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UW and Allen Institute researchers develop new method for large-scale analysis of gene activity to advance disease research

Illustration of split-pool barcoding process

Credit: Jennifer Sunami

A team of researchers at the University of Washington and the Allen Institute have come up with a highly efficient, scalable approach for measuring gene activity at the cellular level that could aid the fight against potentially devastating diseases. The researchers described their novel technique — called SPLiT-seq, short for Split Pool Ligation-based Transcriptome sequencing — in a paper published this week in the journal Science.

SPLiT-seq enables scientists to identify the cellular origin of ribonucleic acid (RNA) molecules, which are essential to the regulation and expression of genes, without having to rely on expensive instrumentation. It employs an approach called combinatorial barcoding, in which the cells go through multiple rounds of sorting and labeling with a DNA identifier, or barcode, through a process known as in-cell ligation. Each time the cells are sorted, all of the cells in a particular pool — and their corresponding RNA — receive the same barcode. Four rounds of sorting and labeling produced a unique barcode combination for each cell that could be used to identify its RNA during bulk sequencing.

“Using SPLiT-seq, it becomes possible to measure gene activity in individual cells, even if there are hundreds of thousands of different cells in a tissue sample,” explained Allen School and Electrical Engineering professor Georg Seelig in a UW News release. “With these ‘split-pool barcoding steps,’ we solve a big problem in measuring gene expression: reliably identifying which RNA molecules came from which cell in the original tissue sample.”

Seelig and his colleagues used SPLiT-seq to profile more than 156,000 mouse brain and spinal cord cells. They were able to identify more than 100 cell types, for which they analyzed gene expression patterns related to cellular function, region, and stage of differentiation.

The process costs around a penny per cell, according to Seelig, and requires no special equipment. By reducing the expense and effort required to analyze gene expression on the cellular level, the team hopes SPLiT-seq will accelerate research into the onset, progression, and treatment of diseases such as cancer, Parkinson’s, and Alzheimer’s.

Co-authors of the paper include Bioengineering Ph.D. students Charles Roco and David Peeler; Electrical Engineering Ph.D. student Sumit Mukherjee and postdocs Alexander Rosenberg, Anna Kuchina, and Paul Sample; former Electrical Engineering postdoc Richard Muscat, now Research Funding Manager at Cancer UK; Wei Chen, a graduate student at the UW Molecular Engineering & Sciences Institute; Bioengineering professors Suzie Pun and Drew Sellers; Allen Institute scientists Zizhen Yao and Lucas Graybuck; and Bosiljka Tasic, Associate Director of Molecular Genetics at the Allen Institute.

Read the full Science paper here, the UW News release here, and a related Allen Institute article here. To learn more about this and related work, visit the Seelig Lab for Synthetic Biology website and follow @seeliglab on Twitter.

Credit: Anna Kuchina


March 16, 2018

Celebrating our first year of innovation as the Paul G. Allen School

Seattle Times front page depicting Paul Allen firing t-shirt gunOn March 9th, 2017, the University of Washington Board of Regents approved the establishment of the Paul G. Allen School of Computer Science & Engineering in recognition of our increasing prominence and impact on campus, in our region, and around the world — and to honor Paul Allen’s many contributions to our university, to science and innovation, and to society.

Today, Allen marked the one-year anniversary of our founding by highlighting 10 exciting innovations from the Allen School that are advancing the field of computer science and helping to make the world a better place. From the article:

“One year ago, with the clink of champagne glasses and the pop of a t-shirt gun, the Paul G. Allen School of Computer Science & Engineering at the University of Washington was christened. With a mission to drive technology forward and a motivation to change the world for the better, the Allen School has already shown itself as global hub for technology innovation. From battery-free cellphones to 3D printed smart objects as well as the development of a digital storage system using DNA, here are just 10 of the many innovations that have come out of the school over the past year.”

See the full list here.

Thanks, Paul, for your ongoing friendship and support — and for highlighting the contributions of our faculty and students.

Happy one-year anniversary to us!

March 9, 2018

Allen School undergrad Christine Betts is geeking out and giving back

Christine BettsAn avid runner, reader, writer, crafter, and scholar — computer science major Christine Betts exemplifies the creativity and academic excellence that are the hallmarks of Allen School students. She also embodies a commitment to service: she has embraced the role of peer adviser, eager to help her fellow CSE students succeed, and also volunteers her time and talents working with kids through non-profit organizations such as Big Brothers Big Sisters.

