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    Research collaboration puts climate-resilient crops in sight

    Any houseplant owner knows that changes in the amount of water or sunlight a plant receives can put it under immense stress. A dying plant brings certain disappointment to anyone with a green thumb. 

    But for farmers who make their living by successfully growing plants, and whose crops may nourish hundreds or thousands of people, the devastation of failing flora is that much greater. As climate change is poised to cause increasingly unpredictable weather patterns globally, crops may be subject to more extreme environmental conditions like droughts, fluctuating temperatures, floods, and wildfire. 

    Climate scientists and food systems researchers worry about the stress climate change may put on crops, and on global food security. In an ambitious interdisciplinary project funded by the Abdul Latif Jameel Water and Food Systems Lab (J-WAFS), David Des Marais, the Gale Assistant Professor in the Department of Civil and Environmental Engineering at MIT, and Caroline Uhler, an associate professor in the MIT Department of Electrical Engineering and Computer Science and the Institute for Data, Systems, and Society, are investigating how plant genes communicate with one another under stress. Their research results can be used to breed plants more resilient to climate change.

    Crops in trouble

    Governing plants’ responses to environmental stress are gene regulatory networks, or GRNs, which guide the development and behaviors of living things. A GRN may be comprised of thousands of genes and proteins that all communicate with one another. GRNs help a particular cell, tissue, or organism respond to environmental changes by signaling certain genes to turn their expression on or off.

    Even seemingly minor or short-term changes in weather patterns can have large effects on crop yield and food security. An environmental trigger, like a lack of water during a crucial phase of plant development, can turn a gene on or off, and is likely to affect many others in the GRN. For example, without water, a gene enabling photosynthesis may switch off. This can create a domino effect, where the genes that rely on those regulating photosynthesis are silenced, and the cycle continues. As a result, when photosynthesis is halted, the plant may experience other detrimental side effects, like no longer being able to reproduce or defend against pathogens. The chain reaction could even kill a plant before it has the chance to be revived by a big rain.

    Des Marais says he wishes there was a way to stop those genes from completely shutting off in such a situation. To do that, scientists would need to better understand how exactly gene networks respond to different environmental triggers. Bringing light to this molecular process is exactly what he aims to do in this collaborative research effort.

    Solving complex problems across disciplines

    Despite their crucial importance, GRNs are difficult to study because of how complex and interconnected they are. Usually, to understand how a particular gene is affecting others, biologists must silence one gene and see how the others in the network respond. 

    For years, scientists have aspired to an algorithm that could synthesize the massive amount of information contained in GRNs to “identify correct regulatory relationships among genes,” according to a 2019 article in the Encyclopedia of Bioinformatics and Computational Biology. 

    “A GRN can be seen as a large causal network, and understanding the effects that silencing one gene has on all other genes requires understanding the causal relationships among the genes,” says Uhler. “These are exactly the kinds of algorithms my group develops.”

    Des Marais and Uhler’s project aims to unravel these complex communication networks and discover how to breed crops that are more resilient to the increased droughts, flooding, and erratic weather patterns that climate change is already causing globally.

    In addition to climate change, by 2050, the world will demand 70 percent more food to feed a booming population. “Food systems challenges cannot be addressed individually in disciplinary or topic area silos,” says Greg Sixt, J-WAFS’ research manager for climate and food systems. “They must be addressed in a systems context that reflects the interconnected nature of the food system.”

    Des Marais’ background is in biology, and Uhler’s in statistics. “Dave’s project with Caroline was essentially experimental,” says Renee J. Robins, J-WAFS’ executive director. “This kind of exploratory research is exactly what the J-WAFS seed grant program is for.”

    Getting inside gene regulatory networks

    Des Marais and Uhler’s work begins in a windowless basement on MIT’s campus, where 300 genetically identical Brachypodium distachyon plants grow in large, temperature-controlled chambers. The plant, which contains more than 30,000 genes, is a good model for studying important cereal crops like wheat, barley, maize, and millet. For three weeks, all plants receive the same temperature, humidity, light, and water. Then, half are slowly tapered off water, simulating drought-like conditions.

    Six days into the forced drought, the plants are clearly suffering. Des Marais’ PhD student Jie Yun takes tissues from 50 hydrated and 50 dry plants, freezes them in liquid nitrogen to immediately halt metabolic activity, grinds them up into a fine powder, and chemically separates the genetic material. The genes from all 100 samples are then sequenced at a lab across the street.

    The team is left with a spreadsheet listing the 30,000 genes found in each of the 100 plants at the moment they were frozen, and how many copies there were. Uhler’s PhD student Anastasiya Belyaeva inputs the massive spreadsheet into the computer program she developed and runs her novel algorithm. Within a few hours, the group can see which genes were most active in one condition over another, how the genes were communicating, and which were causing changes in others. 

    The methodology captures important subtleties that could allow researchers to eventually alter gene pathways and breed more resilient crops. “When you expose a plant to drought stress, it’s not like there’s some canonical response,” Des Marais says. “There’s lots of things going on. It’s turning this physiologic process up, this one down, this one didn’t exist before, and now suddenly is turned on.” 

