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    Machine learning and the microscope

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    With recent advances in imaging, genomics and other technologies, the life sciences are awash in data. If a biologist is studying cells taken from the brain tissue of Alzheimer’s patients, for example, there could be any number of characteristics they want to investigate — a cell’s type, the genes it’s expressing, its location within the tissue, or more. However, while cells can now be probed experimentally using different kinds of measurements simultaneously, when it comes to analyzing the data, scientists usually can only work with one type of measurement at a time.Working with “multimodal” data, as it’s called, requires new computational tools, which is where Xinyi Zhang comes in.The fourth-year MIT PhD student is bridging machine learning and biology to understand fundamental biological principles, especially in areas where conventional methods have hit limitations. Working in the lab of MIT Professor Caroline Uhler in the Department of Electrical Engineering and Computer Science, the Laboratory for Information and Decision Systems, and the Institute for Data, Systems, and Society, and collaborating with researchers at the Eric and Wendy Schmidt Center at the Broad Institute and elsewhere, Zhang has led multiple efforts to build computational frameworks and principles for understanding the regulatory mechanisms of cells.“All of these are small steps toward the end goal of trying to answer how cells work, how tissues and organs work, why they have disease, and why they can sometimes be cured and sometimes not,” Zhang says.The activities Zhang pursues in her down time are no less ambitious. The list of hobbies she has taken up at the Institute include sailing, skiing, ice skating, rock climbing, performing with MIT’s Concert Choir, and flying single-engine planes. (She earned her pilot’s license in November 2022.)“I guess I like to go to places I’ve never been and do things I haven’t done before,” she says with signature understatement.Uhler, her advisor, says that Zhang’s quiet humility leads to a surprise “in every conversation.”“Every time, you learn something like, ‘Okay, so now she’s learning to fly,’” Uhler says. “It’s just amazing. Anything she does, she does for the right reasons. She wants to be good at the things she cares about, which I think is really exciting.”Zhang first became interested in biology as a high school student in Hangzhou, China. She liked that her teachers couldn’t answer her questions in biology class, which led her to see it as the “most interesting” topic to study.Her interest in biology eventually turned into an interest in bioengineering. After her parents, who were middle school teachers, suggested studying in the United States, she majored in the latter alongside electrical engineering and computer science as an undergraduate at the University of California at Berkeley.Zhang was ready to dive straight into MIT’s EECS PhD program after graduating in 2020, but the Covid-19 pandemic delayed her first year. Despite that, in December 2022, she, Uhler, and two other co-authors published a paper in Nature Communications.The groundwork for the paper was laid by Xiao Wang, one of the co-authors. She had previously done work with the Broad Institute in developing a form of spatial cell analysis that combined multiple forms of cell imaging and gene expression for the same cell while also mapping out the cell’s place in the tissue sample it came from — something that had never been done before.This innovation had many potential applications, including enabling new ways of tracking the progression of various diseases, but there was no way to analyze all the multimodal data the method produced. In came Zhang, who became interested in designing a computational method that could.The team focused on chromatin staining as their imaging method of choice, which is relatively cheap but still reveals a great deal of information about cells. The next step was integrating the spatial analysis techniques developed by Wang, and to do that, Zhang began designing an autoencoder.Autoencoders are a type of neural network that typically encodes and shrinks large amounts of high-dimensional data, then expand the transformed data back to its original size. In this case, Zhang’s autoencoder did the reverse, taking the input data and making it higher-dimensional. This allowed them to combine data from different animals and remove technical variations that were not due to meaningful biological differences.In the paper, they used this technology, abbreviated as STACI, to identify how cells and tissues reveal the progression of Alzheimer’s disease when observed under a number of spatial and imaging techniques. The model can also be used to analyze any number of diseases, Zhang says.Given unlimited time and resources, her dream would be to build a fully complete model of human life. Unfortunately, both time and resources are limited. Her ambition isn’t, however, and she says she wants to keep applying her skills to solve the “most challenging questions that we don’t have the tools to answer.”She’s currently working on wrapping up a couple of projects, one focused on studying neurodegeneration by analyzing frontal cortex imaging and another on predicting protein images from protein sequences and chromatin imaging.“There are still many unanswered questions,” she says. “I want to pick questions that are biologically meaningful, that help us understand things we didn’t know before.” More

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      MIT-Takeda Program wraps up with 16 publications, a patent, and nearly two dozen projects completed

