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    Creating new skills and new connections with MIT’s Quantitative Methods Workshop

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    Starting on New Year’s Day, when many people were still clinging to holiday revelry, scores of students and faculty members from about a dozen partner universities instead flipped open their laptops for MIT’s Quantitative Methods Workshop, a jam-packed, weeklong introduction to how computational and mathematical techniques can be applied to neuroscience and biology research. But don’t think of QMW as a “crash course.” Instead the program’s purpose is to help elevate each participant’s scientific outlook, both through the skills and concepts it imparts and the community it creates.

    “It broadens their horizons, it shows them significant applications they’ve never thought of, and introduces them to people whom as researchers they will come to know and perhaps collaborate with one day,” says Susan L. Epstein, a Hunter College computer science professor and education coordinator of MIT’s Center for Brains, Minds, and Machines, which hosts the program with the departments of Biology and Brain and Cognitive Sciences and The Picower Institute for Learning and Memory. “It is a model of interdisciplinary scholarship.”

    This year 83 undergraduates and faculty members from institutions that primarily serve groups underrepresented in STEM fields took part in the QMW, says organizer Mandana Sassanfar, senior lecturer and director of diversity and science outreach across the four hosting MIT entities. Since the workshop launched in 2010, it has engaged more than 1,000 participants, of whom more than 170 have gone on to participate in MIT Summer Research Programs (such as MSRP-BIO), and 39 have come to MIT for graduate school.

    Individual goals, shared experience

    Undergraduates and faculty in various STEM disciplines often come to QMW to gain an understanding of, or expand their expertise in, computational and mathematical data analysis. Computer science- and statistics-minded participants come to learn more about how such techniques can be applied in life sciences fields. In lectures; in hands-on labs where they used the computer programming language Python to process, analyze, and visualize data; and in less formal settings such as tours and lunches with MIT faculty, participants worked and learned together, and informed each other’s perspectives.

    Brain and Cognitive Sciences Professor Nancy Kanwisher delivers a lecture in MIT’s Building 46 on functional brain imaging to QMW participants.

    Photo: Mandana Sassanfar

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    And regardless of their field of study, participants made connections with each other and with the MIT students and faculty who taught and spoke over the course of the week.

    Hunter College computer science sophomore Vlad Vostrikov says that while he has already worked with machine learning and other programming concepts, he was interested to “branch out” by seeing how they are used to analyze scientific datasets. He also valued the chance to learn the experiences of the graduate students who teach QMW’s hands-on labs.

    “This was a good way to explore computational biology and neuroscience,” Vostrikov says. “I also really enjoy hearing from the people who teach us. It’s interesting to hear where they come from and what they are doing.”

    Jariatu Kargbo, a biology and chemistry sophomore at University of Maryland Baltimore County, says when she first learned of the QMW she wasn’t sure it was for her. It seemed very computation-focused. But her advisor Holly Willoughby encouraged Kargbo to attend to learn about how programming could be useful in future research — currently she is taking part in research on the retina at UMBC. More than that, Kargbo also realized it would be a good opportunity to make connections at MIT in advance of perhaps applying for MSRP this summer.

    “I thought this would be a great way to meet up with faculty and see what the environment is like here because I’ve never been to MIT before,” Kargbo says. “It’s always good to meet other people in your field and grow your network.”

    QMW is not just for students. It’s also for their professors, who said they can gain valuable professional education for their research and teaching.

    Fayuan Wen, an assistant professor of biology at Howard University, is no stranger to computational biology, having performed big data genetic analyses of sickle cell disease (SCD). But she’s mostly worked with the R programming language and QMW’s focus is on Python. As she looks ahead to projects in which she wants analyze genomic data to help predict disease outcomes in SCD and HIV, she says a QMW session delivered by biology graduate student Hannah Jacobs was perfectly on point.

    “This workshop has the skills I want to have,” Wen says.

    Moreover, Wen says she is looking to start a machine-learning class in the Howard biology department and was inspired by some of the teaching materials she encountered at QMW — for example, online curriculum modules developed by Taylor Baum, an MIT graduate student in electrical engineering and computer science and Picower Institute labs, and Paloma Sánchez-Jáuregui, a coordinator who works with Sassanfar.

