More stories

  • in

    Improving health outcomes by targeting climate and air pollution simultaneously

    Climate policies are typically designed to reduce greenhouse gas emissions that result from human activities and drive climate change. The largest source of these emissions is the combustion of fossil fuels, which increases atmospheric concentrations of ozone, fine particulate matter (PM2.5) and other air pollutants that pose public health risks. While climate policies may result in lower concentrations of health-damaging air pollutants as a “co-benefit” of reducing greenhouse gas emissions-intensive activities, they are most effective at improving health outcomes when deployed in tandem with geographically targeted air-quality regulations.

    Yet the computer models typically used to assess the likely air quality/health impacts of proposed climate/air-quality policy combinations come with drawbacks for decision-makers. Atmospheric chemistry/climate models can produce high-resolution results, but they are expensive and time-consuming to run. Integrated assessment models can produce results for far less time and money, but produce results at global and regional scales, rendering them insufficiently precise to obtain accurate assessments of air quality/health impacts at the subnational level.

    To overcome these drawbacks, a team of researchers at MIT and the University of California at Davis has developed a climate/air-quality policy assessment tool that is both computationally efficient and location-specific. Described in a new study in the journal ACS Environmental Au, the tool could enable users to obtain rapid estimates of combined policy impacts on air quality/health at more than 1,500 locations around the globe — estimates precise enough to reveal the equity implications of proposed policy combinations within a particular region.

    “The modeling approach described in this study may ultimately allow decision-makers to assess the efficacy of multiple combinations of climate and air-quality policies in reducing the health impacts of air pollution, and to design more effective policies,” says Sebastian Eastham, the study’s lead author and a principal research scientist at the MIT Joint Program on the Science and Policy of Global Change. “It may also be used to determine if a given policy combination would result in equitable health outcomes across a geographical area of interest.”

    To demonstrate the efficiency and accuracy of their policy assessment tool, the researchers showed that outcomes projected by the tool within seconds were consistent with region-specific results from detailed chemistry/climate models that took days or even months to run. While continuing to refine and develop their approaches, they are now working to embed the new tool into integrated assessment models for direct use by policymakers.

    “As decision-makers implement climate policies in the context of other sustainability challenges like air pollution, efficient modeling tools are important for assessment — and new computational techniques allow us to build faster and more accurate tools to provide credible, relevant information to a broader range of users,” says Noelle Selin, a professor at MIT’s Institute for Data, Systems and Society and Department of Earth, Atmospheric and Planetary Sciences, and supervising author of the study. “We are looking forward to further developing such approaches, and to working with stakeholders to ensure that they provide timely, targeted and useful assessments.”

    The study was funded, in part, by the U.S. Environmental Protection Agency and the Biogen Foundation. More

  • in

    Study: Carbon-neutral pavements are possible by 2050, but rapid policy and industry action are needed

    Almost 2.8 million lane-miles, or about 4.6 million lane-kilometers, of the United States are paved.

    Roads and streets form the backbone of our built environment. They take us to work or school, take goods to their destinations, and much more.

    However, a new study by MIT Concrete Sustainability Hub (CSHub) researchers shows that the annual greenhouse gas (GHG) emissions of all construction materials used in the U.S. pavement network are 11.9 to 13.3 megatons. This is equivalent to the emissions of a gasoline-powered passenger vehicle driving about 30 billion miles in a year.

    As roads are built, repaved, and expanded, new approaches and thoughtful material choices are necessary to dampen their carbon footprint. 

    The CSHub researchers found that, by 2050, mixtures for pavements can be made carbon-neutral if industry and governmental actors help to apply a range of solutions — like carbon capture — to reduce, avoid, and neutralize embodied impacts. (A neutralization solution is any compensation mechanism in the value chain of a product that permanently removes the global warming impact of the processes after avoiding and reducing the emissions.) Furthermore, nearly half of pavement-related greenhouse gas (GHG) savings can be achieved in the short term with a negative or nearly net-zero cost.

    The research team, led by Hessam AzariJafari, MIT CSHub’s deputy director, closed gaps in our understanding of the impacts of pavements decisions by developing a dynamic model quantifying the embodied impact of future pavements materials demand for the U.S. road network. 

    The team first split the U.S. road network into 10-mile (about 16 kilometer) segments, forecasting the condition and performance of each. They then developed a pavement management system model to create benchmarks helping to understand the current level of emissions and the efficacy of different decarbonization strategies. 

    This model considered factors such as annual traffic volume and surface conditions, budget constraints, regional variation in pavement treatment choices, and pavement deterioration. The researchers also used a life-cycle assessment to calculate annual state-level emissions from acquiring pavement construction materials, considering future energy supply and materials procurement.

    The team considered three scenarios for the U.S. pavement network: A business-as-usual scenario in which technology remains static, a projected improvement scenario aligned with stated industry and national goals, and an ambitious improvement scenario that intensifies or accelerates projected strategies to achieve carbon neutrality. 

    If no steps are taken to decarbonize pavement mixtures, the team projected that GHG emissions of construction materials used in the U.S. pavement network would increase by 19.5 percent by 2050. Under the projected scenario, there was an estimated 38 percent embodied impact reduction for concrete and 14 percent embodied impact reduction for asphalt by 2050.

    The keys to making the pavement network carbon neutral by 2050 lie in multiple places. Fully renewable energy sources should be used for pavement materials production, transportation, and other processes. The federal government must contribute to the development of these low-carbon energy sources and carbon capture technologies, as it would be nearly impossible to achieve carbon neutrality for pavements without them. 

    Additionally, increasing pavements’ recycled content and improving their design and production efficiency can lower GHG emissions to an extent. Still, neutralization is needed to achieve carbon neutrality.

    Making the right pavement construction and repair choices would also contribute to the carbon neutrality of the network. For instance, concrete pavements can offer GHG savings across the whole life cycle as they are stiffer and stay smoother for longer, meaning they require less maintenance and have a lesser impact on the fuel efficiency of vehicles. 

