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    Improving drug development with a vast map of the immune system

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    The human immune system is a network made up of trillions of cells that are constantly circulating throughout the body. The cellular network orchestrates interactions with every organ and tissue to carry out an impossibly long list of functions that scientists are still working to understand. All that complexity limits our ability to predict which patients will respond to treatments and which ones might suffer debilitating side effects.

    The issue often leads pharmaceutical companies to stop developing drugs that could help certain patients, halting clinical trials even when drugs show promising results for some people.

    Now, Immunai is helping to predict how patients will respond to treatments by building a comprehensive map of the immune system. The company has assembled a vast database it calls AMICA, that combines multiple layers of gene and protein expression data in cells with clinical trial data to match the right drugs to the right patients.

    “Our starting point was creating what I call the Google Maps for the immune system,” Immunai co-founder and CEO Noam Solomon says. “We started with single-cell RNA sequencing, and over time we’ve added more and more ‘omics’: genomics, proteomics, epigenomics, all to measure the immune system’s cellular expression and function, to measure the immune environment holistically. Then we started working with pharmaceutical companies and hospitals to profile the immune systems of patients undergoing treatments to really get to the root mechanisms of action and resistance for therapeutics.”

    Immunai’s big data foundation is a result of its founders’ unique background. Solomon and co-founder Luis Voloch ’13, SM ’15 hold degrees in mathematics and computer science. In fact, Solomon was a postdoc in MIT’s Department of Mathematics at the time of Immunai’s founding.

    Solomon frames Immunai’s mission as stopping the decades-long divergence of computer science and the life sciences. He believes the single biggest factor driving the explosion of computing has been Moore’s Law — our ability to exponentially increase the number of transistors on a chip over the past 60 years. In the pharmaceutical industry, the reverse is happening: By one estimate, the cost of developing a new drug roughly doubles every nine years. The phenomenon has been dubbed Eroom’s Law (“Eroom” for “Moore” spelled backward).

    Solomon sees the trend eroding the case for developing new drugs, with huge consequences for patients.

    “Why should pharmaceutical companies invest in discovery if they won’t get a return on investment?” Solomon asks. “Today, there’s only a 5 to 10 percent chance that any given clinical trial will be successful. What we’ve built through a very robust and granular mapping of the immune system is a chance to improve the preclinical and clinical stages of drug development.”

    A change in plans

    Solomon entered Tel Aviv University when he was 14 and earned his bachelor’s degree in computer science by 19. He earned two PhDs in Israel, one in computer science and the other in mathematics, before coming to MIT in 2017 as a postdoc to continue his mathematical research career.

    That year Solomon met Voloch, who had already earned bachelor’s and master’s degrees in math and computer science from MIT. But the researchers were soon exposed to a problem that would take them out of their comfort zones and change the course of their careers.

    Voloch’s grandfather was receiving a cocktail of treatments for cancer at the time. The cancer went into remission, but he suffered terrible side effects that caused him to stop taking his medication.

    Voloch and Solomon began wondering if their expertise could help patients like Voloch’s grandfather.

    “When we realized we could make an impact, we made the difficult decision to stop our academic pursuits and start a new journey,” Solomon recalls. “That was the starting point for Immunai.”

    Voloch and Solomon soon partnered with Immunai scientific co-founders Ansu Satpathy, a researcher at Stanford University at the time, and Danny Wells, a researcher at the Parker Institute for Cancer Immunotherapy. Satpathy and Wells had shown that single-cell RNA sequencing could be used to gain insights into why patients respond differently to a common cancer treatment.

    The team began analyzing single-cell RNA sequencing data published in scientific papers, trying to link common biomarkers with patient outcomes. Then they integrated data from the United Kingdom’s Biobank public health database, finding they were able to improve their models’ predictions. Soon they were incorporating data from hospitals, academic research institutions, and pharmaceutical companies, analyzing information about the structure, function, and environment of cells — multiomics — to get a clearer picture of immune activity.

    “Single cell sequencing gives you metrics you can measure in thousands of cells, where you can look at 20,000 different genes, and those metrics give you an immune profile,” Solomon explains. “When you measure all of that over time, especially before and after getting therapy, and compare patients who do respond with patients who don’t, you can apply machine learning models to understand why.”

    Those data and models make up AMICA, what Immunai calls the world’s largest cell-level immune knowledge base. AMICA stands for Annotated Multiomic Immune Cell Atlas. It analyzes single cell multiomic data from almost 10,000 patients and bulk-RNA data from 100,000 patients across more than 800 cell types and 500 diseases.

    At the core of Immunai’s approach is a focus on the immune system, which other companies shy away from because of its complexity.

    “We don’t want to be like other groups that are studying mainly tumor microenvironments,” Solomon says. “We look at the immune system because the immune system is the common denominator. It’s the one system that is implicated in every disease, in your body’s response to everything that you encounter, whether it’s a viral infection or bacterial infection or a drug that you are receiving — even how you are aging.”

    Turning data into better treatments

    Immunai has already partnered with some of the largest pharmaceutical companies in the world to help them identify promising treatments and set up their clinical trials for success. Immunai’s insights can help partners make critical decisions about treatment schedules, dosing, drug combinations, patient selection, and more.

    “Everyone is talking about AI, but I think the most exciting aspect of the platform we have built is the fact that it’s vertically integrated, from wet lab to computational modeling with multiple iterations,” Solomon says. “For example, we may do single-cell immune profiling of patient samples, then we upload that data to the cloud and our computational models come up with insights, and with those insights we do in vitro or in vivo validation to see if our models are right and iteratively improve them.”

    Ultimately Immunai wants to enable a future where lab experiments can more reliably turn into impactful new recommendations and treatments for patients.