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      When the Takeda Pharmaceutical Co. and the MIT School of Engineering launched their collaboration focused on artificial intelligence in health care and drug development in February 2020, society was on the cusp of a globe-altering pandemic and AI was far from the buzzword it is today.As the program concludes, the world looks very different. AI has become a transformative technology across industries including health care and pharmaceuticals, while the pandemic has altered the way many businesses approach health care and changed how they develop and sell medicines.For both MIT and Takeda, the program has been a game-changer.When it launched, the collaborators hoped the program would help solve tangible, real-world problems. By its end, the program has yielded a catalog of new research papers, discoveries, and lessons learned, including a patent for a system that could improve the manufacturing of small-molecule medicines.Ultimately, the program allowed both entities to create a foundation for a world where AI and machine learning play a pivotal role in medicine, leveraging Takeda’s expertise in biopharmaceuticals and the MIT researchers’ deep understanding of AI and machine learning.“The MIT-Takeda Program has been tremendously impactful and is a shining example of what can be accomplished when experts in industry and academia work together to develop solutions,” says Anantha Chandrakasan, MIT’s chief innovation and strategy officer, dean of the School of Engineering, and the Vannevar Bush Professor of Electrical Engineering and Computer Science. “In addition to resulting in research that has advanced how we use AI and machine learning in health care, the program has opened up new opportunities for MIT faculty and students through fellowships, funding, and networking.”What made the program unique was that it was centered around several concrete challenges spanning drug development that Takeda needed help addressing. MIT faculty had the opportunity to select the projects based on their area of expertise and general interest, allowing them to explore new areas within health care and drug development.“It was focused on Takeda’s toughest business problems,” says Anne Heatherington, Takeda’s research and development chief data and technology officer and head of its Data Sciences Institute.“They were problems that colleagues were really struggling with on the ground,” adds Simon Davies, the executive director of the MIT-Takeda Program and Takeda’s global head of statistical and quantitative sciences. Takeda saw an opportunity to collaborate with MIT’s world-class researchers, who were working only a few blocks away. Takeda, a global pharmaceutical company with global headquarters in Japan, has its global business units and R&D center just down the street from the Institute.As part of the program, MIT faculty were able to select what issues they were interested in working on from a group of potential Takeda projects. Then, collaborative teams including MIT researchers and Takeda employees approached research questions in two rounds. Over the course of the program, collaborators worked on 22 projects focused on topics including drug discovery and research, clinical drug development, and pharmaceutical manufacturing. Over 80 MIT students and faculty joined more than 125 Takeda researchers and staff on teams addressing these research questions.The projects centered around not only hard problems, but also the potential for solutions to scale within Takeda or within the biopharmaceutical industry more broadly.Some of the program’s findings have already resulted in wider studies. One group’s results, for instance, showed that using artificial intelligence to analyze speech may allow for earlier detection of frontotemporal dementia, while making that diagnosis more quickly and inexpensively. Similar algorithmic analyses of speech in patients diagnosed with ALS may also help clinicians understand the progression of that disease. Takeda is continuing to test both AI applications.Other discoveries and AI models that resulted from the program’s research have already had an impact. Using a physical model and AI learning algorithms can help detect particle size, mix, and consistency for powdered, small-molecule medicines, for instance, speeding up production timelines. Based on their research under the program, collaborators have filed for a patent for that technology.For injectable medicines like vaccines, AI-enabled inspections can also reduce process time and false rejection rates. Replacing human visual inspections with AI processes has already shown measurable impact for the pharmaceutical company.Heatherington adds, “our lessons learned are really setting the stage for what we’re doing next, really embedding AI and gen-AI [generative AI] into everything that we do moving forward.”Over the course of the program, more than 150 Takeda researchers and staff also participated in educational programming organized by the Abdul Latif Jameel Clinic for Machine Learning in Health. In addition to providing research opportunities, the program funded 10 students through SuperUROP, the Advanced Undergraduate Research Opportunities Program, as well as two cohorts from the DHIVE health-care innovation program, part of the MIT Sandbox Innovation Fund Program.Though the formal program has ended, certain aspects of the collaboration will continue, such as the MIT-Takeda Fellows, which supports graduate students as they pursue groundbreaking research related to health and AI. During its run, the program supported 44 MIT-Takeda Fellows and will continue to support MIT students through an endowment fund. Organic collaboration between MIT and Takeda researchers will also carry forward. And the programs’ collaborators are working to create a model for similar academic and industry partnerships to widen the impact of this first-of-its-kind collaboration.  More

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      A community collaboration for progress

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      While decades of discriminatory policies and practices continue to fuel the affordable housing crisis in the United States, less than three miles from the MIT campus exists a beacon of innovation and community empowerment.“We are very proud to continue MIT’s long-standing partnership with Camfield Estates,” says Catherine D’Ignazio, associate professor of urban science and planning. “Camfield has long been an incubator of creative ideas focused on uplifting their community.”D’Ignazio co-leads a research team focused on housing as part of the MIT Initiative for Combatting Systemic Racism (ICSR) led by the Institute for Data, Systems, and Society (IDSS). The group researches the uneven impacts of data, AI, and algorithmic systems on housing in the United States, as well as ways that these same tools could be used to address racial disparities. The Camfield Tenant Association is a research partner providing insight into the issue and relevant data, as well as opportunities for MIT researchers to solve real challenges and make a local impact.

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      MIT Initiative on Combatting Systemic Racism – Housing Video: MIT Sociotechnical Systems Research Center

