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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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      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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      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.

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      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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      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

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      Six MIT students selected as spring 2024 MIT-Pillar AI Collective Fellows

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      The MIT-Pillar AI Collective has announced six fellows for the spring 2024 semester. With support from the program, the graduate students, who are in their final year of a master’s or PhD program, will conduct research in the areas of AI, machine learning, and data science with the aim of commercializing their innovations.

      Launched by MIT’s School of Engineering and Pillar VC in 2022, the MIT-Pillar AI Collective supports faculty, postdocs, and students conducting research on AI, machine learning, and data science. Supported by a gift from Pillar VC and administered by the MIT Deshpande Center for Technological Innovation, the mission of the program is to advance research toward commercialization.

      The spring 2024 MIT-Pillar AI Collective Fellows are:

      Yasmeen AlFaraj

      Yasmeen AlFaraj is a PhD candidate in chemistry whose interest is in the application of data science and machine learning to soft materials design to enable next-generation, sustainable plastics, rubber, and composite materials. More specifically, she is applying machine learning to the design of novel molecular additives to enable the low-cost manufacturing of chemically deconstructable thermosets and composites. AlFaraj’s work has led to the discovery of scalable, translatable new materials that could address thermoset plastic waste. As a Pillar Fellow, she will pursue bringing this technology to market, initially focusing on wind turbine blade manufacturing and conformal coatings. Through the Deshpande Center for Technological Innovation, AlFaraj serves as a lead for a team developing a spinout focused on recyclable versions of existing high-performance thermosets by incorporating small quantities of a degradable co-monomer. In addition, she participated in the National Science Foundation Innovation Corps program and recently graduated from the Clean Tech Open, where she focused on enhancing her business plan, analyzing potential markets, ensuring a complete IP portfolio, and connecting with potential funders. AlFaraj earned a BS in chemistry from University of California at Berkeley.

      Ruben Castro Ornelas

      Ruben Castro Ornelas is a PhD student in mechanical engineering who is passionate about the future of multipurpose robots and designing the hardware to use them with AI control solutions. Combining his expertise in programming, embedded systems, machine design, reinforcement learning, and AI, he designed a dexterous robotic hand capable of carrying out useful everyday tasks without sacrificing size, durability, complexity, or simulatability. Ornelas’s innovative design holds significant commercial potential in domestic, industrial, and health-care applications because it could be adapted to hold everything from kitchenware to delicate objects. As a Pillar Fellow, he will focus on identifying potential commercial markets, determining the optimal approach for business-to-business sales, and identifying critical advisors. Ornelas served as co-director of StartLabs, an undergraduate entrepreneurship club at MIT, where he earned an BS in mechanical engineering.

      Keeley Erhardt

      Keeley Erhardt is a PhD candidate in media arts and sciences whose research interests lie in the transformative potential of AI in network analysis, particularly for entity correlation and hidden link detection within and across domains. She has designed machine learning algorithms to identify and track temporal correlations and hidden signals in large-scale networks, uncovering online influence campaigns originating from multiple countries. She has similarly demonstrated the use of graph neural networks to identify coordinated cryptocurrency accounts by analyzing financial time series data and transaction dynamics. As a Pillar Fellow, Erhardt will pursue the potential commercial applications of her work, such as detecting fraud, propaganda, money laundering, and other covert activity in the finance, energy, and national security sectors. She has had internships at Google, Facebook, and Apple and held software engineering roles at multiple tech unicorns. Erhardt earned an MEng in electrical engineering and computer science and a BS in computer science, both from MIT.

      Vineet Jagadeesan Nair

      Vineet Jagadeesan Nair is a PhD candidate in mechanical engineering whose research focuses on modeling power grids and designing electricity markets to integrate renewables, batteries, and electric vehicles. He is broadly interested in developing computational tools to tackle climate change. As a Pillar Fellow, Nair will explore the application of machine learning and data science to power systems. Specifically, he will experiment with approaches to improve the accuracy of forecasting electricity demand and supply with high spatial-temporal resolution. In collaboration with Project Tapestry @ Google X, he is also working on fusing physics-informed machine learning with conventional numerical methods to increase the speed and accuracy of high-fidelity simulations. Nair’s work could help realize future grids with high penetrations of renewables and other clean, distributed energy resources. Outside academics, Nair is active in entrepreneurship, most recently helping to organize the 2023 MIT Global Startup Workshop in Greece. He earned an MS in computational science and engineering from MIT, an MPhil in energy technologies from Cambridge University as a Gates Scholar, and a BS in mechanical engineering and a BA in economics from University of California at Berkeley.

