1 Year, 10 Innovations From UW’s Paul G. Allen School That’s Making the World a Better Place

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 and 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’s just 10 of the many innovations that have come out of the school over the past year.

1. Mozak: Playing to win at fundamental neuroscience research

mozak-edited Photo credit: University of Washington

One of the first projects to be unveiled to the general public following creation of the Allen School, Mozak is a scientific discovery game that is designed to advance our understanding of the brain’s structure and function. Players produce complete, 3D models of neurons from different regions of the brain from images captured by high-powered microscopes, while receiving real-time feedback from researchers. Working together, Mozak’s community of citizen scientists and neuroscientists are able to reconstruct neurons more than three times faster than previous methods — and create models that are as much as 90 percent complete, compared to 20 percent for the most effective computer-generated reconstructions. One day, this winning combination will enable us to effectively combat neurodegenerative diseases such as Alzheimer’s and Parkinson’s.

A collaboration between the Allen School’s Center for Game Science and the Allen Institute

2. Say hello to the world’s first battery-free phone

cellphones Photo credit: Mark Stone/University of Washington

UW researchers invented a mobile phone that can function continuously on just a few microwatts of power harvested from ambient radio signals or light, eliminating the need for a battery. The clever design is entirely analog — it bypasses the traditional power-hungry process of converting analog voice signals into digital data when a person is talking and of converting digital data into analog sound signals when listening. The system also uses highly efficient backscatter communication: when a person is talking, the same ambient radio signals used to power the phone are modulated by the user’s voice; when listening, the base station’s signal, modulated by the remote speaker’s voice, is directly coupled to the user’s earphones. The team built a functional prototype out of commercially available components and used it to place Skype calls with the help of its custom-built base station. The technology behind this base station could be built into the cellular network infrastructure or WiFi routers — suggesting that truly battery-free communication could be near at hand.

A collaboration with the UW Department of Electrical Engineering

3. DNA circuit boards: A big leap forward for molecular computing

dna-circuit-boards Photo credit: Microsoft Research/Equinox Graphics

A team of researchers at UW and Microsoft Research Cambridge came up with an ingenious approach to building tiny computers out of DNA molecules. They applied the principle of spatial organization, which is at the heart of many human-engineered systems, to create a new “DNA domino” architecture that transmits information in a cascade and reduces computation time from hours to minutes compared to existing approaches to biocompatible computing. The researchers constructed their circuits by laying out short strands of DNA, called staples or hairpins, on long strands of DNA folded into a scaffold known as DNA origami. Using this approach, the team built elementary Boolean logic gates and transmission lines, as well as a two-input, dual-rail XNOR gate that demonstrates the potential for the domino architecture to serve as a building block for a molecular computer — which could spark a new wave of health care innovation, from biosensing capabilities to tiny, DNA therapy-delivery robots.

A collaboration with the UW Department of Electrical Engineering and Microsoft Research

4. Cybersecurity at the nexus of the biological and digital worlds

DNA-Exploit-1 Photo credit: Dennis Wise/University of Washington

In an illustration of how the barrier between the biological and digital worlds continues to fall away, a team of researchers in the Allen School became the first to demonstrate that it is possible to infect software systems with malware delivered via DNA. When processed through commonly available sequencing software, strands of synthetic DNA containing malicious code enabled the team to take over the computer on which the samples were being analyzed. While there are a number of physical and technical challenges that would have to be overcome in order to implement a similar hack in the wild, the project revealed how systems currently in use for processing biological data could be vulnerable to attack — and provided a wake-up call for a growing industry that has yet to contend with significant cybersecurity threats.

5. A palm-sized solution to screening for potentially deadly diseases

BiliScreen Photo credit: Dennis Wise/University of Washington

Eyes may be the window to the soul; thanks to UW researchers, they may soon be a window to one’s health. Allen School researchers partnered with clinicians at UW Medicine to develop an app that detects adult jaundice, a yellowing of the skin and eyes produced when excess bilirubin is present in the bloodstream. Jaundice can be an early symptom of a variety of medical conditions, including hepatitis, Gilbert’s syndrome, and potentially pancreatic cancer. By combining the built-in capabilities of a smartphone camera with computer vision and machine learning techniques, BiliScreen isolates and evaluates the sclera, or white part of the eye, and correlates the color information with bilirubin levels to determine whether an individual has jaundice before it is visible to the naked eye. An early iteration of the app, used in conjunction with a 3D-printed box to control for variations in lighting conditions, correctly identified jaundice nearly 90 percent of the time. The researchers aim to refine the app to work without any accessories — enabling anyone, anywhere, to screen for potentially deadly diseases.