      Formerly known as “Camfield Gardens,” the 102-unit housing development in Roxbury, Massachusetts, was among the pioneering sites in the 1990s to engage in the U.S. Department of Housing and Urban Development’s (HUD) program aimed at revitalizing disrepaired public housing across the country. This also served as the catalyst for their collaboration with MIT, which began in the early 2000s.“The program gave Camfield the money and energy to tear everything on the site down and build it back up anew, in addition to allowing them to buy the property from the city for $1 and take full ownership of the site,” explains Nolen Scruggs, a master’s student in the MIT Department of Urban Studies and Planning (DUSP) who has worked with Camfield over the past few years as part of ICSR’s housing vertical team. “At the time, MIT graduate students helped start a ‘digital divide’ bridge gap program that later evolved into the tech lab that is still there today, continuing to enable residents to learn computer skills and things they might need to get a hand up.”Because of that early collaboration, Camfield Estates reached out to MIT in 2022 to start a new chapter of collaboration with students. Scruggs spent a few months building a team of students from Harvard University, Wentworth Institute of Technology, and MIT to work on a housing design project meant to help the Camfield Tenants Association prepare for their looming redevelopment needs.“One of the things that’s been really important to the work of the ICSR housing vertical is historical context,” says Peko Hosoi, a professor of mechanical engineering and mathematics who co-leads the ICSR Housing vertical with D’Ignazio. “We didn’t get to the place we are right now with housing in an instant. There’s a lot of things that have happened in the U.S. like redlining, predatory lending, and different ways of investing in infrastructure that add important contexts.”“Quantitative methods are a great way to look across macroscale phenomena, but our team recognizes and values qualitative and participatory methods as well, to get a more grounded picture of what community needs really are and what kinds of innovations can bubble up from communities themselves,” D’Ignazio adds. “This is where the partnership with Camfield Estates comes in, which Nolen has been leading.”Finding creative solutionsBefore coming to MIT, Scruggs, a proud New Yorker, worked on housing issues while interning for his local congressperson, House Minority Leader Hakeem Jeffries. He called residents to discuss their housing concerns, learning about the affordability issues that were making it hard for lower- and middle-income families to find places to live.“Having this behind-the-scenes experience set the stage for my involvement in Camfield,” Scruggs says, recalling his start at Camfield conducting participatory action research, meeting with Camfield seniors to discuss and capture their concerns.Scruggs says the biggest issue they have been trying to tackle with Camfield is twofold: creating more space for new residents while also helping current residents achieve their end goal of homeownership.“This speaks to some of the larger issues our group at ICSR is working on in terms of housing affordability,” he says. “With Camfield it is looking at where can people with Section 8 vouchers move, what limits do they have, and what barriers do they face — whether it’s through big tech systems, or individual preferences coming from landlords.”Scruggs adds, “The discrimination those people face while trying to find a house, lock it down, talk to a bank, etc. — it can be very, very difficult and discouraging.” Scruggs says one attempt to combat this issue would be through hiring a caseworker to assist people through the process — one of many ideas that came from a Camfield collaboration with the FHLBank Affordable Housing Development Competition.As part of the competition, the goal for Scruggs’s team was to help Camfield tenants understand all of their options and their potential trade-offs, so that in the end they can make informed decisions about what they want to do with their space.“So often redevelopment schemes don’t ensure people can come back.” Scruggs says. “There are specific design proposals being made to ensure that the structure of people’s lifestyles wouldn’t be disrupted.”Scruggs says that tentative recommendations discussed with tenant association president Paulette Ford include replacing the community center with a high-rise development that would increase the number of units available.“I think they are thinking really creatively about their options,” Hosoi says. “Paulette Ford, and her mother before her, have always referred to Camfield as a ‘hand up,’ with the idea that people come to Camfield to live until they can afford a home of their own locally.”Scruggs’s other partnership with Camfield involves working with MIT undergraduate Amelie Nagle as part of the Undergraduate Research Opportunities Program to create programing that will teach computer design and coding to Camfield community kids — in the very TechLab that goes back to MIT and Camfield’s first collaboration.“Nolen has a real commitment to community-led knowledge production,” says D’Ignazio. “It has been a pleasure to work with him and see how he takes all his urban planning skills (GIS, mapping, urban design, photography, and more) to work in respectful ways that foreground community innovation.”She adds: “We are hopeful that the process will yield some high-quality architectural and planning ideas, and help Camfield take the next step towards realizing their innovative vision.” More

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      Janabel Xia: Algorithms, dance rhythms, and the drive to succeed

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      Senior math major Janabel Xia is a study of a person in constant motion.When she isn’t sorting algorithms and improving traffic control systems for driverless vehicles, she’s dancing as a member of at least four dance clubs. She’s joined several social justice organizations, worked on cryptography and web authentication technology, and created a polling app that allows users to vote anonymously.In her final semester, she’s putting the pedal to the metal, with a green light to lessen the carbon footprint of urban transportation by using sensors at traffic light intersections.First stepsGrowing up in Lexington, Massachusetts, Janabel has been competing on math teams since elementary school. On her math team, which met early mornings before the start of school, she discovered a love of problem-solving that challenged her more than her classroom “plug-and-chug exercises.”At Lexington High School, she was math team captain, a two-time Math Olympiad attendee, and a silver medalist for Team USA at the European Girls’ Mathematical Olympiad.As a math major, she studies combinatorics and theoretical computer science, including theoretical and applied cryptography. In her sophomore year, she was a researcher in the Cryptography and Information Security Group at the MIT Computer Science and Artificial Intelligence Laboratory, where she conducted cryptanalysis research under Professor Vinod Vaikuntanathan.Part of her interests in cryptography stem from the beauty of the underlying mathematics itself — the field feels like clever engineering with mathematical tools. But another part of her interest in cryptography stems from its political dimensions, including its potential to fundamentally change existing power structures and governance. Xia and students at the University of California at Berkeley and Stanford University created zkPoll, a private polling app written with the Circom programming language, that allows users to create polls for specific sets of people, while generating a zero-knowledge proof that keeps personal information hidden to decrease negative voting influences from public perception.Her participation in the PKG Center’s Active Community Engagement Freshman Pre-Orientation Program introduced her to local community organizations focusing on food security, housing for formerly incarcerated individuals, and access to health care. She is also part of Reading for Revolution, a student book club that discusses race, class, and working-class movements within MIT and the Greater Boston area.Xia’s educational journey led to her ongoing pursuit of combining mathematical and computational methods in areas adjacent to urban planning.  “When I realized how much planning was concerned with social justice as it was concerned with design, I became more attracted to the field.”Going on autopilotShe took classes with the Department of Urban Studies and Planning and is currently working on an Undergraduate Research Opportunities Program (UROP) project with Professor Cathy Wu in the Institute for Data, Systems, and Society.Recent work on eco-driving by Wu and doctoral student Vindula Jayawardana investigated semi-autonomous vehicles that communicate with sensors localized at traffic intersections, which in theory could reduce carbon emissions by up to 21 percent.Xia aims to optimize the implementation scheme for these sensors at traffic intersections, considering a graded scheme where perhaps only 20 percent of all sensors are initially installed, and more sensors get added in waves. She wants to maximize the emission reduction rates at each step of the process, as well as ensure there is no unnecessary installation and de-installation of such sensors.  Dance numbersMeanwhile, Xia has been a member of MIT’s Fixation, Ridonkulous, and MissBehavior groups, and as a traditional Chinese dance choreographer for the MIT Asian Dance Team. A dancer since she was 3, Xia started with Chinese traditional dance, and later added ballet and jazz. Because she is as much of a dancer as a researcher, she has figured out how to make her schedule work.“Production weeks are always madness, with dancers running straight from class to dress rehearsals and shows all evening and coming back early next morning to take down lights and roll up marley [material that covers the stage floor],” she says. “As busy as it keeps me, I couldn’t have survived MIT without dance. I love the discipline, creativity, and most importantly the teamwork that dance demands of us. I really love the dance community here with my whole heart. These friends have inspired me and given me the love to power me through MIT.”Xia lives with her fellow Dance Team members at the off-campus Women’s Independent Living Group (WILG).  “I really value WILG’s culture of independence, both in lifestyle — cooking, cleaning up after yourself, managing house facilities, etc. — and thought — questioning norms, staying away from status games, finding new passions.”In addition to her UROP, she’s wrapping up some graduation requirements, finishing up a research paper on sorting algorithms from her summer at the University of Minnesota Duluth Research Experience for Undergraduates in combinatorics, and deciding between PhD programs in math and computer science.  “My biggest goal right now is to figure out how to combine my interests in mathematics and urban studies, and more broadly connect technical perspectives with human-centered work in a way that feels right to me,” she says.“Overall, MIT has given me so many avenues to explore that I would have never thought about before coming here, for which I’m infinitely grateful. Every time I find something new, it’s hard for me not to find it cool. There’s just so much out there to learn about. While it can feel overwhelming at times, I hope to continue that learning and exploration for the rest of my life.” More

