Month: August 2021

CSE Teaching Professor Christine Alvardo along with colleagues at three other Southern California universities received a $1.3 million grant from the National Science Foundation (NSF) to investigate how gender, ethnicity, and other factors impact those who want to study computer science. The researchers will study application, admission, and retention data to better understand how demographics and pre-college preparation influence student success, and specifically what factors create or prevent access to a computer science education.

By Josh Baxt 

Nobody was prepared for the SARS-CoV-2 virus. Suddenly, businesses closed, schools were shut down and people had to find new ways to fulfill their obligations.

The UC San Diego Department of Computer Science and Engineering was on top of it from the start, adopting creative ways to keep classes, conferences and other meetings afloat. But after the initial rush to problem-solve, CSE faculty began assessing how the response could have gone better and bringing in additional tools, both new and old, to address future outbreaks.

A Blank and Endless Void

Imagine giving a presentation and the audience only responds with blank stares – no reaction whatsoever. That’s been a common occurrence for teachers worldwide, as they adapt their classes to Zoom and other online platforms. They put in the work, but they can’t always convince students to turn on their cameras.

“When I’m presenting the lecture content, it feels like I’m talking into a void,” said one professor.

To better understand online classroom dynamics, CSE researchers studied UC San Diego faculty and student attitudes towards online classes. The paper was presented at the Association for Computing Machinery’s Conference on Human Factors in Computing Systems.

“We wanted to understand instructor and student perspectives and see how we can marry them,” said Associate Professor Nadir Weibel, PhD, senior author on the paper. “How can we improve students’ experience and give better tools to instructors?”

The project was initiated by PhD student and first author Matin Yarmand, along with co-authors Scott Klemmer, PhD, a CSE professor, and Carnegie Mellon University PhD student Jaemarie Solyst. The team conducted faculty interviews and distributed student surveys to collect their experiences.

They found faculty were often discouraged by the lack of feedback. Without visual cues, they weren’t sure if they were getting their points across. On the other side, students resisted turning on their cameras and were often muted. Many didn’t want their peers to see them; others were eating or performing unrelated tasks; some were unaware the video feedback helped instructors; and a hardcore few saw no need to turn their cameras on at all.

Students felt awkward asking questions on video but liked the chat functions, which made them more likely to participate. Also, online classes lack opportunities for short conversations and questions, the “hallway time” that is so common before and after live lectures.

Persevering and Pioneering in a Pandemic

By Kimberley Clementi

Shelby Thomas (Ph.D. ’20) is not averse to risk. This is apparent in his chosen sport – toes to the nose surfing. It factored into the decision to take a leave of absence from his UC San Diego Computer Science and Engineering Ph.D. program only a few months shy of completing his dissertation. It also prompted his next move — co-founding a FinTech Blockchain startup, an industry so cutting-edge it lacks adequate language to define it.

Still, timing is everything.  Thomas timed his make-it or break-it move for the winter quarter of 2020, just one month ahead of an unforeseen global pandemic. 

Calculating Risk before COVID-19

Thomas’ gambit was a carefully considered one. After all, the stakes were high. Beginning a startup not only placed his Ph.D. at risk but also the engineering career of his wife, Reetika Agarwal (M.S. ’16). So in the fall of 2019, Thomas turned to his CSE advisors, Associate Professor George Porter and Professor Geoffrey Voelker, for advice.  

“George and Geoff understood the position I was in and grounded me with the reality of the situation. They would support me in doing both the Ph.D. and startup at the same time but warned me that the statistics were not in my favor,” says Thomas. They were willing to take those odds on me.”

Confident they had support from their CSE community, Thomas and his wife packed their bags, broke their San Diego lease and moved to the San Francisco Bay Area. Together, with a combined income of $0, they began searching for an apartment. That was early March.

