IOI
-
An AI-based, Indoor/Outdoor-Integrated (IOI) GPS System to Bring Seismic Waves in the Terrains of Positioning Technology
KAIST breaks new grounds in positioning technology with an AI-integrated GPS board that works both indoors and out
KAIST (President Kwang Hyung Lee) announced on the 8th that Professor Dong-Soo Han's research team (Intelligent Service Integration Lab) from the School of Computing has developed a GPS system that works both indoors and outdoors with quality precision regardless of the environment.
This Indoor/Outdoor-Integrated GPS System, or IOI GPS System, for short, uses the GPS signals outdoors and estimates locations indoors using signals from multiple sources like an inertial sensor, pressure sensors, geomagnetic sensors, and light sensors. To this end, the research team developed techniques to detect environmental changes such as entering a building, and methods to detect entrances, ground floors, stairs, elevators and levels of buildings by utilizing artificial intelligence techniques. Various landmark detecting techniques were also incorporated with pedestrian dead reckoning (PDR), a navigation tool for pedestrians, to devise the so-called “Sensor-Fusion Positioning Algorithm”.
To date, it was common to estimate locations based on wireless LAN signals or base station signals in a space where the GPS signal could not reach. However, the IOI GPS enables positioning even in buildings without signals nor indoor maps.
The algorithm developed by the research team can provide accurate floor information within a building where even big tech companies like Google and Apple's positioning services do not provide. Unlike other positioning methods that rely on visual data, geomagnetic positioning techniques, or wireless LAN, this system also has the advantage of not requiring any prior preparation. In other words, the foundation to enable the usage of a universal GPS system that works both indoors and outdoors anywhere in the world is now ready.
The research team also produced a circuit board for the purpose of operating the IOI GPS System, mounted with chips to receive and process GPS, Wi-Fi, and Bluetooth signals, along with an inertial sensor, a barometer, a magnetometer, and a light sensor. The sensor-fusion positioning algorithm the lab has developed is also incorporated in the board.
When the accuracy of the IOI GPS board was tested in the N1 building of KAIST’s main campus in Daejeon, it achieved an accuracy of about 95% in floor estimation and an accuracy of about 3 to 6 meters in distance estimation. As for the indoor/outdoor transition, the navigational mode change was completed in about 0.3 seconds. When it was combined with the PDR technique, the estimation accuracy improved further down to a scope of one meter.
The research team is now working on assembling a tag with a built-in positioning board and applying it to location-based docent services for visitors at museums, science centers, and art galleries. The IOI GPS tag can be used for the purpose of tracking children and/or the elderly, and it can also be used to locate people or rescue workers lost in disaster-ridden or hazardous sites. On a different note, the sensor-fusion positioning algorithm and positioning board for vehicles are also under development for the tracking of vehicles entering indoor areas like underground parking lots.
When the IOI GPS board for vehicles is manufactured, the research team will work to collaborate with car manufacturers and car rental companies, and will also develop a sensor-fusion positioning algorithm for smartphones. Telecommunication companies seeking to diversify their programs in the field of location-based services will also be interested in the use the IOI GPS.
Professor Dong-Soo Han of the School of Computing, who leads the research team, said, “This is the first time to develop an indoor/outdoor integrated GPS system that can pinpoint locations in a building where there is no wireless signal or an indoor map, and there are an infinite number of areas it can be applied to. When the integration with the Korea Augmentation Satellite System (KASS) and the Korean GPS (KPS) System that began this year, is finally completed, Korea can become the leader in the field of GPS both indoors and outdoors, and we also have plans to manufacture semi-conductor chips for the IOI GPS System to keep the tech-gap between Korea and the followers.”
He added, "The guidance services at science centers, museums, and art galleries that uses IOI GPS tags can provide a set of data that would be very helpful for analyzing the visitors’ viewing traces. It is an essential piece of information required when the time comes to decide when to organize the next exhibit. We will be working on having it applied to the National Science Museum, first.”
The projects to develop the IOI GPS system and the trace analysis system for science centers were supported through Science, Culture, Exhibits and Services Capability Enhancement Program of the Ministry of Science and ICT.