    “Scientists can cure nearly every type of cancer, but only in mice,” Solomon says. “In preclinical models we know how to cure cancer. In human beings, in most cases, we still don’t. To overcome that, most scientists are looking for better ex vivo or in vivo models. Our approach is to be more agnostic as to the model system, but feed the machine with more and more data from multiple model systems. We’re demonstrating that our algorithms can repeatedly beat the top benchmarks in identifying the top preclinical immune features that match to patient outcomes.” More

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      Dealing with the limitations of our noisy world

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      Tamara Broderick first set foot on MIT’s campus when she was a high school student, as a participant in the inaugural Women’s Technology Program. The monthlong summer academic experience gives young women a hands-on introduction to engineering and computer science.

      What is the probability that she would return to MIT years later, this time as a faculty member?

      That’s a question Broderick could probably answer quantitatively using Bayesian inference, a statistical approach to probability that tries to quantify uncertainty by continuously updating one’s assumptions as new data are obtained.

      In her lab at MIT, the newly tenured associate professor in the Department of Electrical Engineering and Computer Science (EECS) uses Bayesian inference to quantify uncertainty and measure the robustness of data analysis techniques.

      “I’ve always been really interested in understanding not just ‘What do we know from data analysis,’ but ‘How well do we know it?’” says Broderick, who is also a member of the Laboratory for Information and Decision Systems and the Institute for Data, Systems, and Society. “The reality is that we live in a noisy world, and we can’t always get exactly the data that we want. How do we learn from data but at the same time recognize that there are limitations and deal appropriately with them?”

      Broadly, her focus is on helping people understand the confines of the statistical tools available to them and, sometimes, working with them to craft better tools for a particular situation.

      For instance, her group recently collaborated with oceanographers to develop a machine-learning model that can make more accurate predictions about ocean currents. In another project, she and others worked with degenerative disease specialists on a tool that helps severely motor-impaired individuals utilize a computer’s graphical user interface by manipulating a single switch.

      A common thread woven through her work is an emphasis on collaboration.

      “Working in data analysis, you get to hang out in everybody’s backyard, so to speak. You really can’t get bored because you can always be learning about some other field and thinking about how we can apply machine learning there,” she says.

      Hanging out in many academic “backyards” is especially appealing to Broderick, who struggled even from a young age to narrow down her interests.

      A math mindset

      Growing up in a suburb of Cleveland, Ohio, Broderick had an interest in math for as long as she can remember. She recalls being fascinated by the idea of what would happen if you kept adding a number to itself, starting with 1+1=2 and then 2+2=4.

      “I was maybe 5 years old, so I didn’t know what ‘powers of two’ were or anything like that. I was just really into math,” she says.

      Her father recognized her interest in the subject and enrolled her in a Johns Hopkins program called the Center for Talented Youth, which gave Broderick the opportunity to take three-week summer classes on a range of subjects, from astronomy to number theory to computer science.

      Later, in high school, she conducted astrophysics research with a postdoc at Case Western University. In the summer of 2002, she spent four weeks at MIT as a member of the first class of the Women’s Technology Program.

      She especially enjoyed the freedom offered by the program, and its focus on using intuition and ingenuity to achieve high-level goals. For instance, the cohort was tasked with building a device with LEGOs that they could use to biopsy a grape suspended in Jell-O.

      The program showed her how much creativity is involved in engineering and computer science, and piqued her interest in pursuing an academic career.

      “But when I got into college at Princeton, I could not decide — math, physics, computer science — they all seemed super-cool. I wanted to do all of it,” she says.

      She settled on pursuing an undergraduate math degree but took all the physics and computer science courses she could cram into her schedule.

      Digging into data analysis

      After receiving a Marshall Scholarship, Broderick spent two years at Cambridge University in the United Kingdom, earning a master of advanced study in mathematics and a master of philosophy in physics.

      In the UK, she took a number of statistics and data analysis classes, including her first class on Bayesian data analysis in the field of machine learning.

      It was a transformative experience, she recalls.

      “During my time in the U.K., I realized that I really like solving real-world problems that matter to people, and Bayesian inference was being used in some of the most important problems out there,” she says.

      Back in the U.S., Broderick headed to the University of California at Berkeley, where she joined the lab of Professor Michael I. Jordan as a grad student. She earned a PhD in statistics with a focus on Bayesian data analysis. 

      She decided to pursue a career in academia and was drawn to MIT by the collaborative nature of the EECS department and by how passionate and friendly her would-be colleagues were.

      Her first impressions panned out, and Broderick says she has found a community at MIT that helps her be creative and explore hard, impactful problems with wide-ranging applications.

      “I’ve been lucky to work with a really amazing set of students and postdocs in my lab — brilliant and hard-working people whose hearts are in the right place,” she says.

      One of her team’s recent projects involves a collaboration with an economist who studies the use of microcredit, or the lending of small amounts of money at very low interest rates, in impoverished areas.

      The goal of microcredit programs is to raise people out of poverty. Economists run randomized control trials of villages in a region that receive or don’t receive microcredit. They want to generalize the study results, predicting the expected outcome if one applies microcredit to other villages outside of their study.

      But Broderick and her collaborators have found that results of some microcredit studies can be very brittle. Removing one or a few data points from the dataset can completely change the results. One issue is that researchers often use empirical averages, where a few very high or low data points can skew the results.

      Using machine learning, she and her collaborators developed a method that can determine how many data points must be dropped to change the substantive conclusion of the study. With their tool, a scientist can see how brittle the results are.

      “Sometimes dropping a very small fraction of data can change the major results of a data analysis, and then we might worry how far those conclusions generalize to new scenarios. Are there ways we can flag that for people? That is what we are getting at with this work,” she explains.

      At the same time, she is continuing to collaborate with researchers in a range of fields, such as genetics, to understand the pros and cons of different machine-learning techniques and other data analysis tools.

      Happy trails

      Exploration is what drives Broderick as a researcher, and it also fuels one of her passions outside the lab. She and her husband enjoy collecting patches they earn by hiking all the trails in a park or trail system.

      “I think my hobby really combines my interests of being outdoors and spreadsheets,” she says. “With these hiking patches, you have to explore everything and then you see areas you wouldn’t normally see. It is adventurous, in that way.”