Betts’ achievements have not gone unnoticed in the local community. Last month, she received the inaugural Allen AI Outstanding Engineer Scholarship from the Allen Institute for Artificial Intelligence and was featured in GeekWire’s Geek of the Week. Between her studies, her extracurricular activities, and her volunteer work, Betts is keeping busy these days. She recently slowed down long enough to share her thoughts with us for the latest edition of the Allen School’s Undergraduate Spotlight — including how coming from a position of privilege inspires her to be a geek who gives back.

Allen School: What are some of your favorite things about being an Allen School student?

Christine Betts: There are so many awesome things about studying CSE. I’ve already been able to get exposure to teaching, research, advising, and some really interesting parts of computer science. I think what I’m most amazed by is how approachable and kind the people I’ve gotten to work with are. For example, the Ph.D. student I’ve been doing research with in the Molecular Information Systems Lab, Max Willsey, is patient and excellent at explaining things. He’s just one example of the many passionate people I’ve had the chance to learn from in the Allen School.

I’m grateful for not only the material I’ve learned, but the forethought with which it’s been taught, as well. It’s so cool to have dipped my toes in many different realms as an undergrad, and I’ve gained much more than CS knowledge through these experiences! I try to be cautious about deeming anything as “meant to be,” because I think that mentality can be dangerous when bad things happen, but after following a really bizarre path to get here, I couldn’t be more grateful to have discovered my inclination towards algorithmic thinking and absolute love of programming. As weird as it is to be a Missourian who took a gap year in the other Washington — DC, that is — here at UW, I feel so incredibly lucky for the things that felt negative at the time, but which led me into STEM even though I previously never saw myself in this field.

Allen School: You recently received the very first AI2 Oustanding Engineer Scholarship. That must be exciting. What impact will this scholarship have on you and your plans for the future?

CB: Holy cow, am I excited! I still can’t really believe it. The scholarship means a ton for my family and me, and the opportunity to intern with AI2 is incredible. I think this scholarship says so much about AI2 as an institution; increasing the voices being heard in tech is about even more than providing financial support, and I think AI2 really recognizes that. I’m beyond excited for this fall and the chance to receive mentorship, learn a ton, and to get a feel for working with a smaller organization.

I’m particularly looking forward to seeing AI in practice and will hopefully have lots of resources to figure out what I want to do after I graduate. Grad school? Research? Industry? I heard Oren Etzioni’s TEDxSeattle talk last year and was inspired and impressed by his message about the problems in the assumptions we make about an AI-controlled future. It really got me thinking about the things that make us human and are hard to replicate. I’ve always been interested in human behavior and cognition, so I’m sure during my internship at AI2 I’ll get all kinds of intellectual stimulation! I feel so much gratitude for this scholarship, and I hope to be able to share the knowledge and opportunities that come from this with other young women.

Allen School: You’ve also joined the ranks of Allen School peer advisers. What does that mean to you?

CB: I’m absolutely stoked to be a new peer adviser! I feel lucky to have had so many opportunities myself as a student, such as the chance to do research as an undergrad. I can’t wait to help others create game plans for their own success regardless of their major or background!

Allen School: Who or what have you found most inspiring during your time here?

CB: I’ve been sitting in on advising appointments and have been really inspired by the advising team; they all have so much compassion and empathy. I think they really reflect the prevailing vibe of the school, where people are accessible, interesting, and excited about CSE. This quarter, I’ve also been attending the Change seminar, which is a weekly presentation and discussion about a topic that pulls together technology and global development. The seminar has been a great reminder of all the meaningful applications of the skills I’m acquiring in my classes. It’s easy to get caught up in free food, cushy jobs, and the latest stories featured in MIT Tech Review. But at the end of the day, when I graduate I’ll have something to offer that can make the world a better place, and I feel I have an obligation to strive for that given how many opportunities I’ve had.

Finally, my peers never fail to inspire me! I’ve made so many great friends within the Allen School community that I think I’ve become an extrovert. I’m amazed by how hard everyone works, but also by my classmates who have the innate desire to invest in other people.

Allen School: It sounds like you stay pretty busy within CSE, but what do you like to do outside of the classrooms and labs?

CB: I love to build things, so I’m drawn to kinetic and creative endeavors like weaving, sewing, knitting, and physical computing. I especially love the intersection of CS and those other types of creative activities; I’m currently working on a project for an English class that’s a woven data visualization about the portrayal of women in the hero’s journey. It’s rooted in The Odyssey, where Penelope is weaving and unweaving Odysseus’ burial shroud while waiting for him to return. (The statement is that I’ll finish the weaving, thereby pushing against a patriarchal structure while still working within it.) I also love to read — mostly poetry and non-fiction books — and listen to podcasts. I used to do other creative and personal projects, including calligraphy and writing about things I think about a lot, but I’ve learned that sometimes we have to lose little parts of ourselves if we want to really grow in other areas. For now, at least, the tradeoff is worth it.

