of Science and Technology (KAIST), developed a computational framework, named DeepDDI, that accurately predicts 86 DDI types for a given drug pair. The research results were published online in Proceedings of the National Academy of Sciences of the United States of America (PNAS) on April 16, 2018, which is entitled “Deep learning improves prediction of drug-drug and drug-food interactions.”
DeepDDI takes structural information and names of two drugs in pair as inputs, and predicts relevant DDI types for the input drug pair. DeepDDI uses deep neural network to predict 86 DDI types with a mean accuracy of 92.4% using the DrugBank gold standard DDI dataset covering 192,284 DDIs contributed by 191,878 drug pairs. Very importantly, DDI types predicted by DeepDDI are generated in the form of human-readable sentences as outputs, which describe changes in pharmacological effects and/or the risk of ADEs as a result of the interaction between two drugs in pair. For example, DeepDDI output sentences describing potential interactions between oxycodone (opioid pain medication) and atazanavir (antiretroviral medication) were generated as follows: “The metabolism of Oxycodone can be decreased when combined with Atazanavir”; and “The risk or severity of adverse effects can be increased when Oxycodone is combined with Atazanavir”. By doing this, DeepDDI can provide more specific information on drug interactions beyond the occurrence chance of DDIs or ADEs typically reported to date.
DeepDDI was first used to predict DDI types of 2,329,561 drug pairs from all possible combinations of 2,159 approved drugs, from which DDI types of 487,632 drug pairs were newly predicted. Also, DeepDDI can be used to suggest which drug or food to avoid during medication in order to minimize the chance of adverse drug events or optimize the drug efficacy. To this end, DeepDDI was used to suggest potential causal mechanisms for the reported ADEs of 9,284 drug pairs, and also predict alternative drug candidates for 62,707 drug pairs having negative health effects to keep only the beneficial effects. Furthermore, DeepDDI was applied to 3,288,157 drug-food constituent pairs (2,159 approved drugs and 1,523 well-characterized food constituents) to predict DFIs. The effects of 256 food constituents on pharmacological effects of interacting drugs and bioactivities of 149 food constituents were also finally predicted. All these prediction results can be useful if an individual is taking medications for a specific (chronic) disease such as hypertension or diabetes mellitus type 2.
Distinguished Professor Sang Yup Lee said, “We have developed a platform technology DeepDDI that will allow precision medicine in the era of Fourth Industrial Revolution. DeepDDI can serve to provide important information on drug prescription and dietary suggestions while taking certain drugs to maximize health benefits and ultimately help maintain a healthy life in this aging society.”
Figure 1. Overall scheme of Deep DDDI and prediction of food constituents that reduce the in vivo concentration of approved drugs
2018.04.18 View 11598 -
Two Professors Receive the Asan Medical Award
(Professor Ho Min Kim and Chair Profesor Eunjoon Kim (from far right)
Chair Professor Eunjoon Kim of the Department of Biological Sciences and Professor Ho Min Kim from the Graduate School of Medical Science & Engineering won the 11th Asan Medical Award in the areas of basic medicine and young medical scholar on March 21.
The Asan Medical Award has been recognizing the most distinguished scholars in the areas of basic and clinical medicines annually since 2007.
Chair Professor Kim won the 300 million KRW award in recognition of his research in the mechanism of synaptic brain dysfunction and its relation with neural diseases.
The young medical scholar’s award recognizes a promising scholar under the age of 40. Professor Kim won the award for identifying the key protein structure and molecular mechanism controlling immunocytes and neurons. He earned a 50 million KRW prize.
2018.03.26 View 8892 -
Developing Flexible Vertical Micro LED
A KAIST research team led by Professor Keon Jae Lee from the Department of Materials Science and Engineering and Professor Daesoo Kim from the Department of Biological Sciences has developed flexible vertical micro LEDs (f-VLEDs) using anisotropic conductive film (ACF)-based transfer and interconnection technology. The team also succeeded in controlling animal behavior via optogenetic stimulation of the f-VLEDs.
Flexible micro LEDs have become a strong candidate for the next-generation display due to their ultra-low power consumption, fast response speed, and excellent flexibility. However, the previous micro LED technology had critical issues such as poor device efficiency, low thermal reliability, and the lack of interconnection technology for high-resolution micro LED displays.
