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Marshaling artificial intelligence in the fight against Covid-19 | MIT News

Artificial intelligence could play a decisive role in stopping the Covid-19 pandemic. To give the technology a push, the MIT-IBM Watson AI Lab is funding 10 projects at MIT aimed at advancing AI’s transformative potential for society. The research will target the immediate public health and economic challenges of this moment. But it could have a lasting impact on how we evaluate and respond to risk long after the crisis has passed. The 10 research projects are highlighted below.

Early detection of sepsis in Covid-19 patients 

Sepsis is a deadly complication of Covid-19, the disease caused by the new coronavirus SARS-CoV-2. About 10 percent of Covid-19 patients get sick with sepsis within a week of showing symptoms, but only about half survive.

Identifying patients at risk for sepsis can lead to earlier, more aggressive treatment and a better chance of survival. Early detection can also help hospitals prioritize intensive-care resources for their sickest patients. In a project led by MIT Professor Daniela Rus, researchers will develop a machine learning system to analyze images of patients’ white blood cells for signs of an activated immune response against sepsis.

Designing proteins to block SARS-CoV-2

Proteins are the basic building blocks of life, and with AI, researchers can explore and manipulate their structures to address longstanding problems. Take perishable food: The MIT-IBM Watson AI Lab recently used AI to discover that a silk protein made by honeybees could double as a coating for quick-to-rot foods to extend their shelf life.

In a related project led by MIT professors Benedetto Marelli and Markus Buehler, researchers will enlist the protein-folding method used in their honeybee-silk discovery to try to defeat the new coronavirus. Their goal is to design proteins able to block the virus from binding to human cells, and to synthesize and test their unique protein creations in the lab.

Saving lives while restarting the U.S. economy

Some states are reopening for business even as questions remain about how to protect those most vulnerable to the coronavirus. In a project led by MIT professors Daron Acemoglu, Simon Johnson and Asu Ozdaglar will model the effects of targeted lockdowns on the economy and public health.

In a recent working paper co-authored by Acemoglu, Victor Chernozhukov, Ivan Werning, and Michael Whinston, MIT economists analyzed the relative risk of infection, hospitalization, and death for different age groups. When they compared uniform lockdown policies against those targeted to protect seniors, they found that a targeted approach could save more lives. Building on this work, researchers will consider how antigen tests and contact tracing apps can further reduce public health risks.

Which materials make the best face masks?

Massachusetts and six other states have ordered residents to wear face masks in public to limit the spread of coronavirus. But apart from the coveted N95 mask, which traps 95 percent of airborne particles 300 nanometers or larger, the effectiveness of many masks remains unclear due to a lack of standardized methods to evaluate them.

In a project led by MIT Associate Professor Lydia Bourouiba, researchers are developing a rigorous set of methods to measure how well homemade and medical-grade masks do at blocking the tiny droplets of saliva and mucus expelled during normal breathing, coughs, or sneezes. The researchers will test materials worn alone and together, and in a variety of configurations and environmental conditions. Their methods and measurements will determine how well materials protect mask wearers and the people around them.

Treating Covid-19 with repurposed drugs

As Covid-19’s global death toll mounts, researchers are racing to find a cure among already-approved drugs. Machine learning can expedite screening by letting researchers quickly predict if promising candidates can hit their target.

In a project led by MIT Assistant Professor Rafael Gomez-Bombarelli, researchers will represent molecules in three dimensions to see if this added spatial information can help to identify drugs most likely to be effective against the disease. They will use NASA’s Ames and U.S. Department of Energy’s NSERC supercomputers to further speed the screening process.

A privacy-first approach to automated contact tracing

Smartphone data can help limit the spread of Covid-19 by identifying people who have come into contact with someone infected with the virus, and thus may have caught the infection themselves. But automated contact tracing also carries serious privacy risks.

In collaboration with MIT Lincoln Laboratory and others, MIT researchers Ronald Rivest and Daniel Weitzner will use encrypted Bluetooth data to ensure personally identifiable information remains anonymous and secure.