I also love to run and enjoy long-distance activities. I’ve done a triathlon, ridden my bike across Iowa, completed a century (a 100-mile bike ride), and, most recently, run a marathon with my buddy, Olga. I hope to one day do a half Ironman; the hardest part will definitely be finishing the swim before the cutoff time, because I’m a super-slow swimmer!

Allen School: You are very service-oriented. How have the opportunities you’ve enjoyed influenced how you approach your volunteer work?

CB: I’m really interested in the larger dynamics of American society and the role I play as someone with a lot of privilege. I don’t come from anything close to a private-school, “coastal elite” type of background, but I am aware of the inequities that exist and the biases that positively affect my outcomes as a straight cis white woman.

A few years ago, I saw an interview with Killer Mike from Run the Jewels in which he discussed how well-educated white folks should spend time mentoring children who might not have the same access, but have a lot of potential — not to “feel good about ourselves,” but to recognize the benefits that come with one’s identity and to try to improve outcomes for those who don’t share that identity. While I was living in Washington, DC, I was a Girls on the Run coach, which I absolutely loved. Since moving to Seattle, I’ve been a Big Sister for a young woman in East Bellevue. I’ve gotten a lot out of my time with my “Little,” and her wit and curiosity are a constant reminder of how important it is to encourage and support success in everyone — not only those who come from the most well-educated or wealthy families.


Christine is clearly going the extra mile inside and outside of the classroom. Thanks, Christine, for being an exemplary member of the Allen School community!


February 23, 2018

New wireless charging system from UW researchers uses a laser to beam power to your cellphone

Demonstration of the laser wireless charging system with a smartphone

UW researchers’ laser-powered charging system can wirelessly charge a smartphone from across a room. Guard beams (illuminated here in red for visibility) prevent human contact with the charging beam by triggering the beam’s automatic shut-off.

Mobile devices and WiFi have given people the freedom to access information and accomplish tasks on the move, but there is still one area in which we remain tethered to the old way of doing things: the power cord. No matter what fancy features or sleek designs are built into the latest devices, they still run on a battery — which means they have to be plugged into the wall to recharge. But that could change thanks to a team of researchers led by Allen School professor Shyam Gollakota and Physics and Electrical Engineering professor Arka Majumdar, who have developed the first laser-powered wireless charging solution to safely and quickly charge mobile devices from across a room — potentially liberating us from those pesky power cords for good.

The team set out to create an end-to-end power delivery system that is practical and efficient as well as safe. To satisfy the first two criteria, the researchers aimed to adhere to the form-factor requirements of a smartphone while minimizing the need for instrumentation of the environment. The resulting system consists of two main components: a laser power source capable of delivering a charge at distance, and a compact receiver that attaches to the back of a smartphone. Power comes from a laser emitter configured produce a focused beam in the near-infrared spectrum. That beam charges the smartphone via a small array of photovoltaic cells mounted on the back of the device to convert the beam’s optical power to electrical power.

To prevent overheating, the cell array is paired with a thermoelectric generator that is mounted on an aluminum heatsink to dissipate excess heat from the beam. The generator harvests some of the heat that would otherwise be wasted. Instead of requiring the laser emitter to scan the room for devices, which is inefficient and time-consuming, the team developed an acoustic localization system that relies on a series of chirps emitted by the device, in this case a smartphone, to be charged. These chirps are inaudible to human ears, but capable of being picked up by the microphones built into the emitter.

The receiver that mounts on the back of a smartphone

The receiver, which consists of a photovoltaic cell array attached to a thermoelectric generator mounted on an aluminum heatsink, is only 8 mm thick and 40 mm wide.

“This acoustic localization system ensures that the emitter can detect when a user has set the smartphone on the charging surface, which can be an ordinary location like a table across the room,” explained Vikram Iyer, a Ph.D. student in electrical engineering who works in the Allen School’s Networks & Mobile Systems Lab. Iyer is co-lead author of the research paper presenting the team’s work, which was published in the Proceedings of the Association for Computing Machinery on Interactive, Mobile, Wearable and Ubiquitous Technologies (IMWUT).

While power delivery and heat dissipation presented interesting technical challenges, the team also had to contend with the significant question of human safety. Due to the level of concentrated power required from the laser to deliver a strong enough charge wirelessly and from distance, the team had to devise a foolproof way to prevent humans and objects from inadvertently coming into contact with the beam.