The research team has designed new transfer equipment and fabricated a f-VLED array (50ⅹ50) using simultaneous transfer and interconnection through the precise alignment of ACF bonding process. These f-VLEDs (thickness: 5 ㎛, size: below 80 ㎛) achieved optical power density (30 mW/mm2) three times higher than that of lateral micro LEDs, improving thermal reliability and lifetime by reducing heat generation within the thin film LEDs.
These f-VLEDs can be applied to optogenetics for controlling the behavior of neuron cells and brains. In contrast to the electrical stimulation that activates all of the neurons in brain, optogenetics can stimulate specific excitatory or inhibitory neurons within the localized cortical areas of the brain, which facilitates precise analysis, high-resolution mapping, and neuron modulation of animal brains. (Refer to the author’s previous ACS Nano paper of “Optogenetic Mapping of Functional Connectivity in Freely Moving Mice via Insertable Wrapping Electrode Array Beneath the Skull.” )
In this work, they inserted the innovative f-VLEDs into the narrow space between the skull and the brain surface and succeeded in controlling mouse behavior by illuminating motor neurons on two-dimensional cortical areas located deep below the brain surface.
Professor Lee said, “The flexible vertical micro LED can be used in low-power smart watches, mobile displays, and wearable lighting. In addition, these flexible optoelectronic devices are suitable for biomedical applications such as brain science, phototherapeutic treatment, and contact lens biosensors.”
He recently established a startup company ( FRONICS Inc. ) based on micro LED technology and is looking for global partnerships for commercialization. This result entitled “ Optogenetic Control of Body Movements via Flexible Vertical Light-Emitting Diodes on Brain Surface ” was published in the February 2018 issue of Nano Energy.
Figure 1. Comparison of μ-LEDs Technology
2018.01.29 View 13056 -
Three Professors Named KAST Fellows
(Professor Dan Keun Sung at the center)
(Professor Y.H. Cho at the center)
(Professor K.H. Cho at the center)
The Korean Academy of Science and Technology (KAST) inducted three KAIST professors as fellows at the New Year’s ceremony held at KAST on January 12. They were among the 24 newly elected fellows of the most distinguished academy in Korea. The new fellows are Professor Dan Keun Sung of the School of Electrical Engineering, Professor Kwang-Hyun Cho of the Department of Bio and Brain Engineering, and Professor Yong-Hoon Cho of the Department of Physics.
Professor Sung was recognized for his lifetime academic achievements in fields related with network protocols and energy ICT. He also played a crucial role in launching the Korean satellites KITSAT-1,2,3 and the establishment of the Satellite Technology Research Center at KAIST.
Professor Y.H.Cho has been a pioneer in the field of low-dimensional semiconductor-powered quantum photonics that enables quantum optical research in solid state. He has been recognized as a renowned scholar in this field internationally.
Professor K.H.Cho has conducted original research that combines IT and BT in systems biology and has applied novel technologies of electronic modeling and computer simulation analysis for investigating complex life sciences. Professor Cho, who is in his 40s, is the youngest fellow among the newly inducted fellows.
2018.01.16 View 13730 -
Harnessing the Strength of KAIST Alumni: New Head of KAA Inaugurated
KAIST alumni gathered in Seoul on January 13 to celebrate the New Year and the newly-elected leadership of the KAIST Alumni Association (KAA). More than 300 alumni, including President Sung-Chul Shin who is also an alumnus of KAIST, joined the gala event held at the Lotte Hotel.
Photo: Ki-Chul Cha(left) and Jung Sik Koh(right)
The KAA inaugurated its new president, Ki-Chul Cha, who was preceded by Jung Sik Koh, the former CEO at the Korea Resources Corporation. His term starts from January 2018 to December 2020.
Cha is the CEO of Inbody Co Ltd., a global company specializing in developing and selling medical instruments, such as a body composition analyzers, and medical solutions. He is also an adjunct professor in the Department of Mechanical Engineering at Yonsei University. Cha obtained a master’s degree in Mechanical Engineering at KAIST in 1980, and a Ph.D. in Bioengineering at the University of Utah, before finishing his post-doc fellowship at Harvard Medical School.