      They’ve discovered some amazing hikes they would never have known about, but also embarked on more than a few “total disaster hikes,” she says. But each hike, whether a hidden gem or an overgrown mess, offers its own rewards.

      And just like in her research, curiosity, open-mindedness, and a passion for problem-solving have never led her astray. More

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      Automated method helps researchers quantify uncertainty in their predictions

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      Pollsters trying to predict presidential election results and physicists searching for distant exoplanets have at least one thing in common: They often use a tried-and-true scientific technique called Bayesian inference.

      Bayesian inference allows these scientists to effectively estimate some unknown parameter — like the winner of an election — from data such as poll results. But Bayesian inference can be slow, sometimes consuming weeks or even months of computation time or requiring a researcher to spend hours deriving tedious equations by hand. 

      Researchers from MIT and elsewhere have introduced an optimization technique that speeds things up without requiring a scientist to do a lot of additional work. Their method can achieve more accurate results faster than another popular approach for accelerating Bayesian inference.

      Using this new automated technique, a scientist could simply input their model and then the optimization method does all the calculations under the hood to provide an approximation of some unknown parameter. The method also offers reliable uncertainty estimates that can help a researcher understand when to trust its predictions.

      This versatile technique could be applied to a wide array of scientific quandaries that incorporate Bayesian inference. For instance, it could be used by economists studying the impact of microcredit loans in developing nations or sports analysts using a model to rank top tennis players.

      “When you actually dig into what people are doing in the social sciences, physics, chemistry, or biology, they are often using a lot of the same tools under the hood. There are so many Bayesian analyses out there. If we can build a really great tool that makes these researchers lives easier, then we can really make a difference to a lot of people in many different research areas,” says senior author Tamara Broderick, an associate professor in MIT’s Department of Electrical Engineering and Computer Science (EECS) and a member of the Laboratory for Information and Decision Systems and the Institute for Data, Systems, and Society.

      Broderick is joined on the paper by co-lead authors Ryan Giordano, an assistant professor of statistics at the University of California at Berkeley; and Martin Ingram, a data scientist at the AI company KONUX. The paper was recently published in the Journal of Machine Learning Research.

      Faster results

      When researchers seek a faster form of Bayesian inference, they often turn to a technique called automatic differentiation variational inference (ADVI), which is often both fast to run and easy to use.

      But Broderick and her collaborators have found a number of practical issues with ADVI. It has to solve an optimization problem and can do so only approximately. So, ADVI can still require a lot of computation time and user effort to determine whether the approximate solution is good enough. And once it arrives at a solution, it tends to provide poor uncertainty estimates.

      Rather than reinventing the wheel, the team took many ideas from ADVI but turned them around to create a technique called deterministic ADVI (DADVI) that doesn’t have these downsides.

      With DADVI, it is very clear when the optimization is finished, so a user won’t need to spend extra computation time to ensure that the best solution has been found. DADVI also permits the incorporation of more powerful optimization methods that give it an additional speed and performance boost.

      Once it reaches a result, DADVI is set up to allow the use of uncertainty corrections. These corrections make its uncertainty estimates much more accurate than those of ADVI.

      DADVI also enables the user to clearly see how much error they have incurred in the approximation to the optimization problem. This prevents a user from needlessly running the optimization again and again with more and more resources to try and reduce the error.

      “We wanted to see if we could live up to the promise of black-box inference in the sense of, once the user makes their model, they can just run Bayesian inference and don’t have to derive everything by hand, they don’t need to figure out when to stop their algorithm, and they have a sense of how accurate their approximate solution is,” Broderick says.

      Defying conventional wisdom

      DADVI can be more effective than ADVI because it uses an efficient approximation method, called sample average approximation, which estimates an unknown quantity by taking a series of exact steps.

      Because the steps along the way are exact, it is clear when the objective has been reached. Plus, getting to that objective typically requires fewer steps.

      Often, researchers expect sample average approximation to be more computationally intensive than a more popular method, known as stochastic gradient, which is used by ADVI. But Broderick and her collaborators showed that, in many applications, this is not the case.

      “A lot of problems really do have special structure, and you can be so much more efficient and get better performance by taking advantage of that special structure. That is something we have really seen in this paper,” she adds.

      They tested DADVI on a number of real-world models and datasets, including a model used by economists to evaluate the effectiveness of microcredit loans and one used in ecology to determine whether a species is present at a particular site.

      Across the board, they found that DADVI can estimate unknown parameters faster and more reliably than other methods, and achieves as good or better accuracy than ADVI. Because it is easier to use than other techniques, DADVI could offer a boost to scientists in a wide variety of fields.

      In the future, the researchers want to dig deeper into correction methods for uncertainty estimates so they can better understand why these corrections can produce such accurate uncertainties, and when they could fall short.

      “In applied statistics, we often have to use approximate algorithms for problems that are too complex or high-dimensional to allow exact solutions to be computed in reasonable time. This new paper offers an interesting set of theory and empirical results that point to an improvement in a popular existing approximate algorithm for Bayesian inference,” says Andrew Gelman ’85, ’86, a professor of statistics and political science at Columbia University, who was not involved with the study. “As one of the team involved in the creation of that earlier work, I’m happy to see our algorithm superseded by something more stable.”

      This research was supported by a National Science Foundation CAREER Award and the U.S. Office of Naval Research.  More

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      Technique could efficiently solve partial differential equations for numerous applications

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      In fields such as physics and engineering, partial differential equations (PDEs) are used to model complex physical processes to generate insight into how some of the most complicated physical and natural systems in the world function.

      To solve these difficult equations, researchers use high-fidelity numerical solvers, which can be very time-consuming and computationally expensive to run. The current simplified alternative, data-driven surrogate models, compute the goal property of a solution to PDEs rather than the whole solution. Those are trained on a set of data that has been generated by the high-fidelity solver, to predict the output of the PDEs for new inputs. This is data-intensive and expensive because complex physical systems require a large number of simulations to generate enough data. 