“Safety was our focus in designing this system,” Gollakota said. “We have designed, constructed and tested this laser-based charging system with a rapid-response safety mechanism, which ensures that the laser emitter will terminate the charging beam before a person comes into the path of the laser.”

The team could not rely on cameras, acoustic tracking, or other motion detection methods, because those approaches would all introduce an unacceptable delay between detection and shut-off. Instead, the team turned to optics, incorporating a set of “guard beams” — harmless, low-power lasers that surround the charging beam. A set of 3D-printed retroflectors arranged around the power cell reflect the guard beams back to photodiodes on the laser emitter. When one of the guard beams detects an object, such as a human arm, moving into its path, it causes the charging beam to automatically shut off. Because the guard beam operates at the speed of light, it can trigger this shut-off within a fraction of a second — faster than the maximum speed of human motion.

Team members, clockwise from top left: Vikram Iyer, Shyam Gollakota holding smartphone, Elyas Bayati, Arka Majumdar, Rajalakshmi Nandakumar

The research team, clockwise from top left: Vikram Iyer, Shyam Gollakota, Elyas Bayati, and Rajalakshmi Nandakumar

The team demonstrated its prototype can charge a smartphone at roughly the same speed as a standard USB cable. The laser charging system is capable of delivering two watts of power in a steady stream from a distance of 4.3 meters, or roughly 14 feet, to an area of roughly 15 square inches in size. The system can be modified to expand the charging area to more than three feet, like a tabletop, from a distance of 12 meters or nearly 40 feet.

The UW team’s laser-based system has several advantages over existing approaches to wireless power. Near-field magnetic induction, for example, is a commercially available technology that is safe and efficient, but also limited in range. Methods for harvesting ambient power from far field microwave sources, on the other hand, can handle a longer range, but are suitable only for ultra-low power applications requiring only a few microwatts of power. The researchers anticipate that their approach can be extended to charging a range of devices, including tablets, cameras, and desktop computers.

In addition to Gollakota, Majumdar, and Iyer, the team includes co-lead author Elyas Bayati, a Ph.D. student in electrical engineering who works in the UW Applied Physics Laboratory, and Allen School Ph.D. student Rajalakshmi Nandakumar.

Read the UW News release here, visit the project website here, and read related coverage in Wired, ForbesNew AtlasDigital TrendsGeekWire, The Engineer, International Business Times, The Daily Mail, R&D Magazine, and SlashGear.

Photo credits: Mark Stone/University of Washington


February 21, 2018

UW and Microsoft researchers achieve random access in large-scale DNA data storage

Two MISL members performing wet-lab experiments

Allen School Ph.D. student Lee Organick (foreground) and Microsoft researcher Yuan-Jyue Chen in the Molecular Information Systems Lab (Dennis Wise/University of Washington)

University of Washington and Microsoft researchers revealed today that they have taken a significant step forward in their quest to develop a DNA-based storage system for digital data. In a paper published in Nature Biotechnology, the members of the Molecular Information Systems Laboratory (MISL) describe the science behind their world record-setting achievement of 200 megabytes stored in synthetic DNA. They also present their system for random access — that is, the selective retrieval of individual data files encoded in more than 13 million DNA oligonucleotides. While this is not the first time researchers have achieved random access in DNA, the UW and Microsoft team have produced the first demonstration of random access at such a large scale.

One of the big advantages to DNA as a digital storage medium is its ability to store vast quantities of information, with a raw limit of one exabyte — equivalent to one billion gigabytes — per cubic millimeter. The data must be converted from digital 0s and 1s to the molecules of DNA: adenine, thymine, cytosine, and guanine. To restore the data to its digital form, the DNA is sequenced and the files decoded back to 0s and 1s. This process becomes more daunting as the amount of data increases — without the ability to perform random access, the entire dataset would have to be sequenced and decoded in bulk in order to find and retrieve specific files. In addition, the DNA synthesis and sequencing processes are error-prone, which can result in data loss.

MISL researchers addressed these problems by designing and validating an extensive library of primers for use in conjunction with polymerase chain reaction (PCR) to achieve random access. Before synthesizing the DNA containing data from a file, the researchers appended both ends of each DNA sequence with PCR primer targets from the primer library. They then used these primers later to select the desired strands through random access, and used a new algorithm designed to more efficiently decode and restore the data to its original, digital state.