      Mahdi Ramadan

      Mahdi Ramadan is a PhD candidate in brain and cognitive sciences whose research interests lie at the intersection of cognitive science, computational modeling, and neural technologies. His work uses novel unsupervised methods for learning and generating interpretable representations of neural dynamics, capitalizing on recent advances in AI, specifically contrastive and geometric deep learning techniques capable of uncovering the latent dynamics underlying neural processes with high fidelity. As a Pillar Fellow, he will leverage these methods to gain a better understanding of dynamical models of muscle signals for generative motor control. By supplementing current spinal prosthetics with generative AI motor models that can streamline, speed up, and correct limb muscle activations in real time, as well as potentially using multimodal vision-language models to infer the patients’ high-level intentions, Ramadan aspires to build truly scalable, accessible, and capable commercial neuroprosthetics. Ramadan’s entrepreneurial experience includes being the co-founder of UltraNeuro, a neurotechnology startup, and co-founder of Presizely, a computer vision startup. He earned a BS in neurobiology from University of Washington.

      Rui (Raymond) Zhou

      Rui (Raymond) Zhou is a PhD candidate in mechanical engineering whose research focuses on multimodal AI for engineering design. As a Pillar Fellow, he will advance models that could enable designers to translate information in any modality or combination of modalities into comprehensive 2D and 3D designs, including parametric data, component visuals, assembly graphs, and sketches. These models could also optimize existing human designs to accomplish goals such as improving ergonomics or reducing drag coefficient. Ultimately, Zhou aims to translate his work into a software-as-a-service platform that redefines product design across various sectors, from automotive to consumer electronics. His efforts have the potential to not only accelerate the design process but also reduce costs, opening the door to unprecedented levels of customization, idea generation, and rapid prototyping. Beyond his academic pursuits, Zhou founded UrsaTech, a startup that integrates AI into education and engineering design. He earned a BS in electrical engineering and computer sciences from University of California at Berkeley. More

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      Generating the policy of tomorrow

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      As first-year students in the Social and Engineering Systems (SES) doctoral program within the MIT Institute for Data, Systems, and Society (IDSS), Eric Liu and Ashely Peake share an interest in investigating housing inequality issues.

      They also share a desire to dive head-first into their research.

      “In the first year of your PhD, you’re taking classes and still getting adjusted, but we came in very eager to start doing research,” Liu says.

      Liu, Peake, and many others found an opportunity to do hands-on research on real-world problems at the MIT Policy Hackathon, an initiative organized by students in IDSS, including the Technology and Policy Program (TPP). The weekend-long, interdisciplinary event — now in its sixth year — continues to gather hundreds of participants from around the globe to explore potential solutions to some of society’s greatest challenges.

      This year’s theme, “Hack-GPT: Generating the Policy of Tomorrow,” sought to capitalize on the popularity of generative AI (like the chatbot ChatGPT) and the ways it is changing how we think about technical and policy-based challenges, according to Dansil Green, a second-year TPP master’s student and co-chair of the event.

      “We encouraged our teams to utilize and cite these tools, thinking about the implications that generative AI tools have on their different challenge categories,” Green says.

      After 2022’s hybrid event, this year’s organizers pivoted back to a virtual-only approach, allowing them to increase the overall number of participants in addition to increasing the number of teams per challenge by 20 percent.

      “Virtual allows you to reach more people — we had a high number of international participants this year — and it helps reduce some of the costs,” Green says. “I think going forward we are going to try and switch back and forth between virtual and in-person because there are different benefits to each.”

      “When the magic hits”

      Liu and Peake competed in the housing challenge category, where they could gain research experience in their actual field of study. 