      In a new paper, “Physics-enhanced deep surrogates for partial differential equations,” published in December in Nature Machine Intelligence, a new method is proposed for developing data-driven surrogate models for complex physical systems in such fields as mechanics, optics, thermal transport, fluid dynamics, physical chemistry, and climate models.

      The paper was authored by MIT’s professor of applied mathematics Steven G. Johnson along with Payel Das and Youssef Mroueh of the MIT-IBM Watson AI Lab and IBM Research; Chris Rackauckas of Julia Lab; and Raphaël Pestourie, a former MIT postdoc who is now at Georgia Tech. The authors call their method “physics-enhanced deep surrogate” (PEDS), which combines a low-fidelity, explainable physics simulator with a neural network generator. The neural network generator is trained end-to-end to match the output of the high-fidelity numerical solver.

      “My aspiration is to replace the inefficient process of trial and error with systematic, computer-aided simulation and optimization,” says Pestourie. “Recent breakthroughs in AI like the large language model of ChatGPT rely on hundreds of billions of parameters and require vast amounts of resources to train and evaluate. In contrast, PEDS is affordable to all because it is incredibly efficient in computing resources and has a very low barrier in terms of infrastructure needed to use it.”

      In the article, they show that PEDS surrogates can be up to three times more accurate than an ensemble of feedforward neural networks with limited data (approximately 1,000 training points), and reduce the training data needed by at least a factor of 100 to achieve a target error of 5 percent. Developed using the MIT-designed Julia programming language, this scientific machine-learning method is thus efficient in both computing and data.

      The authors also report that PEDS provides a general, data-driven strategy to bridge the gap between a vast array of simplified physical models with corresponding brute-force numerical solvers modeling complex systems. This technique offers accuracy, speed, data efficiency, and physical insights into the process.

      Says Pestourie, “Since the 2000s, as computing capabilities improved, the trend of scientific models has been to increase the number of parameters to fit the data better, sometimes at the cost of a lower predictive accuracy. PEDS does the opposite by choosing its parameters smartly. It leverages the technology of automatic differentiation to train a neural network that makes a model with few parameters accurate.”

      “The main challenge that prevents surrogate models from being used more widely in engineering is the curse of dimensionality — the fact that the needed data to train a model increases exponentially with the number of model variables,” says Pestourie. “PEDS reduces this curse by incorporating information from the data and from the field knowledge in the form of a low-fidelity model solver.”

      The researchers say that PEDS has the potential to revive a whole body of the pre-2000 literature dedicated to minimal models — intuitive models that PEDS could make more accurate while also being predictive for surrogate model applications.

      “The application of the PEDS framework is beyond what we showed in this study,” says Das. “Complex physical systems governed by PDEs are ubiquitous, from climate modeling to seismic modeling and beyond. Our physics-inspired fast and explainable surrogate models will be of great use in those applications, and play a complementary role to other emerging techniques, like foundation models.”

      The research was supported by the MIT-IBM Watson AI Lab and the U.S. Army Research Office through the Institute for Soldier Nanotechnologies.  More

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      3 Questions: A new PhD program from the Center for Computational Science and Engineering

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      This fall, the Center for Computational Science and Engineering (CCSE), an academic unit in the MIT Schwarzman College of Computing, is introducing a new standalone PhD degree program that will enable students to pursue research in cross-cutting methodological aspects of computational science and engineering. The launch follows approval of the center’s degree program proposal at the May 2023 Institute faculty meeting.

      Doctoral-level graduate study in computational science and engineering (CSE) at MIT has, for the past decade, been offered through an interdisciplinary program in which CSE students are admitted to one of eight participating academic departments in the School of Engineering or School of Science. While this model adds a strong disciplinary component to students’ education, the rapid growth of the CSE field and the establishment of the MIT Schwarzman College of Computing have prompted an exciting expansion of MIT’s graduate-level offerings in computation.

      The new degree, offered by the college, will run alongside MIT’s existing interdisciplinary offerings in CSE, complementing these doctoral training programs and preparing students to contribute to the leading edge of the field. Here, CCSE co-directors Youssef Marzouk and Nicolas Hadjiconstantinou discuss the standalone program and how they expect it to elevate the visibility and impact of CSE research and education at MIT.

      Q: What is computational science and engineering?

      Marzouk: Computational science and engineering focuses on the development and analysis of state-of-the-art methods for computation and their innovative application to problems of science and engineering interest. It has intellectual foundations in applied mathematics, statistics, and computer science, and touches the full range of science and engineering disciplines. Yet, it synthesizes these foundations into a discipline of its own — one that links the digital and physical worlds. It’s an exciting and evolving multidisciplinary field.

      Hadjiconstantinou: Examples of CSE research happening at MIT include modeling and simulation techniques, the underlying computational mathematics, and data-driven modeling of physical systems. Computational statistics and scientific machine learning have become prominent threads within CSE, joining high-performance computing, mathematically-oriented programming languages, and their broader links to algorithms and software. Application domains include energy, environment and climate, materials, health, transportation, autonomy, and aerospace, among others. Some of our researchers focus on general and widely applicable methodology, while others choose to focus on methods and algorithms motivated by a specific domain of application.

      Q: What was the motivation behind creating a standalone PhD program?

      Marzouk: The new degree focuses on a particular class of students whose background and interests are primarily in CSE methodology, in a manner that cuts across the disciplinary research structure represented by our current “with-departments” degree program. There is a strong research demand for such methodologically-focused students among CCSE faculty and MIT faculty in general. Our objective is to create a targeted, coherent degree program in this field that, alongside our other thriving CSE offerings, will create the leading environment for top CSE students worldwide.

      Hadjiconstantinou: One of CCSE’s most important functions is to recruit exceptional students who are trained in and want to work in computational science and engineering. Experience with our CSE master’s program suggests that students with a strong background and interests in the discipline prefer to apply to a pure CSE program for their graduate studies. The standalone degree aims to bring these students to MIT and make them available to faculty across the Institute.