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      From steel engineering to ovarian tumor research

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      Ashutosh Kumar is a classically trained materials engineer. Having grown up with a passion for making things, he has explored steel design and studied stress fractures in alloys.Throughout Kumar’s education, however, he was also drawn to biology and medicine. When he was accepted into an undergraduate metallurgical engineering and materials science program at Indian Institute of Technology (IIT) Bombay, the native of Jamshedpur was very excited — and “a little dissatisfied, since I couldn’t do biology anymore.”Now a PhD candidate and a MathWorks Fellow in MIT’s Department of Materials Science and Engineering, Kumar can merge his wide-ranging interests. He studies the effect of certain bacteria that have been observed encouraging the spread of ovarian cancer and possibly reducing the effectiveness of chemotherapy and immunotherapy.“Some microbes have an affinity toward infecting ovarian cancer cells, which can lead to changes in the cellular structure and reprogramming cells to survive in stressful conditions,” Kumar says. “This means that cells can migrate to different sites and may have a mechanism to develop chemoresistance. This opens an avenue to develop therapies to see if we can start to undo some of these changes.”Kumar’s research combines microbiology, bioengineering, artificial intelligence, big data, and materials science. Using microbiome sequencing and AI, he aims to define microbiome changes that may correlate with poor patient outcomes. Ultimately, his goal is to engineer bacteriophage viruses to reprogram bacteria to work therapeutically.Kumar started inching toward work in the health sciences just months into earning his bachelor’s degree at IIT Bombay.“I realized engineering is so flexible that its applications extend to any field,” he says, adding that he started working with biomaterials “to respect both my degree program and my interests.”“I loved it so much that I decided to go to graduate school,” he adds.Starting his PhD program at MIT, he says, “was a fantastic opportunity to switch gears and work on more interdisciplinary or ‘MIT-type’ work.”Kumar says he and Angela Belcher, the James Mason Crafts Professor of biological engineering and materials science, began discussing the impact of the microbiome on ovarian cancer when he first arrived at MIT.“I shared my enthusiasm about human health and biology, and we started brainstorming,” he says. “We realized that there’s an unmet need to understand a lot of gynecological cancers. Ovarian cancer is an aggressive cancer, which is usually diagnosed when it’s too late and has already spread.”In 2022, Kumar was awarded a MathWorks Fellowship. The fellowships are awarded to School of Engineering graduate students, preferably those who use MATLAB or Simulink — which were developed by the mathematical computer software company MathWorks — in their research. The philanthropic support fueled Kumar’s full transition into health science research.“The work we are doing now was initially not funded by traditional sources, and the MathWorks Fellowship gave us the flexibility to pursue this field,” Kumar says. “It provided me with opportunities to learn new skills and ask questions about this topic. MathWorks gave me a chance to explore my interests and helped me navigate from being a steel engineer to a cancer scientist.”Kumar’s work on the relationship between bacteria and ovarian cancer started with studying which bacteria are incorporated into tumors in mouse models.“We started looking closely at changes in cell structure and how those changes impact cancer progression,” he says, adding that MATLAB image processing helps him and his collaborators track tumor metastasis.The research team also uses RNA sequencing and MATLAB algorithms to construct a taxonomy of the bacteria.“Once we have identified the microbiome composition,” Kumar says, “we want to see how the microbiome changes as cancer progresses and identify changes in, let’s say, patients who develop chemoresistance.”He says recent findings that ovarian cancer may originate in the fallopian tubes are promising because detecting cancer-related biomarkers or lesions before cancer spreads to the ovaries could lead to better prognoses.As he pursues his research, Kumar says he is extremely thankful to Belcher “for believing in me to work on this project.“She trusted me and my passion for making an impact on human health — even though I come from a materials engineering background — and supported me throughout. It was her passion to take on new challenges that made it possible for me to work on this idea. She has been an amazing mentor and motivated me to continue moving forward.”For her part, Belcher is equally enthralled.“It has been amazing to work with Ashutosh on this ovarian cancer microbiome project,” she says. “He has been so passionate and dedicated to looking for less-conventional approaches to solve this debilitating disease. His innovations around looking for very early changes in the microenvironment of this disease could be critical in interception and prevention of ovarian cancer. We started this project with very little preliminary data, so his MathWorks fellowship was critical in the initiation of the project.”Kumar, who has been very active in student government and community-building activities, believes it is very important for students to feel included and at home at their institutions so they can develop in ways outside of academics. He says that his own involvement helps him take time off from work.“Science can never stop, and there will always be something to do,” he says, explaining that he deliberately schedules time off and that social engagement helps him to experience downtime. “Engaging with community members through events on campus or at the dorm helps set a mental boundary with work.”Regarding his unusual route through materials science to cancer research, Kumar regards it as something that occurred organically.“I have observed that life is very dynamic,” he says. “What we think we might do versus what we end up doing is never consistent. Five years back, I had no idea I would be at MIT working with such excellent scientific mentors around me.” More

