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Zachary Tatlock wins NSF CAREER Award to improve reliability of critical software systems

Zachary Tatlock

Professor Zachary Tatlock, a member of the Allen School’s Programming Languages & Software Engineering (PLSE) group, has earned a CAREER Award from the National Science Foundation to advance the development of a practical verification framework and other methods for improving the reliability of distributed software systems that form the backbone of modern computing applications.

Billions of people around the world rely on distributed systems every day for critical services, including banking, healthcare, transportation, and more. Such systems are designed for optimum scalability and availability, so that when load spikes, machines crash, or networks misbehave, the system is able to compensate for those failures and continue servicing user requests. But these systems are not infallible in practice, and failures can have devastating impacts in human and economic terms — halting essential services and causing significant data loss. On a single day in the summer of 2015, a series of software failures halted trading on the New York Stock Exchange, grounded the entire mainland fleet of United Airlines, and knocked out the website of the The Wall Street Journal. Four years previously, a widespread failure in Amazon’s Elastic Compute Cloud (EC2), part of Amazon Web Services, brought down sites such as Foursquare and Reddit and affected the functionality of others, such as The New York Times. In all, more than 70 sites were affected by that outage.

Tatlock aims to reduce the likelihood and severity of such failures by applying a practical verification-based approach that makes it easier for programmers to implement reliable, high-performance distributed systems. Currently, the set of potential failures is so complex, and the rate of change in software so high, that it is infeasible to effectively test such systems against all scenarios. An alternative approach is to mathematically prove the system works correctly in all cases. But researchers typically only prove the correctness of high-level algorithms for simplified models of these systems, compelled by their complexity to ignore low-level implementation details. This can lead to mismatches between the simplified model and actual implementation which yield subtle errors that may result in large-scale failure. Furthermore, even the most painstakingly constructed proofs eventually become obsolete as the systems they are written for evolve to meet the increasing demand for scale and performance. Tatlock will address these shortcomings by designing compositional verification techniques for independently proving implementation correctness for applications and reliability for fault-tolerance components. This approach would enable programmers to verify the safety and reliability of distributed systems implementations when faced with a variety of network or machine failures — making them less likely in future to ground flights or grind financial markets to a halt.

The NSF’s Faculty Early Career Development Program recognizes and supports junior faculty who exemplify the role of teacher-scholar and demonstrate the potential to be lifelong leaders at the intersection of education and research. Tatlock is the 11th Allen School professor to earn a CAREER Award through the program in the past two years — an incredible success rate that is a testament to the high caliber of our young faculty. A total of 58 current or former Allen School faculty members have earned a CAREER Award or its predecessor, the Presidential/NSF Young Investigator Award.

Read Tatlock’s award abstract here.

Congratulations, Zach!

 

January 19, 2018

James Bornholt and Eunsol Choi named 2018 Facebook Fellows

Facebook Fellowship program logoAllen School Ph.D. students James Bornholt and Eunsol Choi have won 2018 Facebook Fellowships, which are designed to support and recognize promising doctoral students who are pursing innovative research in computer science and engineering. Only 17 students from around the globe were chosen out of more than 800 applicants to receive one of these competitive awards, which provide each fellow with up to two years of tuition, grant support, conference travel support, and multiple opportunities to engage with Facebook researchers.

Bornholt works with professors Emina Torlak, Dan Grossman, and Luis Ceze in the Allen School’s Programming Languages & Software Engineering (PLSE) research group. His research focuses primarily on programming languages and formal methods, with an emphasis on the development of automated program synthesis and verification tools.

James BornholtBornholt was the lead researcher on MemSynth, the first of a new class of synthesis-aided memory model tools for formalizing subtle details of computer processors. Bornholt also co-authored “Push-Button Verification of File Systems via Crash Refinement,” which earned the Best Paper Award at the 12th USENIX Symposium on Operating Systems Design and Implementation (OSDI 2016). In that paper, Bornholt and his colleagues presented Yggdrasil, a new file system automatically proven to be crash-safe. Bornholt branched out from his core research interests to contribute to “A DNA-Based Archival Storage System,” in which a team of researchers in the Molecular Information Systems Lab — a collaboration between UW and Microsoft Research — designed a next-generation storage system for digital data using synthetic DNA.