    In addition to Des Marais and Uhler’s research, J-WAFS has funded projects in food and water from researchers in 29 departments across all five MIT schools as well as the MIT Schwarzman College of Computing. J-WAFS seed grants typically fund seven to eight new projects every year.

    “The grants are really aimed at catalyzing new ideas, providing the sort of support [for MIT researchers] to be pushing boundaries, and also bringing in faculty who may have some interesting ideas that they haven’t yet applied to water or food concerns,” Robins says. “It’s an avenue for researchers all over the Institute to apply their ideas to water and food.”

    Alison Gold is a student in MIT’s Graduate Program in Science Writing. More

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    MIT appoints members of new faculty committee to drive climate action plan

    In May, responding to the world’s accelerating climate crisis, MIT issued an ambitious new plan, “Fast Forward: MIT’s Climate Action Plan for the Decade.” The plan outlines a broad array of new and expanded initiatives across campus to build on the Institute’s longstanding climate work.

    Now, to unite these varied climate efforts, maximize their impact, and identify new ways for MIT to contribute climate solutions, the Institute has appointed more than a dozen faculty members to a new committee established by the Fast Forward plan, named the Climate Nucleus.

    The committee includes leaders of a number of climate- and energy-focused departments, labs, and centers that have significant responsibilities under the plan. Its membership spans all five schools and the MIT Schwarzman College of Computing. Professors Noelle Selin and Anne White have agreed to co-chair the Climate Nucleus for a term of three years.

    “I am thrilled and grateful that Noelle and Anne have agreed to step up to this important task,” says Maria T. Zuber, MIT’s vice president for research. “Under their leadership, I’m confident that the Climate Nucleus will bring new ideas and new energy to making the strategy laid out in the climate action plan a reality.”

    The Climate Nucleus has broad responsibility for the management and implementation of the Fast Forward plan across its five areas of action: sparking innovation, educating future generations, informing and leveraging government action, reducing MIT’s own climate impact, and uniting and coordinating all of MIT’s climate efforts.

    Over the next few years, the nucleus will aim to advance MIT’s contribution to a two-track approach to decarbonizing the global economy, an approach described in the Fast Forward plan. First, humanity must go as far and as fast as it can to reduce greenhouse gas emissions using existing tools and methods. Second, societies need to invest in, invent, and deploy new tools — and promote new institutions and policies — to get the global economy to net-zero emissions by mid-century.

    The co-chairs of the nucleus bring significant climate and energy expertise, along with deep knowledge of the MIT community, to their task.

    Selin is a professor with joint appointments in the Institute for Data, Systems, and Society and the Department of Earth, Atmospheric and Planetary Sciences. She is also the director of the Technology and Policy Program. She began at MIT in 2007 as a postdoc with the Center for Global Change Science and the Joint Program on the Science and Policy of Global Change. Her research uses modeling to inform decision-making on air pollution, climate change, and hazardous substances.

    “Climate change affects everything we do at MIT. For the new climate action plan to be effective, the Climate Nucleus will need to engage the entire MIT community and beyond, including policymakers as well as people and communities most affected by climate change,” says Selin. “I look forward to helping to guide this effort.”

    White is the School of Engineering’s Distinguished Professor of Engineering and the head of the Department of Nuclear Science and Engineering. She joined the MIT faculty in 2009 and has also served as the associate director of MIT’s Plasma Science and Fusion Center. Her research focuses on assessing and refining the mathematical models used in the design of fusion energy devices, such as tokamaks, which hold promise for delivering limitless zero-carbon energy.

    “The latest IPCC report underscores the fact that we have no time to lose in decarbonizing the global economy quickly. This is a problem that demands we use every tool in our toolbox — and develop new ones — and we’re committed to doing that,” says White, referring to an August 2021 report from the Intergovernmental Panel on Climate Change, a UN climate science body, that found that climate change has already affected every region on Earth and is intensifying. “We must train future technical and policy leaders, expand opportunities for students to work on climate problems, and weave sustainability into every one of MIT’s activities. I am honored to be a part of helping foster this Institute-wide collaboration.”

    A first order of business for the Climate Nucleus will be standing up three working groups to address specific aspects of climate action at MIT: climate education, climate policy, and MIT’s own carbon footprint. The working groups will be responsible for making progress on their particular areas of focus under the plan and will make recommendations to the nucleus on ways of increasing MIT’s effectiveness and impact. The working groups will also include student, staff, and alumni members, so that the entire MIT community has the opportunity to contribute to the plan’s implementation.  

    The nucleus, in turn, will report and make regular recommendations to the Climate Steering Committee, a senior-level team consisting of Zuber; Richard Lester, the associate provost for international activities; Glen Shor, the executive vice president and treasurer; and the deans of the five schools and the MIT Schwarzman College of Computing. The new plan created the Climate Steering Committee to ensure that climate efforts will receive both the high-level attention and the resources needed to succeed.

    Together the new committees and working groups are meant to form a robust new infrastructure for uniting and coordinating MIT’s climate action efforts in order to maximize their impact. They replace the Climate Action Advisory Committee, which was created in 2016 following the release of MIT’s first climate action plan.