    Concrete pavements have other use-phase benefits including a cooling effect through an intrinsically high albedo, meaning they reflect more sunlight than regular pavements. Therefore, they can help combat extreme heat and positively affect the earth’s energy balance through positive radiative forcing, making albedo a potential neutralization mechanism.

    At the same time, a mix of fixes, including using concrete and asphalt in different contexts and proportions, could produce significant GHG savings for the pavement network; decision-makers must consider scenarios on a case-by-case basis to identify optimal solutions. 

    In addition, it may appear as though the GHG emissions of materials used in local roads are dwarfed by the emissions of interstate highway materials. However, the study found that the two road types have a similar impact. In fact, all road types contribute heavily to the total GHG emissions of pavement materials in general. Therefore, stakeholders at the federal, state, and local levels must be involved if our roads are to become carbon neutral. 

    The path to pavement network carbon-neutrality is, therefore, somewhat of a winding road. It demands regionally specific policies and widespread investment to help implement decarbonization solutions, just as renewable energy initiatives have been supported. Providing subsidies and covering the costs of premiums, too, are vital to avoid shifts in the market that would derail environmental savings.

    When planning for these shifts, we must recall that pavements have impacts not just in their production, but across their entire life cycle. As pavements are used, maintained, and eventually decommissioned, they have significant impacts on the surrounding environment.

    If we are to meet climate goals such as the Paris Agreement, which demands that we reach carbon-neutrality by 2050 to avoid the worst impacts of climate change, we — as well as industry and governmental stakeholders — must come together to take a hard look at the roads we use every day and work to reduce their life cycle emissions. 

    The study was published in the International Journal of Life Cycle Assessment. In addition to AzariJafari, the authors include Fengdi Guo of the MIT Department of Civil and Environmental Engineering; Jeremy Gregory, executive director of the MIT Climate and Sustainability Consortium; and Randolph Kirchain, director of the MIT CSHub. More

  • in

    Busy GPUs: Sampling and pipelining method speeds up deep learning on large graphs

    Graphs, a potentially extensive web of nodes connected by edges, can be used to express and interrogate relationships between data, like social connections, financial transactions, traffic, energy grids, and molecular interactions. As researchers collect more data and build out these graphical pictures, researchers will need faster and more efficient methods, as well as more computational power, to conduct deep learning on them, in the way of graph neural networks (GNN).  

    Now, a new method, called SALIENT (SAmpling, sLIcing, and data movemeNT), developed by researchers at MIT and IBM Research, improves the training and inference performance by addressing three key bottlenecks in computation. This dramatically cuts down on the runtime of GNNs on large datasets, which, for example, contain on the scale of 100 million nodes and 1 billion edges. Further, the team found that the technique scales well when computational power is added from one to 16 graphical processing units (GPUs). The work was presented at the Fifth Conference on Machine Learning and Systems.

    “We started to look at the challenges current systems experienced when scaling state-of-the-art machine learning techniques for graphs to really big datasets. It turned out there was a lot of work to be done, because a lot of the existing systems were achieving good performance primarily on smaller datasets that fit into GPU memory,” says Tim Kaler, the lead author and a postdoc in the MIT Computer Science and Artificial Intelligence Laboratory (CSAIL).

    By vast datasets, experts mean scales like the entire Bitcoin network, where certain patterns and data relationships could spell out trends or foul play. “There are nearly a billion Bitcoin transactions on the blockchain, and if we want to identify illicit activities inside such a joint network, then we are facing a graph of such a scale,” says co-author Jie Chen, senior research scientist and manager of IBM Research and the MIT-IBM Watson AI Lab. “We want to build a system that is able to handle that kind of graph and allows processing to be as efficient as possible, because every day we want to keep up with the pace of the new data that are generated.”

    Kaler and Chen’s co-authors include Nickolas Stathas MEng ’21 of Jump Trading, who developed SALIENT as part of his graduate work; former MIT-IBM Watson AI Lab intern and MIT graduate student Anne Ouyang; MIT CSAIL postdoc Alexandros-Stavros Iliopoulos; MIT CSAIL Research Scientist Tao B. Schardl; and Charles E. Leiserson, the Edwin Sibley Webster Professor of Electrical Engineering at MIT and a researcher with the MIT-IBM Watson AI Lab.     

    For this problem, the team took a systems-oriented approach in developing their method: SALIENT, says Kaler. To do this, the researchers implemented what they saw as important, basic optimizations of components that fit into existing machine-learning frameworks, such as PyTorch Geometric and the deep graph library (DGL), which are interfaces for building a machine-learning model. Stathas says the process is like swapping out engines to build a faster car. Their method was designed to fit into existing GNN architectures, so that domain experts could easily apply this work to their specified fields to expedite model training and tease out insights during inference faster. The trick, the team determined, was to keep all of the hardware (CPUs, data links, and GPUs) busy at all times: while the CPU samples the graph and prepares mini-batches of data that will then be transferred through the data link, the more critical GPU is working to train the machine-learning model or conduct inference. 

    The researchers began by analyzing the performance of a commonly used machine-learning library for GNNs (PyTorch Geometric), which showed a startlingly low utilization of available GPU resources. Applying simple optimizations, the researchers improved GPU utilization from 10 to 30 percent, resulting in a 1.4 to two times performance improvement relative to public benchmark codes. This fast baseline code could execute one complete pass over a large training dataset through the algorithm (an epoch) in 50.4 seconds.                          