      Q: How will this impact computing education and research at MIT? 

      Hadjiconstantinou: We believe that offering a standalone PhD program in CSE alongside the existing “with-departments” programs will significantly strengthen MIT’s graduate programs in computing. In particular, it will strengthen the methodological core of CSE research and education at MIT, while continuing to support the disciplinary-flavored CSE work taking place in our participating departments, which include Aeronautics and Astronautics; Chemical Engineering; Civil and Environmental Engineering; Materials Science and Engineering; Mechanical Engineering; Nuclear Science and Engineering; Earth, Atmospheric and Planetary Sciences; and Mathematics. Together, these programs will create a stronger CSE student cohort and facilitate deeper exchanges between the college and other units at MIT.

      Marzouk: In a broader sense, the new program is designed to help realize one of the key opportunities presented by the college, which is to create a richer variety of graduate degrees in computation and to involve as many faculty and units in these educational endeavors as possible. The standalone CSE PhD will join other distinguished doctoral programs of the college — such as the Department of Electrical Engineering and Computer Science PhD; the Operations Research Center PhD; and the Interdisciplinary Doctoral Program in Statistics and the Social and Engineering Systems PhD within the Institute for Data, Systems, and Society — and grow in a way that is informed by them. The confluence of these academic programs, and natural synergies among them, will make MIT quite unique. More

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      Bringing the social and ethical responsibilities of computing to the forefront

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      There has been a remarkable surge in the use of algorithms and artificial intelligence to address a wide range of problems and challenges. While their adoption, particularly with the rise of AI, is reshaping nearly every industry sector, discipline, and area of research, such innovations often expose unexpected consequences that involve new norms, new expectations, and new rules and laws.

      To facilitate deeper understanding, the Social and Ethical Responsibilities of Computing (SERC), a cross-cutting initiative in the MIT Schwarzman College of Computing, recently brought together social scientists and humanists with computer scientists, engineers, and other computing faculty for an exploration of the ways in which the broad applicability of algorithms and AI has presented both opportunities and challenges in many aspects of society.

      “The very nature of our reality is changing. AI has the ability to do things that until recently were solely the realm of human intelligence — things that can challenge our understanding of what it means to be human,” remarked Daniel Huttenlocher, dean of the MIT Schwarzman College of Computing, in his opening address at the inaugural SERC Symposium. “This poses philosophical, conceptual, and practical questions on a scale not experienced since the start of the Enlightenment. In the face of such profound change, we need new conceptual maps for navigating the change.”

      The symposium offered a glimpse into the vision and activities of SERC in both research and education. “We believe our responsibility with SERC is to educate and equip our students and enable our faculty to contribute to responsible technology development and deployment,” said Georgia Perakis, the William F. Pounds Professor of Management in the MIT Sloan School of Management, co-associate dean of SERC, and the lead organizer of the symposium. “We’re drawing from the many strengths and diversity of disciplines across MIT and beyond and bringing them together to gain multiple viewpoints.”

      Through a succession of panels and sessions, the symposium delved into a variety of topics related to the societal and ethical dimensions of computing. In addition, 37 undergraduate and graduate students from a range of majors, including urban studies and planning, political science, mathematics, biology, electrical engineering and computer science, and brain and cognitive sciences, participated in a poster session to exhibit their research in this space, covering such topics as quantum ethics, AI collusion in storage markets, computing waste, and empowering users on social platforms for better content credibility.

      Showcasing a diversity of work

      In three sessions devoted to themes of beneficent and fair computing, equitable and personalized health, and algorithms and humans, the SERC Symposium showcased work by 12 faculty members across these domains.

      One such project from a multidisciplinary team of archaeologists, architects, digital artists, and computational social scientists aimed to preserve endangered heritage sites in Afghanistan with digital twins. The project team produced highly detailed interrogable 3D models of the heritage sites, in addition to extended reality and virtual reality experiences, as learning resources for audiences that cannot access these sites.

      In a project for the United Network for Organ Sharing, researchers showed how they used applied analytics to optimize various facets of an organ allocation system in the United States that is currently undergoing a major overhaul in order to make it more efficient, equitable, and inclusive for different racial, age, and gender groups, among others.

      Another talk discussed an area that has not yet received adequate public attention: the broader implications for equity that biased sensor data holds for the next generation of models in computing and health care.

      A talk on bias in algorithms considered both human bias and algorithmic bias, and the potential for improving results by taking into account differences in the nature of the two kinds of bias.

      Other highlighted research included the interaction between online platforms and human psychology; a study on whether decision-makers make systemic prediction mistakes on the available information; and an illustration of how advanced analytics and computation can be leveraged to inform supply chain management, operations, and regulatory work in the food and pharmaceutical industries.

      Improving the algorithms of tomorrow

      “Algorithms are, without question, impacting every aspect of our lives,” said Asu Ozdaglar, deputy dean of academics for the MIT Schwarzman College of Computing and head of the Department of Electrical Engineering and Computer Science, in kicking off a panel she moderated on the implications of data and algorithms.

      “Whether it’s in the context of social media, online commerce, automated tasks, and now a much wider range of creative interactions with the advent of generative AI tools and large language models, there’s little doubt that much more is to come,” Ozdaglar said. “While the promise is evident to all of us, there’s a lot to be concerned as well. This is very much time for imaginative thinking and careful deliberation to improve the algorithms of tomorrow.”

      Turning to the panel, Ozdaglar asked experts from computing, social science, and data science for insights on how to understand what is to come and shape it to enrich outcomes for the majority of humanity.

      Sarah Williams, associate professor of technology and urban planning at MIT, emphasized the critical importance of comprehending the process of how datasets are assembled, as data are the foundation for all models. She also stressed the need for research to address the potential implication of biases in algorithms that often find their way in through their creators and the data used in their development. “It’s up to us to think about our own ethical solutions to these problems,” she said. “Just as it’s important to progress with the technology, we need to start the field of looking at these questions of what biases are in the algorithms? What biases are in the data, or in that data’s journey?”