    In addition to Selin and White, the members of the Climate Nucleus are:

    Bob Armstrong, professor in the Department of Chemical Engineering and director of the MIT Energy Initiative;
    Dara Entekhabi, professor in the departments of Civil and Environmental Engineering and Earth, Atmospheric and Planetary Sciences;
    John Fernández, professor in the Department of Architecture and director of the Environmental Solutions Initiative;
    Stefan Helmreich, professor in the Department of Anthropology;
    Christopher Knittel, professor in the MIT Sloan School of Management and director of the Center for Energy and Environmental Policy Research;
    John Lienhard, professor in the Department of Mechanical Engineering and director of the Abdul Latif Jameel Water and Food Systems Lab;
    Julie Newman, director of the Office of Sustainability and lecturer in the Department of Urban Studies and Planning;
    Elsa Olivetti, professor in the Department of Materials Science and Engineering and co-director of the Climate and Sustainability Consortium;
    Christoph Reinhart, professor in the Department of Architecture and director of the Building Technology Program;
    John Sterman, professor in the MIT Sloan School of Management and director of the Sloan Sustainability Initiative;
    Rob van der Hilst, professor and head of the Department of Earth, Atmospheric and Planetary Sciences; and
    Chris Zegras, professor and head of the Department of Urban Studies and Planning. More

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    A universal system for decoding any type of data sent across a network

    Every piece of data that travels over the internet — from paragraphs in an email to 3D graphics in a virtual reality environment — can be altered by the noise it encounters along the way, such as electromagnetic interference from a microwave or Bluetooth device. The data are coded so that when they arrive at their destination, a decoding algorithm can undo the negative effects of that noise and retrieve the original data.

    Since the 1950s, most error-correcting codes and decoding algorithms have been designed together. Each code had a structure that corresponded with a particular, highly complex decoding algorithm, which often required the use of dedicated hardware.

    Researchers at MIT, Boston University, and Maynooth University in Ireland have now created the first silicon chip that is able to decode any code, regardless of its structure, with maximum accuracy, using a universal decoding algorithm called Guessing Random Additive Noise Decoding (GRAND). By eliminating the need for multiple, computationally complex decoders, GRAND enables increased efficiency that could have applications in augmented and virtual reality, gaming, 5G networks, and connected devices that rely on processing a high volume of data with minimal delay.

    The research at MIT is led by Muriel Médard, the Cecil H. and Ida Green Professor in the Department of Electrical Engineering and Computer Science, and was co-authored by Amit Solomon and Wei Ann, both graduate students at MIT; Rabia Tugce Yazicigil, assistant professor of electrical and computer engineering at Boston University; Arslan Riaz and Vaibhav Bansal, both graduate students at Boston University; Ken R. Duffy, director of the Hamilton Institute at the National University of Ireland at Maynooth; and Kevin Galligan, a Maynooth graduate student. The research will be presented at the European Solid-States Device Research and Circuits Conference next week.

    Focus on noise

    One way to think of these codes is as redundant hashes (in this case, a series of 1s and 0s) added to the end of the original data. The rules for the creation of that hash are stored in a specific codebook.

    As the encoded data travel over a network, they are affected by noise, or energy that disrupts the signal, which is often generated by other electronic devices. When that coded data and the noise that affected them arrive at their destination, the decoding algorithm consults its codebook and uses the structure of the hash to guess what the stored information is.

    Instead, GRAND works by guessing the noise that affected the message, and uses the noise pattern to deduce the original information. GRAND generates a series of noise sequences in the order they are likely to occur, subtracts them from the received data, and checks to see if the resulting codeword is in a codebook.

    While the noise appears random in nature, it has a probabilistic structure that allows the algorithm to guess what it might be.

    “In a way, it is similar to troubleshooting. If someone brings their car into the shop, the mechanic doesn’t start by mapping the entire car to blueprints. Instead, they start by asking, ‘What is the most likely thing to go wrong?’ Maybe it just needs gas. If that doesn’t work, what’s next? Maybe the battery is dead?” Médard says.

    Novel hardware

    The GRAND chip uses a three-tiered structure, starting with the simplest possible solutions in the first stage and working up to longer and more complex noise patterns in the two subsequent stages. Each stage operates independently, which increases the throughput of the system and saves power.

    The device is also designed to switch seamlessly between two codebooks. It contains two static random-access memory chips, one that can crack codewords, while the other loads a new codebook and then switches to decoding without any downtime.

    The researchers tested the GRAND chip and found it could effectively decode any moderate redundancy code up to 128 bits in length, with only about a microsecond of latency.

    Médard and her collaborators had previously demonstrated the success of the algorithm, but this new work showcases the effectiveness and efficiency of GRAND in hardware for the first time.

    Developing hardware for the novel decoding algorithm required the researchers to first toss aside their preconceived notions, Médard says.

    “We couldn’t go out and reuse things that had already been done. This was like a complete whiteboard. We had to really think about every single component from scratch. It was a journey of reconsideration. And I think when we do our next chip, there will be things with this first chip that we’ll realize we did out of habit or assumption that we can do better,” she says.