    Seeking further performance improvements, the researchers set out to examine the bottlenecks that occur at the beginning of the data pipeline: the algorithms for graph sampling and mini-batch preparation. Unlike other neural networks, GNNs perform a neighborhood aggregation operation, which computes information about a node using information present in other nearby nodes in the graph — for example, in a social network graph, information from friends of friends of a user. As the number of layers in the GNN increase, the number of nodes the network has to reach out to for information can explode, exceeding the limits of a computer. Neighborhood sampling algorithms help by selecting a smaller random subset of nodes to gather; however, the researchers found that current implementations of this were too slow to keep up with the processing speed of modern GPUs. In response, they identified a mix of data structures, algorithmic optimizations, and so forth that improved sampling speed, ultimately improving the sampling operation alone by about three times, taking the per-epoch runtime from 50.4 to 34.6 seconds. They also found that sampling, at an appropriate rate, can be done during inference, improving overall energy efficiency and performance, a point that had been overlooked in the literature, the team notes.      

    In previous systems, this sampling step was a multi-process approach, creating extra data and unnecessary data movement between the processes. The researchers made their SALIENT method more nimble by creating a single process with lightweight threads that kept the data on the CPU in shared memory. Further, SALIENT takes advantage of a cache of modern processors, says Stathas, parallelizing feature slicing, which extracts relevant information from nodes of interest and their surrounding neighbors and edges, within the shared memory of the CPU core cache. This again reduced the overall per-epoch runtime from 34.6 to 27.8 seconds.

    The last bottleneck the researchers addressed was to pipeline mini-batch data transfers between the CPU and GPU using a prefetching step, which would prepare data just before it’s needed. The team calculated that this would maximize bandwidth usage in the data link and bring the method up to perfect utilization; however, they only saw around 90 percent. They identified and fixed a performance bug in a popular PyTorch library that caused unnecessary round-trip communications between the CPU and GPU. With this bug fixed, the team achieved a 16.5 second per-epoch runtime with SALIENT.

    “Our work showed, I think, that the devil is in the details,” says Kaler. “When you pay close attention to the details that impact performance when training a graph neural network, you can resolve a huge number of performance issues. With our solutions, we ended up being completely bottlenecked by GPU computation, which is the ideal goal of such a system.”

    SALIENT’s speed was evaluated on three standard datasets ogbn-arxiv, ogbn-products, and ogbn-papers100M, as well as in multi-machine settings, with different levels of fanout (amount of data that the CPU would prepare for the GPU), and across several architectures, including the most recent state-of-the-art one, GraphSAGE-RI. In each setting, SALIENT outperformed PyTorch Geometric, most notably on the large ogbn-papers100M dataset, containing 100 million nodes and over a billion edges Here, it was three times faster, running on one GPU, than the optimized baseline that was originally created for this work; with 16 GPUs, SALIENT was an additional eight times faster. 

    While other systems had slightly different hardware and experimental setups, so it wasn’t always a direct comparison, SALIENT still outperformed them. Among systems that achieved similar accuracy, representative performance numbers include 99 seconds using one GPU and 32 CPUs, and 13 seconds using 1,536 CPUs. In contrast, SALIENT’s runtime using one GPU and 20 CPUs was 16.5 seconds and was just two seconds with 16 GPUs and 320 CPUs. “If you look at the bottom-line numbers that prior work reports, our 16 GPU runtime (two seconds) is an order of magnitude faster than other numbers that have been reported previously on this dataset,” says Kaler. The researchers attributed their performance improvements, in part, to their approach of optimizing their code for a single machine before moving to the distributed setting. Stathas says that the lesson here is that for your money, “it makes more sense to use the hardware you have efficiently, and to its extreme, before you start scaling up to multiple computers,” which can provide significant savings on cost and carbon emissions that can come with model training.

    This new capacity will now allow researchers to tackle and dig deeper into bigger and bigger graphs. For example, the Bitcoin network that was mentioned earlier contained 100,000 nodes; the SALIENT system can capably handle a graph 1,000 times (or three orders of magnitude) larger.

    “In the future, we would be looking at not just running this graph neural network training system on the existing algorithms that we implemented for classifying or predicting the properties of each node, but we also want to do more in-depth tasks, such as identifying common patterns in a graph (subgraph patterns), [which] may be actually interesting for indicating financial crimes,” says Chen. “We also want to identify nodes in a graph that are similar in a sense that they possibly would be corresponding to the same bad actor in a financial crime. These tasks would require developing additional algorithms, and possibly also neural network architectures.”

    This research was supported by the MIT-IBM Watson AI Lab and in part by the U.S. Air Force Research Laboratory and the U.S. Air Force Artificial Intelligence Accelerator. More

  • in

    Investigating at the interface of data science and computing

    A visual model of Guy Bresler’s research would probably look something like a Venn diagram. He works at the four-way intersection where theoretical computer science, statistics, probability, and information theory collide.

    “There are always new things to do be done at the interface. There are always opportunities for entirely new questions to ask,” says Bresler, an associate professor who recently earned tenure in MIT’s Department of Electrical Engineering and Computer Science (EECS).

    A theoretician, he aims to understand the delicate interplay between structure in data, the complexity of models, and the amount of computation needed to learn those models. Recently, his biggest focus has been trying to unveil fundamental phenomena that are broadly responsible for determining the computational complexity of statistics problems — and finding the “sweet spot” where available data and computation resources enable researchers to effectively solve a problem.

    When trying to solve a complex statistics problem, there is often a tug-of-war between data and computation. Without enough data, the computation needed to solve a statistical problem can be intractable, or at least consume a staggering amount of resources. But get just enough data and suddenly the intractable becomes solvable; the amount of computation needed to come up with a solution drops dramatically.

    The majority of modern statistical problems exhibits this sort of trade-off between computation and data, with applications ranging from drug development to weather prediction. Another well-studied and practically important example is cryo-electron microscopy, Bresler says. With this technique, researchers use an electron microscope to take images of molecules in different orientations. The central challenge is how to solve the inverse problem — determining the molecule’s structure given the noisy data. Many statistical problems can be formulated as inverse problems of this sort.