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      Fostering research, careers, and community in materials science

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      Gabrielle Wood, a junior at Howard University majoring in chemical engineering, is on a mission to improve the sustainability and life cycles of natural resources and materials. Her work in the Materials Initiative for Comprehensive Research Opportunity (MICRO) program has given her hands-on experience with many different aspects of research, including MATLAB programming, experimental design, data analysis, figure-making, and scientific writing.Wood is also one of 10 undergraduates from 10 universities around the United States to participate in the first MICRO Summit earlier this year. The internship program, developed by the MIT Department of Materials Science and Engineering (DMSE), first launched in fall 2021. Now in its third year, the program continues to grow, providing even more opportunities for non-MIT undergraduate students — including the MICRO Summit and the program’s expansion to include Northwestern University.“I think one of the most valuable aspects of the MICRO program is the ability to do research long term with an experienced professor in materials science and engineering,” says Wood. “My school has limited opportunities for undergraduate research in sustainable polymers, so the MICRO program allowed me to gain valuable experience in this field, which I would not otherwise have.”Like Wood, Griheydi Garcia, a senior chemistry major at Manhattan College, values the exposure to materials science, especially since she is not able to learn as much about it at her home institution.“I learned a lot about crystallography and defects in materials through the MICRO curriculum, especially through videos,” says Garcia. “The research itself is very valuable, as well, because we get to apply what we’ve learned through the videos in the research we do remotely.”Expanding research opportunitiesFrom the beginning, the MICRO program was designed as a fully remote, rigorous education and mentoring program targeted toward students from underserved backgrounds interested in pursuing graduate school in materials science or related fields. Interns are matched with faculty to work on their specific research interests.Jessica Sandland ’99, PhD ’05, principal lecturer in DMSE and co-founder of MICRO, says that research projects for the interns are designed to be work that they can do remotely, such as developing a machine-learning algorithm or a data analysis approach.“It’s important to note that it’s not just about what the program and faculty are bringing to the student interns,” says Sandland, a member of the MIT Digital Learning Lab, a joint program between MIT Open Learning and the Institute’s academic departments. “The students are doing real research and work, and creating things of real value. It’s very much an exchange.”Cécile Chazot PhD ’22, now an assistant professor of materials science and engineering at Northwestern University, had helped to establish MICRO at MIT from the very beginning. Once at Northwestern, she quickly realized that expanding MICRO to Northwestern would offer even more research opportunities to interns than by relying on MIT alone — leveraging the university’s strong materials science and engineering department, as well as offering resources for biomaterials research through Northwestern’s medical school. The program received funding from 3M and officially launched at Northwestern in fall 2023. Approximately half of the MICRO interns are now in the program with MIT and half are with Northwestern. Wood and Garcia both participate in the program via Northwestern.“By expanding to another school, we’ve been able to have interns work with a much broader range of research projects,” says Chazot. “It has become easier for us to place students with faculty and research that match their interests.”Building communityThe MICRO program received a Higher Education Innovation grant from the Abdul Latif Jameel World Education Lab, part of MIT Open Learning, to develop an in-person summit. In January 2024, interns visited MIT for three days of presentations, workshops, and campus tours — including a tour of the MIT.nano building — as well as various community-building activities.“A big part of MICRO is the community,” says Chazot. “A highlight of the summit was just seeing the students come together.”The summit also included panel discussions that allowed interns to gain insights and advice from graduate students and professionals. The graduate panel discussion included MIT graduate students Sam Figueroa (mechanical engineering), Isabella Caruso (DMSE), and Eliana Feygin (DMSE). The career panel was led by Chazot and included Jatin Patil PhD ’23, head of product at SiTration; Maureen Reitman ’90, ScD ’93, group vice president and principal engineer at Exponent; Lucas Caretta PhD ’19, assistant professor of engineering at Brown University; Raquel D’Oyen ’90, who holds a PhD from Northwestern University and is a senior engineer at Raytheon; and Ashley Kaiser MS ’19, PhD ’21, senior process engineer at 6K.Students also had an opportunity to share their work with each other through research presentations. Their presentations covered a wide range of topics, including: developing a computer program to calculate solubility parameters for polymers used in textile manufacturing; performing a life-cycle analysis of a photonic chip and evaluating its environmental impact in comparison to a standard silicon microchip; and applying machine learning algorithms to scanning transmission electron microscopy images of CrSBr, a two-dimensional magnetic material. “The summit was wonderful and the best academic experience I have had as a first-year college student,” says MICRO intern Gabriella La Cour, who is pursuing a major in chemistry and dual degree biomedical engineering at Spelman College and participates in MICRO through MIT. “I got to meet so many students who were all in grades above me … and I learned a little about how to navigate college as an upperclassman.” “I actually have an extremely close friendship with one of the students, and we keep in touch regularly,” adds La Cour. “Professor Chazot gave valuable advice about applications and recommendation letters that will be useful when I apply to REUs [Research Experiences for Undergraduates] and graduate schools.”Looking to the future, MICRO organizers hope to continue to grow the program’s reach.“We would love to see other schools taking on this model,” says Sandland. “There are a lot of opportunities out there. The more departments, research groups, and mentors that get involved with this program, the more impact it can have.” More