“Our work reduces the effort, both in sequencing capacity and in processing, to completely recover information stored in DNA,” explained Microsoft Senior Researcher Sergey Yekhanin, who was instrumental in creating the codec and algorithms used to achieve the team’s results. “For the latter, we have devised new algorithms that are more tolerant to errors in writing and reading DNA sequences to minimize the effort in recovering this information.”

Snapshot of Ok Go band members splattered with multi-colored paint from music video

A snapshot from Ok Go’s music video for “This Too Shall Pass,” which the MISL team encoded in DNA

Using synthetic DNA supplied by Twist Bioscience, the MISL team encoded and successfully retrieved 35 distinct files ranging in size from 29 kilobytes to over 44 megabytes — amounting to a record-setting 200 megabytes of high-definition video, audio, images, and text. This represents a significant increase over the previous record of 22 megabytes set by researchers from Harvard Medical School and Technicolor Research & Innovation in Germany.

“The intersection of biotech and computer architecture is incredibly promising and we are excited to detail our results to the community,” said Allen School professor Luis Ceze, who co-leads the MISL. “Since this paper was submitted for publication we have reached over 400 megabytes, and we are still growing and learning more about large-scale DNA data storage.”

With this new milestone, MISL researchers have succeeded in demonstrating how DNA-based data storage — known to be significantly denser and more durable than existing digital storage technologies — can be practical, too. The UW and Microsoft team estimates its approach will scale to physically isolated pools of DNA containing several terabytes each. When dehydrated for storage, these pools of data would be several orders of magnitude denser than tape. And as the costs associated with DNA sequencing and synthesis continue to decline, the team foresees substantial activity devoted to the development of DNA-based data storage in future.

“DNA data storage is an incredibly exciting area, and it is great to see our progress recognized by such a reputable publication as Nature Biotechnology,” said Microsoft Senior Researcher Karin Strauss, co-leader of the MISL and an affiliate professor at the Allen School. “We are enthusiastic to continue working at the intersection of biotechnology and IT.”

It was this intersection that initially interested Allen School Ph.D. student Lee Organick, who performed many of the wet-lab experiments the team used to validate its approach. Having made the leap from undergraduate studies in molecular biology to computer science, she is enthusiastic about the potential impact of the MISL’s approach.

Georg Seelig, Luis Ceze, Karin Strauss

Left to right: Allen School and UW Electrical Engineering professor Georg Seelig, Allen School professor Luis Ceze, and Microsoft researcher Karin Strauss (Tara Brown Photography)

“We’re at a time when a lot of groundbreaking research will be done at the intersection of fields,” said Organick. “When I heard about this project it seemed a bit outlandish, but it captured my imagination.”

The makeup of the lab — which unites researchers from multiple disciplines and organizations — is another plus, in Organick’s view.

“Having worked with such a creative and diverse team of people for several years now, they’ve shown me that projects like this one are achievable,” she said. “And it’s just as exciting as it was the first day.”

The MISL draws upon the varied expertise of researchers from the Allen School, UW departments of electrical engineering and bioengineering, and Microsoft. In addition to Ceze, Strauss, Organick, and Yekhanin, contributors to the Nature Biotechnology paper include lab members Siena Dumas Ang, Yuan-Jyue Chen, Randolph Lopez, Konstantin Makarychev, Miklos Racz, Govinda Kamath, Parikshit Gopalan, Bichlien Nguyen, Christopher Takahashi, Sharon Newman, Hsing-Yeh Parker, Cyrus Rashtchian, Kendall Stewart, Gagan Gupta, Robert Carlson, John Mulligan, Douglas Carmean, and Georg Seelig.

Read the Nature Biotechnology paper here and related articles in IEEE Spectrum, ZDNet, and GeekWire.

Support the next phase of the team’s research by submitting an original image to the lab’s digital time capsule, which will be used to develop and refine techniques for processing visual information in DNA molecules, as part of the #MemoriesInDNA Project here.


February 19, 2018

Maya Cakmak named 2018 Sloan Research Fellow

Maya CakmakProfessor Maya Cakmak, director of the Allen School’s Human-Centered Robotics Lab, has earned a 2018 Sloan Research Fellowship from the Alfred P. Sloan Foundation. The fellowship recognizes Cakmak as one of the most outstanding young researchers in North America and a future scientific leader. Cakmak is among 16 computer scientists to receive a 2018 fellowship, out of 126 fellows overall drawn from more than 50 colleges and universities across the United States and Canada.

“The Sloan Research Fellows represent the very best science has to offer,” Sloan Foundation President Adam Falk said in a press release. “The brightest minds, tackling the hardest problems, and succeeding brilliantly — Fellows are quite literally the future of twenty-first century science.”