Cha plans to explore the idea that alumni engagement, saying, “KAIST stays as a home in the memories of 60,000 alumni. I will dedicate myself to stimulating the alumni association to make KAISTians proud.”
At the gala event, the KAA awarded the Alumni of the Year honor to six alumni who distinguished themselves in the areas of professional achievement, humanitarianism, and public service. They are the Director of Startup KAIST Professor Byoung Yoon Kim; President of LG Chem Ltd and Head of Battery Research and Development Myung Hwan Kim; Director of INNOX Advanced Materials Co., Ltd Kyung Ho Chang; Vice President of the Korea International Trade Association Jung-Kwan Kim; CEO of Samsung Electro-Mechanics Yun-Tae Lee; and CEO of ENF Technology Jinbae Jung.
Photo: President Shin(far right) poses with six awardees of the Distinguished Alumni Award and the former President of KAA, Koh(far left)
2018.01.16 View 10394 -
Professor Dong Ho Cho Awarded at the Haedong Conference 2017
Professor Dong Ho Cho of the School of Electrical Engineering at KAIST received an award at the 13th Haedong Conference 2017 in Seoul on the first of December.
The Korean Institute of Communications and Information Sciences recognized Professor Cho for his significant contributions in the field of mobile communication networks. He has carried out groundbreaking research on mobile systems, including architecture, protocols, algorithms, optimization, and efficiency analysis.
As a result, he has produced 73 papers in renowned international journals, 138 papers at international conferences, and filed 52 international patents and 121 domestic patents. In addition, he transferred 14 of the patents he filed to Korean and international companies.
2017.12.07 View 6335 -
In Jin Cho Earned the Best Poster Prize at ME Summit 2017
In Jin Cho, a Ph.D. student in the Department of Chemical and Biomolecular Engineering at KAIST received the best poster prize at the International Metabolic Engineering Summit 2017 held on October 24 in Beijing, China.
The International Metabolic Engineering Summit is a global conference where scientists and corporate researchers in the field of metabolic engineering present their latest research outcomes and build networks.
At this year’s summit, about 500 researchers from around the world participated in active academic exchanges, including giving keynote speeches and presenting posters.
During the poster session, the summit selects one person for the KeAi-synthetic and Systems Biotechnology Poster Award, two for Microbial Cell Factories Poster Awards, and three for Biotechnology Journal Poster Awards among the posters presented by graduate students, post-doctoral fellows and researchers. Cho received the KeAi-synthetic and Systems Biotechnology Poster Award. Her winning poster is on the biotransformation of p-xylene to terephthalic acid using engineered Escherichia coli.
Terephthalic acid is generally produced by p-xylene oxidation; however, this process requires a high temperature and pressure as well as a toxic catalyst during the reaction process.
Cho and Ziwei Luo, a Ph.D. student at KAIST, co-conducted the research and developed a successful biological conversion process. Compared to the existing chemical process, it does not require a high temperature and pressure; and it is environmentally friendly with a relatively high conversion rate of approximately 97%.
Cho’s advisor, Distinguished Professor Sang Yup Lee said, “Further research on glucose-derived terephthalic acid will enable us to produce biomass-based eco-friendly terephthalic acid through engineered Escherichia coli.”
2017.10.31 View 9502 -
KAIST and KOICA Invited Dominican Republic Officials for Workshop
KAIST will host a two-week workshop for Dominican Republic officials and scholars in collaboration with KOICA (Korea International Cooperation Agency) beginning October 23 at KAIST.
The workshop aims to encourage academia-industry cooperation as one of the Projects for Human Resource Development for Science and Technology at KOICA. Dominican participants including the assistant minister of the Ministry of Higher Education, Science and Technology (MESCYT) and deans of engineering colleges at major universities will enjoy lectures from experts and visit enterprises known for excellent academia-industry collaboration.
According to the Center for Overseas Development, at which Professor WonJoon Kim in the School of Business and Technology Management at KAIST holds the position of director, the workshop is designed to develop human resources in the science and technology (S&T) area, share knowledge on research and development in the field of academia-industry cooperation, and help the participants acquire know-how for managing partnerships between related organizations and industries.