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      Advancing technology for aquaculture

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      According to the National Oceanic and Atmospheric Administration, aquaculture in the United States represents a $1.5 billion industry annually. Like land-based farming, shellfish aquaculture requires healthy seed production in order to maintain a sustainable industry. Aquaculture hatchery production of shellfish larvae — seeds — requires close monitoring to track mortality rates and assess health from the earliest stages of life. 

      Careful observation is necessary to inform production scheduling, determine effects of naturally occurring harmful bacteria, and ensure sustainable seed production. This is an essential step for shellfish hatcheries but is currently a time-consuming manual process prone to human error. 

      With funding from MIT’s Abdul Latif Jameel Water and Food Systems Lab (J-WAFS), MIT Sea Grant is working with Associate Professor Otto Cordero of the MIT Department of Civil and Environmental Engineering, Professor Taskin Padir and Research Scientist Mark Zolotas at the Northeastern University Institute for Experiential Robotics, and others at the Aquaculture Research Corporation (ARC), and the Cape Cod Commercial Fishermen’s Alliance, to advance technology for the aquaculture industry. Located on Cape Cod, ARC is a leading shellfish hatchery, farm, and wholesaler that plays a vital role in providing high-quality shellfish seed to local and regional growers.

      Two MIT students have joined the effort this semester, working with Robert Vincent, MIT Sea Grant’s assistant director of advisory services, through the Undergraduate Research Opportunities Program (UROP). 

      First-year student Unyime Usua and sophomore Santiago Borrego are using microscopy images of shellfish seed from ARC to train machine learning algorithms that will help automate the identification and counting process. The resulting user-friendly image recognition tool aims to aid aquaculturists in differentiating and counting healthy, unhealthy, and dead shellfish larvae, improving accuracy and reducing time and effort.

      Vincent explains that AI is a powerful tool for environmental science that enables researchers, industry, and resource managers to address challenges that have long been pinch points for accurate data collection, analysis, predictions, and streamlining processes. “Funding support from programs like J-WAFS enable us to tackle these problems head-on,” he says. 

      ARC faces challenges with manually quantifying larvae classes, an important step in their seed production process. “When larvae are in their growing stages they are constantly being sized and counted,” explains Cheryl James, ARC larval/juvenile production manager. “This process is critical to encourage optimal growth and strengthen the population.” 

      Developing an automated identification and counting system will help to improve this step in the production process with time and cost benefits. “This is not an easy task,” says Vincent, “but with the guidance of Dr. Zolotas at the Northeastern University Institute for Experiential Robotics and the work of the UROP students, we have made solid progress.” 

      The UROP program benefits both researchers and students. Involving MIT UROP students in developing these types of systems provides insights into AI applications that they might not have considered, providing opportunities to explore, learn, and apply themselves while contributing to solving real challenges.

      Borrego saw this project as an opportunity to apply what he’d learned in class 6.390 (Introduction to Machine Learning) to a real-world issue. “I was starting to form an idea of how computers can see images and extract information from them,” he says. “I wanted to keep exploring that.”

      Usua decided to pursue the project because of the direct industry impacts it could have. “I’m pretty interested in seeing how we can utilize machine learning to make people’s lives easier. We are using AI to help biologists make this counting and identification process easier.” While Usua wasn’t familiar with aquaculture before starting this project, she explains, “Just hearing about the hatcheries that Dr. Vincent was telling us about, it was unfortunate that not a lot of people know what’s going on and the problems that they’re facing.”

      On Cape Cod alone, aquaculture is an $18 million per year industry. But the Massachusetts Division of Marine Fisheries estimates that hatcheries are only able to meet 70–80 percent of seed demand annually, which impacts local growers and economies. Through this project, the partners aim to develop technology that will increase seed production, advance industry capabilities, and help understand and improve the hatchery microbiome.

      Borrego explains the initial challenge of having limited data to work with. “Starting out, we had to go through and label all of the data, but going through that process helped me learn a lot.” In true MIT fashion, he shares his takeaway from the project: “Try to get the best out of what you’re given with the data you have to work with. You’re going to have to adapt and change your strategies depending on what you have.”

      Usua describes her experience going through the research process, communicating in a team, and deciding what approaches to take. “Research is a difficult and long process, but there is a lot to gain from it because it teaches you to look for things on your own and find your own solutions to problems.”

      In addition to increasing seed production and reducing the human labor required in the hatchery process, the collaborators expect this project to contribute to cost savings and technology integration to support one of the most underserved industries in the United States. 

      Borrego and Usua both plan to continue their work for a second semester with MIT Sea Grant. Borrego is interested in learning more about how technology can be used to protect the environment and wildlife. Usua says she hopes to explore more projects related to aquaculture. “It seems like there’s an infinite amount of ways to tackle these issues.” More

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      in Data Management & Statistics

      Growing our donated organ supply

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      For those in need of one, an organ transplant is a matter of life and death. 

      Every year, the medical procedure gives thousands of people with advanced or end-stage diseases extended life. This “second chance” is heavily dependent on the availability, compatibility, and proximity of a precious resource that can’t be simply bought, grown, or manufactured — at least not yet.

      Instead, organs must be given — cut from one body and implanted into another. And because living organ donation is only viable in certain cases, many organs are only available for donation after the donor’s death.

