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      in Data Management & Statistics

      Learning the language of molecules to predict their properties

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      Discovering new materials and drugs typically involves a manual, trial-and-error process that can take decades and cost millions of dollars. To streamline this process, scientists often use machine learning to predict molecular properties and narrow down the molecules they need to synthesize and test in the lab.

      Researchers from MIT and the MIT-Watson AI Lab have developed a new, unified framework that can simultaneously predict molecular properties and generate new molecules much more efficiently than these popular deep-learning approaches.

      To teach a machine-learning model to predict a molecule’s biological or mechanical properties, researchers must show it millions of labeled molecular structures — a process known as training. Due to the expense of discovering molecules and the challenges of hand-labeling millions of structures, large training datasets are often hard to come by, which limits the effectiveness of machine-learning approaches.

      By contrast, the system created by the MIT researchers can effectively predict molecular properties using only a small amount of data. Their system has an underlying understanding of the rules that dictate how building blocks combine to produce valid molecules. These rules capture the similarities between molecular structures, which helps the system generate new molecules and predict their properties in a data-efficient manner.

      This method outperformed other machine-learning approaches on both small and large datasets, and was able to accurately predict molecular properties and generate viable molecules when given a dataset with fewer than 100 samples.

      “Our goal with this project is to use some data-driven methods to speed up the discovery of new molecules, so you can train a model to do the prediction without all of these cost-heavy experiments,” says lead author Minghao Guo, a computer science and electrical engineering (EECS) graduate student.

      Guo’s co-authors include MIT-IBM Watson AI Lab research staff members Veronika Thost, Payel Das, and Jie Chen; recent MIT graduates Samuel Song ’23 and Adithya Balachandran ’23; and senior author Wojciech Matusik, a professor of electrical engineering and computer science and a member of the MIT-IBM Watson AI Lab, who leads the Computational Design and Fabrication Group within the MIT Computer Science and Artificial Intelligence Laboratory (CSAIL). The research will be presented at the International Conference for Machine Learning.

      Learning the language of molecules

      To achieve the best results with machine-learning models, scientists need training datasets with millions of molecules that have similar properties to those they hope to discover. In reality, these domain-specific datasets are usually very small. So, researchers use models that have been pretrained on large datasets of general molecules, which they apply to a much smaller, targeted dataset. However, because these models haven’t acquired much domain-specific knowledge, they tend to perform poorly.

      The MIT team took a different approach. They created a machine-learning system that automatically learns the “language” of molecules — what is known as a molecular grammar — using only a small, domain-specific dataset. It uses this grammar to construct viable molecules and predict their properties.

      In language theory, one generates words, sentences, or paragraphs based on a set of grammar rules. You can think of a molecular grammar the same way. It is a set of production rules that dictate how to generate molecules or polymers by combining atoms and substructures.

      Just like a language grammar, which can generate a plethora of sentences using the same rules, one molecular grammar can represent a vast number of molecules. Molecules with similar structures use the same grammar production rules, and the system learns to understand these similarities.

      Since structurally similar molecules often have similar properties, the system uses its underlying knowledge of molecular similarity to predict properties of new molecules more efficiently. 

      “Once we have this grammar as a representation for all the different molecules, we can use it to boost the process of property prediction,” Guo says.

      The system learns the production rules for a molecular grammar using reinforcement learning — a trial-and-error process where the model is rewarded for behavior that gets it closer to achieving a goal.

      But because there could be billions of ways to combine atoms and substructures, the process to learn grammar production rules would be too computationally expensive for anything but the tiniest dataset.

      The researchers decoupled the molecular grammar into two parts. The first part, called a metagrammar, is a general, widely applicable grammar they design manually and give the system at the outset. Then it only needs to learn a much smaller, molecule-specific grammar from the domain dataset. This hierarchical approach speeds up the learning process.

      Big results, small datasets

      In experiments, the researchers’ new system simultaneously generated viable molecules and polymers, and predicted their properties more accurately than several popular machine-learning approaches, even when the domain-specific datasets had only a few hundred samples. Some other methods also required a costly pretraining step that the new system avoids.

      The technique was especially effective at predicting physical properties of polymers, such as the glass transition temperature, which is the temperature required for a material to transition from solid to liquid. Obtaining this information manually is often extremely costly because the experiments require extremely high temperatures and pressures.

      To push their approach further, the researchers cut one training set down by more than half — to just 94 samples. Their model still achieved results that were on par with methods trained using the entire dataset.

      “This grammar-based representation is very powerful. And because the grammar itself is a very general representation, it can be deployed to different kinds of graph-form data. We are trying to identify other applications beyond chemistry or material science,” Guo says.

      In the future, they also want to extend their current molecular grammar to include the 3D geometry of molecules and polymers, which is key to understanding the interactions between polymer chains. They are also developing an interface that would show a user the learned grammar production rules and solicit feedback to correct rules that may be wrong, boosting the accuracy of the system.

      This work is funded, in part, by the MIT-IBM Watson AI Lab and its member company, Evonik. More

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      A better way to study ocean currents

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

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

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

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

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

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

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

      Diving into the data

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

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

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

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

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

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

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

      Buoyant performance

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

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

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

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

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

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

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

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

    • 63 Shares179 Views

      in Data Management & Statistics

      Strengthening trust in machine-learning models

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      Probabilistic machine learning methods are becoming increasingly powerful tools in data analysis, informing a range of critical decisions across disciplines and applications, from forecasting election results to predicting the impact of microloans on addressing poverty.

      This class of methods uses sophisticated concepts from probability theory to handle uncertainty in decision-making. But the math is only one piece of the puzzle in determining their accuracy and effectiveness. In a typical data analysis, researchers make many subjective choices, or potentially introduce human error, that must also be assessed in order to cultivate users’ trust in the quality of decisions based on these methods.

