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    AI model identifies certain breast tumor stages likely to progress to invasive cancer

    Ductal carcinoma in situ (DCIS) is a type of preinvasive tumor that sometimes progresses to a highly deadly form of breast cancer. It accounts for about 25 percent of all breast cancer diagnoses.Because it is difficult for clinicians to determine the type and stage of DCIS, patients with DCIS are often overtreated. To address this, an interdisciplinary team of researchers from MIT and ETH Zurich developed an AI model that can identify the different stages of DCIS from a cheap and easy-to-obtain breast tissue image. Their model shows that both the state and arrangement of cells in a tissue sample are important for determining the stage of DCIS.Because such tissue images are so easy to obtain, the researchers were able to build one of the largest datasets of its kind, which they used to train and test their model. When they compared its predictions to conclusions of a pathologist, they found clear agreement in many instances.In the future, the model could be used as a tool to help clinicians streamline the diagnosis of simpler cases without the need for labor-intensive tests, giving them more time to evaluate cases where it is less clear if DCIS will become invasive.“We took the first step in understanding that we should be looking at the spatial organization of cells when diagnosing DCIS, and now we have developed a technique that is scalable. From here, we really need a prospective study. Working with a hospital and getting this all the way to the clinic will be an important step forward,” says Caroline Uhler, a professor in the Department of Electrical Engineering and Computer Science (EECS) and the Institute for Data, Systems, and Society (IDSS), who is also director of the Eric and Wendy Schmidt Center at the Broad Institute of MIT and Harvard and a researcher at MIT’s Laboratory for Information and Decision Systems (LIDS).Uhler, co-corresponding author of a paper on this research, is joined by lead author Xinyi Zhang, a graduate student in EECS and the Eric and Wendy Schmidt Center; co-corresponding author GV Shivashankar, professor of mechogenomics at ETH Zurich jointly with the Paul Scherrer Institute; and others at MIT, ETH Zurich, and the University of Palermo in Italy. The open-access research was published July 20 in Nature Communications.Combining imaging with AI   Between 30 and 50 percent of patients with DCIS develop a highly invasive stage of cancer, but researchers don’t know the biomarkers that could tell a clinician which tumors will progress.Researchers can use techniques like multiplexed staining or single-cell RNA sequencing to determine the stage of DCIS in tissue samples. However, these tests are too expensive to be performed widely, Shivashankar explains.In previous work, these researchers showed that a cheap imagining technique known as chromatin staining could be as informative as the much costlier single-cell RNA sequencing.For this research, they hypothesized that combining this single stain with a carefully designed machine-learning model could provide the same information about cancer stage as costlier techniques.First, they created a dataset containing 560 tissue sample images from 122 patients at three different stages of disease. They used this dataset to train an AI model that learns a representation of the state of each cell in a tissue sample image, which it uses to infer the stage of a patient’s cancer.However, not every cell is indicative of cancer, so the researchers had to aggregate them in a meaningful way.They designed the model to create clusters of cells in similar states, identifying eight states that are important markers of DCIS. Some cell states are more indicative of invasive cancer than others. The model determines the proportion of cells in each state in a tissue sample.Organization matters“But in cancer, the organization of cells also changes. We found that just having the proportions of cells in every state is not enough. You also need to understand how the cells are organized,” says Shivashankar.With this insight, they designed the model to consider proportion and arrangement of cell states, which significantly boosted its accuracy.“The interesting thing for us was seeing how much spatial organization matters. Previous studies had shown that cells which are close to the breast duct are important. But it is also important to consider which cells are close to which other cells,” says Zhang.When they compared the results of their model with samples evaluated by a pathologist, it had clear agreement in many instances. In cases that were not as clear-cut, the model could provide information about features in a tissue sample, like the organization of cells, that a pathologist could use in decision-making.This versatile model could also be adapted for use in other types of cancer, or even neurodegenerative conditions, which is one area the researchers are also currently exploring.“We have shown that, with the right AI techniques, this simple stain can be very powerful. There is still much more research to do, but we need to take the organization of cells into account in more of our studies,” Uhler says.This research was funded, in part, by the Eric and Wendy Schmidt Center at the Broad Institute, ETH Zurich, the Paul Scherrer Institute, the Swiss National Science Foundation, the U.S. National Institutes of Health, the U.S. Office of Naval Research, the MIT Jameel Clinic for Machine Learning and Health, the MIT-IBM Watson AI Lab, and a Simons Investigator Award. More