Then, two weeks later, the first cases of COVID-19 were reported in the United States. Markets instantly dipped. The World Health Organization declared a pandemic. Life and work began to shut down. By the second week of March, massive selloffs in the stock market resulted in plunging Dow Jones Industry averages. 

For Thomas’ fledgling startup, the global crisis could not have come at a worse moment. Thomas and his long-term friend and business co-founder, and CEO Thomas Scaria, had just begun to raise funding for their company, Prysm.  

Surviving a Crisis within a Crisis

At the inception of a startup company, the early months are critical. When COVID-19 hit, venture capitalists quickly focused on helping existing companies which dramatically hurt the funding market for new companies. Thomas leaned on his wife and CSE community for their unwavering support.

“A key source of motivation that helped me keep my head up was my advisors. They remained optimistic and encouraged me to continue to press forward,” says Thomas. “The structure they gave helped to keep my work scheduled and consistent.”

Thomas explains that professors Porter and Voelker set weekly meetings to help him complete his dissertation as well as two additional research papers. With their continuous encouragement and motivation, Thomas was able to defend his Ph.D. and meet every standard for graduation before the close of 2020.   

Thomas’ advisors, while pivotal to his success, were not his only pillar of support from within the CSE community. In the early days of the pandemic, when concerns for safety and resource scarcity were at their peak, Thomas relied on his CSE friends and classmates for access to essential supplies.

“My labmates were an incredible support during this period,” says Thomas. “If one person got masks or PPE they would ask in the group if anyone needed it, even though they knew it would put their own supply in peril. There was strength in numbers.”

Playing the Numbers
Today, from the vantage of summer 2021 and the 17th floor window of their downtown San Francisco office, Thomas acknowledges that Prysm survived the pandemic “by the skin of our teeth.” The company was able to secure early investments through relentless shipping. They were smart with their money. Now, Thomas says, investors are clearly seeing the potential that inspired him to take risk in the first place – an opportunity to revolutionize the financial services industry.

Long before COVID-19 brought information and resource inequities into sharp focus, Thomas and his co-founder Scaria were examining disparity within the finance industry. Thomas cites the number 0.1%. He explains that traditional finance systems such as brokerages, exchanges and banks limit wealth acquisition to the top 0.1% by acting as gatekeepers to sophisticated financial tools. 

Thomas and Scaria are breaking ground – and the prevailing Wall Street model – working in an area called Decentralized Finance, or DeFi. Their company, Prysm, offers a platform based on blockchain technology which eliminates third-party middlemen previously indispensable to financial transactions. Users can discover credible investors, create a community, and invest together. Put simply, the third-party is replaced by code. The code authenticates the transactions. 

“We can have zero-trust applications,” says Thomas, citing some of the lingo that is burgeoning within this financial frontier. “Two parties don’t have to trust each other. But they can trust that the code is working correctly. And that allows us to facilitate the transaction.”

Thomas contends that computer coding can bring financial equity by enabling users around the world to invest with little effort and little capital. Rather than a one-size-fits-all approach to finance, code provides access to financial tools while making no assumptions about the individual using them. 

“The beauty of DeFi is that financial tools can be recreated in code and made specific for every individual and group regardless of background, goals and ideology,” says Thomas.

Thomas is confident DeFi will also transform ordinary, day-to-day transactions, like shopping online, paying for food deliveries and completing real estate deals. He foresees applications that will benefit everyone, everywhere. Once again, Thomas credits CSE for expanding his altruistic outlook.

“CSE shaped me by helping me obtain a nuanced understanding of several issues facing the world today – from economic and public policy to energy and social justice,” says Thomas. “Contrary to popular belief, a nuanced understanding of these issues makes me believe that change is possible rather than succumbing to cynicism.”

“Change is possible.”  Thomas firmly holds onto this conviction a year into the pandemic. He pairs this message with one on perseverance, written on his office whiteboard: “Be patient and tough; someday this pain will be useful to you.”

He also keeps an eye on the surf report in Santa Cruz. Thirty minutes to the next swell.