Cakmak’s research focuses on the development of general-purpose robots that can be programmed by their end-users, including people living with motor impairments, older adults who wish to age in place, and others who may require assistance in order to maintain their independence. According to Cakmak, it’s an idea whose time has come — one that is made possible by recent advances in the field.

“Within the last decade, developments in robotics, such as common hardware platforms and open-source software, have fueled a great deal of progress towards this vision,” Cakmak explained, citing examples of robots capable of performing household tasks such as folding laundry or emptying a dishwasher. “However, these capabilities are far from ready for the real world for two important reasons: they are tailored to a particular environment in which the robot operates, meaning that they can’t be easily adapted to other settings, and they involve long development cycles and programmers capable of using specialized software.”

The first problem, Cakmak says, is already being addressed through mainstream robotics research that aims to develop universal capabilities that will work correctly in every potential scenario. But those efforts are hampered by the difficulty for researchers of anticipating every variable a robot might encounter in the course of its work. For her part, Cakmak is interested in eliminating the first problem altogether by tackling the second: empowering users to program their own robots to suit their individual needs and environment. To that end, she is working on ways to enable anyone to do what currently can be done only by skilled programmers. Her approach includes teaching robots to physically manipulate objects through demonstration and verbal commands, and the development of new visual and textual robot programming languages that make programming robots simpler and faster than current software engineering practices.

Ultimately, Cakmak’s work is guided by her desire to have a real impact on real people.

“I deeply care about the relevance and usefulness of my research,” Cakmak said. “We try to evaluate systems we develop in my lab with realistic and diverse sets of tasks, putting them in front of potential users with diverse backgrounds and abilities, and we take every opportunity to demonstrate and deploy them in the real world.”

Cakmak and her students collaborate with robotics startups like Savioke and Fetch Robotics to develop tools that can be useful for these companies and their customers. She also runs a summer camp where high school students with diverse disabilities learn to program robots using tools developed in her lab.

Cakmak is the 32nd current or former Allen School faculty member to have earned one of these prestigious awards, for which candidates are evaluated by senior scientists based on their research accomplishments, creativity, and potential to be a leader in their respective fields. She joins recent recipients Ali Farhadi and Jon Froehlich (2017), Emina Torlak (2016) and Emily Fox, Shyam Gollakota, and Thomas Rothvoss (2015).

Cakmak is not the only computer scientist with an Allen School connection to be honored by the Sloan Foundation this year. Former postdoc Simon Peter, who worked with Allen School professors Tom Anderson and Arvind Krishnamurthy, also received a 2018 fellowship. Peter is a faculty member at the University of Texas at Austin, where he focuses on operating systems and networks.

Four other UW faculty members are among the current class of fellows: Jiun Haw-Chu of the Clean Energy Institute, Arka Majumdar of Electrical Engineering and Physics, Jessica Werk of Astronomy, and Chelsea Wood of Aquatic & Fishery Sciences.

Read the Sloan Foundation press release here and the UW News release here. View the complete list of 2018 Fellows here.

Congratulations, Maya and Simon!


February 16, 2018

Professor Michael Ernst honored for extraordinary contributions to student mentorship

Michael ErnstAllen School professor Michael Ernst has earned the 2018 CRA-E Undergraduate Research Faculty Mentoring Award from the Computing Research Association. The award recognizes faculty who provide exceptional mentorship and support to student researchers. Ernst is a member of the Allen School’s Programming Languages & Software Engineering (PLSE) group.

Recipients of the CRA-E mentorship award are chosen based on their track record of providing a high-quality, rewarding research experience to aspiring computer scientists. The CRA cited Ernst’s combination of research accomplishments and caring demeanor in its award announcement, which also praised his record of mentorship across multiple institutions, projects, and publications. To date, Ernst has mentored 123 undergraduate students over the course of his research career, co-authoring more than 50 publications with them along the way.

“He is typically described as a caring and careful mentor who is selfless, patient, quality-driven, and student-focused,” the CRA said of Ernst, noting that nearly half of his undergraduate mentees have gone on to attend graduate school in computer science.

Ernst’s success can be attributed in part to his holistic approach to student mentorship. In addition to providing direct guidance to mentees, he cultivates an environment and a team that is welcoming and supportive of young researchers — including instructing graduate students, postdoctoral researchers, and faculty colleagues on how to successfully work with undergraduates. He also incorporates state-of-the-art research tools and project-based exploration in his undergraduate classes.

“I’m passionate about mentoring because doing research as an undergraduate changed the course of my career and my life,” said Ernst. “I love making new discoveries — and I get a vicarious thrill from helping others to experience that same wonder.”