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    Machine learning and the microscope

    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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    When to trust an AI model

    Because machine-learning models can give false predictions, researchers often equip them with the ability to tell a user how confident they are about a certain decision. This is especially important in high-stake settings, such as when models are used to help identify disease in medical images or filter job applications.But a model’s uncertainty quantifications are only useful if they are accurate. If a model says it is 49 percent confident that a medical image shows a pleural effusion, then 49 percent of the time, the model should be right.MIT researchers have introduced a new approach that can improve uncertainty estimates in machine-learning models. Their method not only generates more accurate uncertainty estimates than other techniques, but does so more efficiently.In addition, because the technique is scalable, it can be applied to huge deep-learning models that are increasingly being deployed in health care and other safety-critical situations.This technique could give end users, many of whom lack machine-learning expertise, better information they can use to determine whether to trust a model’s predictions or if the model should be deployed for a particular task.“It is easy to see these models perform really well in scenarios where they are very good, and then assume they will be just as good in other scenarios. This makes it especially important to push this kind of work that seeks to better calibrate the uncertainty of these models to make sure they align with human notions of uncertainty,” says lead author Nathan Ng, a graduate student at the University of Toronto who is a visiting student at MIT.Ng wrote the paper with Roger Grosse, an assistant professor of computer science at the University of Toronto; and senior author Marzyeh Ghassemi, an associate professor in the Department of Electrical Engineering and Computer Science and a member of the Institute of Medical Engineering Sciences and the Laboratory for Information and Decision Systems. The research will be presented at the International Conference on Machine Learning.Quantifying uncertaintyUncertainty quantification methods often require complex statistical calculations that don’t scale well to machine-learning models with millions of parameters. These methods also require users to make assumptions about the model and data used to train it.The MIT researchers took a different approach. They use what is known as the minimum description length principle (MDL), which does not require the assumptions that can hamper the accuracy of other methods. MDL is used to better quantify and calibrate uncertainty for test points the model has been asked to label.The technique the researchers developed, known as IF-COMP, makes MDL fast enough to use with the kinds of large deep-learning models deployed in many real-world settings.MDL involves considering all possible labels a model could give a test point. If there are many alternative labels for this point that fit well, its confidence in the label it chose should decrease accordingly.“One way to understand how confident a model is would be to tell it some counterfactual information and see how likely it is to believe you,” Ng says.For example, consider a model that says a medical image shows a pleural effusion. If the researchers tell the model this image shows an edema, and it is willing to update its belief, then the model should be less confident in its original decision.With MDL, if a model is confident when it labels a datapoint, it should use a very short code to describe that point. If it is uncertain about its decision because the point could have many other labels, it uses a longer code to capture these possibilities.The amount of code used to label a datapoint is known as stochastic data complexity. If the researchers ask the model how willing it is to update its belief about a datapoint given contrary evidence, the stochastic data complexity should decrease if the model is confident.But testing each datapoint using MDL would require an enormous amount of computation.Speeding up the processWith IF-COMP, the researchers developed an approximation technique that can accurately estimate stochastic data complexity using a special function, known as an influence function. They also employed a statistical technique called temperature-scaling, which improves the calibration of the model’s outputs. This combination of influence functions and temperature-scaling enables high-quality approximations of the stochastic data complexity.In the end, IF-COMP can efficiently produce well-calibrated uncertainty quantifications that reflect a model’s true confidence. The technique can also determine whether the model has mislabeled certain data points or reveal which data points are outliers.The researchers tested their system on these three tasks and found that it was faster and more accurate than other methods.“It is really important to have some certainty that a model is well-calibrated, and there is a growing need to detect when a specific prediction doesn’t look quite right. Auditing tools are becoming more necessary in machine-learning problems as we use large amounts of unexamined data to make models that will be applied to human-facing problems,” Ghassemi says.IF-COMP is model-agnostic, so it can provide accurate uncertainty quantifications for many types of machine-learning models. This could enable it to be deployed in a wider range of real-world settings, ultimately helping more practitioners make better decisions.“People need to understand that these systems are very fallible and can make things up as they go. A model may look like it is highly confident, but there are a ton of different things it is willing to believe given evidence to the contrary,” Ng says.In the future, the researchers are interested in applying their approach to large language models and studying other potential use cases for the minimum description length principle.  More