    A chip for the future

    Since GRAND only uses codebooks for verification, the chip not only works with legacy codes but could also be used with codes that haven’t even been introduced yet.

    In the lead-up to 5G implementation, regulators and communications companies struggled to find consensus as to which codes should be used in the new network. Regulators ultimately chose to use two types of traditional codes for 5G infrastructure in different situations. Using GRAND could eliminate the need for that rigid standardization in the future, Médard says.

    The GRAND chip could even open the field of coding to a wave of innovation.

    “For reasons I’m not quite sure of, people approach coding with awe, like it is black magic. The process is mathematically nasty, so people just use codes that already exist. I’m hoping this will recast the discussion so it is not so standards-oriented, enabling people to use codes that already exist and create new codes,” she says.

    Moving forward, Médard and her collaborators plan to tackle the problem of soft detection with a retooled version of the GRAND chip. In soft detection, the received data are less precise.

    They also plan to test the ability of GRAND to crack longer, more complex codes and adjust the structure of the silicon chip to improve its energy efficiency.

    The research was funded by the Battelle Memorial Institute and Science Foundation of Ireland. More

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    MIT welcomes nine MLK Visiting Professors and Scholars for 2021-22

    In its 31st year, the Martin Luther King Jr. (MLK) Visiting Professors and Scholars Program will host nine outstanding scholars from across the Americas. The flagship program honors the life and legacy of Martin Luther King Jr. by increasing the presence and recognizing the contributions of underrepresented minority scholars at MIT. Throughout the year, the cohort will enhance their scholarship through intellectual engagement with the MIT community and enrich the cultural, academic, and professional experience of students.

    The 2021-22 scholars

    Sanford Biggers is an interdisciplinary artist hosted by the Department of Architecture. His work is an interplay of narrative, perspective, and history that speaks to current social, political, and economic happenings while examining their contexts. His diverse practice positions him as a collaborator with the past through explorations of often-overlooked cultural and political narratives from American history. Through collaboration with his faculty host, Brandon Clifford, he will spend the year contributing to projects with Architecture; Art, Culture and Technology; the Transmedia Storytelling initiatives; and community workshops and engagement with local K-12 education.

    Kristen Dorsey is an assistant professor of engineering at Smith College. She will be hosted by the Program in Media Arts and Sciences at the MIT Media Lab. Her research focuses on the fabrication and characterization of microscale sensors and microelectromechanical systems. Dorsey tries to understand “why things go wrong” by investigating device reliability and stability. At MIT, Dorsey is interested in forging collaborations to consider issues of access and equity as they apply to wearable health care devices.

    Omolola “Lola” Eniola-Adefeso is the associate dean for graduate and professional education and associate professor of chemical engineering at the University of Michigan. She will join MIT’s Department of Chemical Engineering (ChemE). Eniola-Adefeso will work with Professor Paula Hammond on developing electrostatically assembled nanoparticle coatings that enable targeting of specific immune cell types. A co-founder and chief scientific officer of Asalyxa Bio, she is interested in the interactions between blood leukocytes and endothelial cells in vessel lumen lining, and how they change during inflammation response. Eniola-Adefeso will also work with the Diversity in Chemical Engineering (DICE) graduate student group in ChemE and the National Organization of Black Chemists and Chemical Engineers.

    Robert Gilliard Jr. is an assistant professor of chemistry at the University of Virginia and will join the MIT chemistry department, working closely with faculty host Christopher Cummins. His research focuses on various aspects of group 15 element chemistry. He was a founding member of the National Organization of Black Chemists and Chemical Engineers UGA section, and he has served as an American Chemical Society (ACS) Bridge Program mentor as well as an ACS Project Seed mentor. Gilliard has also collaborated with the Cleveland Public Library to expose diverse young scholars to STEM fields.

    Valencia Joyner Koomson ’98, MNG ’99 will return for the second semester of her appointment this fall in MIT’s Department of Electrical Engineering and Computer Science. Based at Tufts University, where she is an associate professor in the Department of Electrical and Computer Engineering, Koomson has focused her research on microelectronic systems for cell analysis and biomedical applications. In the past semester, she has served as a judge for the Black Alumni/ae of MIT Research Slam and worked closely with faculty host Professor Akintunde Akinwande.

    Luis Gilberto Murillo-Urrutia will continue his appointment in MIT’s Environmental Solutions Initiative. He has 30 years of experience in public policy design, implementation, and advocacy, most notably in the areas of sustainable regional development, environmental protection and management of natural resources, social inclusion, and peace building. At MIT, he has continued his research on environmental justice, with a focus on carbon policy and its impacts on Afro-descendant communities in Colombia.

    Sonya T. Smith was the first female professor of mechanical engineering at Howard University. She will join the Department of Aeronautics and Astronautics at MIT. Her research involves computational fluid dynamics and thermal management of electronics for air and space vehicles. She is looking forward to serving as a mentor to underrepresented students across MIT and fostering new research collaborations with her home lab at Howard.