      Unsurprisingly, the logistical and ethical complexity of distributing a limited number of transplant organs to a growing wait list of patients has received much attention. There’s an important part of the process that has received less focus, however, and which may hold significant untapped potential: organ procurement itself.

      “If you have a donated organ, who should you give it to? This question has been extensively studied in operations research, economics, and even applied computer science,” says Hammaad Adam, a graduate student in the Social and Engineering Systems (SES) doctoral program at the MIT Institute for Data, Systems, and Society (IDSS). “But there’s been a lot less research on where that organ comes from in the first place.”

      In the United States, nonprofits called organ procurement organizations, or OPOs, are responsible for finding and evaluating potential donors, interacting with grieving families and hospital administrations, and recovering and delivering organs — all while following the federal laws that serve as both their mandate and guardrails. Recent studies estimate that obstacles and inefficiencies lead to thousands of organs going uncollected every year, even as the demand for transplants continues to grow.

      “There’s been little transparent data on organ procurement,” argues Adam. Working with MIT computer science professors Marzyeh Ghassemi and Ashia Wilson, and in collaboration with stakeholders in organ procurement, Adam led a project to create a dataset called ORCHID: Organ Retrieval and Collection of Health Information for Donation. ORCHID contains a decade of clinical, financial, and administrative data from six OPOs.

      “Our goal is for the ORCHID database to have an impact in how organ procurement is understood, internally and externally,” says Ghassemi.

      Efficiency and equity 

      It was looking to make an impact that drew Adam to SES and MIT. With a background in applied math and experience in strategy consulting, solving problems with technical components sits right in his wheelhouse.

      “I really missed challenging technical problems from a statistics and machine learning standpoint,” he says of his time in consulting. “So I went back and got a master’s in data science, and over the course of my master’s got involved in a bunch of academic research projects in a few different fields, including biology, management science, and public policy. What I enjoyed most were some of the more social science-focused projects that had immediate impact.”

      As a grad student in SES, Adam’s research focuses on using statistical tools to uncover health-care inequities, and developing machine learning approaches to address them. “Part of my dissertation research focuses on building tools that can improve equity in clinical trials and other randomized experiments,” he explains.

      One recent example of Adam’s work: developing a novel method to stop clinical trials early if the treatment has an unintended harmful effect for a minority group of participants. “I’ve also been thinking about ways to increase minority representation in clinical trials through improved patient recruitment,” he adds.

      Racial inequities in health care extend into organ transplantation, where a majority of wait-listed patients are not white — far in excess of their demographic groups’ proportion to the overall population. There are fewer organ donations from many of these communities, due to various obstacles in need of better understanding if they are to be overcome. 

      “My work in organ transplantation began on the allocation side,” explains Adam. “In work under review, we examined the role of race in the acceptance of heart, liver, and lung transplant offers by physicians on behalf of their patients. We found that Black race of the patient was associated with significantly lower odds of organ offer acceptance — in other words, transplant doctors seemed more likely to turn down organs offered to Black patients. This trend may have multiple explanations, but it is nevertheless concerning.”

      Adam’s research has also found that donor-candidate race match was associated with significantly higher odds of offer acceptance, an association that Adam says “highlights the importance of organ donation from racial minority communities, and has motivated our work on equitable organ procurement.”

      Working with Ghassemi through the IDSS Initiative on Combatting Systemic Racism, Adam was introduced to OPO stakeholders looking to collaborate. “It’s this opportunity to impact not only health-care efficiency, but also health-care equity, that really got me interested in this research,” says Adam.

      Play video

      MIT Initiative on Combatting Systemic Racism – HealthcareVideo: IDSS

      Making an impact

      Creating a database like ORCHID means solving problems in multiple domains, from the technical to the political. Some efforts never overcome the first step: getting data in the first place. Thankfully, several OPOs were already seeking collaborations and looking to improve their performance.

      “We have been lucky to have a strong partnership with the OPOs, and we hope to work together to find important insights to improve efficiency and equity,” says Ghassemi.

      The value of a database like ORCHID is in its potential for generating new insights, especially through quantitative analysis with statistics and computing tools like machine learning. The potential value in ORCHID was recognized with an MIT Prize for Open Data, an MIT Libraries award highlighting the importance and impact of research data that is openly shared.

      “It’s nice that the work got some recognition,” says Adam of the prize. “And it was cool to see some of the other great open data work that’s happening at MIT. I think there’s real impact in releasing publicly available data in an important and understudied domain.”

      All the same, Adam knows that building the database is only the first step.

      “I’m very interested in understanding the bottlenecks in the organ procurement process,” he explains. “As part of my thesis research, I’m exploring this by modeling OPO decision-making using causal inference and structural econometrics.”

      Using insights from this research, Adam also aims to evaluate policy changes that can improve both equity and efficiency in organ procurement. “And we’re hoping to recruit more OPOs, and increase the amount of data we’re releasing,” he says. “The dream state is every OPO joins our collaboration and provides updated data every year.”

      Adam is excited to see how other researchers might use the data to address inefficiencies in organ procurement. “Every organ donor saves between three and four lives,” he says. “So every research project that comes out of this dataset could make a real impact.” More

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      in Data Management & Statistics

      Q&A: How refusal can be an act of design

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      This month in the ACM Journal on Responsible Computing, MIT graduate student Jonathan Zong SM ’20 and co-author J. Nathan Matias SM ’13, PhD ’17 of the Cornell Citizens and Technology Lab examine how the notion of refusal can open new avenues in the field of data ethics. In their open-access report, “Data Refusal From Below: A Framework for Understanding, Evaluating, and Envisioning Refusal as Design,” the pair proposes a framework in four dimensions to map how individuals can say “no” to technology misuses. At the same time, the researchers argue that just like design, refusal is generative, and has the potential to create alternate futures.