Computing a Response to COVID-19

By Kimberley Clementi

Not many people were thinking about antibodies in 2019. Back then, if the average person even contemplated the human body’s response to infectious disease, it was likely only to consider preventative and palliative care – immune boosters like zinc, elderberry, Vitamin C and plenty of rest.

Natalie Castellana (Ph.D. ’12) was the exception. When COVID-19 brought antibodies to the forefront of the pandemic discussion, Castellana was well ahead of the curve. She had been studying antibodies for over a decade and, in 2009, founded Abterra Biosciences (formerly Digital Proteomics) to translate innovations in bioinformatics into applications for the pharmaceutical and biotech industries.

Leading the Science

Throughout 2020, while world leaders looked to science to inform their response to COVID-19, Castellana viewed the pandemic from a parallel perspective. The UC San Diego Computer Science and Engineering graduate and CEO of Abterra Bio believed that computer science, in conjunction with other scientific fields, had a critical role to play in ameliorating the global health crisis.

Prior to the pandemic, Castellana and her team at Abterra Bio – including two CSE classmates, Stefano Bonissone and Anand Patel – were already looking to computer science to deconvolute the adaptive immune response to infectious diseases. They had developed a platform, Alicanto®, that uses mass spectrometry and next generation sequencing to rapidly identify which proteins could be most effective in neutralizing viruses. When COVID-19 emerged, Castellana recognized that Abterra Bio’s innovations were relevant and timely.

“COVID happened. And it happened to be right in our path – our line of sight,” Castellana says. “We were already looking at finding antibodies that have therapeutic potential by looking directly at people who had overcome a disease. So it was not that hard to recognize that we should do this for COVID, too.” 

Throughout the pandemic, Abterra Bio worked with the San Diego Blood Bank to obtain blood samples from local San Diego patients who had recovered from COVID-19. The company then analyzed these samples for virus-neutralizing antibodies. While the research is ongoing, Castellana is intrigued by the challenge COVID-19 variants present to therapeutic treatments and believes her team can help.

“With our approach, we can look at an antibody protein directly. We can pick out an individual antibody and determine whether it is neutralizing all the different variants or just a subset,” says Castellana.

Not only can Castellana’s team identify promising antibodies, but they can find them faster.  Abterra Bio’s platform employs algorithmic and machine learning approaches to accelerate the pace of biological research, which can otherwise be like looking for the proverbial “needle in a haystack.” Computer science, and the computational speed it provides, could potentially shorten the timeline to develop new treatments and drugs.

“While biology is not any different now than 100 years ago, we now have better tools to understand the science,” Castellana explains. “That’s what drives innovation, the technology.”

Harnessing Protein Power

Technology is only one aspect of Castellana and Abterra Bio’s groundbreaking work. Their interdisciplinary team of data scientists and biologists are pushing the boundaries of bioinformatics by starting with a different thesis: one based in proteomics rather than genomics.

Treating infectious diseases like measles and diphtheria, and now COVID-19, generally follows the long-proven method of using antibodies from survivors of the disease. Most studies then focus on gene sequencing and look at the B cells that produce antibodies. The challenge is that B cells can be exceedingly rare and elusive, or even irrelevant, to overcoming the disease.

In contrast, Abterra Bio’s platform, Alicanto®, mines the antibody proteins directly. This allows researchers to examine the antibody molecule and the proteins within an organism. It’s a game-changer in the way science tackles potentially deadly diseases – one that essentially harnesses the power of the human immune response system. 

“Every human generates billions of different antibodies to a variety of different challenges, from vaccines to pathogens to cancer cells,” says Castellana. “Our technology is built to identify the antibodies that have been fully optimized by the immune system and therefore are nature’s solution to overcoming a disease.”

Sequencing a Company’s Path

As Castellana looks to the future, she is optimistic Abterra Bio’s technology will not only impact treatment of infectious diseases but oncology as well. Over the next two years, the company will continue validating and extending their platforms and will soon have antibodies in preclinical development for several therapeutic areas. 