      Shifting focus to generative models and whether the development and use of these technologies should be regulated, the panelists — which also included MIT’s Srini Devadas, professor of electrical engineering and computer science, John Horton, professor of information technology, and Simon Johnson, professor of entrepreneurship — all concurred that regulating open-source algorithms, which are publicly accessible, would be difficult given that regulators are still catching up and struggling to even set guardrails for technology that is now 20 years old.

      Returning to the question of how to effectively regulate the use of these technologies, Johnson proposed a progressive corporate tax system as a potential solution. He recommends basing companies’ tax payments on their profits, especially for large corporations whose massive earnings go largely untaxed due to offshore banking. By doing so, Johnson said that this approach can serve as a regulatory mechanism that discourages companies from trying to “own the entire world” by imposing disincentives.

      The role of ethics in computing education

      As computing continues to advance with no signs of slowing down, it is critical to educate students to be intentional in the social impact of the technologies they will be developing and deploying into the world. But can one actually be taught such things? If so, how?

      Caspar Hare, professor of philosophy at MIT and co-associate dean of SERC, posed this looming question to faculty on a panel he moderated on the role of ethics in computing education. All experienced in teaching ethics and thinking about the social implications of computing, each panelist shared their perspective and approach.

      A strong advocate for the importance of learning from history, Eden Medina, associate professor of science, technology, and society at MIT, said that “often the way we frame computing is that everything is new. One of the things that I do in my teaching is look at how people have confronted these issues in the past and try to draw from them as a way to think about possible ways forward.” Medina regularly uses case studies in her classes and referred to a paper written by Yale University science historian Joanna Radin on the Pima Indian Diabetes Dataset that raised ethical issues on the history of that particular collection of data that many don’t consider as an example of how decisions around technology and data can grow out of very specific contexts.

      Milo Phillips-Brown, associate professor of philosophy at Oxford University, talked about the Ethical Computing Protocol that he co-created while he was a SERC postdoc at MIT. The protocol, a four-step approach to building technology responsibly, is designed to train computer science students to think in a better and more accurate way about the social implications of technology by breaking the process down into more manageable steps. “The basic approach that we take very much draws on the fields of value-sensitive design, responsible research and innovation, participatory design as guiding insights, and then is also fundamentally interdisciplinary,” he said.

      Fields such as biomedicine and law have an ethics ecosystem that distributes the function of ethical reasoning in these areas. Oversight and regulation are provided to guide front-line stakeholders and decision-makers when issues arise, as are training programs and access to interdisciplinary expertise that they can draw from. “In this space, we have none of that,” said John Basl, associate professor of philosophy at Northeastern University. “For current generations of computer scientists and other decision-makers, we’re actually making them do the ethical reasoning on their own.” Basl commented further that teaching core ethical reasoning skills across the curriculum, not just in philosophy classes, is essential, and that the goal shouldn’t be for every computer scientist be a professional ethicist, but for them to know enough of the landscape to be able to ask the right questions and seek out the relevant expertise and resources that exists.

      After the final session, interdisciplinary groups of faculty, students, and researchers engaged in animated discussions related to the issues covered throughout the day during a reception that marked the conclusion of the symposium. More

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      in Data Management & Statistics

      Using data to write songs for progress

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      A three-year recipient of MIT’s Emerson Classical Vocal Scholarships, senior Ananya Gurumurthy recalls getting ready to step onto the Carnegie Hall stage to sing a Mozart opera that she once sang with the New York All-State Choir. The choir conductor reminded her to articulate her words and to engage her diaphragm.

      “If you don’t project your voice, how are people going to hear you when you perform?” Gurumurthy recalls her conductor telling her. “This is your moment, your chance to connect with such a tremendous audience.”

      Gurumurthy reflects on the universal truth of those words as she adds her musical talents to her math and computer science studies to campaign for social and economic justice.

      The daughter of immigrants

      Growing up in Edgemont, New York, she was inspired to fight on behalf of others by her South Asian immigrant parents, who came to the United States in the 1980s. Her father is a management consultant and her mother has experience as an investment banker.

      “They came barely 15 years after the passage of the 1965 Immigration and Nationality Act, which removed national origin quotas from the American immigration system,” she says. “I would not be here if it had not been for the Civil Rights Movement, which preceded both me and my parents.”

      Her parents told her about their new home’s anti-immigrant sentiments; for example, her father was a graduate student in Dallas exiting a store when he was pelted with glass bottles and racial slurs.

      “I often consider the amount of bravery that it must have taken them to abandon everything they knew to immigrate to a new, but still imperfect, country in search of something better,” she says. “As a result, I have always felt so grounded in my identity both as a South Asian American and a woman of color. These identities have allowed me to think critically about how I can most effectively reform the institutions surrounding me.”

      Gurumurthy has been singing since she was 11, but in high school, she decided to also build her political voice by working for New York Senator Andrea Stewart-Cousins. At one point, Gurumurthy noted a log was kept for the subjects of constituent calls, such as “affordable housing” and  “infrastructure,” and it was then that she became aware that Stewart-Cousins would address the most pressing of these callers’ issues before the Senate.

      “This experience was my first time witnessing how powerful the mobilization of constituents in vast numbers was for influencing meaningful legislative change,” says Gurumurthy.

      After she began applying her math skills to political campaigns, Gurumurthy was soon tapped to run analytics for the Democratic National Committee’s (DNC) midterm election initiative. As a lead analyst for the New York DNC, she adapted an interactive activation-competition (IAC) model to understand voting patterns in the 2018 and 2020 elections. She collected data from public voting records to predict how constituents would cast their ballots and used an IAC algorithm to strategize alongside grassroots organizations and allocate resources to empower historically disenfranchised groups in municipal, state, and federal elections to encourage them to vote.