      Zong, a PhD candidate in electrical engineering and computer science, 2022-23 MIT Morningside Academy for Design Design Fellow, and member of the MIT Visualization Group, describes his latest work in this Q&A.

      Q: How do you define the concept of “refusal,” and where does it come from?

      A: Refusal was developed in feminist and Indigenous studies. It’s this idea of saying “no,” without being given permission to say “no.” Scholars like Ruha Benjamin write about refusal in the context of surveillance, race, and bioethics, and talk about it as a necessary counterpart to consent. Others, like the authors of the “Feminist Data Manifest-No,” think of refusal as something that can help us commit to building better futures.

      Benjamin illustrates cases where the choice to refuse is not equally possible for everyone, citing examples involving genetic data and refugee screenings in the U.K. The imbalance of power in these situations underscores the broader concept of refusal, extending beyond rejecting specific options to challenging the entire set of choices presented.

      Q: What inspired you to work on the notion of refusal as an act of design?

      A: In my work on data ethics, I’ve been thinking about how to incorporate processes into research data collection, particularly around consent and opt-out, with a focus on individual autonomy and the idea of giving people choices about the way that their data is used. But when it comes to data privacy, simply making choices available is not enough. Choices can be unequally available, or create no-win situations where all options are bad. This led me to the concept of refusal: questioning the authority of data collectors and challenging their legitimacy.

      The key idea of my work is that refusal is an act of design. I think of refusal as deliberate actions to redesign our socio-technical landscape by exerting some sort of influence. Like design, refusal is generative. Like design, it’s oriented towards creating alternate possibilities and alternate futures. Design is a process of exploring or traversing a space of possibility. Applying a design framework to cases of refusal drawn from scholarly and journalistic sources allowed me to establish a common language for talking about refusal and to imagine refusals that haven’t been explored yet.

      Q: What are the stakes around data privacy and data collection?

      A: The use of data for facial recognition surveillance in the U.S. is a big example we use in the paper. When people do everyday things like post on social media or walk past cameras in public spaces, they might be contributing their data to training facial recognition systems. For instance, a tech company may take photos from a social media site and build facial recognition that they then sell to the government. In the U.S., these systems are disproportionately used by police to surveil communities of color. It is difficult to apply concepts like consent and opt out of these processes, because they happen over time and involve multiple kinds of institutions. It’s also not clear that individual opt-out would do anything to change the overall situation. Refusal then becomes a crucial avenue, at both individual and community levels, to think more broadly of how affected people still exert some kind of voice or agency, without necessarily having an official channel to do so.

      Q: Why do you think these issues are more particularly affecting disempowered communities?

      A: People who are affected by technologies are not always included in the design process for those technologies. Refusal then becomes a meaningful expression of values and priorities for those who were not part of the early design conversations. Actions taken against technologies like face surveillance — be it legal battles against companies, advocacy for stricter regulations, or even direct action like disabling security cameras — may not fit the conventional notion of participating in a design process. And yet, these are the actions available to refusers who may be excluded from other forms of participation.

      I’m particularly inspired by the movement around Indigenous data sovereignty. Organizations like the First Nations Information Governance Centre work towards prioritizing Indigenous communities’ perspectives in data collection, and refuse inadequate representation in official health data from the Canadian government. I think this is a movement that exemplifies the potential of refusal, not only as a way to reject what’s being offered, but also as a means to propose a constructive alternative, very much like design. Refusal is not merely a negation, but a pathway to different futures.

      Q: Can you elaborate on the design framework you propose?

      A: Refusals vary widely across contexts and scales. Developing a framework for refusal is about helping people see actions that are seemingly very different as instances of the same broader idea. Our framework consists of four facets: autonomy, time, power, and cost.

      Consider the case of IBM creating a facial recognition dataset using people’s photos without consent. We saw multiple forms of refusal emerge in response. IBM allowed individuals to opt out by withdrawing their photos. People collectively refused by creating a class-action lawsuit against IBM. Around the same time, many U.S. cities started passing local legislation banning the government use of facial recognition. Evaluating these cases through the framework highlights commonalities and differences. The framework highlights varied approaches to autonomy, like individual opt-out and collective action. Regarding time, opt-outs and lawsuits react to past harm, while legislation might proactively prevent future harm. Power dynamics differ; withdrawing individual photos minimally influences IBM, while legislation could potentially cause longer-term change. And as for cost, individual opt-out seems less demanding, while other approaches require more time and effort, balanced against potential benefits.

      The framework facilitates case description and comparison across these dimensions. I think its generative nature encourages exploration of novel forms of refusal as well. By identifying the characteristics we want to see in future refusal strategies — collective, proactive, powerful, low-cost… — we can aspire to shape future approaches and change the behavior of data collectors. We may not always be able to combine all these criteria, but the framework provides a means to articulate our aspirational goals in this context.

      Q: What impact do you hope this research will have?

      A: I hope to expand the notion of who can participate in design, and whose actions are seen as legitimate expressions of design input. I think a lot of work so far in the conversation around data ethics prioritizes the perspective of computer scientists who are trying to design better systems, at the expense of the perspective of people for whom the systems are not currently working. So, I hope designers and computer scientists can embrace the concept of refusal as a legitimate form of design, and a source of inspiration. There’s a vital conversation happening, one that should influence the design of future systems, even if expressed through unconventional means.

      One of the things I want to underscore in the paper is that design extends beyond software. Taking a socio-technical perspective, the act of designing encompasses software, institutions, relationships, and governance structures surrounding data use. I want people who aren’t software engineers, like policymakers or activists, to view themselves as integral to the technology design process. More