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    MIT researchers introduce generative AI for databases

    A new tool makes it easier for database users to perform complicated statistical analyses of tabular data without the need to know what is going on behind the scenes.GenSQL, a generative AI system for databases, could help users make predictions, detect anomalies, guess missing values, fix errors, or generate synthetic data with just a few keystrokes.For instance, if the system were used to analyze medical data from a patient who has always had high blood pressure, it could catch a blood pressure reading that is low for that particular patient but would otherwise be in the normal range.GenSQL automatically integrates a tabular dataset and a generative probabilistic AI model, which can account for uncertainty and adjust their decision-making based on new data.Moreover, GenSQL can be used to produce and analyze synthetic data that mimic the real data in a database. This could be especially useful in situations where sensitive data cannot be shared, such as patient health records, or when real data are sparse.This new tool is built on top of SQL, a programming language for database creation and manipulation that was introduced in the late 1970s and is used by millions of developers worldwide.“Historically, SQL taught the business world what a computer could do. They didn’t have to write custom programs, they just had to ask questions of a database in high-level language. We think that, when we move from just querying data to asking questions of models and data, we are going to need an analogous language that teaches people the coherent questions you can ask a computer that has a probabilistic model of the data,” says Vikash Mansinghka ’05, MEng ’09, PhD ’09, senior author of a paper introducing GenSQL and a principal research scientist and leader of the Probabilistic Computing Project in the MIT Department of Brain and Cognitive Sciences.When the researchers compared GenSQL to popular, AI-based approaches for data analysis, they found that it was not only faster but also produced more accurate results. Importantly, the probabilistic models used by GenSQL are explainable, so users can read and edit them.“Looking at the data and trying to find some meaningful patterns by just using some simple statistical rules might miss important interactions. You really want to capture the correlations and the dependencies of the variables, which can be quite complicated, in a model. With GenSQL, we want to enable a large set of users to query their data and their model without having to know all the details,” adds lead author Mathieu Huot, a research scientist in the Department of Brain and Cognitive Sciences and member of the Probabilistic Computing Project.They are joined on the paper by Matin Ghavami and Alexander Lew, MIT graduate students; Cameron Freer, a research scientist; Ulrich Schaechtel and Zane Shelby of Digital Garage; Martin Rinard, an MIT professor in the Department of Electrical Engineering and Computer Science and member of the Computer Science and Artificial Intelligence Laboratory (CSAIL); and Feras Saad ’15, MEng ’16, PhD ’22, an assistant professor at Carnegie Mellon University. The research was recently presented at the ACM Conference on Programming Language Design and Implementation.Combining models and databasesSQL, which stands for structured query language, is a programming language for storing and manipulating information in a database. In SQL, people can ask questions about data using keywords, such as by summing, filtering, or grouping database records.However, querying a model can provide deeper insights, since models can capture what data imply for an individual. For instance, a female developer who wonders if she is underpaid is likely more interested in what salary data mean for her individually than in trends from database records.The researchers noticed that SQL didn’t provide an effective way to incorporate probabilistic AI models, but at the same time, approaches that use probabilistic models to make inferences didn’t support complex database queries.They built GenSQL to fill this gap, enabling someone to query both a dataset and a probabilistic model using a straightforward yet powerful formal programming language.A GenSQL user uploads their data and probabilistic model, which the system automatically integrates. Then, she can run queries on data that also get input from the probabilistic model running behind the scenes. This not only enables more complex queries but can also provide more accurate answers.For instance, a query in GenSQL might be something like, “How likely is it that a developer from Seattle knows the programming language Rust?” Just looking at a correlation between columns in a database might miss subtle dependencies. Incorporating a probabilistic model can capture more complex interactions.   Plus, the probabilistic models GenSQL utilizes are auditable, so people can see which data the model uses for decision-making. In addition, these models provide measures of calibrated uncertainty along with each answer.For instance, with this calibrated uncertainty, if one queries the model for predicted outcomes of different cancer treatments for a patient from a minority group that is underrepresented in the dataset, GenSQL would tell the user that it is uncertain, and how uncertain it is, rather than overconfidently advocating for the wrong treatment.Faster and more accurate resultsTo evaluate GenSQL, the researchers compared their system to popular baseline methods that use neural networks. GenSQL was between 1.7 and 6.8 times faster than these approaches, executing most queries in a few milliseconds while providing more accurate results.They also applied GenSQL in two case studies: one in which the system identified mislabeled clinical trial data and the other in which it generated accurate synthetic data that captured complex relationships in genomics.Next, the researchers want to apply GenSQL more broadly to conduct largescale modeling of human populations. With GenSQL, they can generate synthetic data to draw inferences about things like health and salary while controlling what information is used in the analysis.They also want to make GenSQL easier to use and more powerful by adding new optimizations and automation to the system. In the long run, the researchers want to enable users to make natural language queries in GenSQL. Their goal is to eventually develop a ChatGPT-like AI expert one could talk to about any database, which grounds its answers using GenSQL queries.   This research is funded, in part, by the Defense Advanced Research Projects Agency (DARPA), Google, and the Siegel Family Foundation. More