      “While I am doing housing research, I haven’t necessarily had a lot of opportunities to work with actual housing data before,” says Peake, who recently joined the SES doctoral program after completing an undergraduate degree in applied math last year. “It was a really good experience to get involved with an actual data problem, working closer with Eric, who’s also in my lab group, in addition to meeting people from MIT and around the world who are interested in tackling similar questions and seeing how they think about things differently.”

      Joined by Adrian Butterton, a Boston-based paralegal, as well as Hudson Yuen and Ian Chan, two software engineers from Canada, Liu and Peake formed what would end up being the winning team in their category: “Team Ctrl+Alt+Defeat.” They quickly began organizing a plan to address the eviction crisis in the United States.

      “I think we were kind of surprised by the scope of the question,” Peake laughs. “In the end, I think having such a large scope motivated us to think about it in a more realistic kind of way — how could we come up with a solution that was adaptable and therefore could be replicated to tackle different kinds of problems.”

      Watching the challenge on the livestream together on campus, Liu says they immediately went to work, and could not believe how quickly things came together.

      “We got our challenge description in the evening, came out to the purple common area in the IDSS building and literally it took maybe an hour and we drafted up the entire project from start to finish,” Liu says. “Then our software engineer partners had a dashboard built by 1 a.m. — I feel like the hackathon really promotes that really fast dynamic work stream.”

      “People always talk about the grind or applying for funding — but when that magic hits, it just reminds you of the part of research that people don’t talk about, and it was really a great experience to have,” Liu adds.

      A fresh perspective

      “We’ve organized hackathons internally at our company and they are great for fostering innovation and creativity,” says Letizia Bordoli, senior AI product manager at Veridos, a German-based identity solutions company that provided this year’s challenge in Data Systems for Human Rights. “It is a great opportunity to connect with talented individuals and explore new ideas and solutions that we might not have thought about.”

      The challenge provided by Veridos was focused on finding innovative solutions to universal birth registration, something Bordoli says only benefited from the fact that the hackathon participants were from all over the world.

      “Many had local and firsthand knowledge about certain realities and challenges [posed by the lack of] birth registration,” Bordoli says. “It brings fresh perspectives to existing challenges, and it gave us an energy boost to try to bring innovative solutions that we may not have considered before.”

      New frontiers

      Alongside the housing and data systems for human rights challenges was a challenge in health, as well as a first-time opportunity to tackle an aerospace challenge in the area of space for environmental justice.

      “Space can be a very hard challenge category to do data-wise since a lot of data is proprietary, so this really developed over the last few months with us having to think about how we could do more with open-source data,” Green explains. “But I am glad we went the environmental route because it opened the challenge up to not only space enthusiasts, but also environment and climate people.”

      One of the participants to tackle this new challenge category was Yassine Elhallaoui, a system test engineer from Norway who specializes in AI solutions and has 16 years of experience working in the oil and gas fields. Elhallaoui was a member of Team EcoEquity, which proposed an increase in policies supporting the use of satellite data to ensure proper evaluation and increase water resiliency for vulnerable communities.

      “The hackathons I have participated in in the past were more technical,” Elhallaoui says. “Starting with [MIT Science and Technology Policy Institute Director Kristen Kulinowski’s] workshop about policy writers and the solutions they came up with, and the analysis they had to do … it really changed my perspective on what a hackathon can do.”

      “A policy hackathon is something that can make real changes in the world,” she adds. More

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      Leveraging language to understand machines

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      Natural language conveys ideas, actions, information, and intent through context and syntax; further, there are volumes of it contained in databases. This makes it an excellent source of data to train machine-learning systems on. Two master’s of engineering students in the 6A MEng Thesis Program at MIT, Irene Terpstra ’23 and Rujul Gandhi ’22, are working with mentors in the MIT-IBM Watson AI Lab to use this power of natural language to build AI systems.