Overcoming manufacturing and supply hurdles to provide global access to a coronavirus vaccine

A vaccine against SARS-CoV-2 would be a crucial turning point in the fight against Covid-19. Yet, its potential impact will be determined by the ability to rapidly and equitably distribute billions of doses globally. This is an unprecedented challenge in biomanufacturing. 

In a project led by MIT professors Anthony Sinskey and Stacy Springs, researchers will build data-driven statistical models to evaluate tradeoffs in scaling the manufacture and supply of vaccine candidates. Questions include how much production capacity will need to be added, the impact of centralized versus distributed operations, and how to design strategies for fair vaccine distribution. The goal is to give decision-makers the evidence needed to cost-effectively achieve global access.

Leveraging electronic medical records to find a treatment for Covid-19

Developed as a treatment for Ebola, the anti-viral drug remdesivir is now in clinical trials in the United States as a treatment for Covid-19. Similar efforts to repurpose already-approved drugs to treat or prevent the disease are underway.

In a project led by MIT professors Roy Welsch and Stan Finkelstein, researchers will use statistics, machine learning, and simulated clinical drug trials to find and test already-approved drugs as potential therapeutics against Covid-19. Researchers will sift through millions of electronic health records and medical claims for signals indicating that drugs used to fight chronic conditions like hypertension, diabetes, and gastric influx might also work against Covid-19 and other diseases.

Finding better ways to treat Covid-19 patients on ventilators 

Troubled breathing from acute respiratory distress syndrome is one of the complications that brings Covid-19 patients to the ICU. There, life-saving machines help patients breathe by mechanically pumping oxygen into the lungs. But even as towns and cities lower their Covid-19 infections through social distancing, there remains a national shortage of mechanical ventilators and serious health risks of ventilation itself.

In collaboration with IBM researchers Zach Shahn and Daby Sow, MIT researchers Li-Wei Lehman and Roger Mark will develop an AI tool to help doctors find better ventilator settings for Covid-19 patients and decide how long to keep them on a machine. Shortened ventilator use can limit lung damage while freeing up machines for others. To build their models, researchers will draw on data from intensive-care patients with acute respiratory distress syndrome, as well as Covid-19 patients at a local Boston hospital.

Returning to normal via targeted lockdowns, personalized treatments, and mass testing

In a few short months, Covid-19 has devastated towns and cities around the world. Researchers are now piecing together the data to understand how government policies can limit new infections and deaths and how targeted policies might protect the most vulnerable.

In a project led by MIT Professor Dimitris Bertsimas, researchers will study the effects of lockdowns and other measures meant to reduce new infections and deaths and prevent the health-care system from being swamped. In a second phase of the project, they will develop machine learning models to predict how vulnerable a given patient is to Covid-19, and what personalized treatments might be most effective. They will also develop an inexpensive, spectroscopy-based test for Covid-19 that can deliver results in minutes and pave the way for mass testing. The project will draw on clinical data from four hospitals in the United States and Europe, including Codogno Hospital, which reported Italy’s first infection.

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Undergraduates develop next-generation intelligence tools | MIT News

The coronavirus pandemic has driven us apart physically while reminding us of the power of technology to connect. When MIT shut its doors in March, much of campus moved online, to virtual classes, labs, and chatrooms. Among those making the pivot were students engaged in independent research under MIT’s Undergraduate Research Opportunities Program (UROP). 

With regular check-ins with their advisors via Slack and Zoom, many students succeeded in pushing through to the end. One even carried on his experiments from his bedroom, after schlepping his Sphero Bolt robots home in a backpack. “I’ve been so impressed by their resilience and dedication,” says Katherine Gallagher, one of three artificial intelligence engineers at MIT Quest for Intelligence who works with students each semester on intelligence-related applications. “There was that initial week of craziness and then they were right back to work.” Four projects from this spring are highlighted below.

Learning to explore the world with open eyes and ears

Robots rely heavily on images beamed through their built-in cameras, or surrogate “eyes,” to get around. MIT senior Alon Kosowsky-Sachs thinks they could do a lot more if they also used their microphone “ears.” 