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    Fotini Christia named director of the Institute for Data, Systems, and Society

    Fotini Christia, the Ford International Professor of Social Sciences in the Department of Political Science, has been named the new director of the Institute for Data, Systems, and Society (IDSS), effective July 1.“Fotini is well-positioned to guide IDSS into the next chapter. With her tenure as the director of the Sociotechnical Systems Research Center and as an associate director of IDSS since 2020, she has actively forged connections between the social sciences, data science, and computation,” says Daniel Huttenlocher, dean of the MIT Schwarzman College of Computing and the Henry Ellis Warren Professor of Electrical Engineering and Computer Science. “I eagerly anticipate the ways in which she will advance and champion IDSS in alignment with the spirit and mission of the Schwarzman College of Computing.”“Fotini’s profound expertise as a social scientist and her adept use of data science, computational tools, and novel methodologies to grasp the dynamics of societal evolution across diverse fields, makes her a natural fit to lead IDSS,” says Asu Ozdaglar, deputy dean of the MIT Schwarzman College of Computing and head of the Department of Electrical Engineering and Computer Science.Christia’s research has focused on issues of conflict and cooperation in the Muslim world, for which she has conducted fieldwork in Afghanistan, Bosnia, Iraq, the Palestinian Territories, and Yemen, among others. More recently, her research has been directed at examining how to effectively integrate artificial intelligence tools in public policy.She was appointed the director of the Sociotechnical Systems Research Center (SSRC) and an associate director of IDSS in October 2020. SSRC, an interdisciplinary center housed within IDSS in the MIT Schwarzman College of Computing, focuses on the study of high-impact, complex societal challenges that shape our world.As part of IDSS, she is co-organizer of a cross-disciplinary research effort, the Initiative on Combatting Systemic Racism. Bringing together faculty and researchers from all of MIT’s five schools and the college, the initiative builds on extensive social science literature on systemic racism and uses big data to develop and harness computational tools that can help effect structural and normative change toward racial equity across housing, health care, policing, and social media. Christia is also chair of IDSS’s doctoral program in Social and Engineering Systems.Christia is the author of “Alliance Formation in Civil War” (Cambridge University Press, 2012), which was awarded the Luebbert Award for Best Book in Comparative Politics, the Lepgold Prize for Best Book in International Relations, and a Distinguished Book Award from the International Studies Association. She is co-editor with Graeme Blair (University of California, Los Angeles) and Jeremy Weinstein (incoming dean at Harvard Kennedy School) of “Crime, Insecurity, and Community Policing: Experiments on Building Trust,” forthcoming in August 2024 with Cambridge University Press.Her research has also appeared in Science, Nature Human Behavior, Review of Economic Studies, American Economic Journal: Applied Economics, NeurIPs, Communications Medicine, IEEE Transactions on Network Science and Engineering, American Political Science Review, and Annual Review of Political Science, among other journals. Her opinion pieces have been published in Foreign Affairs, The New York Times, The Washington Post, and The Boston Globe, among other outlets.A native of Greece, where she grew up in the port city of Salonika, Christia moved to the United States to attend college at Columbia University. She graduated magna cum laude in 2001 with a joint BA in economics–operations research and an MA in international affairs. She joined the MIT faculty in 2008 after receiving her PhD in public policy from Harvard University.Christia succeeds Noelle Selin, a professor in IDSS and the Department of Earth, Atmospheric, and Planetary Sciences. Selin has led IDSS as interim director for the 2023-24 academic year since July 2023, following Professor Martin Wainwright.“I am incredibly grateful to Noelle for serving as interim director this year. Her contributions in this role, as well as her time leading the Technology and Policy Program, have been invaluable. I’m delighted she will remain part of the IDSS community as a faculty member,” says Huttenlocher. More