    Tiziana Ligorio, a Hunter College computer science doctoral lecturer who together with Epstein teaches a deep machine-learning class at the City University of New York campus, felt similarly. Rather than require a bunch of prerequisites that might drive students away from the class, Ligorio was looking to QMW’s intense but introductory curriculum as a resource for designing a more inclusive way of getting students ready for the class.

    Instructive interactions

    Each day runs from 9 a.m. to 5 p.m., including morning and afternoon lectures and hands-on sessions. Class topics ranged from statistical data analysis and machine learning to brain-computer interfaces, brain imaging, signal processing of neural activity data, and cryogenic electron microscopy.

    “This workshop could not happen without dedicated instructors — grad students, postdocs, and faculty — who volunteer to give lectures, design and teach hands-on computer labs, and meet with students during the very first week of January,” Saassanfar says.

    MIT assistant professor of biology Brady Weissbourd (center) converses with QMW student participants during a lunch break.

    Photo: Mandana Sassanfar

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    The sessions surround student lunches with MIT faculty members. For example, at midday Jan. 2, assistant professor of biology Brady Weissbourd, an investigator in the Picower Institute, sat down with seven students in one of Building 46’s curved sofas to field questions about his neuroscience research in jellyfish and how he uses quantitative techniques as part of that work. He also described what it’s like to be a professor, and other topics that came to the students’ minds.

    Then the participants all crossed Vassar Street to Building 26’s Room 152, where they formed different but similarly sized groups for the hands-on lab “Machine learning applications to studying the brain,” taught by Baum. She guided the class through Python exercises she developed illustrating “supervised” and “unsupervised” forms of machine learning, including how the latter method can be used to discern what a person is seeing based on magnetic readings of brain activity.

    As students worked through the exercises, tablemates helped each other by supplementing Baum’s instruction. Ligorio, Vostrikov, and Kayla Blincow, assistant professor of biology at the University of the Virgin Islands, for instance, all leapt to their feet to help at their tables.

    Hunter College lecturer of computer science Tiziana Ligorio (standing) explains a Python programming concept to students at her table during a workshop session.

    Photo: David Orenstein

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    At the end of the class, when Baum asked students what they had learned, they offered a litany of new knowledge. Survey data that Sassanfar and Sánchez-Jáuregui use to anonymously track QMW outcomes, revealed many more such attestations of the value of the sessions. With a prompt asking how one might apply what they’ve learned, one respondent wrote: “Pursue a research career or endeavor in which I apply the concepts of computer science and neuroscience together.”

    Enduring connections

    While some new QMW attendees might only be able to speculate about how they’ll apply their new skills and relationships, Luis Miguel de Jesús Astacio could testify to how attending QMW as an undergraduate back in 2014 figured into a career where he is now a faculty member in physics at the University of Puerto Rico Rio Piedras Campus. After QMW, he returned to MIT that summer as a student in the lab of neuroscientist and Picower Professor Susumu Tonegawa. He came back again in 2016 to the lab of physicist and Francis Friedman Professor Mehran Kardar. What’s endured for the decade has been his connection to Sassanfar. So while he was once a student at QMW, this year he was back with a cohort of undergraduates as a faculty member.

    Michael Aldarondo-Jeffries, director of academic advancement programs at the University of Central Florida, seconded the value of the networking that takes place at QMW. He has brought students for a decade, including four this year. What he’s observed is that as students come together in settings like QMW or UCF’s McNair program, which helps to prepare students for graduate school, they become inspired about a potential future as researchers.

    “The thing that stands out is just the community that’s formed,” he says. “For many of the students, it’s the first time that they’re in a group that understands what they’re moving toward. They don’t have to explain why they’re excited to read papers on a Friday night.”

    Or why they are excited to spend a week including New Year’s Day at MIT learning how to apply quantitative methods to life sciences data. More

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      Image recognition accuracy: An unseen challenge confounding today’s AI

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      Imagine you are scrolling through the photos on your phone and you come across an image that at first you can’t recognize. It looks like maybe something fuzzy on the couch; could it be a pillow or a coat? After a couple of seconds it clicks — of course! That ball of fluff is your friend’s cat, Mocha. While some of your photos could be understood in an instant, why was this cat photo much more difficult?