Other recent projects to which Bornholt has contributed include Hyperkernel, an automatically verified OS kernel, and Ferrite, a toolkit for constructing crash-consistency models to improve file system performance and correctness.

Choi is a member of the Allen School’s Natural Language Processing group, where she works with professors Luke Zettlemoyer and Yejin Choi. Her research interests broadly span natural language processing, computational social science, and machine learning. She is particularly interested in developing methods for extracting structured representations of human information such as scientific findings, historical facts, and opinions, and retrieving them using natural language questions.

Eunsol ChoiIn “Truth of Varying Shades: Analyzing Language in Fake News and Political Fact-Checking,” which was presented at the Conference on Empirical Methods in Natural Language Processing (EMNLP 2017), Choi and a group of colleagues at the Allen School and Pacific Northwest National Laboratory analyzed the linguistic patterns of articles and political statements to identify cues that indicate whether a news story is trustworthy, unreliable, or satire. As an intern at Google, Choi was lead author on “Coarse-to-Fine Question Answering for Long Documents,” which presented a new framework for question answering that efficiently scales to longer documents while matching or exceeding the performance of current models.

Choi’s research contributions also include TriviaQA, a robust, large-scale reading comprehension data set, and “Zero-Shot Relation Extraction via Reading Comprehension,” which demonstrated how reducing relation extraction to a reading comprehension problem allows generalization to unseen relations that are defined on-the-fly in natural language.

Past Allen School winners of the Facebook Fellowship include Aditya Vashistha (2016), for his work on social media tools for people in developing communities; Lydia Chilton and Nicki Dell (2013), for their work on crowdsourcing algorithms and applications for improving quality of life in low-resource communities, respectively; and Adrian Sampson (2012), for his work in energy-efficient computing.

Read more about the 2018 Facebook Fellowship recipients here and learn more about the fellowship program here.

Congratulations, James and Eunsol!

 

January 18, 2018

Kurtis Heimerl recognized with College of Engineering Diamond Award for Early Career Achievement

Kurtis HeimerlAllen School professor and undergraduate alumnus Kurtis Heimerl (B.S., ’07) has been recognized with a 2018 Diamond Award from the University of Washington’s College of Engineering. Each year, the Diamond Awards recognizes alumni and friends of the college who have made significant contributions to the field of engineering. The college is honoring Heimerl with its Early Career Achievement Award, which is given each year to an outstanding graduate of the college who has made exceptional professional contributions through research, teaching or service within the first 10 years of their career.

Heimerl is a member of the Allen School’s Information & Communication Technology for Development ICTD) Lab, which focuses on improving the lives of underserved populations in low-income communities through technology. He is particularly interested in harnessing the potential for technology to alleviate poverty by bringing mobile internet access to people in some of the most remote regions on earth.

“Growing up in Alaska, I developed a deep understanding and appreciation of rural life and the difficulties of connectivity in these environments. This background, in areas where people are forced to improvise and resolve their local issues, has always informed my research,” Heimerl explained. “I’m happy and grateful that UW was there to foster my technical skills as a student and now continues to support my work to empower people and communities to own their infrastructure.”

That work began in earnest during his time as a Ph.D. student at the University of California, Berkeley working with professors Eric Brewer and Tapan Parikh (Ph.D., ’07). There, Heimerl became known for his efforts to develop community-based cellular networks. These small-scale networks, which he designed to be locally owned and operated, brought the benefits of cellular connectivity to people in resource-constrained areas that previously lacked coverage. Heimerl founded the startup Endaga, Inc. to commercialize his “cell network in a box,” deploying the technology in rural Pakistan, Indonesia, the Philippines, and other areas without existing wireless infrastructure.

Men attaching a community cellular box to a tree“Cellular communication has revolutionized the way people communicate and connect to essential services, and the benefits are particularly important for people in developing countries,” noted Allen School professor Richard Anderson. “But cell towers are expensive, and if the ‘economic density’ is too low, telecommunication companies won’t invest in connecting those communities. So what can be done to connect the billion people who are still outside of cellular coverage? That’s where Kurtis comes in, developing a ‘local cellular’ technology to address this inequality and bring the benefits of connectivity to more people around the globe.”