Profile: Dong-Soo Han, Ph.D.Professorddsshhan@kaist.ac.krhttp://isilab.kaist.ac.kr
Intelligent Service Integration Lab.School of Computing
http://kaist.ac.kr/en/
Korea Advanced Institute of Science and Technology (KAIST)Daejeon, Republic of Korea
2022.07.13 View 8103 -
Machine Learning-Based Algorithm to Speed up DNA Sequencing
The algorithm presents the first full-fledged, short-read alignment software that leverages learned indices for solving the exact match search problem for efficient seeding
The human genome consists of a complete set of DNA, which is about 6.4 billion letters long. Because of its size, reading the whole genome sequence at once is challenging. So scientists use DNA sequencers to produce hundreds of millions of DNA sequence fragments, or short reads, up to 300 letters long. Then the DNA sequencer assembles all the short reads like a giant jigsaw puzzle to reconstruct the entire genome sequence. Even with very fast computers, this job can take hours to complete.
A research team at KAIST has achieved up to 3.45x faster speeds by developing the first short-read alignment software that uses a recent advance in machine-learning called a learned index.
The research team reported their findings on March 7, 2022 in the journal Bioinformatics. The software has been released as open source and can be found on github (https://github.com/kaist-ina/BWA-MEME).
Next-generation sequencing (NGS) is a state-of-the-art DNA sequencing method. Projects are underway with the goal of producing genome sequencing at population scale. Modern NGS hardware is capable of generating billions of short reads in a single run. Then the short reads have to be aligned with the reference DNA sequence. With large-scale DNA sequencing operations running hundreds of next-generation sequences, the need for an efficient short read alignment tool has become even more critical. Accelerating the DNA sequence alignment would be a step toward achieving the goal of population-scale sequencing. However, existing algorithms are limited in their performance because of their frequent memory accesses.
BWA-MEM2 is a popular short-read alignment software package currently used to sequence the DNA. However, it has its limitations. The state-of-the-art alignment has two phases – seeding and extending. During the seeding phase, searches find exact matches of short reads in the reference DNA sequence. During the extending phase, the short reads from the seeding phase are extended. In the current process, bottlenecks occur in the seeding phase. Finding the exact matches slows the process.
The researchers set out to solve the problem of accelerating the DNA sequence alignment. To speed the process, they applied machine learning techniques to create an algorithmic improvement. Their algorithm, BWA-MEME (BWA-MEM emulated) leverages learned indices to solve the exact match search problem. The original software compared one character at a time for an exact match search. The team’s new algorithm achieves up to 3.45x faster speeds in seeding throughput over BWA-MEM2 by reducing the number of instructions by 4.60x and memory accesses by 8.77x. “Through this study, it has been shown that full genome big data analysis can be performed faster and less costly than conventional methods by applying machine learning technology,” said Professor Dongsu Han from the School of Electrical Engineering at KAIST.
The researchers’ ultimate goal was to develop efficient software that scientists from academia and industry could use on a daily basis for analyzing big data in genomics. “With the recent advances in artificial intelligence and machine learning, we see so many opportunities for designing better software for genomic data analysis. The potential is there for accelerating existing analysis as well as enabling new types of analysis, and our goal is to develop such software,” added Han.
Whole genome sequencing has traditionally been used for discovering genomic mutations and identifying the root causes of diseases, which leads to the discovery and development of new drugs and cures. There could be many potential applications. Whole genome sequencing is used not only for research, but also for clinical purposes. “The science and technology for analyzing genomic data is making rapid progress to make it more accessible for scientists and patients. This will enhance our understanding about diseases and develop a better cure for patients of various diseases.”
The research was funded by the National Research Foundation of the Korean government’s Ministry of Science and ICT.
-PublicationYoungmok Jung, Dongsu Han, “BWA-MEME:BWA-MEM emulated with a machine learning approach,” Bioinformatics, Volume 38, Issue 9, May 2022
(https://doi.org/10.1093/bioinformatics/btac137)
-ProfileProfessor Dongsu HanSchool of Electrical EngineeringKAIST
2022.05.10 View 6949 -
Baemin CEO Endows a Scholarship in Honor of the Late Professor Chwa
CEO Beom-Jun Kim of Woowa Brothers also known as ‘Baemin,’ a leading meal delivery app company, made a donation of 100 million KRW in honor of the late Professor Kyong-Yong Chwa from the School of Computing who passed away last year. The fund will be established for the “Kyong-Yong Chwa - Beom-Jun Kim Scholarship” to provide scholarships for four students over five years.