A collaboration with the UW Department of Electrical Engineering and UW Medicine

6. Breaking the long-range communication barrier for low-power computing

Long-range-Backscatter Photo credit: Dennis Wise/University of Washington

In another first, UW researchers broke a barrier to long-range communication from devices that run on almost zero power. Their innovative system, called long-range backscatter, uses a combination of sensors and reflected radio signals to transmit data at extremely low power — and at very low cost — over distances of up to 2.8 kilometers. Using sensors that cost between 10 and 20 cents each and consume 1000 times less power than existing technologies capable of transmitting over a similar distance, the team demonstrated the reliability of long-range backscatter throughout a 4,800 square-foot house, a 41-room office area, and a one-acre vegetable farm. The project represents a significant breakthrough toward our ability to embed connectivity into everyday objects for a range of potential applications, from smart agriculture and smart cities, to medical devices capable of monitoring and transmitting information on a patient’s condition.

A collaboration with the UW Department of Electrical Engineering

7. A head start in responding to traumatic brain injury

PupilScreen Photo credit: Dennis Wise/University of Washington

Building on UW’s leadership in mobile health innovation, members of the team that brought us BiliScreen also partnered with a group of UW Medicine physicians to develop PupilScreen, the first smartphone app for real-time detection of traumatic brain injury. Currently, the best screening protocols we have for potential cases of brain injury — for example, among athletes injured on the field of play — are subjective. The goal of PupilScreen is to provide an objective assessment of an individual’s condition, using a combination of a smartphone’s built-in video camera and machine learning to quantify changes in the pupillary light response that are imperceptible to the human eye. The research team has been working with doctors to gather more data on which pupillary response characteristics are most helpful in assessing ambiguous cases of concussion, with the goal of making PupilScreen widely available within the next two years.

A collaboration with the UW Department of Electrical Engineering and UW Medicine

8. Now, that’s smart: 3-D printed objects that communicate over WiFi

3D-Printed-Objects Photo credit: Mark Stone/University of Washington

In yet another example of UW’s leadership in battery-free computing, researchers demonstrated how to create smart objects capable of communicating over WiFi out of 3-D printed parts. To eliminate the need for batteries or built-in electronics, the researchers melded the old with the new, combining the physical action of gears, coil springs, and other components — reminiscent of how a mechanical watch keeps time — with their own pioneering work on backscatter, a method of wireless communication in which devices transmit data by reflecting ambient radio signals. The team printed the parts using commercially available filaments that combine plastic with a conductive material. Mechanical action produces signal patterns that can be decoded by a WiFi receiver — actions that also generate energy that can be harvested to power the objects. To prove the concept, the team produced working prototypes of a flow meter to monitor the level of laundry detergent remaining in a bottle, and wireless buttons, knobs and sliders for controlling lighting and other systems throughout the home.

A collaboration with the UW Department of Electrical Engineering

9. MERGE-ing machine learning with medicine for personalized cancer treatment

MERGE Photo credit: Dennis Wise/University of Washington

Allen School researchers developed a new machine learning algorithm to deliver personalized cancer treatment based on a patient’s individual molecular profile. The algorithm — MERGE, short for “Mutation, Expression hubs, known Regulators, Genomic CNV, and mEthylation” — is a novel approach for identifying genes that drive disease progression and therapeutic response. When the researchers evaluated MERGE using a combination of gene expression data from patients with acute myeloid leukemia and sensitivity data for 160 chemotherapy drugs, they found that not only did their algorithm outperform existing methods for predicting drug response, but it also uncovered previously unknown, yet clinically important, gene-drug associations. This breakthrough work could transform how we approach cancer by enabling physicians to match patients with the most effective treatments.

A collaboration with the UW Department of Genome Sciences and UW Medicine

10. Revolutionizing how we store and process data with DNA

Memories-in-DNA-1 Photo credit: Dennis Wise/University of Washington

A group of UW and Microsoft researchers are pioneering new approaches to digital data storage using synthetic DNA — a medium that promises to be a thousand times denser and significantly more durable than traditional approaches. Having set a world record for the amount of digital data successfully encoded in and retrieved from synthetic DNA, the team recently launched the #MemoriesInDNA Project, asking people around the world to submit photos that they want to remember forever. The researchers plan to store 10,000 of these crowdsourced images in DNA to explore new methods for image classification and search directly within DNA molecules. The project is an exciting next step in their efforts to leverage nature’s perfect storage medium to revolutionize our approach to preserving the world’s data, including vital scientific, historical, and cultural artifacts.

A collaboration with UW Department of Electrical Engineering, Microsoft Research and Twist Bioscience