In 2014, Heimerl’s efforts earned him the notice of MIT Technology Review, which recognized his contributions with a TR35 Humanitarian Award. Endaga raised $1.2 million in seed funding before eventually joining forces with Facebook in 2015, which gave Heimerl the opportunity to continue his work as a visiting scientist focused on the company’s rural access initiatives. The following year, he joined the UW faculty, where he continues his focus on increasing connectivity and improving economic opportunity for people living in underserved areas.

Most recently, Heimerl and his colleagues began investigating the increasing adoption of smartphones in rural areas that currently lack the bandwidth to support many of the features that are built into those devices. By developing a better understanding of subscribers’ behavior and motivation, the team aims to provide useful guidance for the deployment of new or upgraded cellular infrastructure to support the preferences of people living in these communities.

“Kurtis combines a thorough knowledge of computer systems and infrastructure with creativity and a strong commitment to a set of social values. This allows him to identify and work on research problems that can have a deep and lasting impact on society,” observed Parikh, now a faculty member at Cornell Tech. “Kurtis has frequently challenged my ideas and perspective, and often he has been right. He is also willing to listen and adapt, which is a testament to his maturity as a researcher and the personal ideals for which he works.”

Heimerl and his fellow Diamond Awards honorees will be formally recognized at a gala hosted by the college on May 10th. He joins a distinguished list of past Allen School recipients, including recent Early Career Achievement winners Ben Hindman, founder of Mesosphere (2016), big data pioneer Christophe Bisciglia (2015), LiveJournal creator Brad Fitzpatrick (2014), and consumer technology leader Greg Badros (2012); Distinguished Service winners Yaw Anokwa, one of the creators of Open Data Kit (2015), and Washington FIRST Robotics volunteer Kevin Ross (2013); and Anne Condon, professor at University of British Columbia, who was recognized for Distinguished Achievement in Academia (2012).

Read more about the 2018 Diamond Award recipients here.

Congratulations, Kurtis!

 

January 18, 2018

Balancing a research career and chronic illness: Jennifer Mankoff’s personal journey to professional success

Jennifer Mankoff in the Allen Center atriumAllen School professor Jennifer Mankoff is an award-winning researcher in human-computer interaction and accessibility. But her road to a successful academic research career was bumpier than most promising young faculty. In addition to navigating the demands of teaching and research while raising a young family — she and spouse Anind Dey, the new Dean of the University of Washington’s Information School, have two children — she had another obstacle to overcome: her health.

According to the U.S. Centers for Disease Control and Prevention, roughly half of all adults in the United States have one or more chronic illnesses — some of which may be “invisible” to others yet are no less debilitating. A little over a decade ago, Mankoff was diagnosed with Lyme disease, a tick-borne illness that is tricky to diagnose and just as tricky to manage, with symptoms that over time ranged from extreme fatigue, to loss of hearing, memory, and fine motor control. She recently spoke with Nature as part of the journal’s in-depth look at how scientists balance the demands of research with long-term illness. It’s a topic that has received very little attention — a situation Mankoff and the other featured researchers hope to rectify by speaking out about their experiences.

As the article makes clear, chronic illness takes a heavy emotional as well as physical toll. Although Mankoff continued doing those things that define success in academic research circles — writing grants, publishing research, and earning tenure — her battle with Lyme cause her to question who she is and what she is capable of.

“My image of who I could or should be didn’t match up with reality in terms of my productivity,” she explained.

For Mankoff and the others who went on the record for the story, finding their way often means finding a way around the limitations brought on by their condition. Mankoff says she “long ago learned that one aspect of managing a chronic illness is accepting the ‘disability’ label and working within that structure to make things easier.”

For example, she requests a classroom near her office so she does not have to contend with a long trek across campus on days when her Lyme-induced fatigue is particularly acute. She also has become adept at prioritizing tasks and at breaking down large tasks into smaller ones, both of which help her to take full advantage of times when her illness takes a back seat.

Jennifer Mankoff works with students in her 3D printing classMankoff, who arrived at the Allen School last fall after 12 years on the faculty of Carnegie Mellon University, in part credits her colleagues’ support for enabling her to carve out a career that works for her.