Kim finished his BS in 1997 and MS in 1999 at the School of Computing and Professor Chwa was his advisor. The late Professor Chwa was a pioneering scholar who brought the concept of computer algorithms to Korea. After graduating from Seoul National University in electric engineering, Professor Chwa earned his PhD at Northwestern University and began teaching at KAIST in 1980. Professor Chwa served as the President of the Korean Institute of Information Scientists and Engineers and a fellow emeritus at the Korean Academy of Science and Technology.
Professor Chwa encouraged younger students to participate in international computer programming contests. Under his wing, Team Korea, which was comprised of four high school students, including Kim, placed fourth in the International Olympiad Informatics (IOI). Kim, who participated in the contest as high school junior, won an individual gold medal in the fourth IOI competition in 1992. Since then, Korean students have actively participated in many competitions including the International Collegiate Programming Contest (ICPC) hosted by the Association for Computing Machinery.
Kim said, “I feel fortunate to have met so many good friends and distinguished professors. With them, I had opportunities to grow. I would like to provide such opportunities to my juniors at KAIST. Professor Chwa was a larger than life figure in the field of computer programming. He was always caring and supported us with a warm heart. I want this donation to help carry on his legacy for our students and for them to seek greater challenges and bigger dreams.”
2022.03.25 View 5838 -
3D Visualization and Quantification of Bioplastic PHA in a Living Bacterial Cell
3D holographic microscopy leads to in-depth analysis of bacterial cells accumulating the bacterial bioplastic, polyhydroxyalkanoate (PHA)
A research team at KAIST has observed how bioplastic granule is being accumulated in living bacteria cells through 3D holographic microscopy. Their 3D imaging and quantitative analysis of the bioplastic ‘polyhydroxyalkanoate’ (PHA) via optical diffraction tomography provides insights into biosynthesizing sustainable substitutes for petroleum-based plastics.
The bio-degradable polyester polyhydroxyalkanoate (PHA) is being touted as an eco-friendly bioplastic to replace existing synthetic plastics. While carrying similar properties to general-purpose plastics such as polyethylene and polypropylene, PHA can be used in various industrial applications such as container packaging and disposable products.
PHA is synthesized by numerous bacteria as an energy and carbon storage material under unbalanced growth conditions in the presence of excess carbon sources. PHA exists in the form of insoluble granules in the cytoplasm. Previous studies on investigating in vivo PHA granules have been performed by using fluorescence microscopy, transmission electron microscopy (TEM), and electron cryotomography.
These techniques have generally relied on the statistical analysis of multiple 2D snapshots of fixed cells or the short-time monitoring of the cells. For the TEM analysis, cells need to be fixed and sectioned, and thus the investigation of living cells was not possible. Fluorescence-based techniques require fluorescence labeling or dye staining. Thus, indirect imaging with the use of reporter proteins cannot show the native state of PHAs or cells, and invasive exogenous dyes can affect the physiology and viability of the cells. Therefore, it was difficult to fully understand the formation of PHA granules in cells due to the technical limitations, and thus several mechanism models based on the observations have been only proposed.
The team of metabolic engineering researchers led by Distinguished Professor Sang Yup Lee and Physics Professor YongKeun Park, who established the startup Tomocube with his 3D holographic microscopy, reported the results of 3D quantitative label-free analysis of PHA granules in individual live bacterial cells by measuring the refractive index distributions using optical diffraction tomography. The formation and growth of PHA granules in the cells of Cupriavidus necator, the most-studied native PHA (specifically, poly(3-hydroxybutyrate), also known as PHB) producer, and recombinant Escherichia coli harboring C. necator PHB biosynthesis pathway were comparatively examined.
From the reconstructed 3D refractive index distribution of the cells, the team succeeded in the 3D visualization and quantitative analysis of cells and intracellular PHA granules at a single-cell level. In particular, the team newly presented the concept of “in vivo PHA granule density.” Through the statistical analysis of hundreds of single cells accumulating PHA granules, the distinctive differences of density and localization of PHA granules in the two micro-organisms were found. Furthermore, the team identified the key protein that plays a major role in making the difference that enabled the characteristics of PHA granules in the recombinant E. coli to become similar to those of C. necator.