    One aim of Bresler’s work is to elucidate relationships between the wide variety of different statistics problems currently being studied. The dream is to classify statistical problems into equivalence classes, as has been done for other types of computational problems in the field of computational complexity. Showing these sorts of relationships means that, instead of trying to understand each problem in isolation, researchers can transfer their understanding from a well-studied problem to a poorly understood one, he says.

    Adopting a theoretical approach

    For Bresler, a desire to theoretically understand various basic phenomena inspired him to follow a path into academia.

    Both of his parents worked as professors and showed how fulfilling academia can be, he says. His earliest introduction to the theoretical side of engineering came from his father, who is an electrical engineer and theoretician studying signal processing. Bresler was inspired by his work from an early age. As an undergraduate at the University of Illinois at Urbana-Champaign, he bounced between physics, math, and computer science courses. But no matter the topic, he gravitated toward the theoretical viewpoint.

    In graduate school at the University of California at Berkeley, Bresler enjoyed the opportunity to work in a wide variety of topics spanning probability, theoretical computer science, and mathematics. His driving motivator was a love of learning new things.

    “Working at the interface of multiple fields with new questions, there is a feeling that one had better learn as much as possible if one is to have any chance of finding the right tools to answer those questions,” he says.

    That curiosity led him to MIT for a postdoc in the Laboratory for Information and Decision Systems (LIDS) in 2013, and then he joined the faculty two years later as an assistant professor in EECS. He was named an associate professor in 2019.

    Bresler says he was drawn to the intellectual atmosphere at MIT, as well as the supportive environment for launching bold research quests and trying to make progress in new areas of study.

    Opportunities for collaboration

    “What really struck me was how vibrant and energetic and collaborative MIT is. I have this mental list of more than 20 people here who I would love to have lunch with every single week and collaborate with on research. So just based on sheer numbers, joining MIT was a clear win,” he says.

    He’s especially enjoyed collaborating with his students, who continually teach him new things and ask deep questions that drive exciting research projects. One such student, Matthew Brennan, who was one of Bresler’s closest collaborators, tragically and unexpectedly passed away in January, 2021.

    The shock from Brennan’s death is still raw for Bresler, and it derailed his research for a time.

    “Beyond his own prodigious capabilities and creativity, he had this amazing ability to listen to an idea of mine that was almost completely wrong, extract from it a useful piece, and then pass the ball back,” he says. “We had the same vision for what we wanted to achieve in the work, and we were driven to try to tell a certain story. At the time, almost nobody was pursuing this particular line of work, and it was in a way kind of lonely. But he trusted me, and we encouraged one another to keep at it when things seemed bleak.”

    Those lessons in perseverance fuel Bresler as he and his students continue exploring questions that, by their nature, are difficult to answer.

    One area he’s worked in on-and-off for over a decade involves learning graphical models from data. Models of certain types of data, such as time-series data consisting of temperature readings, are often constructed by domain experts who have relevant knowledge and can build a reasonable model, he explains.

    But for many types of data with complex dependencies, such as social network or biological data, it is not at all clear what structure a model should take. Bresler’s work seeks to estimate a structured model from data, which could then be used for downstream applications like making recommendations or better predicting the weather.

    The basic question of identifying good models, whether algorithmically in a complex setting or analytically, by specifying a useful toy model for theoretical analysis, connects the abstract work with engineering practice, he says.

    “In general, modeling is an art. Real life is complicated and if you write down some super-complicated model that tries to capture every feature of a problem, it is doomed,” says Bresler. “You have to think about the problem and understand the practical side of things on some level to identify the correct features of the problem to be modeled, so that you can hope to actually solve it and gain insight into what one should do in practice.”

    Outside the lab, Bresler often finds himself solving very different kinds of problems. He is an avid rock climber and spends much of his free time bouldering throughout New England.

    “I really love it. It is a good excuse to get outside and get sucked into a whole different world. Even though there is problem solving involved, and there are similarities at the philosophical level, it is totally orthogonal to sitting down and doing math,” he says. More

  • in

    AI that can learn the patterns of human language

    Human languages are notoriously complex, and linguists have long thought it would be impossible to teach a machine how to analyze speech sounds and word structures in the way human investigators do.

    But researchers at MIT, Cornell University, and McGill University have taken a step in this direction. They have demonstrated an artificial intelligence system that can learn the rules and patterns of human languages on its own.

    When given words and examples of how those words change to express different grammatical functions (like tense, case, or gender) in one language, this machine-learning model comes up with rules that explain why the forms of those words change. For instance, it might learn that the letter “a” must be added to end of a word to make the masculine form feminine in Serbo-Croatian.

    This model can also automatically learn higher-level language patterns that can apply to many languages, enabling it to achieve better results.

    The researchers trained and tested the model using problems from linguistics textbooks that featured 58 different languages. Each problem had a set of words and corresponding word-form changes. The model was able to come up with a correct set of rules to describe those word-form changes for 60 percent of the problems.

    This system could be used to study language hypotheses and investigate subtle similarities in the way diverse languages transform words. It is especially unique because the system discovers models that can be readily understood by humans, and it acquires these models from small amounts of data, such as a few dozen words. And instead of using one massive dataset for a single task, the system utilizes many small datasets, which is closer to how scientists propose hypotheses — they look at multiple related datasets and come up with models to explain phenomena across those datasets.

    “One of the motivations of this work was our desire to study systems that learn models of datasets that is represented in a way that humans can understand. Instead of learning weights, can the model learn expressions or rules? And we wanted to see if we could build this system so it would learn on a whole battery of interrelated datasets, to make the system learn a little bit about how to better model each one,” says Kevin Ellis ’14, PhD ’20, an assistant professor of computer science at Cornell University and lead author of the paper.