“I’ve been lucky to receive a tremendous amount of positive support from the faculty at CMU and again at UW during my interview and since I arrived,” Mankoff told the Allen School News. “Equally important was the support I received at home from my family. That said, negotiating something like this is a personal process, and one for which there are no easy answers.”

Mankoff points out that the lines between work and personal life can get blurred. From her perspective, that is not a bad thing — in fact, she says, it has made her a better researcher. It also opened up new avenues of inquiry that she may not have considered otherwise, including the impact of chronic disease on quality of life, the development of tools for managing chronic illness and physical therapy, and predictors of trust in health care content based on whether it was produced by practitioners or peers.

“Life outside work sometimes – often – impacts work, and for me it has never made sense to keep them separate,” she explained. “My research is often inspired and driven by my personal experiences, and that in turn helped my motivation to get through this.”

Speaking of motivation, Mankoff believes it is important to talk about her journey to give hope and support to others who find themselves in a similar position. While in Pittsburgh, she blogged about Lyme disease and helped to organize local support group efforts. She also has taken on a prominent role in the academic community leading an accessibility group that advocates for access to conferences and online materials.

Although going public can be scary, Mankoff says she does it because, “If my story, or any of the other information in this well researched article, can help someone, then I hope it reaches them.”

Read the full Nature article here and learn more at Chronically Academic, a support network for people with chronic illnesses working in academia.

 

January 17, 2018

Allen School junior Christine Betts champions creativity and diversity as GeekWire’s “Geek of the Week”

Christine BettsChristine Betts, a computer science major who earlier this week received the inaugural Allen Institute for Artificial Intelligence (AI2) Outstanding Software Engineer Scholarship for underrepresented groups, is profiled in GeekWire’s latest “Geek of the Week” feature.

Betts, who hails from Kansas City, Missouri, is an active contributor to the Allen School community, serving as a teaching assistant for our popular introductory programming courses and engaging in undergraduate research in the Molecular Information Systems Lab. In talking about her chosen field, she likes to point out that programming is inherently a creative endeavor — and that people don’t necessarily have to be the “STEM type” to be good at it. She is especially eager to engage more young people from underrepresented groups in computer science.

“Now that I’ve started programming, I can’t imagine doing anything else in a career, but more broadly I’m motivated by the voices I hope to lift up in whatever capacity I can,” Betts told GeekWire. “There are so many perspectives that aren’t being heard because of how poorly the field as a whole reflects the larger population, which is why in the future, no matter what I do, I hope to mentor and lift up young women.”

Betts knows first-hand how uplifting such support can be as one of the TUNE Scholars, a program that supports undergraduate women pursuing computer science and other tech-focused degrees at the University of Washington with housing, mentorship, and networking opportunities.

“I find inspiration in all of the young women I’ve gotten to work with, the awesome, hard-working and motivated women I get to live with as a TUNE Scholar, and in thinking about how much I have to be grateful for.”

Read the full article here, and check out profiles of recent Allen School “Geeks of the Week” Alex Mariakakis, Ira Kemelmacher-Shlizerman, Shyam Gollakota, and 2017 “Geek of the Year” Ed Lazowska.

 

January 12, 2018

Vikram Iyer wins 2018 Microsoft Research Ph.D. Fellowship

Vikram IyerVikram Iyer, a Ph.D. student in Electrical Engineering who works with professor Shyam Gollakota in the Allen School’s Networks & Mobile Systems Lab, has earned a prestigious Microsoft Research Ph.D. Fellowship. He is one of only 10 graduate students from across North America to be selected as a member of the class of 2018 fellows.

The Microsoft Research Ph.D. Fellowship program is designed to promote the careers of promising student researchers in computer science, electrical engineering, mathematics, and related fields. For the class of 2018 fellows, the company specifically sought applicants in two key areas of interest: systems and networking, and artificial intelligence. Iyer has already made significant contributions to the former through his work on wireless power, communication, and localization.