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    Arvind, longtime MIT professor and prolific computer scientist, dies at 77

    Arvind Mithal, the Charles W. and Jennifer C. Johnson Professor in Computer Science and Engineering at MIT, head of the faculty of computer science in the Department of Electrical Engineering and Computer Science (EECS), and a pillar of the MIT community, died on June 17. Arvind, who went by the mononym, was 77 years old.A prolific researcher who led the Computation Structures Group in the Computer Science and Artificial Intelligence Laboratory (CSAIL), Arvind served on the MIT faculty for nearly five decades.“He was beloved by countless people across the MIT community and around the world who were inspired by his intellectual brilliance and zest for life,” President Sally Kornbluth wrote in a letter to the MIT community today.As a scientist, Arvind was well known for important contributions to dataflow computing, which seeks to optimize the flow of data to take advantage of parallelism, achieving faster and more efficient computation.In the last 25 years, his research interests broadened to include developing techniques and tools for formal modeling, high-level synthesis, and formal verification of complex digital devices like microprocessors and hardware accelerators, as well as memory models and cache coherence protocols for parallel computing architectures and programming languages.Those who knew Arvind describe him as a rare individual whose interests and expertise ranged from high-level, theoretical formal systems all the way down through languages and compilers to the gates and structures of silicon hardware.The applications of Arvind’s work are far-reaching, from reducing the amount of energy and space required by data centers to streamlining the design of more efficient multicore computer chips.“Arvind was both a tremendous scholar in the fields of computer architecture and programming languages and a dedicated teacher, who brought systems-level thinking to our students. He was also an exceptional academic leader, often leading changes in curriculum and contributing to the Engineering Council in meaningful and impactful ways. I will greatly miss his sage advice and wisdom,” says Anantha Chandrakasan, chief innovation and strategy officer, dean of engineering, and the Vannevar Bush Professor of Electrical Engineering and Computer Science.“Arvind’s positive energy, together with his hearty laugh, brightened so many people’s lives. He was an enduring source of wise counsel for colleagues and for generations of students. With his deep commitment to academic excellence, he not only transformed research in computer architecture and parallel computing but also brought that commitment to his role as head of the computer science faculty in the EECS department. He left a lasting impact on all of us who had the privilege of working with him,” says Dan Huttenlocher, dean of the MIT Schwarzman College of Computing and the Henry Ellis Warren Professor of Electrical Engineering and Computer Science.Arvind developed an interest in parallel computing while he was a student at the Indian Institute of Technology in Kanpur, from which he received his bachelor’s degree in 1969. He earned a master’s degree and PhD in computer science in 1972 and 1973, respectively, from the University of Minnesota, where he studied operating systems and mathematical models of program behavior. He taught at the University of California at Irvine from 1974 to 1978 before joining the faculty at MIT.At MIT, Arvind’s group studied parallel computing and declarative programming languages, and he led the development of two parallel computing languages, Id and pH. He continued his work on these programming languages through the 1990s, publishing the book “Implicit Parallel Programming in pH” with co-author R.S. Nikhil in 2001, the culmination of more than 20 years of research.In addition to his research, Arvind was an important academic leader in EECS. He served as head of computer science faculty in the department and played a critical role in helping with the reorganization of EECS after the establishment of the MIT Schwarzman College of Computing.