During the workshop, KAIST plans to transfer know-how and share knowledge on its academia-industry cooperation R&D system, in hopes that the workshop will help the Dominican Republic foster its manpower in higher education. The workshop organizers hope that the officers and scholars will be able to apply what they will learn for establishing and carrying out detailed action plans for academia-industry cooperation policies in an effective manner.
“This workshop provides an opportunity to learn about the development of S&T in Korea, academia-industry cooperation R&D, and fostering manpower in advanced S&T. Through the knowledge sharing, we can have a better understanding of academia-industry cooperation as well as education on advanced manpower,” said Pedro Antonio Eduardo, the assistant minister of MESCYT.
He added, “I hope that this workshop will further detailed cooperation between the two countries for Korean high-tech enterprises’ overseas expansion and advanced manpower education. The development model in Korea has many essential elements, so learning its engine for growth and polytechnic manpower education will help develop my country’s industry sector.”
The Project for Human Resource Development for Science and Technology is one of the official development assistance projects running from last year until 2019. It promotes R&D activities for S&T in the Dominican Republic, encouraging academia-industry cooperation by improving trainers in charge of advanced manpower education.
2017.10.30 View 7786 -
Distinguished Professor Lee Named International Fellow of the CAS
Distinguished Professor Sang Yup Lee from the Department of Chemical and Biomolecular Engineering at KAIST was awarded the title of distinguished professor and international fellow from the Chinese Academy of Sciences (CAS), and honorary professor from its affiliated organization the Tianjin Institute of Industrial Biotechnology (TIB).
The CAS recognized Distinguished Professor Lee for his significant contributions to biotechnology. He has made significant pioneering academic achievements in the area of systems metabolic engineering, which produces useful chemicals from microorganisms. Not only did he develop the first and best source technology in that field, but also came out with processes for the production of biofuel and environmentally-friendly chemicals.”
As a global leader in systems metabolic engineering, Distinguished Professor Lee has also been appointed as an honorary professor at Jiangnan University in Wuxi, China.
Distinguished Professor Lee was listed in the ‘Top 20 Translational Researchers of 2014’ selected by the renowned international journal Nature Biotechnology. Moreover, he was the first Asian recipient of the James E. Bailey Award in 2016 and Marvin J. Johnson Award in 2012, which are given to scholars in the field of biotechnology.
He is also one of 13 global scientists who are foreign members of the renowned academic societies the National Academy of Engineering and the National Academy of Sciences in the US. Furthermore, he received the ‘2017 Korea Best Scientist Award’ from the president of Korea in July. Finally, his founding field, systems metabolic engineering, was chosen as one of the ‘Top 10 Emerging Technologies of 2016’ by the World Economic Forum.
The Chinese Academy of Sciences, established in November 1949, is an academic organization that carries out research on basic sciences and natural sciences in China. It defined its science and technology system to include the fields of basic sciences, natural sciences, and high technology. While having a base in Beijing, its branch academies are located in 12 main cities along with 117 affiliates and 100 national key labs.
2017.10.26 View 11188 -
Sangeun Oh Recognized as a 2017 Google Fellow
Sangeun Oh, a Ph.D. candidate in the School of Computing was selected as a Google PhD Fellow in 2017. He is one of 47 awardees of the Google PhD Fellowship in the world.
The Google PhD Fellowship awards students showing outstanding performance in the field of computer science and related research. Since being established in 2009, the program has provided various benefits, including scholarships worth $10,000 USD and one-to-one research discussion with mentors from Google.
His research work on a mobile system that allows interactions among various kinds of smart devices was recognized in the field of mobile computing. He developed a mobile platform that allows smart devices to share diverse functions, including logins, payments, and sensors. This technology provides numerous user experiences that existing mobile platforms could not offer. Through cross-device functionality sharing, users can utilize multiple smart devices in a more convenient manner. The research was presented at The Annual International Conference on Mobile Systems, Applications, and Services (MobiSys) of the Association for Computing Machinery in July, 2017.