In one recent, high-profile example, printed Wi-Fi, Iyer and his colleagues demonstrated how to create smart objects made entirely out of 3D printed plastic parts. To enable the objects to communicate over Wi-Fi without the need for batteries, the team relied on an ingenious combination of old and new techniques. They harvested power from the physical action of gears, coil springs, and other components — not unlike how a mechanical watch keeps time — and leveraged the lab’s pioneering work on backscatter, a method of wireless communication in which devices reflect ambient radio frequency signals that can be decoded by a Wi-Fi receiver.

Backscatter formed the basis of Iyer’s work on another project, interscatter, that enables implantable and other devices to communicate with smartphones and smartwatches by converting Bluetooth transmissions into Wi-Fi and Zigbee-compatible signals. Iyer and his colleagues built several prototypes to demonstrate the technology’s potential, including the first smart contact lens that can monitor and transmit information on the wearer’s medical condition and an implantable neural recording interface. The team, which included Allen School and EE professor Josh Smith of the Sensor Systems Lab, earned the Best Paper Award at SIGCOMM 2016, the annual flagship conference of the Association for Computing Machinery’s Special Interest Group on Data Communication.

In addition to unlocking new applications in battery-free communication, Iyer helped demonstrate that wireless signals can literally unlock a door through on-body transmissions. In this project, Iyer and his colleagues developed a way to securely transmit passwords via the human body using low-frequency signals generated by fingerprint sensors and touchpads on mobile devices. The technology has the potential to do more than open doors; it would also make it easier to link a medical device such as a glucose monitor or insulin pump with a smartphone by eliminating the need to manually type complicated serial numbers or passwords. Other projects that illustrate the range and impact of Iyer’s contributions include FM backscatter, which introduces connectivity to everyday objects using FM radio signals to enable smart fabrics and smart cities applications, and FingerIO, a system for fine-grained finger tracking on mobile devices using sonar that earned an Honorable Mention at CHI 2016, the ACM’s flagship conference on human-computer interaction.

“These are incredibly talented students, the top students from North America,” said Microsoft Principal Researcher and Research Manager Bill Dolan, director of the fellowship program, in a blog post announcing the class of 2018. “We really do want to promote the careers of these great students. It is good for all of us.”

The Microsoft Ph.D. Fellowship provides tuition support, an annual stipend, and funding to cover attendance at professional conferences and seminars. Fellows also have an opportunity to pursue an internship with Microsoft researchers in their field of study. The company has a history of supporting students engaged in leading-edge research at the Allen School, including past fellowship winners Kira Goldner (2017) in theory of computation; Lilian de Greef (2015), Mayank Goel (2014), and Gabe Cohn (2012) in ubiquitous computing; Irene Zhang in computer systems (2015); Yoav Artzi (2014) in natural language processing, and Franziska Roesner (2012) in security and privacy.

Read the Microsoft Research announcement here and learn more about the 2018 fellows here.

Congratulations, Vikram!

 

January 10, 2018

Christine Betts receives inaugural Allen AI Outstanding Engineer Scholarship

AI2 scholarship recipient Christine Betts and AI2 CEO Oren Etzioni

This afternoon the Allen Institute for Artificial Intelligence (AI2) awarded the inaugural Allen AI Outstanding Engineer Scholarship for women and underrepresented minorities to Allen School undergraduate Christine Betts.

The Allen Institute for AI created this scholarship to encourage underrepresented groups to excel in computer science and engineering, and become leaders and role models in their fields. The scholarship covers full tuition, fees, and textbooks for one academic year. It is accompanied by mentorship and a paid summer internship at AI2.

AI2 believes that diversity is fundamental to the greatest advances in science; a variety of backgrounds, perspectives, and experiences are necessary to combat the echo chamber effect so prevalent in technology companies. Encouraging diversity demonstrably results in teams with greater resilience and adaptability, and produces a wider range of tools and strategies. AI2 also believes it is important not just to attract diversity to CSE programs, but to nurture lifelong careers, and lend assistance to those who might not have equal access to opportunity.

Congratulations to Christine, and thanks to AI2, its CEO Oren Etzioni, and its founder Paul G. Allen!