From his home in Sharon, Massachusetts, where he retreated after MIT closed in March, Kosowsky-Sachs is training four baseball-sized Sphero Bolt robots to roll around a homemade arena. His goal is to teach the robots to pair sights with sounds, and to exploit this information to build better representations of their environment. He’s working with Pulkit Agrawal, an assistant professor in MIT’s Department of Electrical Engineering and Computer Science, who is interested in designing algorithms with human-like curiosity.

While Kosowsky-Sachs sleeps, his robots putter away, gliding through an object-strewn rink he built for them from two-by-fours. Each burst of movement becomes a pair of one-second video and audio clips. By day, Kosowsky-Sachs trains a “curiosity” model aimed at pushing the robots to become bolder, and more skillful, at navigating their obstacle course.

“I want them to see something through their camera, and hear something from their microphone, and know that these two things happen together,” he says. “As humans, we combine a lot of sensory information to get added insight about the world. If we hear a thunder clap, we don’t need to see lightning to know that a storm has arrived. Our hypothesis is that robots with a better model of the world will be able to accomplish more difficult tasks.”

Training a robot agent to design a more efficient nuclear reactor 

One important factor driving the cost of nuclear power is the layout of its reactor core. If fuel rods are arranged in an optimal fashion, reactions last longer, burn less fuel, and need less maintenance. As engineers look for ways to bring down the cost of nuclear energy, they are eying the redesign of the reactor core.

“Nuclear power emits very little carbon and is surprisingly safe compared to other energy sources, even solar or wind,” says third-year student Isaac Wolverton. “We wanted to see if we could use AI to make it more efficient.” 

In a project with Josh Joseph, an AI engineer at the MIT Quest, and Koroush Shirvan, an assistant professor in MIT’s Department of Nuclear Science and Engineering, Wolverton spent the year training a reinforcement learning agent to find the best way to lay out fuel rods in a reactor core. To simulate the process, he turned the problem into a game, borrowing a machine learning technique for producing agents with superhuman abilities at chess and Go.

He started by training his agent on a simpler problem: arranging colored tiles on a grid so that as few tiles as possible of the same color would touch. As Wolverton increased the number of options, from two colors to five, and four tiles to 225, he grew excited as the agent continued to find the best strategy. “It gave us hope we could teach it to swap the cores into an optimal arrangement,” he says.

Eventually, Wolverton moved to an environment meant to simulate a 36-rod reactor core, with two enrichment levels and 2.1 million possible core configurations. With input from researchers in Shirvan’s lab, Wolverton trained an agent that arrived at the optimal solution.

The lab is now building on Wolverton’s code to try to train an agent in a life-sized 100-rod environment with 19 enrichment levels. “There’s no breakthrough at this point,” he says. “But we think it’s possible, if we can find enough compute resources.”

Making more livers available to patients who need them

About 8,000 patients in the United States receive liver transplants each year, but that’s only half the number who need one. Many more livers might be made available if hospitals had a faster way to screen them, researchers say. In a collaboration with Massachusetts General Hospital, MIT Quest is evaluating whether automation could help to boost the nation’s supply of viable livers.  

In approving a liver for transplant, pathologists estimate its fat content from a slice of tissue. If it’s low enough, the liver is deemed ready for transplant. But there are often not enough qualified doctors to review tissue samples on the tight timeline needed to match livers with recipients. A shortage of doctors, coupled with the subjective nature of analyzing tissue, means that viable livers are inevitably discarded.

This loss represents a huge opportunity for machine learning, says third-year student Kuan Wei Huang, who joined the project to explore AI applications in health care. The project involves training a deep neural network to pick out globules of fat on liver tissue slides to estimate the liver’s overall fat content.

One challenge, says Huang, has been figuring out how to handle variations in how various pathologists classify fat globules. “This makes it harder to tell whether I’ve created the appropriate masks to feed into the neural net,” he says. “However, after meeting with experts in the field, I received clarifications and was able to continue working.”