    Lawrence Udeigwe is an associate professor of mathematics at Manhattan College and will join MIT’s Department of Brain and Cognitive Sciences. He plans to co-teach a graduate seminar course with Professor James DiCarlo to explore practical and philosophical questions regarding the use of simulations to build theories in neuroscience. Udeigwe also leads the Lorens Chuno group; as a singer-songwriter, his work tackles intersectionality issues faced by contemporary Africans.

    S. Craig Watkins is an internationally recognized expert in media and a professor at the University of Texas at Austin. He will join MIT’s Institute for Data, Systems, and Society to assist in researching the role of big data in enabling deep structural changes with regard to systemic racism. He will continue to expand on his work as founding director of the Institute for Media Innovation at the University of Texas at Austin, exploring the intersections of critical AI studies, critical race studies, and design. He will also work with MIT’s Center for Advanced Virtuality to develop computational systems that support social perspective-taking.

    Community engagement

    Throughout the 2021-22 academic year, MLK professors and scholars will be presenting their research at a monthly speaker series. Events will be held in an in-person/Zoom hybrid environment. All members of the MIT community are encouraged to attend and hear directly from this year’s cohort of outstanding scholars. To hear more about upcoming events, subscribe to their mailing list.

    On Sept. 15, all are invited to join the Institute Community and Equity Office in welcoming the scholars to campus by attending a welcome luncheon. More

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    3 Questions: Peko Hosoi on the data-driven reasoning behind MIT’s Covid-19 policies for the fall

    As students, faculty, and staff prepare for a full return to the MIT campus in the weeks ahead, procedures for entering buildings, navigating classrooms and labs, and interacting with friends and colleagues will likely take some getting used to.

    The Institute recently reinforced its policies for indoor masking and has also continued to require regular testing for people who live, work, or study on campus — procedures that apply to both vaccinated and unvaccinated individuals. Vaccination is required for all students, faculty, and staff on campus unless a medical or religious exemption is granted.

    These and other policies adopted by MIT to control the spread of Covid-19 have been informed by modeling efforts from a volunteer group of MIT faculty, students, and postdocs. The collaboration, dubbed Isolat, was co-founded by Anette “Peko” Hosoi, the Neil and Jane Pappalardo Professor of Mechanical Engineering and associate dean in the School of Engineering.

    The group, which is organized through MIT’s Institute for Data, Systems, and Society (IDSS), has run numerous models to show how measures such as mask wearing, testing, ventilation, and quarantining could affect Covid-19’s spread. These models have helped to shape MIT’s Covid-19 policies throughout the pandemic, including its procedures for returning to campus this fall.

    Hosoi spoke with MIT News about the data-backed reasoning behind some of these procedures, including indoor masking and regular testing, and how a “generous community” will help MIT safely weather the virus and its variants.

    Q: Take us through how you have been modeling Covid-19 and its variants, in regard to helping MIT shape its Covid policies. What’s the approach you’ve taken, and why?

    A: The approach we’re taking uses a simple counting exercise developed in IDSS to estimate the balance of testing, masking, and vaccination that is required to keep the virus in check. The underlying objective is to find infected people faster, on average, than they can infect others, which is captured in a simple algebraic expression. Our objective can be accomplished either by speeding up the rate of finding infected people (i.e. increasing testing frequency) or slowing down the rate of infection (i.e. increasing masking and vaccination) or by a combination of both. To give you a sense of the numbers, balances for different levels of testing are shown in the chart below for a vaccine efficacy of 67 percent and a contagious period of 18 days (which are the CDC’s latest parameters for the Delta variant).

    The vertical axis shows the now-famous reproduction number R0, i.e. the average number of people that one infected person will infect throughout the course of their illness. These R0 are averages for the population, and in specific circumstances the spreading could be more than that.

    Each blue line represents a different testing frequency: Below the line, the virus is controlled; above the line, it spreads. For example, the dotted blue line shows the boundary if we rely solely on vaccination with no testing. In that case, even if everyone is vaccinated, we can only control up to an R0 of about 3.  Unfortunately, the CDC places R0 of the Delta variant somewhere between 5 and 9, so vaccination alone is insufficient to control the spread. (As an aside, this also means that given the efficacy estimates for the current vaccines, herd immunity is not possible.)

    Next consider the dashed blue line, which represents the stability boundary if we test everyone once per week. If our vaccination rate is greater than about 90 percent, testing one time per week can control even the CDC’s most pessimistic estimate for the Delta variant’s R0.

    Q: In returning to campus over the next few weeks, indoor masking and regular testing are required of every MIT community member, even those who are vaccinated. What in your modeling has shown that each of these policies is necessary?

    A: Given that the chart above shows that vaccination and weekly testing are sufficient to control the virus, one should certainly ask “Why have we reinstated indoor masking?” The answer is related to the fact that, as a university, our population turns over once a year; every September we bring in a few thousand new people. Those people are coming from all over the world, and some of them may not have had the opportunity to get vaccinated yet. The good news is that MIT Medical has vaccines and will be administering them to any unvaccinated students as soon as they arrive; the bad news is that, as we all know, it takes three to five weeks for resistance to build up, depending on the vaccine. This means that we should think of August and September as a transition period during which the vaccination rates may fluctuate as new people arrive. 