    Joining Ellis on the paper are MIT faculty members Adam Albright, a professor of linguistics; Armando Solar-Lezama, a professor and associate director of the Computer Science and Artificial Intelligence Laboratory (CSAIL); and Joshua B. Tenenbaum, the Paul E. Newton Career Development Professor of Cognitive Science and Computation in the Department of Brain and Cognitive Sciences and a member of CSAIL; as well as senior author

    Timothy J. O’Donnell, assistant professor in the Department of Linguistics at McGill University, and Canada CIFAR AI Chair at the Mila – Quebec Artificial Intelligence Institute.

    The research is published today in Nature Communications.

    Looking at language 

    In their quest to develop an AI system that could automatically learn a model from multiple related datasets, the researchers chose to explore the interaction of phonology (the study of sound patterns) and morphology (the study of word structure).

    Data from linguistics textbooks offered an ideal testbed because many languages share core features, and textbook problems showcase specific linguistic phenomena. Textbook problems can also be solved by college students in a fairly straightforward way, but those students typically have prior knowledge about phonology from past lessons they use to reason about new problems.

    Ellis, who earned his PhD at MIT and was jointly advised by Tenenbaum and Solar-Lezama, first learned about morphology and phonology in an MIT class co-taught by O’Donnell, who was a postdoc at the time, and Albright.

    “Linguists have thought that in order to really understand the rules of a human language, to empathize with what it is that makes the system tick, you have to be human. We wanted to see if we can emulate the kinds of knowledge and reasoning that humans (linguists) bring to the task,” says Albright.

    To build a model that could learn a set of rules for assembling words, which is called a grammar, the researchers used a machine-learning technique known as Bayesian Program Learning. With this technique, the model solves a problem by writing a computer program.

    In this case, the program is the grammar the model thinks is the most likely explanation of the words and meanings in a linguistics problem. They built the model using Sketch, a popular program synthesizer which was developed at MIT by Solar-Lezama.

    But Sketch can take a lot of time to reason about the most likely program. To get around this, the researchers had the model work one piece at a time, writing a small program to explain some data, then writing a larger program that modifies that small program to cover more data, and so on.

    They also designed the model so it learns what “good” programs tend to look like. For instance, it might learn some general rules on simple Russian problems that it would apply to a more complex problem in Polish because the languages are similar. This makes it easier for the model to solve the Polish problem.

    Tackling textbook problems

    When they tested the model using 70 textbook problems, it was able to find a grammar that matched the entire set of words in the problem in 60 percent of cases, and correctly matched most of the word-form changes in 79 percent of problems.

    The researchers also tried pre-programming the model with some knowledge it “should” have learned if it was taking a linguistics course, and showed that it could solve all problems better.

    “One challenge of this work was figuring out whether what the model was doing was reasonable. This isn’t a situation where there is one number that is the single right answer. There is a range of possible solutions which you might accept as right, close to right, etc.,” Albright says.

    The model often came up with unexpected solutions. In one instance, it discovered the expected answer to a Polish language problem, but also another correct answer that exploited a mistake in the textbook. This shows that the model could “debug” linguistics analyses, Ellis says.

    The researchers also conducted tests that showed the model was able to learn some general templates of phonological rules that could be applied across all problems.

    “One of the things that was most surprising is that we could learn across languages, but it didn’t seem to make a huge difference,” says Ellis. “That suggests two things. Maybe we need better methods for learning across problems. And maybe, if we can’t come up with those methods, this work can help us probe different ideas we have about what knowledge to share across problems.”

    In the future, the researchers want to use their model to find unexpected solutions to problems in other domains. They could also apply the technique to more situations where higher-level knowledge can be applied across interrelated datasets. For instance, perhaps they could develop a system to infer differential equations from datasets on the motion of different objects, says Ellis.

    “This work shows that we have some methods which can, to some extent, learn inductive biases. But I don’t think we’ve quite figured out, even for these textbook problems, the inductive bias that lets a linguist accept the plausible grammars and reject the ridiculous ones,” he adds.

    “This work opens up many exciting venues for future research. I am particularly intrigued by the possibility that the approach explored by Ellis and colleagues (Bayesian Program Learning, BPL) might speak to how infants acquire language,” says T. Florian Jaeger, a professor of brain and cognitive sciences and computer science at the University of Rochester, who was not an author of this paper. “Future work might ask, for example, under what additional induction biases (assumptions about universal grammar) the BPL approach can successfully achieve human-like learning behavior on the type of data infants observe during language acquisition. I think it would be fascinating to see whether inductive biases that are even more abstract than those considered by Ellis and his team — such as biases originating in the limits of human information processing (e.g., memory constraints on dependency length or capacity limits in the amount of information that can be processed per time) — would be sufficient to induce some of the patterns observed in human languages.”

    This work was funded, in part, by the Air Force Office of Scientific Research, the Center for Brains, Minds, and Machines, the MIT-IBM Watson AI Lab, the Natural Science and Engineering Research Council of Canada, the Fonds de Recherche du Québec – Société et Culture, the Canada CIFAR AI Chairs Program, the National Science Foundation (NSF), and an NSF graduate fellowship. More

  • in

    Taking a magnifying glass to data center operations

    When the MIT Lincoln Laboratory Supercomputing Center (LLSC) unveiled its TX-GAIA supercomputer in 2019, it provided the MIT community a powerful new resource for applying artificial intelligence to their research. Anyone at MIT can submit a job to the system, which churns through trillions of operations per second to train models for diverse applications, such as spotting tumors in medical images, discovering new drugs, or modeling climate effects. But with this great power comes the great responsibility of managing and operating it in a sustainable manner — and the team is looking for ways to improve.

    “We have these powerful computational tools that let researchers build intricate models to solve problems, but they can essentially be used as black boxes. What gets lost in there is whether we are actually using the hardware as effectively as we can,” says Siddharth Samsi, a research scientist in the LLSC. 