Trained on images labeled by pathologists, the model will eventually learn to isolate fat globules in unlabeled images on its own. The final output will be a fat content estimate with pictures of highlighted fat globules showing how the model arrived at its final count. “That’s the easy part — we just count up the pixels in the highlighted globules as a percentage of the overall biopsy and we have our fat content estimate,” says the Quest’s Gallagher, who is leading the project.

Huang says he’s excited by the project’s potential to help people. “Using machine learning to address medical problems is one of the best ways that a computer scientist can impact the world.”

Exposing the hidden constraints of what we mean in what we say

Language shapes our understanding of the world in subtle ways, with slight variations in the words we use conveying sharply different meanings. The sentence, “Elephants live in Africa and Asia,” looks a lot like the sentence “Elephants eat twigs and leaves.” But most readers will conclude that the elephants in the first sentence are split into distinct groups living on separate continents but not apply the same reasoning to the second sentence, because eating twigs and eating leaves can both be true of the same elephant in a way that living on different continents cannot.

Karen Gu is a senior majoring in computer science and molecular biology, but instead of putting cells under a microscope for her SuperUROP project, she chose to look at sentences like the ones above. “I’m fascinated by the complex and subtle things that we do to constrain language understanding, almost all of it subconsciously,” she says.

Working with Roger Levy, a professor in MIT’s Department of Brain and Cognitive Sciences, and postdoc MH Tessler, Gu explored how prior knowledge guides our interpretation of syntax and ultimately, meaning. In the sentences above, prior knowledge about geography and mutual exclusivity interact with syntax to produce different meanings.

After steeping herself in linguistics theory, Gu built a model to explain how, word by word, a given sentence produces meaning. She then ran a set of online experiments to see how human subjects would interpret analogous sentences in a story. Her experiments, she says, largely validated intuitions from linguistic theory.

One challenge, she says, was having to reconcile two approaches for studying language. “I had to figure out how to combine formal linguistics, which applies an almost mathematical approach to understanding how words combine, and probabilistic semantics-pragmatics, which has focused more on how people interpret whole utterances.’ “

After MIT closed in March, she was able to finish the project from her parents’ home in East Hanover, New Jersey. “Regular meetings with my advisor have been really helpful in keeping me motivated and on track,” she says. She says she also got to improve her web-development skills, which will come in handy when she starts work at Benchling, a San Francisco-based software company, this summer.

Spring semester Quest UROP projects were funded, in part, by the MIT-IBM Watson AI Lab and Eric Schmidt, technical advisor to Alphabet Inc., and his wife, Wendy.

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Bringing the predictive power of artificial intelligence to health care | MIT News

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An important aspect of treating patients with conditions like diabetes and heart disease is helping them stay healthy outside of the hospital — before they to return to the doctor’s office with further complications.

But reaching the most vulnerable patients at the right time often has more to do with probabilities than clinical assessments. Artificial intelligence (AI) has the potential to help clinicians tackle these types of problems, by analyzing large datasets to identify the patients that would benefit most from preventative measures. However, leveraging AI has often required health care organizations to hire their own data scientists or settle for one-size-fits-all solutions that aren’t optimized for their patients.

Now the startup ClosedLoop.ai is helping health care organizations tap into the power of AI with a flexible analytics solution that lets hospitals quickly plug their data into machine learning models and get actionable results.

The platform is being used to help hospitals determine which patients are most likely to miss appointments, acquire infections like sepsis, benefit from periodic check ups, and more. Health insurers, in turn, are using ClosedLoop to make population-level predictions around things like patient readmissions and the onset or progression of chronic diseases.

“We built a health care data science platform that can take in whatever data an organization has, quickly build models that are specific to [their patients], and deploy those models,” says ClosedLoop co-founder and Chief Technology Officer Dave DeCaprio ’94. “Being able to take somebody’s data the way it lives in their system and convert that into a model that can be readily used is still a problem that requires a lot of [health care] domain knowledge, and that’s a lot of what we bring to the table.”

In light of the Covid-19 pandemic, ClosedLoop has also created a model that helps organizations identify the most vulnerable people in their region and prepare for patient surges. The open source tool, called the C-19 Index, has been used to connect high-risk patients with local resources and helped health care systems create risk scores for tens of millions of people overall.

