Columbia Data Science Institute alumni use machine learning to discover coronavirus treatments

Two graduates of the Data Science Institute (DSI) at Columbia University are using computational design to quickly discover treatments for the coronavirus.

Andrew Satz and Brett Averso are chief executive officer and chief technology officer, respectively, of EVQLV, a startup creating algorithms capable of computationally generating, screening, and optimizing hundreds of millions of therapeutic antibodies. They apply their technology to discover treatments most likely to help those infected by the virus responsible for COVID-19. The machine learning algorithms rapidly screen for therapeutic antibodies with a high probability of success.

Conducting antibody discovery in a laboratory typically takes years; it takes just a week for the algorithms to identify antibodies that can fight against the virus. Expediting the development of a treatment that could help infected people is critical says Satz, who is a 2018 DSI alumnus and 2015 graduate of Columbia's School of General Studies. {module INSIDE STORY}

"We are reducing the time it takes to identify promising antibody candidates," he says. "Studies show it takes an average of five years and a half-billion dollars to discover and optimize antibodies in a lab. Our algorithms can significantly reduce that time and cost."

Speeding up the first stage of the process--antibody discovery--goes a long way toward expediting the discovery of a treatment for COVID-19. After EVQLV performs computational antibody discovery and optimization, it sends the promising antibody gene sequences to its laboratory partners. Laboratory technicians then engineer and test the antibodies, a process that takes a few months, as opposed to several years. Antibodies found to be successful will move onto animal studies and, finally, human studies.

Given the international urgency to combat the coronavirus, Satz says it may be possible to have a treatment ready for patients before the end of 2020.

"What our algorithms do is reduce the likelihood of drug-discovery failure in the lab," he adds. "We fail on the computer as much as possible to reduce the possibility of downstream failure in the laboratory. And that shaves a significant amount of time from laborious and time-consuming work."

Averso, who is also a 2018 DSI alumnus, says some of the antibodies EVQLV is designing are intended to prevent the coronavirus from attaching to the human body. "The right-shaped antibodies bind to proteins that sit on the surface of human cells and the coronavirus, similar to a lock and key. Such binding can prevent the proliferation of the virus in the human body, potentially limiting the effects of the disease."

He also noted that the scientific community and the biotech industry are galvanized to forge collaborations that bring about therapeutics, diagnostics, and vaccines as quickly as possible.

EVQLV collaborates with Immunoprecise Antibodies (IPA), a company focused on the discovery of therapeutic antibodies. The collaboration will accelerate the effort to develop therapeutic candidates against COVID-19. EVQLV will identify and screen hundreds of millions of potential antibody treatments in only a few days--far beyond the capacity of any laboratory. IPA will produce and test the most promising antibody candidates.

Satz and Averso, who met while students at DSI, are deeply committed to using "data for good." The pair have worked together for several years at the intersection of data science and health care and formed EVQLV in December 2019 to use AI to accelerate the speed at which healing is discovered, developed, and delivered. The company has already grown to 12 team members with skills ranging from machine learning and molecular biology to software engineering and antibody design, cloud supercomputing, and clinical development.

Both DSI graduates typically put in 100-hour workweeks because they are passionate about and committed to using data science to "help heal those in need."

"We are building a company that sits at the frontiers of AI and biotech," Satz says. "We are hard at work accelerating the speed at which healing is discovered and delivered and could not ask for a more fulfilling mission."

Bennett, Brassard and Shor win the Frontiers of Knowledge Award in Basic Sciences

The BBVA Foundation Frontiers of Knowledge Award in Basic Sciences has gone in this twelfth edition to Charles Bennett, Gilles Brassard and Peter Shor for their "outstanding contributions to the field of quantum computation and communication," said the committee in its citation.

Bennett and Brassard, a chemical physicist and the computer scientist respectively, invented quantum cryptography in the 1980s to ensure the physical inviolability of data communications. The importance of their work became apparent ten years later when mathematician Peter Shor discovered that a hypothetical quantum computer would render effectively useless the conventional cryptography systems underpinning the privacy and security of today's Internet communications. In other words, when a true quantum supercomputer is eventually built, quantum cryptography will be the only means to keep communications secure.

The award committee, chaired by Nobel Physics laureate Theodor Hänsch with quantum physicist Ignacio Cirac acting as its secretary, remarked on the leap forward in quantum technologies witnessed in these last few years, an advance which draws heavily on the new laureates' pioneering contributions. Their work, says the committee, "spans multiple disciplines and brings together concepts from mathematics, physics and computer science. Their ideas are playing a key role in the development of quantum technologies for communication and computation."