    To gain insight into this challenge, the LLSC has been collecting detailed data on TX-GAIA usage over the past year. More than a million user jobs later, the team has released the dataset open source to the computing community.

    Their goal is to empower computer scientists and data center operators to better understand avenues for data center optimization — an important task as processing needs continue to grow. They also see potential for leveraging AI in the data center itself, by using the data to develop models for predicting failure points, optimizing job scheduling, and improving energy efficiency. While cloud providers are actively working on optimizing their data centers, they do not often make their data or models available for the broader high-performance computing (HPC) community to leverage. The release of this dataset and associated code seeks to fill this space.

    “Data centers are changing. We have an explosion of hardware platforms, the types of workloads are evolving, and the types of people who are using data centers is changing,” says Vijay Gadepally, a senior researcher at the LLSC. “Until now, there hasn’t been a great way to analyze the impact to data centers. We see this research and dataset as a big step toward coming up with a principled approach to understanding how these variables interact with each other and then applying AI for insights and improvements.”

    Papers describing the dataset and potential applications have been accepted to a number of venues, including the IEEE International Symposium on High-Performance Computer Architecture, the IEEE International Parallel and Distributed Processing Symposium, the Annual Conference of the North American Chapter of the Association for Computational Linguistics, the IEEE High-Performance and Embedded Computing Conference, and International Conference for High Performance Computing, Networking, Storage and Analysis. 

    Workload classification

    Among the world’s TOP500 supercomputers, TX-GAIA combines traditional computing hardware (central processing units, or CPUs) with nearly 900 graphics processing unit (GPU) accelerators. These NVIDIA GPUs are specialized for deep learning, the class of AI that has given rise to speech recognition and computer vision.

    The dataset covers CPU, GPU, and memory usage by job; scheduling logs; and physical monitoring data. Compared to similar datasets, such as those from Google and Microsoft, the LLSC dataset offers “labeled data, a variety of known AI workloads, and more detailed time series data compared with prior datasets. To our knowledge, it’s one of the most comprehensive and fine-grained datasets available,” Gadepally says. 

    Notably, the team collected time-series data at an unprecedented level of detail: 100-millisecond intervals on every GPU and 10-second intervals on every CPU, as the machines processed more than 3,000 known deep-learning jobs. One of the first goals is to use this labeled dataset to characterize the workloads that different types of deep-learning jobs place on the system. This process would extract features that reveal differences in how the hardware processes natural language models versus image classification or materials design models, for example.   

    The team has now launched the MIT Datacenter Challenge to mobilize this research. The challenge invites researchers to use AI techniques to identify with 95 percent accuracy the type of job that was run, using their labeled time-series data as ground truth.

    Such insights could enable data centers to better match a user’s job request with the hardware best suited for it, potentially conserving energy and improving system performance. Classifying workloads could also allow operators to quickly notice discrepancies resulting from hardware failures, inefficient data access patterns, or unauthorized usage.

    Too many choices

    Today, the LLSC offers tools that let users submit their job and select the processors they want to use, “but it’s a lot of guesswork on the part of users,” Samsi says. “Somebody might want to use the latest GPU, but maybe their computation doesn’t actually need it and they could get just as impressive results on CPUs, or lower-powered machines.”

    Professor Devesh Tiwari at Northeastern University is working with the LLSC team to develop techniques that can help users match their workloads to appropriate hardware. Tiwari explains that the emergence of different types of AI accelerators, GPUs, and CPUs has left users suffering from too many choices. Without the right tools to take advantage of this heterogeneity, they are missing out on the benefits: better performance, lower costs, and greater productivity.

    “We are fixing this very capability gap — making users more productive and helping users do science better and faster without worrying about managing heterogeneous hardware,” says Tiwari. “My PhD student, Baolin Li, is building new capabilities and tools to help HPC users leverage heterogeneity near-optimally without user intervention, using techniques grounded in Bayesian optimization and other learning-based optimization methods. But, this is just the beginning. We are looking into ways to introduce heterogeneity in our data centers in a principled approach to help our users achieve the maximum advantage of heterogeneity autonomously and cost-effectively.”

    Workload classification is the first of many problems to be posed through the Datacenter Challenge. Others include developing AI techniques to predict job failures, conserve energy, or create job scheduling approaches that improve data center cooling efficiencies.

    Energy conservation 

    To mobilize research into greener computing, the team is also planning to release an environmental dataset of TX-GAIA operations, containing rack temperature, power consumption, and other relevant data.

    According to the researchers, huge opportunities exist to improve the power efficiency of HPC systems being used for AI processing. As one example, recent work in the LLSC determined that simple hardware tuning, such as limiting the amount of power an individual GPU can draw, could reduce the energy cost of training an AI model by 20 percent, with only modest increases in computing time. “This reduction translates to approximately an entire week’s worth of household energy for a mere three-hour time increase,” Gadepally says.

    They have also been developing techniques to predict model accuracy, so that users can quickly terminate experiments that are unlikely to yield meaningful results, saving energy. The Datacenter Challenge will share relevant data to enable researchers to explore other opportunities to conserve energy.

    The team expects that lessons learned from this research can be applied to the thousands of data centers operated by the U.S. Department of Defense. The U.S. Air Force is a sponsor of this work, which is being conducted under the USAF-MIT AI Accelerator.

    Other collaborators include researchers at MIT Computer Science and Artificial Intelligence Laboratory (CSAIL). Professor Charles Leiserson’s Supertech Research Group is investigating performance-enhancing techniques for parallel computing, and research scientist Neil Thompson is designing studies on ways to nudge data center users toward climate-friendly behavior.

    Samsi presented this work at the inaugural AI for Datacenter Optimization (ADOPT’22) workshop last spring as part of the IEEE International Parallel and Distributed Processing Symposium. The workshop officially introduced their Datacenter Challenge to the HPC community.

