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#437171 Scientists Tap the World’s Most ...
In The Hitchhiker’s Guide to the Galaxy by Douglas Adams, the haughty supercomputer Deep Thought is asked whether it can find the answer to the ultimate question concerning life, the universe, and everything. It replies that, yes, it can do it, but it’s tricky and it’ll have to think about it. When asked how long it will take it replies, “Seven-and-a-half million years. I told you I’d have to think about it.”
Real-life supercomputers are being asked somewhat less expansive questions but tricky ones nonetheless: how to tackle the Covid-19 pandemic. They’re being used in many facets of responding to the disease, including to predict the spread of the virus, to optimize contact tracing, to allocate resources and provide decisions for physicians, to design vaccines and rapid testing tools, and to understand sneezes. And the answers are needed in a rather shorter time frame than Deep Thought was proposing.
The largest number of Covid-19 supercomputing projects involves designing drugs. It’s likely to take several effective drugs to treat the disease. Supercomputers allow researchers to take a rational approach and aim to selectively muzzle proteins that SARS-CoV-2, the virus that causes Covid-19, needs for its life cycle.
The viral genome encodes proteins needed by the virus to infect humans and to replicate. Among these are the infamous spike protein that sniffs out and penetrates its human cellular target, but there are also enzymes and molecular machines that the virus forces its human subjects to produce for it. Finding drugs that can bind to these proteins and stop them from working is a logical way to go.
The Summit supercomputer at Oak Ridge National Laboratory has a peak performance of 200,000 trillion calculations per second—equivalent to about a million laptops. Image credit: Oak Ridge National Laboratory, U.S. Dept. of Energy, CC BY
I am a molecular biophysicist. My lab, at the Center for Molecular Biophysics at the University of Tennessee and Oak Ridge National Laboratory, uses a supercomputer to discover drugs. We build three-dimensional virtual models of biological molecules like the proteins used by cells and viruses, and simulate how various chemical compounds interact with those proteins. We test thousands of compounds to find the ones that “dock” with a target protein. Those compounds that fit, lock-and-key style, with the protein are potential therapies.
The top-ranked candidates are then tested experimentally to see if they indeed do bind to their targets and, in the case of Covid-19, stop the virus from infecting human cells. The compounds are first tested in cells, then animals, and finally humans. Computational drug discovery with high-performance computing has been important in finding antiviral drugs in the past, such as the anti-HIV drugs that revolutionized AIDS treatment in the 1990s.
World’s Most Powerful Computer
Since the 1990s the power of supercomputers has increased by a factor of a million or so. Summit at Oak Ridge National Laboratory is presently the world’s most powerful supercomputer, and has the combined power of roughly a million laptops. A laptop today has roughly the same power as a supercomputer had 20-30 years ago.
However, in order to gin up speed, supercomputer architectures have become more complicated. They used to consist of single, very powerful chips on which programs would simply run faster. Now they consist of thousands of processors performing massively parallel processing in which many calculations, such as testing the potential of drugs to dock with a pathogen or cell’s proteins, are performed at the same time. Persuading those processors to work together harmoniously is a pain in the neck but means we can quickly try out a lot of chemicals virtually.
Further, researchers use supercomputers to figure out by simulation the different shapes formed by the target binding sites and then virtually dock compounds to each shape. In my lab, that procedure has produced experimentally validated hits—chemicals that work—for each of 16 protein targets that physician-scientists and biochemists have discovered over the past few years. These targets were selected because finding compounds that dock with them could result in drugs for treating different diseases, including chronic kidney disease, prostate cancer, osteoporosis, diabetes, thrombosis and bacterial infections.
Scientists are using supercomputers to find ways to disable the various proteins—including the infamous spike protein (green protrusions)—produced by SARS-CoV-2, the virus responsible for Covid-19. Image credit: Thomas Splettstoesser scistyle.com, CC BY-ND
Billions of Possibilities
So which chemicals are being tested for Covid-19? A first approach is trying out drugs that already exist for other indications and that we have a pretty good idea are reasonably safe. That’s called “repurposing,” and if it works, regulatory approval will be quick.