    The other revelation that has informed our policies for September is the recent report from the CDC that infected vaccinated people carry roughly the same viral load as unvaccinated infected people. This suggests that vaccinated people — although they are highly unlikely to get seriously ill — are a consequential part of the transmission chain and can pass the virus along to others. So, in order to avoid giving the virus to people who are not yet fully vaccinated during the transition period, we all need to exercise a little extra care to give the newly vaccinated time for their immune systems to ramp up. 

    Q: As the fall progresses, what signs are you looking for that might shift decisions on masking and testing on campus?

    A: Eventually we will have to shift responsibility toward individuals rather than institutions, and allow people to make decisions about masks and testing based on their own risk tolerance. The success of the vaccines in suppressing severe illness will enable us to shift to a position in which our objective is not necessarily to control the spread of the virus, but rather to reduce the risk of serious outcomes to an acceptable level. There are many people who believe we need to make this adjustment and wean ourselves off pandemic living. They are right; we cannot continue like this forever. However, we have not played all our cards yet, and, in my opinion, we need to carefully consider what’s left in our hand before we abdicate institutional responsibility.

    The final ace we have to play is vaccinating kids. It is important to remember that we have many people in our community with kids who are too young to be vaccinated and, understandably, those parents do not want to bring Covid home to their children. Furthermore, our campus is not just a workplace; it is also home to thousands of people, some of whom have children living in our residences or attending an MIT childcare center. Given that context, and the high probability that a vaccine will be approved for children in the near future, it is my belief that our community has the empathy and fortitude to try to keep the virus in check until parents have the option to protect their children with vaccines. 

    Bearing in mind that children constitute an unprotected portion of our population, let me return to the original question and speculate on the fate of masks and testing in the fall. Regarding testing, the analysis suggests that we cannot give that up entirely if we would like to control the spread of the virus. Second, control of the virus is not the only benefit we get from testing. It also gives us situational awareness, serves as an early warning beacon, and provides information that individual members of the community can use as they make decisions about their own risk budget. Personally, I’ve been testing for a year now and I find it easy and reassuring. Honestly, it’s nice to know that I’m Covid-free before I see friends (outside!) or go home to my family.

    Regarding masks, there is always uncertainty around whether a new variant will arise or whether vaccine efficacy will fade, but, given the current parameters and our analysis, my hope is that we will be in a position to provide some relief on the mask mandate once the incoming members of our population have been fully vaccinated. I also suspect that whenever the mask mandate is lifted, masks are not likely to go away. There are certainly situations in which I will continue to wear a mask regardless of the mandate, and many in our community will continue to feel safer wearing masks even when they are not required.

    I believe that we are a generous community and that we will be willing to take precautions to help keep each other healthy. The students who were on campus last year did an outstanding job, and they have given me a tremendous amount of faith that we can be considerate and good to one another even in extremely trying times.

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    Last-mile routing research challenge awards $175,000 to three winning teams

    Routing is one of the most studied problems in operations research; even small improvements in routing efficiency can save companies money and result in energy savings and reduced environmental impacts. Now, three teams of researchers from universities around the world have received prize money totaling $175,000 for their innovative route optimization models.

    The three teams were the winners of the Amazon Last-Mile Routing Research Challenge, through which the MIT Center for Transportation & Logistics (MIT CTL) and Amazon engaged with a global community of researchers across a range of disciplines, from computer science to business operations to supply chain management, challenging them to build data-driven route optimization models leveraging massive historical route execution data.

    First announced in February, the research challenge attracted more than 2,000 participants from around the world. Two hundred twenty-nine researcher teams formed during the spring to independently develop solutions that incorporated driver know-how into route optimization models with the intent that they would outperform traditional optimization approaches. Out of the 48 teams whose models qualified for the final round of the challenge, three teams’ work stood out above the rest. Amazon provided real operational training data for the models and evaluated submissions, with technical support from MIT CTL scientists.

    In real life, drivers frequently deviate from planned and mathematically optimized route sequences. Drivers carry information about which roads are hard to navigate when traffic is bad, when and where they can easily find parking, which stops can be conveniently served together, and many other factors that existing optimization models simply don’t capture.

    Each model addressed the challenge data in a unique way. The methodological approaches chosen by the participants frequently combined traditional exact and heuristic optimization approaches with nontraditional machine learning methods. On the machine learning side, the most commonly adopted methods were different variants of artificial neural networks, as well as inverse reinforcement learning approaches.

    There were 45 submissions that reached the finalist phase, with team members hailing from 29 countries. Entrants spanned all levels of higher education from final-year undergraduate students to retired faculty. Entries were assessed in a double-blind review process so that the judges would not know what team was attached to each entry.

    The third-place prize of $25,000 was awarded to Okan Arslan and Rasit Abay. Okan is a professor at HEC Montréal, and Rasit is a doctoral student at the University of New South Wales in Australia. The runner-up prize at $50,000 was awarded to MIT’s own Xiaotong Guo, Qingyi Wang, and Baichuan Mo, all doctoral students. The top prize of $100,000 was awarded to Professor William Cook of the University of Waterloo in Canada, Professor Stephan Held of the University of Bonn in Germany, and Professor Emeritus Keld Helsgaun of Roskilde University in Denmark. Congratulations to all winners and contestants were held via webinar on July 30.