The research team also presented 3D time-lapse movies showing the actual processes of PHA granule formation combined with cell growth and division. Movies showing the living cells synthesizing and accumulating PHA granules in their native state had never been reported before.
Professor Lee said, “This study provides insights into the morphological and physical characteristics of in vivo PHA as well as the unique mechanisms of PHA granule formation that undergo the phase transition from soluble monomers into the insoluble polymer, followed by granule formation. Through this study, a deeper understanding of PHA granule formation within the bacterial cells is now possible, which has great significance in that a convergence study of biology and physics was achieved. This study will help develop various bioplastics production processes in the future.”
This work was supported by the Technology Development Program to Solve Climate Changes on Systems Metabolic Engineering for Biorefineries (Grants NRF-2012M1A2A2026556 and NRF-2012M1A2A2026557) and the Bio & Medical Technology Development Program (Grant No. 2021M3A9I4022740) from the Ministry of Science and ICT (MSIT) through the National Research Foundation (NRF) of Korea to S.Y.L. This work was also supported by the KAIST Cross-Generation Collaborative Laboratory project.
-PublicationSo Young Choi, Jeonghun Oh, JaeHwang Jung, YongKeun Park, and Sang Yup Lee. Three-dimensional label-free visualization and quantification of polyhydroxyalkanoates in individualbacterial cell in its native state. PNAS(https://doi.org./10.1073/pnas.2103956118)
-ProfileDistinguished Professor Sang Yup LeeMetabolic Engineering and Synthetic Biologyhttp://mbel.kaist.ac.kr/
Department of Chemical and Biomolecular Engineering KAIST
Endowed Chair Professor YongKeun ParkBiomedical Optics Laboratoryhttps://bmokaist.wordpress.com/
Department of PhysicsKAIST
2021.07.28 View 10265 -
KAIST Researchers Receive Awards at the 13th Asian Congress on Biotechnology
(From left: Seon Young Park, Dr. So Young Choi, and Yoojin Choi)
Researchers in the laboratory of KAIST Distinguished Professor Sang Yup Lee from the Department of Chemical and Biomolecular Engineering swept awards at the 13th Asian Congress on Biotechnology held in Thailand last month. The conference awarded a total of eight prizes in the areas of best research and best poster presentation. This is an exceptional case in which members of one research team received almost half of the awards at an international conference.
Dr. So Young Choi received the Best Research Award, while Ph.D. candidates Yoojin Choi and Seon Young Park each received the Best Poster Presentation Award at the conference held in Khon Kaen, Thailand from July 23 to 27.
The Asian Congress on Biotechnology is an international conference in which scientists and industry experts in Asia and from around the world gather to present recent research findings in the field of biotechnology. At the conference, around 400 researchers in biotechnology from 25 countries, including Korea, gathered to present and discuss various research findings under the theme of “Bioinnovation and Bioeconomy.”
Distinguished Professor Sang Yup Lee attended the conference to give the opening plenary lecture on the topic of ‘Systems Strategies in Biotechnology.’ Professor Lee announced, “I have attended international conferences with students for the last 20 years, but this is the first in which my team received three awards at an international conference that only honors a total of eight awards, three for Best Research and five for Best Presentation.”
Dr. Choi presented research results on poly (lactate-co-glycolate) (PLGA) synthesis through a biological method using micro-organisms and received the Best Research Award. PLGA is a random copolymer of DL-lactic and glycolic acids and is a biopolymer widely used for biomedical applications. PLGA is biodegradable, biocompatible, and nontoxic, and thus has been approved by the US Food and Drug Administration (FDA) for its use in implants, drug delivery, and sutures.
Dr. Choi’s research was deemed to be innovative for synthesizing PLGA from glucose and xylose in cells through metabolic engineering of E.Coli. Dr. Choi received her Ph.D. under the supervision of Distinguished Professor Lee this February and is currently conducting post-doc research.