“Arvind was a force of nature, larger than life in every sense. His relentless positivity, unwavering optimism, boundless generosity, and exceptional strength as a researcher was truly inspiring and left a profound mark on all who had the privilege of knowing him. I feel enormous gratitude for the light he brought into our lives and his fundamental impact on our community,” says Daniela Rus, the Andrew and Erna Viterbi Professor of Electrical Engineering and Computer Science and the director of CSAIL.His work on dataflow and parallel computing led to the Monsoon project in the late 1980s and early 1990s. Arvind’s group, in collaboration with Motorola, built 16 dataflow computing machines and developed their associated software. One Monsoon dataflow machine is now in the Computer History Museum in Mountain View, California.Arvind’s focus shifted in the 1990s when, as he explained in a 2012 interview for the Institute of Electrical and Electronics Engineers (IEEE), funding for research into parallel computing began to dry up.“Microprocessors were getting so much faster that people thought they didn’t need it,” he recalled.Instead, he began applying techniques his team had learned and developed for parallel programming to the principled design of digital hardware.In addition to mentoring students and junior colleagues at MIT, Arvind also advised universities and governments in many countries on research in parallel programming and semiconductor design.Based on his work on digital hardware design, Arvind founded Sandburst in 2000, a fabless manufacturing company for semiconductor chips. He served as the company’s president for two years before returning to the MIT faculty, while continuing as an advisor. Sandburst was later acquired by Broadcom.Arvind and his students also developed Bluespec, a programming language designed to automate the design of chips. Building off this work, he co-founded the startup Bluespec, Inc., in 2003, to develop practical tools that help engineers streamline device design.Over the past decade, he was dedicated to advancing undergraduate education at MIT by bringing modern design tools to courses 6.004 (Computation Structures) and 6.191 (Introduction to Deep Learning), and incorporating Minispec, a programming language that is closely related to Bluespec.Arvind was honored for these and other contributions to data flow and multithread computing, and the development of tools for the high-level synthesis of hardware, with membership in the National Academy of Engineering in 2008 and the American Academy of Arts and Sciences in 2012. He was also named a distinguished alumnus of IIT Kanpur, his undergraduate alma mater.“Arvind was more than a pillar of the EECS community and a titan of computer science; he was a beloved colleague and a treasured friend. Those of us with the remarkable good fortune to work and collaborate with Arvind are devastated by his sudden loss. His kindness and joviality were unwavering; his mentorship was thoughtful and well-considered; his guidance was priceless. We will miss Arvind deeply,” says Asu Ozdaglar, deputy dean of the MIT Schwarzman College of Computing and head of EECS.Among numerous other awards, including membership in the Indian National Academy of Sciences and fellowship in the Association for Computing Machinery and IEEE, he received the Harry H. Goode Memorial Award from IEEE in 2012, which honors significant contributions to theory or practice in the information processing field.A humble scientist, Arvind was the first to point out that these achievements were only possible because of his outstanding and brilliant collaborators. Chief among those collaborators were the undergraduate and graduate students he felt fortunate to work with at MIT. He maintained excellent relationships with them both professionally and personally, and valued these relationships more than the work they did together, according to family members.In summing up the key to his scientific success, Arvind put it this way in the 2012 IEEE interview: “Really, one has to do what one believes in. I think the level at which most of us work, it is not sustainable if you don’t enjoy it on a day-to-day basis. You can’t work on it just because of the results. You have to work on it because you say, ‘I have to know the answer to this,’” he said.He is survived by his wife, Gita Singh Mithal, their two sons Divakar ’01 and Prabhakar ’04, their wives Leena and Nisha, and two grandchildren, Maya and Vikram.  More

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

    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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    Researchers use large language models to help robots navigate