      MIT Computer Science and Artificial Intelligence Laboratory (CSAIL) researchers were surprised to find that despite the critical importance of understanding visual data in pivotal areas ranging from health care to transportation to household devices, the notion of an image’s recognition difficulty for humans has been almost entirely ignored. One of the major drivers of progress in deep learning-based AI has been datasets, yet we know little about how data drives progress in large-scale deep learning beyond that bigger is better.

      In real-world applications that require understanding visual data, humans outperform object recognition models despite the fact that models perform well on current datasets, including those explicitly designed to challenge machines with debiased images or distribution shifts. This problem persists, in part, because we have no guidance on the absolute difficulty of an image or dataset. Without controlling for the difficulty of images used for evaluation, it’s hard to objectively assess progress toward human-level performance, to cover the range of human abilities, and to increase the challenge posed by a dataset.

      To fill in this knowledge gap, David Mayo, an MIT PhD student in electrical engineering and computer science and a CSAIL affiliate, delved into the deep world of image datasets, exploring why certain images are more difficult for humans and machines to recognize than others. “Some images inherently take longer to recognize, and it’s essential to understand the brain’s activity during this process and its relation to machine learning models. Perhaps there are complex neural circuits or unique mechanisms missing in our current models, visible only when tested with challenging visual stimuli. This exploration is crucial for comprehending and enhancing machine vision models,” says Mayo, a lead author of a new paper on the work.

      This led to the development of a new metric, the “minimum viewing time” (MVT), which quantifies the difficulty of recognizing an image based on how long a person needs to view it before making a correct identification. Using a subset of ImageNet, a popular dataset in machine learning, and ObjectNet, a dataset designed to test object recognition robustness, the team showed images to participants for varying durations from as short as 17 milliseconds to as long as 10 seconds, and asked them to choose the correct object from a set of 50 options. After over 200,000 image presentation trials, the team found that existing test sets, including ObjectNet, appeared skewed toward easier, shorter MVT images, with the vast majority of benchmark performance derived from images that are easy for humans.

      The project identified interesting trends in model performance — particularly in relation to scaling. Larger models showed considerable improvement on simpler images but made less progress on more challenging images. The CLIP models, which incorporate both language and vision, stood out as they moved in the direction of more human-like recognition.

      “Traditionally, object recognition datasets have been skewed towards less-complex images, a practice that has led to an inflation in model performance metrics, not truly reflective of a model’s robustness or its ability to tackle complex visual tasks. Our research reveals that harder images pose a more acute challenge, causing a distribution shift that is often not accounted for in standard evaluations,” says Mayo. “We released image sets tagged by difficulty along with tools to automatically compute MVT, enabling MVT to be added to existing benchmarks and extended to various applications. These include measuring test set difficulty before deploying real-world systems, discovering neural correlates of image difficulty, and advancing object recognition techniques to close the gap between benchmark and real-world performance.”

      “One of my biggest takeaways is that we now have another dimension to evaluate models on. We want models that are able to recognize any image even if — perhaps especially if — it’s hard for a human to recognize. We’re the first to quantify what this would mean. Our results show that not only is this not the case with today’s state of the art, but also that our current evaluation methods don’t have the ability to tell us when it is the case because standard datasets are so skewed toward easy images,” says Jesse Cummings, an MIT graduate student in electrical engineering and computer science and co-first author with Mayo on the paper.

      From ObjectNet to MVT

      A few years ago, the team behind this project identified a significant challenge in the field of machine learning: Models were struggling with out-of-distribution images, or images that were not well-represented in the training data. Enter ObjectNet, a dataset comprised of images collected from real-life settings. The dataset helped illuminate the performance gap between machine learning models and human recognition abilities, by eliminating spurious correlations present in other benchmarks — for example, between an object and its background. ObjectNet illuminated the gap between the performance of machine vision models on datasets and in real-world applications, encouraging use for many researchers and developers — which subsequently improved model performance.

      Fast forward to the present, and the team has taken their research a step further with MVT. Unlike traditional methods that focus on absolute performance, this new approach assesses how models perform by contrasting their responses to the easiest and hardest images. The study further explored how image difficulty could be explained and tested for similarity to human visual processing. Using metrics like c-score, prediction depth, and adversarial robustness, the team found that harder images are processed differently by networks. “While there are observable trends, such as easier images being more prototypical, a comprehensive semantic explanation of image difficulty continues to elude the scientific community,” says Mayo.