    Top-performing teams may be interviewed by Amazon for research roles in the company’s Last Mile organization. MIT CTL will publish and promote short technical papers written by all finalists and might invite top-performing teams to present at MIT. Further, a team led by Matthias Winkenbach, director of the MIT Megacity Logistics Lab, will guest-edit a special issue of Transportation Science, one of the most renowned academic journals in this field, featuring academic papers on topics related to the problem tackled by the research challenge. More

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    Helping companies optimize their websites and mobile apps

    Creating a good customer experience increasingly means creating a good digital experience. But metrics like pageviews and clicks offer limited insight into how much customers actually like a digital product.

    That’s the problem the digital optimization company Amplitude is solving. Amplitude gives companies a clearer picture into how users interact with their digital products to help them understand exactly which features to promote or improve.

    “It’s all about using product data to drive your business,” says Amplitude CEO Spenser Skates ’10, who co-founded the company with Curtis Liu ’10 and Stanford University graduate Jeffrey Wang. “Mobile apps and websites are really complex. The average app or website will have thousands of things you can do with it. The question is how you know which of those things are driving a great user experience and which parts are really frustrating for users.”

    Amplitude’s database can gather millions of details about how users behave inside an app or website and allow customers to explore that information without needing data science degrees.

    “It provides an interface for very easy, accessible ways of looking at your data, understanding your data, and asking questions of that data,” Skates says.

    Amplitude, which recently announced it will be going public, is already helping 23 of the 100 largest companies in the U.S. Customers include media companies like NBC, tech companies like Twitter, and retail companies like Walmart.

    “Our platform helps businesses understand how people are using their apps and websites so they can create better versions of their products,” Skates says. “It’s all about creating a really compelling product.”

    Learning entrepreneurship

    The founders say their years at MIT were among the best of their lives. Skates and Liu were undergraduates from 2006 to 2010. Skates majored in biological engineering while Liu majored in mathematics and electrical engineering and computer science. The two first met as opponents in MIT’s Battlecode competition, in which students use artificial intelligence algorithms to control teams of robots that compete in a strategy game against other teams. The following year they teamed up.

    “There are a lot of parallels between what you’re trying to do in Battlecode and what you end up having to do in the early stages of a startup,” Liu says. “You have limited resources, limited time, and you’re trying to accomplish a goal. What we found is trying a lot of different things, putting our ideas out there and testing them with real data, really helped us focus on the things that actually mattered. That method of iteration and continual improvement set the foundation for how we approach building products and startups.”

    Liu and Skates next participated in the MIT $100K Entrepreneurship Competition with an idea for a cloud-based music streaming service. After graduation, Skates began working in finance and Liu got a job at Google, but they continued pursuing startup ideas on the side, including a website that let alumni see where their classmates ended up and a marketplace for finding photographers.

    A year after graduation, the founders decided to quit their jobs and work on a startup full time. Skates moved into Liu’s apartment in San Francisco, setting up a mattress on the floor, and they began working on a project that became Sonalight, a voice recognition app. As part of the project, the founders built an internal system to understand where users got stuck in the app and what features were used the most.

    Despite getting over 100,000 downloads, the founders decided Sonalight was a little too early for its time and started thinking their analytics feature could be useful to other companies. They spoke with about 30 different product teams to learn more about what companies wanted from their digital analytics. Amplitude was officially founded in 2012.

    Amplitude gathers fine details about digital product usage, parsing out individual features and actions to give customers a better view of how their products are being used. Using the data in Amplitude’s intuitive, no-code interface, customers can make strategic decisions like whether to launch a feature or change a distribution channel.

    The platform is designed to ease the bottlenecks that arise when executives, product teams, salespeople, and marketers want to answer questions about customer experience or behavior but need the data science team to crunch the numbers for them.

    “It’s a very collaborative interface to encourage customers to work together to understand how users are engaging with their apps,” Skates says.

    Amplitude’s database also uses machine learning to segment users, predict user outcomes, and uncover novel correlations. Earlier this year, the company unveiled a service called Recommend that helps companies create personalized user experiences across their entire platform in minutes. The service goes beyond demographics to personalize customer experiences based on what users have done or seen before within the product.

    “We’re very conscious on the privacy front,” Skates says. “A lot of analytics companies will resell your data to third parties or use it for advertising purposes. We don’t do any of that. We’re only here to provide product insights to our customers. We’re not using data to track you across the web. Everyone expects Netflix to use the data on what you’ve watched before to recommend what to watch next. That’s effectively what we’re helping other companies do.”

    Optimizing digital experiences

    The meditation app Calm is on a mission to help users build habits that improve their mental wellness. Using Amplitude, the company learned that users most often use the app to get better sleep and reduce stress. The insights helped Calm’s team double down on content geared toward those goals, launching “sleep stories” to help users unwind at the end of each day and adding content around anxiety relief and relaxation. Sleep stories are now Calm’s most popular type of content, and Calm has grown rapidly to millions of people around the world.