    “We hope this research will allow us and others who run supercomputing centers to be more responsive to user needs while also reducing the energy consumption at the center level,” Samsi says. More

  • in

    Companies use MIT research to identify and respond to supply chain risks

    In February 2020, MIT professor David Simchi-Levi predicted the future. In an article in Harvard Business Review, he and his colleague warned that the new coronavirus outbreak would throttle supply chains and shutter tens of thousands of businesses across North America and Europe by mid-March.

    For Simchi-Levi, who had developed new models of supply chain resiliency and advised major companies on how to best shield themselves from supply chain woes, the signs of disruption were plain to see. Two years later, the professor of engineering systems at the MIT Schwarzman College of Computing and the Department of Civil and Environmental Engineering, and director of the MIT Data Science Lab has found a “flood of interest” from companies anxious to apply his Risk Exposure Index (REI) research to identify and respond to hidden risks in their own supply chains.

    His work on “stress tests” for critical supply chains and ways to guide global supply chain recovery were included in the 2022 Economic Report of the President presented to the U.S. Congress in April.

    It is rare that data science research can influence policy at the highest levels, Simchi-Levi says, but his models reflect something that business needs now: a new world of continuing global crisis, without relying on historical precedent.

    “What the last two years showed is that you cannot plan just based on what happened last year or the last two years,” Simchi-Levi says.

    He recalled the famous quote, sometimes attributed to hockey great Wayne Gretzsky, that good players don’t skate to where the puck is, but where the puck is going to be. “We are not focusing on the state of the supply chain right now, but what may happen six weeks from now, eight weeks from now, to prepare ourselves today to prevent the problems of the future.”

    Finding hidden risks

    At the heart of REI is a mathematical model of the supply chain that focuses on potential failures at different supply chain nodes — a flood at a supplier’s factory, or a shortage of raw materials at another factory, for instance. By calculating variables such as “time-to-recover” (TTR), which measures how long it will take a particular node to be back at full function, and time-to-survive (TTS), which identifies the maximum duration that the supply chain can match supply with demand after a disruption, the model focuses on the impact of disruption on the supply chain, rather than the cause of disruption.

    Even before the pandemic, catastrophic events such as the 2010 Iceland volcanic eruption and the 2011 Tohoku earthquake and tsunami in Japan were threatening these nodes. “For many years, companies from a variety of industries focused mostly on efficiency, cutting costs as much as possible, using strategies like outsourcing and offshoring,” Simchi-Levi says. “They were very successful doing this, but it has dramatically increased their exposure to risk.”

    Using their model, Simchi-Levi and colleagues began working with Ford Motor Company in 2013 to improve the company’s supply chain resiliency. The partnership uncovered some surprising hidden risks.

    To begin with, the researchers found out that Ford’s “strategic suppliers” — the nodes of the supply chain where the company spent large amount of money each year — had only moderate exposure to risk. Instead, the biggest risk “tended to come from tiny suppliers that provide Ford with components that cost about 10 cents,” says Simchi-Levi.

    The analysis also found that risky suppliers are everywhere across the globe. “There is this idea that if you just move suppliers closer to market, to demand, to North America or to Mexico, you increase the resiliency of your supply chain. That is not supported by our data,” he says.

    Rewards of resiliency

    By creating a virtual representation, or “digital twin,” of the Ford supply chain, the researchers were able to test out strategies at each node to see what would increase supply chain resiliency. Should the company invest in more warehouses to store a key component? Should it shift production of a component to another factory?

    Companies are sometimes reluctant to invest in supply chain resiliency, Simchi-Levi says, but the analysis isn’t just about risk. “It’s also going to help you identify savings opportunities. The company may be building a lot of misplaced, costly inventory, for instance, and our method helps them to identify these inefficiencies and cut costs.”

    Since working with Ford, Simchi-Levi and colleagues have collaborated with many other companies, including a partnership with Accenture, to scale the REI technology to a variety of industries including high-tech, industrial equipment, home improvement retailers, fashion retailers, and consumer packaged goods.

    Annette Clayton, the CEO of Schneider Electric North America and previously its chief supply chain officer, has worked with Simchi-Levi for 17 years. “When I first went to work for Schneider, I asked David and his team to help us look at resiliency and inventory positioning in order to make the best cost, delivery, flexibility, and speed trade-offs for the North American supply chain,” she says. “As the pandemic unfolded, the very learnings in supply chain resiliency we had worked on before became even more important and we partnered with David and his team again,”

    “We have used TTR and TTS to determine places where we need to develop and duplicate supplier capability, from raw materials to assembled parts. We increased inventories where our time-to-recover because of extended logistics times exceeded our time-to-survive,” Clayton adds. “We have used TTR and TTS to prioritize our workload in supplier development, procurement and expanding our own manufacturing capacity.”

    The REI approach can even be applied to an entire country’s economy, as the U.N. Office for Disaster Risk Reduction has done for developing countries such as Thailand in the wake of disastrous flooding in 2011.

    Simchi-Levi and colleagues have been motivated by the pandemic to enhance the REI model with new features. “Because we have started collaborating with more companies, we have realized some interesting, company-specific business constraints,” he says, which are leading to more efficient ways of calculating hidden risk. More

  • in

    New CRISPR-based map ties every human gene to its function

    The Human Genome Project was an ambitious initiative to sequence every piece of human DNA. The project drew together collaborators from research institutions around the world, including MIT’s Whitehead Institute for Biomedical Research, and was finally completed in 2003. Now, over two decades later, MIT Professor Jonathan Weissman and colleagues have gone beyond the sequence to present the first comprehensive functional map of genes that are expressed in human cells. The data from this project, published online June 9 in Cell, ties each gene to its job in the cell, and is the culmination of years of collaboration on the single-cell sequencing method Perturb-seq.