The invention of quantum cryptography

Quantum cryptography emerged in the realm of basic science, but in a few decades has produced a whole new technology that is now commercially available and tipped as a rising market. When Bennett, at IBM Research for over forty years, and Brassard, Canada Research Chair in Quantum Information Science at the University of Montreal, began working together in 1979, there was not the least hint of this future scenario. Quantum physics and computer science were separate, even distant fields, and any work on the linkages between them was confined to the fringes of established research. Yet by 1984, Bennett and Brassard had come up with an intriguing result: a cryptographic system which, as the committee describes it, "allows encoding and transmitting messages using the laws of quantum physics in a way that makes them unreadable to eavesdroppers, even if they had quantum computational resources."

To create quantum cryptography, Bennett and Brassard made use of one of those strange phenomena of the quantum world: superposition, which, in simplified terms, makes it possible for a single particle to be in two or more places at once. Quantum theory holds that this dual state is lost as soon as somebody observes the particle, which will then appear in one position or the other. And if the same particle was in the midst of being transmitted, any attempted hack would collapse the superposition, alerting the interlocutors that same instant.

Bennett and Brassard's protocol, known as BB84 after its inventors and year of publication, is today generally acknowledged as the first practical application of the science of quantum information.

"Quantum information is a kind of information that is disturbed by observation and cannot be copied," explained Bennett on the phone yesterday after hearing of the award. "Gilles Brassard and I realized that it could be used for the practical purpose of sending messages, in such a way that the sender and receiver could tell immediately whether anyone had listened to the message en route. And that, in essence, is quantum key distribution or quantum cryptography."

The importance of BB84 was not immediately recognized by the scientific community. The cryptographic protocols now in use, which underpin the security of all our Internet communications and transactions, are based on the existence of mathematical problems that computers cannot solve, and in the mid-1980s there was nothing to suggest that this might one day change. However ten years later change it did, thanks to the work of Peter Shor. Peter Shor, winner of the BBVA Foundation Frontiers of Knowledge Award in Basic Sciences.{module INSIDE STORY}

The algorithm that challenged classical cryptography

Shor, Professor of Applied Mathematics at MIT, discovered that the supposedly intractable problem on which standard cryptography was based, the prime factorization of large numbers -i.e. the decomposition of a large number into its prime factors - would be within the scope of a hypothetical quantum computer. As the citation states, "Shor discovered that quantum computers could factorize integers much faster than any supercomputer, therefore compromising the security of conventional cryptographic schemes."

Shor's algorithm, so named for its author, is now one of the quantum algorithms that comprise the fast-developing language to be spoken by tomorrow's quantum computers.

"When Shor discovered that if you could build a quantum computer", explains Bennett, "it would defeat certain cryptographic systems in widespread use, that stimulated a lot more research because the cryptographers wanted to find more secure systems that were harder to break. And at the same time, other people wanted to build a better quantum computer to see what it could be used for besides code-breaking."

In a phone conversation, Gilles Brassard also recalled this time in his career: "We created the BB84 system ten years before Peter Shor discovered that quantum computers if they could be built, would completely undermine the cryptographic infrastructure that protects Internet communications. The importance of our work became much more evident after Shor destroyed everything else. It's sort of funny, because in 1984 quantum theory led to the most secure confidentiality possible in inter-machine transmission. And ten years later the same quantum theory challenged all the cryptographic systems invented, except for ours!"

Bennett and Brassard would go on working closely together for several decades. Both have also collaborated with Shor, who explains his own contribution as follows: "Current cryptographic systems depend on the difficulty of factoring numbers. If you could factor numbers quickly, you could break all the codes of today's systems. What I showed is that a quantum computer could factor large numbers fairly quickly. Of course, nobody has actually built a big enough quantum computer to factor those numbers yet, and it will probably be years or decades before they do."

Shortly after devising his algorithm, Shor made another landmark contribution, known as quantum error correction; "an essential requirement," in the words of the committee. "for enabling and scaling quantum computations."

By their very nature, quantum supercomputers are exposed to a large volume of noise, causing numerous errors. Before Shor's finding, it was not believed theoretically possible to isolate quantum computers to such an extent that errors could be eradicated. So Shor, in essence, gave hope to the field and propelled it forward.

"Everyone thought that you couldn't correct errors on quantum computers," recalls Shore, "because as soon as you try to measure a quantum system you disturb it. In other words, if you try to measure the error so as to correct it, you disturb it and computation is interrupted. My algorithm showed that you can isolate and fix the error and still preserve the computation".

The promise of a rising technology

Quantum cryptography is right now one of the most advanced branches of quantum technology, with several companies up and running in Europe and the United States. In China a quantum communication terrestrial system known as Backbone has been laid between Beijing and Shanghai is already being used for commercial applications, and in 2016 the country launched an experimental satellite link with Europe.