Oh said, “I would like to express my gratitude to my advisor, the professors in the School of Computing, and my lab colleagues. I will devote myself to carrying out more research in order to contribute to society.”
His advisor, Insik Shin, a professor in the School of Computing said, “Being recognized as a Google PhD Fellow is an honor to both the student as well as KAIST. I strongly anticipate and believe that Oh will make the next step by carrying out good quality research.”
2017.09.27 View 11771 -
Professor Jin Woo Kim Wins the 14th Macrogen Scientist Award
Professor Jin Woo Kim of the Department of Biological Sciences at KAIST received the 14th Macrogen Scientist Award at the 2017 KSMCB International Conference held in COEX on September 12, 2017.
The award is given by the Korean Society for Molecular and Cellular Biology (KSMCB) and sponsored by Macrogen, a service provider of genome research. The award was established in 2004 to recognize biological scientists who have accomplished excellent performance in the field of basic life sciences.
Professor Kim has achieved outstanding research performances on nerve development, such as identifying the cause of senile retinal degenerative disease and finding retinal nerve cells that distinguish light and darkness in dark conditions.
Recently, he discovered intercellular communication, which controls the development of retinal neurons. His findings have contributed to addressing the principles of maintenance and regeneration of retinal neurons.
Since joining KAIST, he has presented approximately 20 papers and published in numerous international journals including Cell Reports, Genes and Development, and EMBO Journal. Moreover, he delivered special lectures at international conferences, universities, and institutes around the world.
2017.09.14 View 8626 -
A Novel and Practical Fab-route for Superomniphobic Liquid-free Surfaces
(clockwise from left: Jaeho Choi, Hee Tak Kim, Shin-Hyun Kim)
A joint research team led by Professor Hee Tak Kim and Shin-Hyun Kim in the Department of Chemical and Biomolecular Engineering at KAIST developed a fabrication technology that can inexpensively produce surfaces capable of repelling liquids, including water and oil.
The team used the photofluidization of azobenzene molecule-containing polymers to generate a superomniphobic surface which can be applied for developing stain-free fabrics, non-biofouling medical tubing, and corrosion-free surfaces.
Mushroom-shaped surface textures, also called doubly re-entrant structures, are known to be the most effective surface structure that enhances resistance against liquid invasion, thereby exhibiting superior superomniphobic property.
However, the existing procedures for their fabrication are highly delicate, time-consuming, and costly. Moreover, the materials required for the fabrication are restricted to an inflexible and expensive silicon wafer, which limits the practical use of the surface.
To overcome such limitations, the research team used a different approach to fabricate the re-entrant structures called localized photofludization by using the peculiar optical phenomenon of azobenzene molecule-containing polymers (referred to as azopolymers). It is a phenomenon where an azopolymer becomes fluidized under irradiation, and the fluidization takes place locally within the thin surface layer of the azopolymer.
With this novel approach, the team facilitated the localized photofluidization in the top surface layer of azopolymer cylindrical posts, successfully reconfiguring the cylindrical posts to doubly re-entrant geometry while the fluidized thin top surface of an azopolymer is flowing down.
The structure developed by the team exhibits a superior superomniphobic property even for liquids infiltrating the surface immediately.
Moreover, the superomniphobic property can be maintained on a curved target surface because its surficial materials are based on high molecules.
Furthermore, the fabrication procedure of the structure is highly reproducible and scalable, providing a practical route to creating robust omniphobic surfaces.
Professor Hee Tak Kim said, “Not only does the novel photo-fluidization technology in this study produce superior superomniphobic surfaces, but it also possesses many practical advantages in terms of fab-procedures and material flexibility; therefore, it could greatly contribute to real uses in diverse applications.”
Professor Shin-Hyun Kim added, “The designed doubly re-entrant geometry in this study was inspired by the skin structure of springtails, insects dwelling in soil that breathe through their skin. As I carried out this research, I once again realized that humans can learn from nature to create new engineering designs.”
The paper (Jaeho Choi as a first author) was published in ACS Nano, an international journal for Nano-technology, in August.
(Schematic diagram of mushroom-shaped structure fabrication)
(SEM image of mushroom-shaped structure)
(Image of superomniphobic property of different types of liquid)
2017.09.08 View 7616