    Calm’s story shows the power of letting user behavior drive product decisions. Amplitude has also helped the online fundraising site GoFundMe increase donations by showing users more compelling campaigns and the exercise bike company Peloton realize the importance of social features like leaderboards.

    Moving forward, the founders believe Amplitude’s platform will continue helping companies adapt to an increasingly digital world in which users expect more compelling, personalized experiences.

    “If you think about the online experience for companies today compared to 10 years ago, now [digital] is the main point of contact, whether you’re a media company streaming content, a retail company, or a finance company,” Skates says. “That’s only going to continue. That’s where we’re trying to help.” More

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    Exact symbolic artificial intelligence for faster, better assessment of AI fairness

    The justice system, banks, and private companies use algorithms to make decisions that have profound impacts on people’s lives. Unfortunately, those algorithms are sometimes biased — disproportionately impacting people of color as well as individuals in lower income classes when they apply for loans or jobs, or even when courts decide what bail should be set while a person awaits trial.

    MIT researchers have developed a new artificial intelligence programming language that can assess the fairness of algorithms more exactly, and more quickly, than available alternatives.

    Their Sum-Product Probabilistic Language (SPPL) is a probabilistic programming system. Probabilistic programming is an emerging field at the intersection of programming languages and artificial intelligence that aims to make AI systems much easier to develop, with early successes in computer vision, common-sense data cleaning, and automated data modeling. Probabilistic programming languages make it much easier for programmers to define probabilistic models and carry out probabilistic inference — that is, work backward to infer probable explanations for observed data.

    “There are previous systems that can solve various fairness questions. Our system is not the first; but because our system is specialized and optimized for a certain class of models, it can deliver solutions thousands of times faster,” says Feras Saad, a PhD student in electrical engineering and computer science (EECS) and first author on a recent paper describing the work. Saad adds that the speedups are not insignificant: The system can be up to 3,000 times faster than previous approaches.

    SPPL gives fast, exact solutions to probabilistic inference questions such as “How likely is the model to recommend a loan to someone over age 40?” or “Generate 1,000 synthetic loan applicants, all under age 30, whose loans will be approved.” These inference results are based on SPPL programs that encode probabilistic models of what kinds of applicants are likely, a priori, and also how to classify them. Fairness questions that SPPL can answer include “Is there a difference between the probability of recommending a loan to an immigrant and nonimmigrant applicant with the same socioeconomic status?” or “What’s the probability of a hire, given that the candidate is qualified for the job and from an underrepresented group?”

    SPPL is different from most probabilistic programming languages, as SPPL only allows users to write probabilistic programs for which it can automatically deliver exact probabilistic inference results. SPPL also makes it possible for users to check how fast inference will be, and therefore avoid writing slow programs. In contrast, other probabilistic programming languages such as Gen and Pyro allow users to write down probabilistic programs where the only known ways to do inference are approximate — that is, the results include errors whose nature and magnitude can be hard to characterize.

    Error from approximate probabilistic inference is tolerable in many AI applications. But it is undesirable to have inference errors corrupting results in socially impactful applications of AI, such as automated decision-making, and especially in fairness analysis.

    Jean-Baptiste Tristan, associate professor at Boston College and former research scientist at Oracle Labs, who was not involved in the new research, says, “I’ve worked on fairness analysis in academia and in real-world, large-scale industry settings. SPPL offers improved flexibility and trustworthiness over other PPLs on this challenging and important class of problems due to the expressiveness of the language, its precise and simple semantics, and the speed and soundness of the exact symbolic inference engine.”

    SPPL avoids errors by restricting to a carefully designed class of models that still includes a broad class of AI algorithms, including the decision tree classifiers that are widely used for algorithmic decision-making. SPPL works by compiling probabilistic programs into a specialized data structure called a “sum-product expression.” SPPL further builds on the emerging theme of using probabilistic circuits as a representation that enables efficient probabilistic inference. This approach extends prior work on sum-product networks to models and queries expressed via a probabilistic programming language. However, Saad notes that this approach comes with limitations: “SPPL is substantially faster for analyzing the fairness of a decision tree, for example, but it can’t analyze models like neural networks. Other systems can analyze both neural networks and decision trees, but they tend to be slower and give inexact answers.”

    “SPPL shows that exact probabilistic inference is practical, not just theoretically possible, for a broad class of probabilistic programs,” says Vikash Mansinghka, an MIT principal research scientist and senior author on the paper. “In my lab, we’ve seen symbolic inference driving speed and accuracy improvements in other inference tasks that we previously approached via approximate Monte Carlo and deep learning algorithms. We’ve also been applying SPPL to probabilistic programs learned from real-world databases, to quantify the probability of rare events, generate synthetic proxy data given constraints, and automatically screen data for probable anomalies.”

    The new SPPL probabilistic programming language was presented in June at the ACM SIGPLAN International Conference on Programming Language Design and Implementation (PLDI), in a paper that Saad co-authored with MIT EECS Professor Martin Rinard and Mansinghka. SPPL is implemented in Python and is available open source. More