Ernst’s approach has made him a role model for the next generation of computer science faculty. As one former mentee who went on to become a faculty member said, “I strive to use as much of prof. Ernst’s mentoring style in my own advising as I can.” If imitation is the highest form of flattery, you can’t get much higher praise than that.

In addition to Ernst, the CRA recognized Catherine Putonti, a professor of computer science and biology at Loyola University Chicago and the Stritch School of Medicine, with a 2018 faculty mentoring award. Read the full CRA announcement here.

Congratulations, Mike — and thank you for delivering an exceptional research experience to so many Allen School undergraduates!


February 13, 2018

Allen School undergraduates earn national recognition for research excellence

Computing Research Association logoIn keeping with the Allen School’s commitment to provide an unparalleled educational experience to students, many undergraduates participate in leading-edge research in our labs. Undergraduate researchers work alongside faculty, postdocs, and graduate students and often submit their work to major academic research conferences and scientific journals. This year, three of these talented student researchers — Kimberly Ruth, Preston Jiang, and Deric Pang — were recognized as part of the Computing Research Association’s 2018 Outstanding Undergraduate Researcher Awards, which highlight exceptional potential among young computer scientists.

Kimberly RuthKimberly Ruth, a junior who is double-majoring in computer engineering and mathematics, was named a finalist in this year’s CRA awards competition. For the past two years, she has worked with professors Tadayoshi Kohno and Franziska Roesner in the Allen School’s Security and Privacy Research Lab as part of a team focused on security for emerging augmented reality platforms.

Ruth collaborated with Ph.D. student Kiron Lebeck on the development of Arya, an AR system that protects against buggy or malicious output by applications. As part of that work, Ruth contributed to the prototype built on the Unity game engine, including a selection of applications in C# to run on the system. The team’s results were published last year at the 38th IEEE Symposium on Security & Privacy, with Ruth as the second author, and subsequently invited for publication in an upcoming issue of IEEE Security & Privacy Magazine. She also worked with Lebeck to design and execute a user study to evaluate people’s reactions and concerns related to AR technology, with an emphasis on multi-user scenarios, using the Microsoft HoloLens. Inspired by the results of that user study, Ruth has taken the lead on a new project examining a set of open questions related to the design of multi-user AR platforms that span computer privacy and security, operating system design, and human-computer interaction.

Outside of the lab, Ruth volunteers as a peer tutor for the Allen School’s Foundations of Computing course. She previously earned a 2017 Mary Gates Research Scholarship, a competitive award that recognizes University of Washington students engaged in undergraduate research, and a 2017-18 Washington Research Foundation Fellowship, which supports students engaged in sophisticated science and engineering research projects.

Preston JiangPreston Jiang is a transfer student from Seattle Central College who works with Rajesh Rao, the Hwang Professor of Computer Science & Engineering and Electrical Engineering and director of both the Allen School’s Neural Systems Lab and the National Science Foundation’s Center for Sensorimotor Neural Engineering. He also works with professor Andrea Stocco, co-director of the Cognition & Cortical Dynamics Laboratory. Jiang was recognized with an Honorable Mention from CRA for his research on brain-computer interfaces (BCIs) and brain-to-brain interfaces (BBIs).

Jiang started out applying his knowledge of signal processing, machine learning and systems integration to create a new BCI for controlling a cursor based on electroencephalography (EEG) signals from the scalp. Rao subsequently tapped him to serve as the lead student researcher on the third generation of their BBI project, which seeks to enable individuals to communicate directly using EEG and signals transmitted to the visual cortex via a transcranial magnetic stimulator (TMS). Jiang’s contributions focused on BrainNet, a system for linking three or more brains to collaboratively solve a task through visual brain signals. As part of this work, he helped to assess the viability and performance of the BrainNet, managed integration of the EEG, BCI, and TMS systems, and ran experiments with human subjects. Jiang also contributed to another ambitious project, this time exploring the potential for brain-based virtual reality, by cataloguing the variety of artificial visual sensations known as “phosphenes” that humans experience to enable the future development of VR systems based on direct brain stimulation.

The team plans to publish journal papers on both BrainNet and the brain-based VR project with Jiang as co-author. Jiang previously was recognized for research excellence with a 2017 WRF Innovation Undergraduate Fellowship in Neuroengineering and a 2017-18 Levinson Emerging Scholars Award, which supports juniors and seniors pursuing advanced research in bioscience and related areas.