Ph.D. candidate Choi presented her research on the use of recombinant E.Coli for the biological synthesis of various nanoparticles and received the Best Poster Presentation award. Choi used recombinant E.Coli-expressing proteins and peptides that adsorb to heavy metals to biologically synthesize diverse metal nanoparticles such as single-nanoparticle including gold and silver, quantum dots, and magnetic nanoparticles for the first time. The synthesized nanoparticles can be used in the fields of bio-imaging, diagnosis, environment, and energy.
Ph.D. candidate Park, who also received the Best Poster Presentation award, synthesized and increased production of astanxanthin, a strong antioxidant found in nature, in E.Coli using metabolic engineering. Astanxanthin is a carotenoid pigment found in salmon and shrimp that widely used in health products and cosmetics.
2017.08.01 View 12759 -
A Technology Holding Company Establishes Two Companies Based on Technologies Developed at KAIST
Mirae Holdings is a technology holding company created by four science and technology universities, KAIST, DIGIST (Daegu Gyeongbuk Institute of Science and Technology), GIST (Gwangju Institute of Science and Technology), and UNIST (Ulsan National Institute of Science and Technology) in 2014 to commercialize the universities’ research achievements. The company identifies promising technologies for commercialization, makes business plans, establishes venture capitals, and invests in startup companies.
Over the past year, Mirae Holdings has established two venture companies based on the technologies developed at KAIST. In September 2014, it founded Cresem Inc., a company used the anisotropic conductive film (ACF) bonding technology, which was developed by Professor Kyung-Wook Paik of the Material Science and Engineering Department at KAIST. Cresem provides a technology to bond electronic parts ultrasonically. The company is expected to have 860,000 USD worth of sales within the first year of its launching.
Last June, Mirae Holdings created another company, Doctor Kitchen, with the technology developed by Professor Gwan-Su Yi of the Bio and Brain Engineering Department at KAIST. Doctor Kitchen supplies precooked food, which helps diabetic patients regulate their diet. The company offers a personalized diet plan to customers so that they can effectively manage their disease and monitor their blood sugar level efficiently.
The Chief Executive Officer of Mirae Holdings, Young-Ho Kim, said, “We can assist KAIST researchers who aspire to create a company based on their research outcomes through various stages of startup services such as making business plans, securing venture capitals, and networking with existing businesses.”
Young-Ho Kim (left in the picture), the Chief Executive Officer of Mirae Holdings, holds a certificate of company registration with Sang-Min Oh (right in the picture), the Chief Executive Officer of Cresem.
Young-Ho Kim (left in the picture), the Chief Executive Officer of Mirae Holdings, holds a certificate of company registration with Jae-Yeun Park (right in the picture), the Chief Executive Officer of Dr. Kitchen.
2015.07.29 View 10902 -
KAIST to support the Genetic Donguibogam Research Project for global market entry of a new natural drug produced by Green Cross Corporation HS
In the wake of the spread of the Middle East Respiratory Syndrome (MERS), sales of immune-enhancing products in Korea such as red and white ginseng have risen dramatically. Ginseng is one of Korea’s major health supplement it exports, but due to the lack of precise scientific knowledge of its mechanism, sales of ginseng account for less than 2% of the global market share.
The Genetic Donguibogam Research Project represents a group of research initiatives to study genes and environmental factors that contribute to diseases and to discover alternative treatments through Eastern medicine. The project is being led by KAIST’s Department of Bio & Brain Engineering Professor Do-Heon Lee.
Professor Lee and Chief Executive Officer Young-Hyo Yoo of Green Cross Corporation HS, a Korean pharmaceutical company, signed a memorandum of understanding (MOU), as well as a non-disclosure agreement (NDA) to develop a naturally derived drug with an enhanced ginsenoside, pharmacological compounds of ginseng, for the global market entry of BST204 on June 10, 2015.
Donguibogam is the traditional Korean source for the principles and practice of Eastern medicine, which was compiled by the royal physician Heo Jun and first published in 1613 during the Joseon Dynasty of Korea.
Cooperating with Green Cross Co., HS, KAIST researchers will use a multi-component, multi-target (MCMT)-based development platform to produce the new natural drug, BST204. This cooperation is expected to assist the entry of the drug into the European market.