January 9, 2018

Allen School launches UW Reality Lab to advance augmented and virtual reality research

Student working with VR headset on a telepresence applicationThe Allen School has partnered with leading technology companies to create a new academic research center aimed at advancing the state of the art in augmented and virtual reality. The UW Reality Lab, which launched today with $6 million in funding provided by Facebook, Google, and Huawei, will focus on the pursuit of leading-edge research and educating the next generation of innovators in this burgeoning field. The center will build upon the Allen School’s established leadership in computer vision and graphics, object recognition, game science, computer architecture, privacy and security, and more. It will also pave the way for new academic and industry collaborations in a region known as a hub of AR and VR innovation.

The UW Reality Lab will be co-led by Allen School professors Brian Curless, Ira Kemelmacher-Shlizerman, and Steve Seitz. According to Seitz, who serves as chair of the new center and divides his time between the Allen School and Google, academic researchers are uniquely positioned to advance AR and VR by tackling the fundamental research problems that will underpin this growing field.

“We’re seeing some really compelling and high quality AR and VR experiences being built today,” Seitz said in a UW News release. “But there are still many core research advances needed to move the industry forward — tools for easily creating content, infrastructure solutions for streaming 3D video, and privacy and security safeguards.”

Seitz and his colleagues were inspired to create the center in part by their experience in launching the Allen School’s first virtual and augmented reality capstone course. Students in the course worked together in teams to produce new AR applications using the latest devices. Projects ranged from original games, to how-to programs for music and cooking, to art and industrial design tools.

Brian Curless, Ira Kemelmacher-Shlizerman, and Steve Seitz

The UW Reality Lab leadership team, left to right: Brian Curless, Ira Kemelmacher-Shlizerman, and Steve Seitz

Kemelmacher-Shlizerman, the new center’s director of research and education, said the faculty quickly recognized an opportunity to expand beyond the capstone course to accelerate new developments in the field.

“This opened our eyes to the potential of investing deeper in development of algorithms and applications for AR and VR,” observed Kemelmacher-Shlizerman, who splits her time between the Allen School and Facebook. “We realized there were so many cool things we could do if only we had more resources, more time and more devices.”

The team will have all three thanks to a partnership with Facebook, Google, and Huawei. The funding will be used to develop new courses and provide the infrastructure and access to emerging technologies that will enable UW researchers and students to develop and test new ideas and applications. The companies are also contributing time and expertise to the UW Reality Lab’s advisory board, a group of leaders drawn from across the AR/VR community who will assist the center in remaining at the forefront of new developments in the field.

As director of the new center, Curless is enthusiastic about the opportunity to help shape the future of AR and VR. “It’s big, it’s happening now and there’s a lot of research to be done,” he said. “We’re thrilled to take a leading role in making it all happen.”

Visit the UW Reality Lab website and read the UW News release to learn more, and see coverage in The Seattle TimesGeekWire, Xconomy, and the Puget Sound Business Journal.

January 8, 2018

UW researchers “MERGE” machine learning and medicine to enable targeted treatment of cancer

Su-In Lee and Safiye Celik discuss the MERGE formula written on a whiteboard

Allen School and Genome Sciences professor Su-In Lee, left, and Allen School Ph.D. student Safiye Celik discuss the key formula for their MERGE algorithm to match patients with cancer drugs based on their molecular profiles. Credit: Dennis Wise

In the latest example of computing’s potential to transform health care, a team of researchers at the Allen School, UW Department of Genome Sciences, and UW Medicine is applying a combination of machine learning and big data to improve outcomes for cancer patients. The team’s approach, detailed in a new paper published in the journal Nature Communications, helps physicians deliver targeted treatment to patients based on their individual molecular profiles.

Allen School and Genome Sciences professor Su-In Lee, first and corresponding author, and Allen School Ph.D. candidate Safiye Celik, co-first author, have developed a new machine learning algorithm called MERGE to identify reliable biomarkers of therapeutic response to 160 anti-cancer drugs in cases of acute myeloid leukemia (AML) — an aggressive form of cancer of the blood and bone marrow cells that is predominantly found in older adults — in collaboration with UW Hematology and Institute for Stem Cell & Regenerative Medicine professors Pamela S. Becker and C. Anthony Blau. MERGE “recycles” publicly available genomic data from many AML patients and biological knowledge databases to find the best drugs for AML patients and opens promising avenues to improve patient care for many other diseases in the era of precision medicine.