The index is just the latest way that ClosedLoop is accelerating the health care industry’s adoption of AI to improve patient health, a goal DeCaprio has worked toward for the better part of his career.

Designing a strategy

After working as a software engineer for several private companies through the internet boom of the early 2000s, DeCaprio was looking to make a career change when he came across a project focused on genome annotation at the Broad Institute of MIT and Harvard.

The project was DeCaprio’s first professional exposure to the power of artificial intelligence. It blossomed into a six year stint at the Broad, after which he continued exploring the intersection of big data and health care.

“After a year in health care, I realized it was going to be really hard to do anything else,” DeCaprio says. “I’m not going to be able to get excited about selling ads on the internet or anything like that. Once you start dealing with human health, that other stuff just feels insignificant.”

In the course of his work, DeCaprio began noticing problems with the ways machine learning and other statistical techniques were making their way into health care, notably in the fact that predictive models were being applied without regard for hospitals’ patient populations.

“Someone would say, ‘I know how to predict diabetes’ or ‘I know how to predict readmissions,’ and they’d sell a model,” DeCaprio says. “I knew that wasn’t going to work, because the reason readmissions happen in a low-income population of New York City is very different from the reason readmissions happen in a retirement community in Florida. The important thing wasn’t to build one magic model but to build a system that can quickly take somebody’s data and train a model that’s specific for their problems.”

With that approach in mind, DeCaprio joined forces with former co-worker and serial entrepreneur Andrew Eye, and started ClosedLoop in 2017. The startup’s first project involved creating models that predicted patient health outcomes for the Medical Home Network (MHN), a not-for-profit hospital collaboration focused on improving care for Medicaid recipients in Chicago.

As the founders created their modeling platform, they had to address many of the most common obstacles that have slowed health care’s adoption of AI solutions.

Often the first problems startups run into is making their algorithms work with each health care system’s data. Hospitals vary in the type of data they collect on patients and the way they store that information in their system. Hospitals even store the same types of data in vastly different ways.

DeCaprio credits his team’s knowledge of the health care space with helping them craft a solution that allows customers to upload raw data sets into ClosedLoop’s platform and create things like patient risk scores with a few clicks.

Another limitation of AI in health care has been the difficulty of understanding how models get to results. With ClosedLoop’s models, users can see the biggest factors contributing to each prediction, giving them more confidence in each output.

Overall, to become ingrained in customer’s operations, the founders knew their analytics platform needed to give simple, actionable insights. That has translated into a system that generates lists, risk scores, and rankings that care managers can use when deciding which interventions are most urgent for which patients.

“When someone walks into the hospital, it’s already too late [to avoid costly treatments] in many cases,” DeCaprio says. “Most of your best opportunities to lower the cost of care come by keeping them out of the hospital in the first place.”

Customers like health insurers also use ClosedLoop’s platform to predict broader trends in disease risk, emergency room over-utilization, and fraud.

Stepping up for Covid-19

In March, ClosedLoop began exploring ways its platform could help hospitals prepare for and respond to Covid-19. The efforts culminated in a company hackathon over the weekend of March 16. By Monday, ClosedLoop had an open source model on GitHub that assigned Covid-19 risk scores to Medicare patients. By that Friday, it had been used to make predictions on more than 2 million patients.

Today, the model works with all patients, not just those on Medicare, and it has been used to assess the vulnerability of communities around the country. Care organizations have used the model to project patient surges and help individuals at the highest risk understand what they can do to prevent infection.

“Some of it is just reaching out to people who are socially isolated to see if there’s something they can do,” DeCaprio says. “Someone who is 85 years old and shut in may not know there’s a community based organization that will deliver them groceries.”

For DeCaprio, bringing the predictive power of AI to health care has been a rewarding, if humbling, experience.

“The magnitude of the problems are so large that no matter what impact you have, you don’t feel like you’ve moved the needle enough,” he says. “At the same time, every time an organization says, ‘This is the primary tool our care managers have been using to figure out who to reach out to,’ it feels great.”

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