      In the realm of health care, for example, the pertinence of understanding visual complexity becomes even more pronounced. The ability of AI models to interpret medical images, such as X-rays, is subject to the diversity and difficulty distribution of the images. The researchers advocate for a meticulous analysis of difficulty distribution tailored for professionals, ensuring AI systems are evaluated based on expert standards, rather than layperson interpretations.

      Mayo and Cummings are currently looking at neurological underpinnings of visual recognition as well, probing into whether the brain exhibits differential activity when processing easy versus challenging images. The study aims to unravel whether complex images recruit additional brain areas not typically associated with visual processing, hopefully helping demystify how our brains accurately and efficiently decode the visual world.

      Toward human-level performance

      Looking ahead, the researchers are not only focused on exploring ways to enhance AI’s predictive capabilities regarding image difficulty. The team is working on identifying correlations with viewing-time difficulty in order to generate harder or easier versions of images.

      Despite the study’s significant strides, the researchers acknowledge limitations, particularly in terms of the separation of object recognition from visual search tasks. The current methodology does concentrate on recognizing objects, leaving out the complexities introduced by cluttered images.

      “This comprehensive approach addresses the long-standing challenge of objectively assessing progress towards human-level performance in object recognition and opens new avenues for understanding and advancing the field,” says Mayo. “With the potential to adapt the Minimum Viewing Time difficulty metric for a variety of visual tasks, this work paves the way for more robust, human-like performance in object recognition, ensuring that models are truly put to the test and are ready for the complexities of real-world visual understanding.”

      “This is a fascinating study of how human perception can be used to identify weaknesses in the ways AI vision models are typically benchmarked, which overestimate AI performance by concentrating on easy images,” says Alan L. Yuille, Bloomberg Distinguished Professor of Cognitive Science and Computer Science at Johns Hopkins University, who was not involved in the paper. “This will help develop more realistic benchmarks leading not only to improvements to AI but also make fairer comparisons between AI and human perception.” 

      “It’s widely claimed that computer vision systems now outperform humans, and on some benchmark datasets, that’s true,” says Anthropic technical staff member Simon Kornblith PhD ’17, who was also not involved in this work. “However, a lot of the difficulty in those benchmarks comes from the obscurity of what’s in the images; the average person just doesn’t know enough to classify different breeds of dogs. This work instead focuses on images that people can only get right if given enough time. These images are generally much harder for computer vision systems, but the best systems are only a bit worse than humans.”

      Mayo, Cummings, and Xinyu Lin MEng ’22 wrote the paper alongside CSAIL Research Scientist Andrei Barbu, CSAIL Principal Research Scientist Boris Katz, and MIT-IBM Watson AI Lab Principal Researcher Dan Gutfreund. The researchers are affiliates of the MIT Center for Brains, Minds, and Machines.

      The team is presenting their work at the 2023 Conference on Neural Information Processing Systems (NeurIPS). More

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      in Data Management & Statistics

      Summer research offers a springboard to advanced studies

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      Doctoral studies at MIT aren’t a calling for everyone, but they can be for anyone who has had opportunities to discover that science and technology research is their passion and to build the experience and skills to succeed. For Taylor Baum, Josefina Correa Menéndez, and Karla Alejandra Montejo, three graduate students in just one lab of The Picower Institute for Learning and Memory, a pivotal opportunity came via the MIT Summer Research Program in Biology and Neuroscience (MSRP-Bio). When a student finds MSRP-Bio, it helps them find their future in research. 

      In the program, undergraduate STEM majors from outside MIT spend the summer doing full-time research in the departments of Biology, Brain and Cognitive Sciences (BCS), or the Center for Brains, Minds and Machines (CBMM). They gain lab skills, mentoring, preparation for graduate school, and connections that might last a lifetime. Over the last two decades, a total of 215 students from underrepresented minority groups, who are from economically disadvantaged backgrounds, first-generation or nontraditional college students, or students with disabilities have participated in research in BCS or CBMM labs.  