The laureates, however, view the development of quantum computation as essentially a long-term prospect, unlikely to immediately fulfill the expectations stoked by the prototypes of leading tech firms. As Bennett reflects, "I really welcome the number of smart people working in this field, because back in the days when there were only half a dozen of us it didn't progress. But I think people are too eager to know what it's going to be used for right away, especially considering that quantum information is very delicate. It requires very precise hardware resistant to error and well insulated from environmental influences. These are tough engineering problems. Not necessarily impossible, but they are hard and will take years to achieve."

That said, they have no doubts about the future potential of quantum computers. For Brassard, "the 19th century was the era of steam power, the 20th century was the era of information, and the 21st century will go down in history as the quantum age, the age in which quantum technologies dominate all the changes occurring in society, in a way we cannot yet foresee."

Shor, meantime, believes that "it will be 5 or 10 years before a quantum supercomputer can do anything approaching useful." With time, however, he is convinced that these machines will deliver revolutionary applications, in biomedicine, for instance: "At the moment, it takes enormous amounts of computer time to simulate the behavior of molecules, but quantum computers could achieve that, and help design new drugs."

Computer science classes break down cultural barriers

In a Kenyan refugee camp, a teenaged Burundian boy, a Somali boy and two girls from the Dinka ethnic group in South Sudan worked together to create a rudimentary video game about malaria.

The girls suggested the players' goal should be indigenous plant medicine; the Somali boy said they should instead seek pills since plant medicine is "old-fashioned."

The others eventually agreed with him, and their resulting design depicted characters trying to avoid mosquitoes and reach little red pills. The teens' collaboration, disagreement, and finished product illustrated some of the opportunities and challenges of computational education, which can break down and expose cultural barriers in unexpected ways, a new study from Cornell University researchers has found. {module In-article}

"Friction is not just a source of conflict - it's a source of learning," said Ian Arawjo, doctoral student in the field of information science and first author of "Computing Education for Intercultural Learning: Lessons From the Nairobi Play Project," which won an honorable mention for best paper at the upcoming Association for Computing Machinery Conference on Computer-Supported Cooperative Work and Social Computing, Nov. 9-13 in Austin, Texas.

The paper was co-authored by Ariam Mogos of the Nairobi Play Project; Steven Jackson, associate professor and chair of the Department of Information Science; Tapan Parikh, associate professor at Cornell Tech; and Kentaro Toyama of the University of Michigan.

The Nairobi Play Project, funded by the United Nations Children's Fund Kenya Country Program, seeks to foster intercultural learning between groups in or at risk of conflict. In 30 after-school sessions led by teachers who are themselves, refugees, students learn basic computing concepts and develop video games with community-based themes.

The perceived importance of computing, the novelty of the devices, the need to share equipment, unfamiliar modes of thinking and opportunity for laughter are among the factors that contribute to intercultural cooperation, Arawjo said. Many students - whose regular classes in refugee camps have student-teacher ratios of around 100 to 1 - said they likely wouldn't have been allowed to participate in any other kind of class.

"My mother is OK with [the class] because I am the first person in the family using a computer," a Somali girl told interviewers.

For the study, researchers observed classes, interviewed teachers and students and conducted surveys both before and after the program. They found that despite resistance - or in some cases, because of it - the structure of the computational class enabled unlikely friendships between students from very different backgrounds.

For example, a Somali girl initially expressed resistance to working with a South Sudanese boy but said he "was my computer mate and become my best friend" after the two shared a laptop for a month. A Congolese boy and a Sudanese boy bonded over language difficulties. Two Dinka students stopped attending the class after learning their teacher was from the Nuer tribe because their two tribes were in active conflict. The teacher visited the boys to encourage them to return and finish the program, which they did.

The limited number of devices meant the students had to sit together and cooperate. When asked how he made friends from different backgrounds, a boy said, "Our teacher told us you must sit together - for example, you're Congolese, you're Sudanese. They mix us. ... We have to communicate. Because there is only one computer. You cannot make something without the computer."

Programming requires students to consider a problem from the computer's perspective - similar to seeing from other people's points of view, Arawjo said. Teachers built on these connections. Unfamiliar tools and debugging programs also tended to inspire humor, the researchers wrote.

A teacher demonstrates computational tools to students in the Nairobi Play Project.

"One thing that emerged from this work is that the line between computational learning and intercultural learning is not so clear," Arawjo said.

None of these connections happened automatically. The researchers found that, as in the United States, cultural power hierarchies could be reproduced if teachers didn't recognize and avert them. Teachers needed to be capable and experienced enough to take advantage of opportunities for intercultural learning. And the devices could distract the students, especially if the internet was available.

Teachers also faced the challenge of conflicts erupting in class. One cross-cultural team of boys created a video game in which migrants reclaim their lands by killing all male members of another tribe; concerned about reinforcing xenophobia, the teachers encouraged them to find another solution.

"Conflict is present," Arawjo said. "But it also can be resolved, and the resolution of conflict offers powerful opportunities for learning."