Deric PangDeric Pang is a student enrolled in the Allen School’s combined bachelor’s/master’s program who earned an Honorable Mention in the CRA awards competition. He has contributed to research projects on fault localization, programming by natural language, and software testing under the guidance of professor Michael Ernst in the Programming Languages & Software Engineering (PLSE) group.

Pang was part of a team that changed our understanding of fault localization, an approach for identifying defective lines of code to save substantial effort in the debugging process. Previous research into fault localization techniques has tended to use artificial faults for ease of evaluation. However, Pang and his colleagues discovered that a technique’s performance on artificial faults is not a good predictor of how well it will handle real faults. After replicating previous work, the team found that only 30 percent of the evaluated techniques were statistically and practically significant for artificial faults — and none met this threshold for real faults. Pang and his fellow researchers used their findings to develop new, more effective techniques and presented their work at the 39th International Conference of Software Engineering (ICSE 2017). Pang also contributed to Tellina, a code translation tool that is the result of a collaboration between PLSE and a group of researchers led by professor Luke Zettlemoyer of the Allen School’s Natural Language Processing group. Tellina translates the natural language description of a desired operation into programming language using recurrent neural networks. The system enables programmers to be more productive by allowing them to describe an intended operation using their own words rather than having to memorize the details of increasingly complex systems. In a controlled user study, Pang and his colleagues found that, even in cases where Tellina’s predictions were not completely correct, programmers who used the tool significantly outperformed those who did not.

Pang previously completed internships at Marchex and Amazon, where he worked on automatic speech recognition and the Alexa Machine Learning team, and studied abroad as a computer science exchange student at ETH Zürich. He plans to spend this spring as an intern at NVIDIA working on autonomous drone research.

Since 2000, a total of 58 Allen School students have been honored by CRA for excellence in undergraduate research. Congratulations to Kimberly, Preston, and Deric — and thanks to the faculty and graduate students who serve as mentors and enthusiastically support undergraduate research!


February 12, 2018

Yin Tat Lee wins NSF CAREER Award to develop new, efficient algorithms for convex optimization

Yin Tat Lee head shotProfessor Yin Tat Lee of the Allen School’s Theory of Computation research group has received a CAREER Award from the National Science Foundation to develop faster, more efficient algorithms for solving convex and other optimization problems. The outcome of Lee’s research, which seeks to increase the scientific community’s understanding of the relationship between convex geometry and optimization algorithms and improve upon current techniques drawn from continuous and discrete optimization, will have broad impact across the sciences and beyond.

Convex optimization techniques have applications in a range of fields, including machine learning, statistics, mathematics, economics, and operations research. However, many of these techniques historically tended to be inefficient and expensive to implement. Recent advances yielding faster algorithms have enabled Lee to break the long-standing running time barriers for specific problems, such as linear programming and maximum flow problems, and to apply optimization techniques to a broader class of problems than was previously feasible. Lee aims to build upon that past work by tackling a set of significant problems in convex geometry and optimization in order to push the state of the art even further. His approach will draw from techniques used in a variety of domains, including combinatorial and convex optimization, convex and Riemannian geometry, spectral graph theory, stochastic processes, and more.

One major goal of Lee’s CAREER proposal is to make progress towards resolving the Kannan-Lovasz-Simononoviz (KLS) conjecture — a central problem not only to the field of optimization but to theoretical computer science and mathematics, and one that implies several other well-known conjectures. Such progress would represent a significant breakthrough in researchers’ understanding of convex optimization and yield immediate running-time improvements for several problems in convex geometry. Lee also aims to resolve a number of algorithmic barriers to optimization, most notably the square-root iterations barrier for solving linear programs. This work would overcome a major obstacle to achieving nearly linear-time algorithms for the maximum flow problem, which is a key subroutine in many other algorithms and promises to have broad theoretical and practical implications.

Finally, Lee will apply a geometry perspective to the study of complex optimization algorithms, such as first-order methods and cutting-plane methods, in order to better understand their complexity and aid in the discovery of new applications. He also intends to explore the use of sampling algorithms for non-convex optimization, which is a rapidly developing area in machine learning.

The CAREER Award is administered through NSF’s Faculty Early Career Development Program and is designed to recognize and support promising junior faculty who successfully blend teaching and research and demonstrate the potential to be leaders in their respective fields. Including Lee, 59 Allen School faculty members have received one of these prestigious awards or their predecessor, the Presidential/NSF Young Investigator Award.

Read Lee’s award abstract here.

Congratulations, Yin Tat!


February 7, 2018

All work and no play …

The antidote to becoming a dull computer scientist: the Allen School’s annual ski day at Stevens Pass!

January 27, 2018

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