      Like Baum, Correa Menéndez, and Montejo, the vast majority go on to pursue graduate studies, says Diversity and Outreach Coordinator Mandana Sassanfar, who runs the program. For instance, among 91 students who have worked in Picower Institute labs, 81 have completed their undergraduate studies. Of those, 46 enrolled in PhD programs at MIT or other schools such as Cornell, Yale, Stanford, and Princeton universities, and the University of California System. Another 12 have gone to medical school, another seven are in MD/PhD programs, and three have earned master’s degrees. The rest are studying as post-baccalaureates or went straight into the workforce after earning their bachelor’s degree. 

      After participating in the program, Baum, Correa Menéndez, and Montejo each became graduate students in the research group of Emery N. Brown, the Edward Hood Taplin Professor of Computational Neuroscience and Medical Engineering in The Picower Institute and the Institute for Medical Engineering and Science. The lab combines statistical, computational, and experimental neuroscience methods to study how general anesthesia affects the central nervous system to ultimately improve patient care and advance understanding of the brain. Brown says the students have each been doing “off-the-scale” work, in keeping with the excellence he’s seen from MSRP BIO students over the years. For example, on Aug. 10 Baum and Correa Menéndez were honored with MathWorks Fellowships.

      “I think MSRP is fantastic. Mandana does this amazing job of getting students who are quite talented to come to MIT to realize that they can move their game to the next level. They have the capacity to do it. They just need the opportunities,” Brown says. “These students live up to the expectations that you have of them. And now as graduate students, they’re taking on hard problems and they’re solving them.” 

      Paths to PhD studies 

      Pursuing a PhD is hardly a given. Many young students have never considered graduate school or specific fields of study like neuroscience or electrical engineering. But Sassanfar engages students across the country to introduce them to the opportunity MSRP-Bio provides to gain exposure, experience, and mentoring in advanced fields. Every fall, after the program’s students have returned to their undergraduate institutions, she visits schools in places as far flung as Florida, Maryland, Puerto Rico, and Texas and goes to conferences for diverse science communities such as ABRCMS and SACNAS to spread the word. 

      Taylor Baum

      Photo courtesy of Taylor Baum.

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      When Baum first connected with the program in 2017, she was finding her way at Penn State University. She had been majoring in biology and music composition but had just switched the latter to engineering following a conversation over coffee exposing her to brain-computer interfacing technology, in which detecting brain signals of people with full-body paralysis could improve their quality of life by enabling control of computers or wheelchairs. Baum became enthusiastic about the potential to build similar systems, but as a new engineering student, she struggled to find summer internships and research opportunities. 

      “I got rejected from every single progam except the MIT Center for Brains, Minds and Machines MSRP,” she recalls with a chuckle. 

      Baum thrived in MSRP-Bio, working in Brown’s lab for three successive summers. At each stage, she said, she gained more research skills, experience, and independence. When she graduated, she was sure she wanted to go to graduate school and applied to four of her dream schools. She accepted MIT’s offer to join the Department of Electrical Engineering and Computer Science, where she is co-advised by faculty members there and by Brown. She is now working to develop a system grounded in cardiovascular physiology that can improve blood pressure management. A tool for practicing anesthesiologists, the system automates the dosing of drugs to maintain a patient’s blood pressure at safe levels in the operating room or intensive care unit. 

      More than that, Baum not only is leading an organization advancing STEM education in Puerto Rico, but also is helping to mentor a current MSRP-Bio student in the Brown lab. 

      “MSRP definitely bonds everyone who has participated in it,” Baum says. “If I see anyone who I know participated in MSRP, we could have an immediate conversation. I know that most of us, if we needed help, we’d feel comfortable asking for help from someone from MSRP. With that shared experience, we have a sense of camaraderie, and community.” 

      In fact, a few years ago when a former MSRP-Bio student named Karla Montejo was applying to MIT, Baum provided essential advice and feedback about the application process, Montejo says. Now, as a graduate student, Montejo has become a mentor for the program in her own right, Sassanfar notes. For instance, Montejo serves on program alumni panels that advise new MSRP-Bio students. 

      Karla Alejandra Montejo

      Photo courtesy of Karla Alejandra Montejo.

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      Montejo’s family immigrated to Miami from Cuba when she was a child. The magnet high school she attended was so new that students were encouraged to help establish the school’s programs. She forged a path into research. 

      “I didn’t even know what research was,” she says. “I wanted to be a doctor, and I thought maybe it would help me on my resume. I thought it would be kind of like shadowing, but no, it was really different. So I got really captured by research when I was in high school.” 