      Research and student organizing at MIT

      When she arrived at MIT in 2019 to study mathematics with computer science, along with minors in music and economics, she admits she was saddled with the naïve notion that she would “build digital tools that could single-handedly alleviate all of the collective pressures of systemic injustice in this country.” 

      Since then, she has learned to create what she calls “a more nuanced view.” She picked up data analytics skills to build mobilization platforms for organizations that pursued social and economic justice, including working in Fulton County, Georgia, with Fair Fight Action (through the Kelly-Douglas Fund Scholarship) to analyze patterns of voter suppression, and MIT’s ethics laboratories in the Computer Science and Artificial Intelligence Laboratory to build symbolic artificial intelligence protocols to better understand bias in artificial intelligence algorithms. For her work on the International Monetary Fund (through the MIT Washington Summer Internship Program), Gurumurthy was awarded second place for the 2022 S. Klein Prize in Technical Writing for her paper “The Rapid Rise of Cryptocurrency.”

      “The outcomes of each project gave me more hope to begin the next because I could see the impact of these digital tools,” she says. “I saw people feel empowered to use their voices whether it was voting for the first time, protesting exploitative global monetary policy, or fighting gender discrimination. I’ve been really fortunate to see the power of mathematical analysis firsthand.”

      “I have come to realize that the constructive use of technology could be a powerful voice of resistance against injustice,” she says. “Because numbers matter, and when people bear witness to them, they are pushed to take action in meaningful ways.”

      Hoping to make a difference in her own community, she joined several Institute committees. As co-chair of the Undergraduate Association’s education committee, she propelled MIT’s first-ever digital petition for grade transparency and worked with faculty members on Institute committees to ensure that all students were being provided adequate resources to participate in online education in the wake of the Covid-19 pandemic. The digital petition inspired her to begin a project, called Insite, to develop a more centralized digital means of data collection on student life at MIT to better inform policies made by its governing bodies. As Ring Committee chair, she ensured that the special traditions of the “Brass Rat” were made economically accessible to all class members by helping the committee nearly triple its financial aid budget. For her efforts at MIT, last May she received the William L. Stewart, Jr. Award for “[her] contributions [as] an individual student at MIT to extracurricular activities and student life.”

      Ananya plans on going to law school after graduation, to study constitutional law so that she can use her technical background to build quantitative evidence in cases pertaining to voting rights, social welfare, and ethical technology, and set legal standards ”for the humane use of data,” she says.

      “In building digital tools for a variety of social and economic justice organizations, I hope that we can challenge our existing systems of power and realize the progress we so dearly need to witness. There is strength in numbers, both algorithmically and organizationally. I believe it is our responsibility to simultaneously use these strengths to change the world.”

      Her ambitions, however, began when she began singing lessons when she was 11; without her background as a vocalist, she says she would be voiceless.

      “Operatic performance has given me the ability to truly step into my character and convey powerful emotions in my performance. In the process, I have realized that my voice is most powerful when it reflects my true convictions, whether I am performing or publicly speaking. I truly believe that this honesty has allowed me to become an effective community organizer. I’d like to believe that this voice is what compels those around me to act.”

      Private musical study is available for students through the Emerson/Harris Program, which offers merit-based financial awards to students of outstanding achievement on their instruments or voice in classical, jazz, or world music. The Emerson/Harris Program is funded by the late Cherry L. Emerson Jr. SM ’41, in response to an appeal from Associate Provost Ellen T. Harris (Class of 1949 professor emeritus of music). More

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      A better way to study ocean currents

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      To study ocean currents, scientists release GPS-tagged buoys in the ocean and record their velocities to reconstruct the currents that transport them. These buoy data are also used to identify “divergences,” which are areas where water rises up from below the surface or sinks beneath it.

      By accurately predicting currents and pinpointing divergences, scientists can more precisely forecast the weather, approximate how oil will spread after a spill, or measure energy transfer in the ocean. A new model that incorporates machine learning makes more accurate predictions than conventional models do, a new study reports.

      A multidisciplinary research team including computer scientists at MIT and oceanographers has found that a standard statistical model typically used on buoy data can struggle to accurately reconstruct currents or identify divergences because it makes unrealistic assumptions about the behavior of water.

      The researchers developed a new model that incorporates knowledge from fluid dynamics to better reflect the physics at work in ocean currents. They show that their method, which only requires a small amount of additional computational expense, is more accurate at predicting currents and identifying divergences than the traditional model.

      This new model could help oceanographers make more accurate estimates from buoy data, which would enable them to more effectively monitor the transportation of biomass (such as Sargassum seaweed), carbon, plastics, oil, and nutrients in the ocean. This information is also important for understanding and tracking climate change.

      “Our method captures the physical assumptions more appropriately and more accurately. In this case, we know a lot of the physics already. We are giving the model a little bit of that information so it can focus on learning the things that are important to us, like what are the currents away from the buoys, or what is this divergence and where is it happening?” says senior author Tamara Broderick, an associate professor in MIT’s Department of Electrical Engineering and Computer Science (EECS) and a member of the Laboratory for Information and Decision Systems and the Institute for Data, Systems, and Society.

      Broderick’s co-authors include lead author Renato Berlinghieri, an electrical engineering and computer science graduate student; Brian L. Trippe, a postdoc at Columbia University; David R. Burt and Ryan Giordano, MIT postdocs; Kaushik Srinivasan, an assistant researcher in atmospheric and ocean sciences at the University of California at Los Angeles; Tamay Özgökmen, professor in the Department of Ocean Sciences at the University of Miami; and Junfei Xia, a graduate student at the University of Miami. The research will be presented at the International Conference on Machine Learning.

      Diving into the data

      Oceanographers use data on buoy velocity to predict ocean currents and identify “divergences” where water rises to the surface or sinks deeper.

      To estimate currents and find divergences, oceanographers have used a machine-learning technique known as a Gaussian process, which can make predictions even when data are sparse. To work well in this case, the Gaussian process must make assumptions about the data to generate a prediction.