Green Cross Co., HS has applied a bio-conversion technique to ginseng to develop BST204, which is a drug with enhanced active constituent of aginsenosides. The drug is the first produced by any Korean pharmaceutical company to complete the first phase of clinical trials in Germany and is about to start the second phase of trials.
Professor Do-Heon Lee, the Director of the project said, “Genetic Donguibogam Research Project seeks to create new innovative healthcare material for the future using integrated fundamental technologies such as virtual human body computer modelling and multi-omics to explain the mechanism in which natural ingredients affect the human body.” He continued, “Especially, by employing the virtual human body computer modelling, we can develop an innovative new technology that will greatly assist Korean pharmaceutical industry and make it the platform technology in entering global markets.”
Young-Hyo Yoo, the CEO of Green Cross Co., HS, said, “For a new naturally derived drug to be acknowledged in the global market, such as Europe and the US, its mechanism, as well as its effectiveness and safety, should be proven. However, it is difficult and costly to explain the mechanism in which the complex composition of a natural substance influences the body. Innovative technology is needed to solve this problem.”
Professor Do-Heon Lee (left in the picture), the Director of Genetic Donguibogam Research Project, stands abreast Young-Hyo Yoo (right in the picture), the CEO of Green Cross Co., HS.
2015.06.10 View 7712 -
Collaboration with Korea Institute of Energy Research
KAIST and the Korea Institute of Energy Research (KIER) agreed on September 4th to further collaboration on energy research such as the development of nano-based hybrid solar cells, bio-fuels, artificial photosynthesis, and carbon dioxide reduction.
The two institutions will select 11 research projects to focus on their cooperation. President Steve Kang (in the right) stood with Jooho Whang, the president of KIER (in the left), holding the signed memorandum of understanding.
2013.11.04 View 7271 -
Ultra High Speed Nanomaterial Synthesis Process Developed Using Laser
Dr. Jun-Yeop, Yeo and the research team led by Professor Seung-Hwan, Ko (both of the Department of Mechanical Engineering) successfully developed a process enabling the location-determinable, ultra high speed synthesis of nanomaterials using concentrated laser beams.
The result of the research effort was published as the frontispiece in the July 9th issue of Advanced Functional Materials, a world renowned material science and engineering academic journal.
Application of the technology reduced the time needed to process nanomaterial synthesis from a few hours to a mere five minutes. In addition, unlike conventional nanomaterial synthesis processes, it is simple enough to enable mass production and commercialization.
Conventional processes require the high temperatures of 900~1,000 °C and the use of toxic or explosive vapors. Complex processes such as separation after synthesis and patterning are needed for application in electronic devices. The multi-step, expensive, environmentally unfriendly characteristics of nanomaterial synthesis served as road blocks to its mass production and commercialization.
Exposing the precursor to concentrated continuous laser beam (green wavelength) resulted in the synthesis of nanowires in the desired location; the first instance in the world to accomplish this feat. The technology, according to the research team, makes possible the production, integration and patterning of nanomaterials using a single process. Applicable to various surfaces and substrates, nanowires have been successfully synthesized on flexible plastic substrates and controlled patterning on the surface of 3-dimensional structures.
Dr. Yeo commented that the research effort has “yielded the creation of a nanomaterial synthesis process capable of synthesis, integration, pattern, and material production using light energy” and has “reduced the synthesis process time of nanomaterial to one tenths of the conventional process.” Dr. Yeo continues to devise steps to commercialize the new multifunctional electronic material and methods for mass production.
The research effort, led by Dr. Yeo and Professor Ko, received contribution from Professor Hyung-Jin Sung (KAIST Department of Mechanical Engineering), Seok-Joon Hong, a Ph.D. candidate, Hyun-Wook Kang, also a Ph.D. candidate, Professor Costas Grigoropoulos of UC Berkeley, and Dr. Dae Ho Lee. In addition, the team received support from the National Research Foundation, Ministry of Knowledge Economy, Global Frontier Program, and KAIST EEWS.
Picture I: Synthesized nanomaterials produced at a desirable location by laser beams
Picture 2: Synthesized nanomaterials built on the 3D structure by using the developed technology
Picture 3: Functional electric circuit made with synthesized nanomaterials
Picture 4: Cover page of July 9th issue of Advanced Functional Materials
2013.08.23 View 9386