      Despite continuing to pursue research in college at Florida International University, Montejo didn’t get into graduate school on her first attempt because she hadn’t yet learned how to focus her application. But Sassanfar had visited FIU to recruit students and through that relationship Montejo had already gone through MIT’s related Quantitative Methods Workshop (QMW). So Montejo enrolled in MSRP-Bio, working in the CBMM-affiliated lab of Gabriel Kreiman at Boston Children’s Hospital. 

      “I feel like Mandana really helped me out, gave me a break, and the MSRP experience pretty much solidified that I really wanted to come to MIT,” Montejo says. 

      In the QMW, Montejo learned she really liked computational neuroscience, and in Kreiman’s lab she got to try her hand at computational modeling of the cognition involved in making perceptual sense of complex scenes. Montejo realized she wanted to work on more biologically based neuroscience problems. When the summer ended, because she was off the normal graduate school cycle for now, she found a two-year post-baccalaurate program at Mayo Clinic studying the role a brain cell type called astrocytes might have in the Parkinson’s disease treatment deep brain stimulation. 

      When it came time to reapply to graduate schools (with the help of Baum and others in the BCS Application Assistance Program) Montejo applied to MIT and got in, joining the Brown lab. Now she’s working on modeling the role of  metabolic processes in the changing of brain rhythms under anesthesia, taking advantage of how general anesthesia predictably changes brain states. The effects anesthetic drugs have on cell metabolism and the way that ultimately affects levels of consciousness reveals important aspects of how metabolism affects brain circuits and systems. Earlier this month, for instance, Montejo co-led a paper the lab published in The Proceedings of the National Academy of Sciences detailing the neuroscience of a patient’s transition into an especially deep state of unconsciousness called “burst suppression.” 

      Josefina Correa Menendez

      Photo: David Orenstein

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      A signature of the Brown lab’s work is rigorous statistical analysis and methods, for instance to discern brain arousal states from EEG measures of brain rhythms. A PhD candidate in MIT’s Interdisciplinary Doctoral Program in Statistics, Correa Menéndez is advancing the use of Bayesian hierarchical models for neural data analysis. These statistical models offer a principled way of pooling information across datasets. One of her models can help scientists better understand the way neurons can “spike” with electrical activity when the brain is presented with a stimulus. The other’s power is in discerning critical features such as arousal states of the brain under general anesthesia from electrophysiological recordings. 

      Though she now works with complex equations and computations as a PhD candidate in neuroscience and statistics, Correa Menéndez was mostly interested in music art as a high school student at Academia María Reina in San Juan and then architecture in college at the University of Puerto Rico at Río Piedras. It was discussions at the intersection of epistemology and art during an art theory class that inspired Correa Menéndez to switch her major to biology and to take computer science classes, too. 

      When Sassanfar visited Puerto Rico in 2017, a computer science professor (Patricia Ordóñez) suggested that Correa Menéndez apply for a chance to attend the QMW. She did, and that led her to also participate in MSRP-Bio in the lab of Sherman Fairchild Professor Matt Wilson (a faculty member in BCS, CBMM, and the Picower Institute). She joined in the lab’s studies of how spatial memories are represented in the hippocampus and how the brain makes use of those memories to help understand the world around it. With mentoring from then-postdoc Carmen Varela (now a faculty member at Florida State University), the experience not only exposed her to neuroscience, but also helped her gain skills and experience with lab experiments, building research tools, and conducting statistical analyses. She ended up working in the Wilson lab as a research scholar for a year and began her graduate studies in September 2018.  

      Classes she took with Brown as a research scholar inspired her to join his lab as a graduate student. 

      “Taking the classes with Emery and also doing experiments made me aware of the role of statistics in the scientific process: from the interpretation of results to the analysis and the design of experiments,” she says. “More often than not, in science, statistics becomes this sort of afterthought — this ‘annoying’ thing that people need to do to get their paper published. But statistics as a field is actually a lot more than that. It’s a way of thinking about data. Particularly, Bayesian modeling provides a principled inference framework for combining prior knowledge into a hypothesis that you can test with data.” 

      To be sure, no one starts out with such inspiration about scientific scholarship, but MSRP-Bio helps students find that passion for research and the paths that opens up.   More