While the road ahead looks promising, Castellana is quick to recognize that Abterra Bio is building on research and algorithms conceived a decade earlier at CSE. She credits her co-founders and advisors, CSE Professors Pavel Pevzner, Vineet Bafna and Nuno Bandeira for their ground-breaking work in bioinformatics and computational tools. 

“From their pioneering work, a variety of tools emerged – from sequencing antibodies directly from the protein, to using next generation sequencing to look at patient response to disease, to trying to find virus neutralizing antibodies,” she said. “A whole body of work came out of their labs. And that’s where the company started – with the technology developed from UCSD.”

In addition to licensing intellectual property to Abterra Bio, UC San Diego has provided support to commercialize the fledgling company’s technology. The company worked with UC San Diego Office of Innovation and Commercialization to license software and patents developed by the campus team. 

Castellana acknowledges one more valuable legacy from CSE: its interdisciplinary learning environment. She describes CSE as “entrepreneurial” and “collaborative across disciplines” – a combination Castellana has replicated at Abterra Bio, noting almost all the company’s employees come from the amazing talent pool at UC San Diego across a variety of disciplines. 

“One thing I thoroughly enjoyed about CSE was the opportunity for interaction across subfields within computer science. It was exciting to be just down the hall from world class research in cryptography, computer graphics, and machine learning,” says Castellana. “Exposure to people thinking about things in different ways is so important to innovation.”

For Castellana, applying her computer science background to biological problems was more than a cross disciplinary approach to problem solving. It was personal, too. As Castellana is fond of saying, she wanted to be a “computer scientist with a soul.” 

“I knew I wanted to switch into bioinformatics, to apply my knowledge about computer science to biological problems,” says Castellana. “How do we live healthier and fuller lives? That was the answer I wanted to solve.”

Viera Kair joined CSE in 2003 and was a fixture of the  undergraduate advising team for nearly 20 years before her retirement in June.  During her tenure in the department, Kair advised thousands of students and mentored many colleagues.  Kair has been an essential and valued resource for CSE students, faculty, and other campus stakeholders.

Kair was among the first people on campus to be certified by UC San Diego’s yoga teacher training and she taught yoga on campus at the library consistently from the date of her certification up until the pandemic hit. In retirement she is looking forward to traveling with her husband, Steve, and spending more time with her family in Serbia.

Bridget Benson (Ph.D. ’10) is now an Associate Professor at Cal Poly SLO.

Tom Ristenpart (Ph.D. ’10), an associate professor at Cornell Tech, was honored with two distinguished paper awards at the Usenix Security Symposium.

Alexandra Boldyreva, a professor at Georgia Tech, has won a PKC Test of Time Award for work she completed as a CSE Ph.D. student in 2003.

Two alumni were honored with the Distinguished Alumni Award at this spring’s CSE Research Open House: Darrell Long (Ph.D. ’88), currently a Distinguished Professor of Engineering at the University of California Santa Cruz, and Jeff Carter (B.A. ’86), the vice president overseeing relational database services at Amazon. They were honored for their contributions to academia and industry, and continue to be active in the CSE alumni network.

CSE’s Stefan Savage has been recognized at UC San Diego and internationally for his acclaimed work in cybersecurity. For the past 240 years, the American Academy of Arts and Sciences (AAS) has honored individuals whose work has advanced the public good, and this year Savage was elected into the class of 2021 fellows. Savage was also honored with the prestigious Distinguished Researcher award from the UC San Diego Academic Senate. These awards are a sign of respect from peers for groundbreaking research conducted by members of UC San Diego faculty. Savage’s research is particularly noted for his usage of both computer science and the social sciences to pinpoint security vulnerabilities in cars, track fraudulent financial transactions, and design methods of measuring distributed denial of service attacks.