    The data are available for other scientists to use. “It’s a big resource in the way the human genome is a big resource, in that you can go in and do discovery-based research,” says Weissman, who is also a member of the Whitehead Institute and an investigator with the Howard Hughes Medical Institute. “Rather than defining ahead of time what biology you’re going to be looking at, you have this map of the genotype-phenotype relationships and you can go in and screen the database without having to do any experiments.”

    The screen allowed the researchers to delve into diverse biological questions. They used it to explore the cellular effects of genes with unknown functions, to investigate the response of mitochondria to stress, and to screen for genes that cause chromosomes to be lost or gained, a phenotype that has proved difficult to study in the past. “I think this dataset is going to enable all sorts of analyses that we haven’t even thought up yet by people who come from other parts of biology, and suddenly they just have this available to draw on,” says former Weissman Lab postdoc Tom Norman, a co-senior author of the paper.

    Pioneering Perturb-seq

    The project takes advantage of the Perturb-seq approach that makes it possible to follow the impact of turning on or off genes with unprecedented depth. This method was first published in 2016 by a group of researchers including Weissman and fellow MIT professor Aviv Regev, but could only be used on small sets of genes and at great expense.

    The massive Perturb-seq map was made possible by foundational work from Joseph Replogle, an MD-PhD student in Weissman’s lab and co-first author of the present paper. Replogle, in collaboration with Norman, who now leads a lab at Memorial Sloan Kettering Cancer Center; Britt Adamson, an assistant professor in the Department of Molecular Biology at Princeton University; and a group at 10x Genomics, set out to create a new version of Perturb-seq that could be scaled up. The researchers published a proof-of-concept paper in Nature Biotechnology in 2020. 

    The Perturb-seq method uses CRISPR-Cas9 genome editing to introduce genetic changes into cells, and then uses single-cell RNA sequencing to capture information about the RNAs that are expressed resulting from a given genetic change. Because RNAs control all aspects of how cells behave, this method can help decode the many cellular effects of genetic changes.

    Since their initial proof-of-concept paper, Weissman, Regev, and others have used this sequencing method on smaller scales. For example, the researchers used Perturb-seq in 2021 to explore how human and viral genes interact over the course of an infection with HCMV, a common herpesvirus.

    In the new study, Replogle and collaborators including Reuben Saunders, a graduate student in Weissman’s lab and co-first author of the paper, scaled up the method to the entire genome. Using human blood cancer cell lines as well noncancerous cells derived from the retina, he performed Perturb-seq across more than 2.5 million cells, and used the data to build a comprehensive map tying genotypes to phenotypes.

    Delving into the data

    Upon completing the screen, the researchers decided to put their new dataset to use and examine a few biological questions. “The advantage of Perturb-seq is it lets you get a big dataset in an unbiased way,” says Tom Norman. “No one knows entirely what the limits are of what you can get out of that kind of dataset. Now, the question is, what do you actually do with it?”

    The first, most obvious application was to look into genes with unknown functions. Because the screen also read out phenotypes of many known genes, the researchers could use the data to compare unknown genes to known ones and look for similar transcriptional outcomes, which could suggest the gene products worked together as part of a larger complex.

    The mutation of one gene called C7orf26 in particular stood out. Researchers noticed that genes whose removal led to a similar phenotype were part of a protein complex called Integrator that played a role in creating small nuclear RNAs. The Integrator complex is made up of many smaller subunits — previous studies had suggested 14 individual proteins — and the researchers were able to confirm that C7orf26 made up a 15th component of the complex.

    They also discovered that the 15 subunits worked together in smaller modules to perform specific functions within the Integrator complex. “Absent this thousand-foot-high view of the situation, it was not so clear that these different modules were so functionally distinct,” says Saunders.

    Another perk of Perturb-seq is that because the assay focuses on single cells, the researchers could use the data to look at more complex phenotypes that become muddied when they are studied together with data from other cells. “We often take all the cells where ‘gene X’ is knocked down and average them together to look at how they changed,” Weissman says. “But sometimes when you knock down a gene, different cells that are losing that same gene behave differently, and that behavior may be missed by the average.”

    The researchers found that a subset of genes whose removal led to different outcomes from cell to cell were responsible for chromosome segregation. Their removal was causing cells to lose a chromosome or pick up an extra one, a condition known as aneuploidy. “You couldn’t predict what the transcriptional response to losing this gene was because it depended on the secondary effect of what chromosome you gained or lost,” Weissman says. “We realized we could then turn this around and create this composite phenotype looking for signatures of chromosomes being gained and lost. In this way, we’ve done the first genome-wide screen for factors that are required for the correct segregation of DNA.”

    “I think the aneuploidy study is the most interesting application of this data so far,” Norman says. “It captures a phenotype that you can only get using a single-cell readout. You can’t go after it any other way.”

    The researchers also used their dataset to study how mitochondria responded to stress. Mitochondria, which evolved from free-living bacteria, carry 13 genes in their genomes. Within the nuclear DNA, around 1,000 genes are somehow related to mitochondrial function. “People have been interested for a long time in how nuclear and mitochondrial DNA are coordinated and regulated in different cellular conditions, especially when a cell is stressed,” Replogle says.

    The researchers found that when they perturbed different mitochondria-related genes, the nuclear genome responded similarly to many different genetic changes. However, the mitochondrial genome responses were much more variable. 

    “There’s still an open question of why mitochondria still have their own DNA,” said Replogle. “A big-picture takeaway from our work is that one benefit of having a separate mitochondrial genome might be having localized or very specific genetic regulation in response to different stressors.”

    “If you have one mitochondria that’s broken, and another one that is broken in a different way, those mitochondria could be responding differentially,” Weissman says.

    In the future, the researchers hope to use Perturb-seq on different types of cells besides the cancer cell line they started in. They also hope to continue to explore their map of gene functions, and hope others will do the same. “This really is the culmination of many years of work by the authors and other collaborators, and I’m really pleased to see it continue to succeed and expand,” says Norman. More