      A standard way of applying a Gaussian process to oceans data assumes the latitude and longitude components of the current are unrelated. But this assumption isn’t physically accurate. For instance, this existing model implies that a current’s divergence and its vorticity (a whirling motion of fluid) operate on the same magnitude and length scales. Ocean scientists know this is not true, Broderick says. The previous model also assumes the frame of reference matters, which means fluid would behave differently in the latitude versus the longitude direction.

      “We were thinking we could address these problems with a model that incorporates the physics,” she says.

      They built a new model that uses what is known as a Helmholtz decomposition to accurately represent the principles of fluid dynamics. This method models an ocean current by breaking it down into a vorticity component (which captures the whirling motion) and a divergence component (which captures water rising or sinking).

      In this way, they give the model some basic physics knowledge that it uses to make more accurate predictions.

      This new model utilizes the same data as the old model. And while their method can be more computationally intensive, the researchers show that the additional cost is relatively small.

      Buoyant performance

      They evaluated the new model using synthetic and real ocean buoy data. Because the synthetic data were fabricated by the researchers, they could compare the model’s predictions to ground-truth currents and divergences. But simulation involves assumptions that may not reflect real life, so the researchers also tested their model using data captured by real buoys released in the Gulf of Mexico.

      This shows the trajectories of approximately 300 buoys released during the Grand LAgrangian Deployment (GLAD) in the Gulf of Mexico in the summer of 2013, to learn about ocean surface currents around the Deepwater Horizon oil spill site. The small, regular clockwise rotations are due to Earth’s rotation.Credit: Consortium of Advanced Research for Transport of Hydrocarbons in the Environment

      In each case, their method demonstrated superior performance for both tasks, predicting currents and identifying divergences, when compared to the standard Gaussian process and another machine-learning approach that used a neural network. For example, in one simulation that included a vortex adjacent to an ocean current, the new method correctly predicted no divergence while the previous Gaussian process method and the neural network method both predicted a divergence with very high confidence.

      The technique is also good at identifying vortices from a small set of buoys, Broderick adds.

      Now that they have demonstrated the effectiveness of using a Helmholtz decomposition, the researchers want to incorporate a time element into their model, since currents can vary over time as well as space. In addition, they want to better capture how noise impacts the data, such as winds that sometimes affect buoy velocity. Separating that noise from the data could make their approach more accurate.

      “Our hope is to take this noisily observed field of velocities from the buoys, and then say what is the actual divergence and actual vorticity, and predict away from those buoys, and we think that our new technique will be helpful for this,” she says.

      “The authors cleverly integrate known behaviors from fluid dynamics to model ocean currents in a flexible model,” says Massimiliano Russo, an associate biostatistician at Brigham and Women’s Hospital and instructor at Harvard Medical School, who was not involved with this work. “The resulting approach retains the flexibility to model the nonlinearity in the currents but can also characterize phenomena such as vortices and connected currents that would only be noticed if the fluid dynamic structure is integrated into the model. This is an excellent example of where a flexible model can be substantially improved with a well thought and scientifically sound specification.”

      This research is supported, in part, by the Office of Naval Research, a National Science Foundation (NSF) CAREER Award, and the Rosenstiel School of Marine, Atmospheric, and Earth Science at the University of Miami. More

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      Martin Wainwright named director of the Institute for Data, Systems, and Society

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      Martin Wainwright, the Cecil H. Green Professor in MIT’s departments of Electrical Engineering and Computer Science (EECS) and Mathematics, has been named the new director of the Institute for Data, Systems, and Society (IDSS), effective July 1.

      “Martin is a widely recognized leader in statistics and machine learning — both in research and in education. In taking on this leadership role in the college, Martin will work to build up the human and institutional behavior component of IDSS, while strengthening initiatives in both policy and statistics, and collaborations within the institute, across MIT, and beyond,” says Daniel Huttenlocher, dean of the MIT Schwarzman College of Computing and the Henry Ellis Warren Professor of Electrical Engineering and Computer Science. “I look forward to working with him and supporting his efforts in this next chapter for IDSS.”

      “Martin holds a strong belief in the value of theoretical, experimental, and computational approaches to research and in facilitating connections between them. He also places much importance in having practical, as well as academic, impact,” says Asu Ozdaglar, deputy dean of academics for the MIT Schwarzman College of Computing, department head of EECS, and the MathWorks Professor of Electrical Engineering and Computer Science. “As the new director of IDSS, he will undoubtedly bring these tenets to the role in advancing the mission of IDSS and helping to shape its future.”

      A principal investigator in the Laboratory for Information and Decision Systems and the Statistics and Data Science Center, Wainwright joined the MIT faculty in July 2022 from the University of California at Berkeley, where he held the Howard Friesen Chair with a joint appointment between the departments of Electrical Engineering and Computer Science and Statistics.

      Wainwright received his bachelor’s degree in mathematics from the University of Waterloo, Canada, and doctoral degree in electrical engineering and computer science from MIT. He has received a number of awards and recognition, including an Alfred P. Sloan Foundation Fellowship, and best paper awards from the IEEE Signal Processing Society, IEEE Communications Society, and IEEE Information Theory and Communication Societies. He has also been honored with the Medallion Lectureship and Award from the Institute of Mathematical Statistics, and the COPSS Presidents’ Award from the Joint Statistical Societies. He was a section lecturer with the International Congress of Mathematicians in 2014 and received the Blackwell Award from the Institute of Mathematical Statistics in 2017.

      He is the author of “High-dimensional Statistics: A Non-Asymptotic Viewpoint” (Cambridge University Press, 2019), and is coauthor on several books, including on graphical models and on sparse statistical modeling.

      Wainwright succeeds Munther Dahleh, the William A. Coolidge Professor in EECS, who has helmed IDSS since its founding in 2015.

      “I am grateful to Munther and thank him for his leadership of IDSS. As the founding director, he has led the creation of a remarkable new part of MIT,” says Huttenlocher. More