    Someday, you may want your home robot to carry a load of dirty clothes downstairs and deposit them in the washing machine in the far-left corner of the basement. The robot will need to combine your instructions with its visual observations to determine the steps it should take to complete this task.For an AI agent, this is easier said than done. Current approaches often utilize multiple hand-crafted machine-learning models to tackle different parts of the task, which require a great deal of human effort and expertise to build. These methods, which use visual representations to directly make navigation decisions, demand massive amounts of visual data for training, which are often hard to come by.To overcome these challenges, researchers from MIT and the MIT-IBM Watson AI Lab devised a navigation method that converts visual representations into pieces of language, which are then fed into one large language model that achieves all parts of the multistep navigation task.Rather than encoding visual features from images of a robot’s surroundings as visual representations, which is computationally intensive, their method creates text captions that describe the robot’s point-of-view. A large language model uses the captions to predict the actions a robot should take to fulfill a user’s language-based instructions.Because their method utilizes purely language-based representations, they can use a large language model to efficiently generate a huge amount of synthetic training data.While this approach does not outperform techniques that use visual features, it performs well in situations that lack enough visual data for training. The researchers found that combining their language-based inputs with visual signals leads to better navigation performance.“By purely using language as the perceptual representation, ours is a more straightforward approach. Since all the inputs can be encoded as language, we can generate a human-understandable trajectory,” says Bowen Pan, an electrical engineering and computer science (EECS) graduate student and lead author of a paper on this approach.Pan’s co-authors include his advisor, Aude Oliva, director of strategic industry engagement at the MIT Schwarzman College of Computing, MIT director of the MIT-IBM Watson AI Lab, and a senior research scientist in the Computer Science and Artificial Intelligence Laboratory (CSAIL); Philip Isola, an associate professor of EECS and a member of CSAIL; senior author Yoon Kim, an assistant professor of EECS and a member of CSAIL; and others at the MIT-IBM Watson AI Lab and Dartmouth College. The research will be presented at the Conference of the North American Chapter of the Association for Computational Linguistics.Solving a vision problem with languageSince large language models are the most powerful machine-learning models available, the researchers sought to incorporate them into the complex task known as vision-and-language navigation, Pan says.But such models take text-based inputs and can’t process visual data from a robot’s camera. So, the team needed to find a way to use language instead.Their technique utilizes a simple captioning model to obtain text descriptions of a robot’s visual observations. These captions are combined with language-based instructions and fed into a large language model, which decides what navigation step the robot should take next.The large language model outputs a caption of the scene the robot should see after completing that step. This is used to update the trajectory history so the robot can keep track of where it has been.The model repeats these processes to generate a trajectory that guides the robot to its goal, one step at a time.To streamline the process, the researchers designed templates so observation information is presented to the model in a standard form — as a series of choices the robot can make based on its surroundings.For instance, a caption might say “to your 30-degree left is a door with a potted plant beside it, to your back is a small office with a desk and a computer,” etc. The model chooses whether the robot should move toward the door or the office.“One of the biggest challenges was figuring out how to encode this kind of information into language in a proper way to make the agent understand what the task is and how they should respond,” Pan says.Advantages of languageWhen they tested this approach, while it could not outperform vision-based techniques, they found that it offered several advantages.First, because text requires fewer computational resources to synthesize than complex image data, their method can be used to rapidly generate synthetic training data. In one test, they generated 10,000 synthetic trajectories based on 10 real-world, visual trajectories.The technique can also bridge the gap that can prevent an agent trained with a simulated environment from performing well in the real world. This gap often occurs because computer-generated images can appear quite different from real-world scenes due to elements like lighting or color. But language that describes a synthetic versus a real image would be much harder to tell apart, Pan says. Also, the representations their model uses are easier for a human to understand because they are written in natural language.“If the agent fails to reach its goal, we can more easily determine where it failed and why it failed. Maybe the history information is not clear enough or the observation ignores some important details,” Pan says.In addition, their method could be applied more easily to varied tasks and environments because it uses only one type of input. As long as data can be encoded as language, they can use the same model without making any modifications.But one disadvantage is that their method naturally loses some information that would be captured by vision-based models, such as depth information.However, the researchers were surprised to see that combining language-based representations with vision-based methods improves an agent’s ability to navigate.“Maybe this means that language can capture some higher-level information than cannot be captured with pure vision features,” he says.This is one area the researchers want to continue exploring. They also want to develop a navigation-oriented captioner that could boost the method’s performance. In addition, they want to probe the ability of large language models to exhibit spatial awareness and see how this could aid language-based navigation.This research is funded, in part, by the MIT-IBM Watson AI Lab. More