      As computing is becoming more advanced, researchers are looking to improve the hardware that they run on; this means innovating to create new computer chips. And, since there is literature already available on modifications that can be made to achieve certain parameters and performance, Terpstra and her mentors and advisors Anantha Chandrakasan, MIT School of Engineering dean and the Vannevar Bush Professor of Electrical Engineering and Computer Science, and IBM’s researcher Xin Zhang, are developing an AI algorithm that assists in chip design.

      “I’m creating a workflow to systematically analyze how these language models can help the circuit design process. What reasoning powers do they have, and how can it be integrated into the chip design process?” says Terpstra. “And then on the other side, if that proves to be useful enough, [we’ll] see if they can automatically design the chips themselves, attaching it to a reinforcement learning algorithm.”

      To do this, Terpstra’s team is creating an AI system that can iterate on different designs. It means experimenting with various pre-trained large language models (like ChatGPT, Llama 2, and Bard), using an open-source circuit simulator language called NGspice, which has the parameters of the chip in code form, and a reinforcement learning algorithm. With text prompts, researchers will be able to query how the physical chip should be modified to achieve a certain goal in the language model and produced guidance for adjustments. This is then transferred into a reinforcement learning algorithm that updates the circuit design and outputs new physical parameters of the chip.

      “The final goal would be to combine the reasoning powers and the knowledge base that is baked into these large language models and combine that with the optimization power of the reinforcement learning algorithms and have that design the chip itself,” says Terpstra.

      Rujul Gandhi works with the raw language itself. As an undergraduate at MIT, Gandhi explored linguistics and computer sciences, putting them together in her MEng work. “I’ve been interested in communication, both between just humans and between humans and computers,” Gandhi says.

      Robots or other interactive AI systems are one area where communication needs to be understood by both humans and machines. Researchers often write instructions for robots using formal logic. This helps ensure that commands are being followed safely and as intended, but formal logic can be difficult for users to understand, while natural language comes easily. To ensure this smooth communication, Gandhi and her advisors Yang Zhang of IBM and MIT assistant professor Chuchu Fan are building a parser that converts natural language instructions into a machine-friendly form. Leveraging the linguistic structure encoded by the pre-trained encoder-decoder model T5, and a dataset of annotated, basic English commands for performing certain tasks, Gandhi’s system identifies the smallest logical units, or atomic propositions, which are present in a given instruction.

      “Once you’ve given your instruction, the model identifies all the smaller sub-tasks you want it to carry out,” Gandhi says. “Then, using a large language model, each sub-task can be compared against the available actions and objects in the robot’s world, and if any sub-task can’t be carried out because a certain object is not recognized, or an action is not possible, the system can stop right there to ask the user for help.”

      This approach of breaking instructions into sub-tasks also allows her system to understand logical dependencies expressed in English, like, “do task X until event Y happens.” Gandhi uses a dataset of step-by-step instructions across robot task domains like navigation and manipulation, with a focus on household tasks. Using data that are written just the way humans would talk to each other has many advantages, she says, because it means a user can be more flexible about how they phrase their instructions.

      Another of Gandhi’s projects involves developing speech models. In the context of speech recognition, some languages are considered “low resource” since they might not have a lot of transcribed speech available, or might not have a written form at all. “One of the reasons I applied to this internship at the MIT-IBM Watson AI Lab was an interest in language processing for low-resource languages,” she says. “A lot of language models today are very data-driven, and when it’s not that easy to acquire all of that data, that’s when you need to use the limited data efficiently.” 

      Speech is just a stream of sound waves, but humans having a conversation can easily figure out where words and thoughts start and end. In speech processing, both humans and language models use their existing vocabulary to recognize word boundaries and understand the meaning. In low- or no-resource languages, a written vocabulary might not exist at all, so researchers can’t provide one to the model. Instead, the model can make note of what sound sequences occur together more frequently than others, and infer that those might be individual words or concepts. In Gandhi’s research group, these inferred words are then collected into a pseudo-vocabulary that serves as a labeling method for the low-resource language, creating labeled data for further applications.

      The applications for language technology are “pretty much everywhere,” Gandhi says. “You could imagine people being able to interact with software and devices in their native language, their native dialect. You could imagine improving all the voice assistants that we use. You could imagine it being used for translation or interpretation.” More