Safiye Celik, Su-In Lee, C. Anthony Blau, and Pamela Becker

Clockwise from top left: Safiye Celik, Su-In Lee, C. Anthony Blau, and Pamela S. Becker

MERGE — short for “Mutation, Expression hubs, known Regulators, Genomic CNV, and mEthylation” — is a novel computational approach for prioritizing genes based on their relevance as drivers of disease progression and observed drug response. The system models a weighted combination of these features to learn each gene’s MERGE score, which indicates its potential reliability as a biomarker for drug sensitivity. Celik trained MERGE using publicly available AML data and gene annotation databases, along with gene expression data from 30 patients diagnosed with AML and their in vitro sensitivity data for 160 approved or experimental chemotherapy drugs. She then tested its performance against that of four existing methods for predicting patient drug response: correlation-based methods, ElasticNet, multi-task learning, and Bayesian multi-task multiple kernel learning (MKL).

Not only did MERGE outperform the current state of the art in its ability to accurately identify reliable biomarkers for drug response, but it discovered new gene-drug associations that those other methods failed to identify; these novel associations were validated in a biological laboratory. These findings are clinically important because they involve the drugs included in nearly all upfront AML treatment regimens today — mitoxantrone and etoposide.

“We ranked the top eight genes that were likely to be biologically significant for leukemia in several major drug classes,” explained Celik. “For five of those genes, MERGE was the only system capable of identifying their role in predicting treatment response and patient sensitivity to certain drugs — a significant improvement over existing approaches.”

One of those genes is the SMARCA4 gene expression, which the researchers determined and experimentally validated to be a sensitivity marker for a class of chemotherapy drugs known as topoisomerase II inhibitors. The MERGE analysis revealed that cell lines genetically engineered to show high SMARCA4 expression exhibit dramatically higher sensitivity to such drugs — making them excellent candidates for treating AML patients with high SMARCA4 expression.

“Drug development is an expensive and challenging process, and cancers that appear pathologically similar can respond to the same drug regimen in different ways,” noted Lee. “There are more than 1,200 potential cancer medicines in development in the United States alone. We need better methods for matching patients to the most effective treatment, and that has been our goal in developing MERGE.”

Lee Lab contributors, from left: Benjamin Logsdon, Scott Lundberg, and Javad Hosseini

In addition to Lee, Celik, Blau, and Becker, contributors to the project include former Lee Lab postdoc Benjamin A. Logsdon of Sage Bionetworks; Allen School Ph.D. student Scott Lundberg; former Allen School Ph.D. student Javad Hosseini; Timothy Martins of the Quellos High Throughput Screening Core at UW’s Institute for Stem Cell & Regenerative Medicine; Vivian Oehler and Elihu Estey of Fred Hutchinson Cancer Research Center and UW Medicine; and Chris Miller, Sylvia Chien, Jin Dai, and Akanksha Saxena of UW Medicine. This work was supported by the National Institutes of Health, National Science Foundation, American Cancer Society, Life Sciences Discovery Fund, and philanthropic funding from Norman Metcalfe.

Read the full paper here, and visit the MERGE website here. Read a related UW Medicine story here and The Huddle article here.

 

January 5, 2018

Wheelchair-using Allen School alums Doug Ferry, Chris Schlechty featured by Google, Microsoft

In a remarkable coincidence, Google and Microsoft each published articles describing the accomplishments of wheelchair-using computer scientists in their engineering organizations – each of whom is an Allen School alum.

Doug Ferry, ’91, is quadriplegic as a result of a bodysurfing accident when he was 20 years old. He steers a motorized chair with his head and codes with a mouth stick. He spent 18 years at Microsoft before moving to Google 18 months ago. Read more about Doug in the Google post here.

Chris Schlechty, ’08, has been at Microsoft since graduation. A full-stack developer on the Sharepoint team, Chris has muscular dystrophy and uses an onscreen keyboard and other assistive technology. Read more about Chris in the Microsoft post here.

Doug Ferry and Chris Schlechty – wonderful examples of Allen School alums overcoming adversity and using their education to craft technology that helps others to do the same.

Thanks to Google and Microsoft for highlighting these amazing alums.

January 3, 2018

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