      To address this issue, MIT computer scientist Tamara Broderick, associate professor in the Department of Electrical Engineering and Computer Science (EECS) and a member of the Laboratory for Information and Decision Systems (LIDS), and a team of researchers have developed a classification system — a “taxonomy of trust” — that defines where trust might break down in a data analysis and identifies strategies to strengthen trust at each step. The other researchers on the project are Professor Anna Smith at the University of Kentucky, professors Tian Zheng and Andrew Gelman at Columbia University, and Professor Rachael Meager at the London School of Economics. The team’s hope is to highlight concerns that are already well-studied and those that need more attention.

      In their paper, published in February in Science Advances, the researchers begin by detailing the steps in the data analysis process where trust might break down: Analysts make choices about what data to collect and which models, or mathematical representations, most closely mirror the real-life problem or question they are aiming to answer. They select algorithms to fit the model and use code to run those algorithms. Each of these steps poses unique challenges around building trust. Some components can be checked for accuracy in measurable ways. “Does my code have bugs?”, for example, is a question that can be tested against objective criteria. Other times, problems are more subjective, with no clear-cut answers; analysts are confronted with numerous strategies to gather data and decide whether a model reflects the real world.

      “What I think is nice about making this taxonomy, is that it really highlights where people are focusing. I think a lot of research naturally focuses on this level of ‘are my algorithms solving a particular mathematical problem?’ in part because it’s very objective, even if it’s a hard problem,” Broderick says.

      “I think it’s really hard to answer ‘is it reasonable to mathematize an important applied problem in a certain way?’ because it’s somehow getting into a harder space, it’s not just a mathematical problem anymore.”

      Capturing real life in a model

      The researchers’ work in categorizing where trust breaks down, though it may seem abstract, is rooted in real-world application.

      Meager, a co-author on the paper, analyzed whether microfinances can have a positive effect in a community. The project became a case study for where trust could break down, and ways to reduce this risk.

      At first look, measuring the impact of microfinancing might seem like a straightforward endeavor. But like any analysis, researchers meet challenges at each step in the process that can affect trust in the outcome. Microfinancing — in which individuals or small businesses receive small loans and other financial services in lieu of conventional banking — can offer different services, depending on the program. For the analysis, Meager gathered datasets from microfinance programs in countries across the globe, including in Mexico, Mongolia, Bosnia, and the Philippines.

      When combining conspicuously distinct datasets, in this case from multiple countries and across different cultures and geographies, researchers must evaluate whether specific case studies can reflect broader trends. It is also important to contextualize the data on hand. For example, in rural Mexico, owning goats may be counted as an investment.

      “It’s hard to measure the quality of life of an individual. People measure things like, ‘What’s the business profit of the small business?’ Or ‘What’s the consumption level of a household?’ There’s this potential for mismatch between what you ultimately really care about, and what you’re measuring,” Broderick says. “Before we get to the mathematical level, what data and what assumptions are we leaning on?”

      With data on hand, analysts must define the real-world questions they seek to answer. In the case of evaluating the benefits of microfinancing, analysts must define what they consider a positive outcome. It is standard in economics, for example, to measure the average financial gain per business in communities where a microfinance program is introduced. But reporting an average might suggest a net positive effect even if only a few (or even one) person benefited, instead of the community as a whole.

      “What you really wanted was that a lot of people are benefiting,” Broderick says. “It sounds simple. Why didn’t we measure the thing that we cared about? But I think it’s really common that practitioners use standard machine learning tools, for a lot of reasons. And these tools might report a proxy that doesn’t always agree with the quantity of interest.”

      Analysts may consciously or subconsciously favor models they are familiar with, especially after investing a great deal of time learning their ins and outs. “Someone might be hesitant to try a nonstandard method because they might be less certain they will use it correctly. Or peer review might favor certain familiar methods, even if a researcher might like to use nonstandard methods,” Broderick says. “There are a lot of reasons, sociologically. But this can be a concern for trust.”

      Final step, checking the code 

      While distilling a real-life problem into a model can be a big-picture, amorphous problem, checking the code that runs an algorithm can feel “prosaic,” Broderick says. But it is another potentially overlooked area where trust can be strengthened.

      In some cases, checking a coding pipeline that executes an algorithm might be considered outside the purview of an analyst’s job, especially when there is the option to use standard software packages.

      One way to catch bugs is to test whether code is reproducible. Depending on the field, however, sharing code alongside published work is not always a requirement or the norm. As models increase in complexity over time, it becomes harder to recreate code from scratch. Reproducing a model becomes difficult or even impossible.

      “Let’s just start with every journal requiring you to release your code. Maybe it doesn’t get totally double-checked, and everything isn’t absolutely perfect, but let’s start there,” Broderick says, as one step toward building trust.

      Paper co-author Gelman worked on an analysis that forecast the 2020 U.S. presidential election using state and national polls in real-time. The team published daily updates in The Economist magazine, while also publishing their code online for anyone to download and run themselves. Throughout the season, outsiders pointed out both bugs and conceptual problems in the model, ultimately contributing to a stronger analysis.

      The researchers acknowledge that while there is no single solution to create a perfect model, analysts and scientists have the opportunity to reinforce trust at nearly every turn.

      “I don’t think we expect any of these things to be perfect,” Broderick says, “but I think we can expect them to be better or to be as good as possible.” More

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      Improving health outcomes by targeting climate and air pollution simultaneously

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      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

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

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      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

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

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      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

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      Investigating at the interface of data science and computing

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      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

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      AI that can learn the patterns of human language

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      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