But repurposing isn’t necessarily being done in the most rational way. One idea researchers are considering is that drugs that work against protein targets of some other virus, such as the flu, hepatitis or Ebola, will automatically work against Covid-19, even when the SARS-CoV-2 protein targets don’t have the same shape.
Our own work has now expanded to about 10 targets on SARS-CoV-2, and we’re also looking at human protein targets for disrupting the virus’s attack on human cells. Top-ranked compounds from our calculations are being tested experimentally for activity against the live virus. Several of these have already been found to be active.The best approach is to check if repurposed compounds will actually bind to their intended target. To that end, my lab published a preliminary report of a supercomputer-driven docking study of a repurposing compound database in mid-February. The study ranked 8,000 compounds in order of how well they bind to the viral spike protein. This paper triggered the establishment of a high-performance computing consortium against our viral enemy, announced by President Trump in March. Several of our top-ranked compounds are now in clinical trials.
Also, we and others are venturing out into the wild world of new drug discovery for Covid-19—looking for compounds that have never been tried as drugs before. Databases of billions of these compounds exist, all of which could probably be synthesized in principle but most of which have never been made. Billion-compound docking is a tailor-made task for massively parallel supercomputing.
Dawn of the Exascale Era
Work will be helped by the arrival of the next big machine at Oak Ridge, called Frontier, planned for next year. Frontier should be about 10 times more powerful than Summit. Frontier will herald the “exascale” supercomputing era, meaning machines capable of 1,000,000,000,000,000,000 calculations per second.
Although some fear supercomputers will take over the world, for the time being, at least, they are humanity’s servants, which means that they do what we tell them to. Different scientists have different ideas about how to calculate which drugs work best—some prefer artificial intelligence, for example—so there’s quite a lot of arguing going on.
Hopefully, scientists armed with the most powerful computers in the world will, sooner rather than later, find the drugs needed to tackle Covid-19. If they do, then their answers will be of more immediate benefit, if less philosophically tantalizing, than the answer to the ultimate question provided by Deep Thought, which was, maddeningly, simply 42.
This article is republished from The Conversation under a Creative Commons license. Read the original article.
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#437136 Researchers develop real-time physics ...
Motion picture animation and video games are impressively lifelike nowadays, capturing a wisp of hair falling across a heroine's eyes or a canvas sail snapping crisply in the wind. Collaborators from the University of California, Los Angeles (UCLA) and Carnegie Mellon University have adapted this sophisticated computer graphics technology to simulate the movements of soft, limbed robots for the first time. Continue reading
#437120 The New Indiana Jones? AI. Here’s How ...
Archaeologists have uncovered scores of long-abandoned settlements along coastal Madagascar that reveal environmental connections to modern-day communities. They have detected the nearly indiscernible bumps of earthen mounds left behind by prehistoric North American cultures. Still other researchers have mapped Bronze Age river systems in the Indus Valley, one of the cradles of civilization.
All of these recent discoveries are examples of landscape archaeology. They’re also examples of how artificial intelligence is helping scientists hunt for new archaeological digs on a scale and at a pace unimaginable even a decade ago.
“AI in archaeology has been increasing substantially over the past few years,” said Dylan Davis, a PhD candidate in the Department of Anthropology at Penn State University. “One of the major uses of AI in archaeology is for the detection of new archaeological sites.”
The near-ubiquitous availability of satellite data and other types of aerial imagery for many parts of the world has been both a boon and a bane to archaeologists. They can cover far more ground, but the job of manually mowing their way across digitized landscapes is still time-consuming and laborious. Machine learning algorithms offer a way to parse through complex data far more quickly.
AI Gives Archaeologists a Bird’s Eye View
Davis developed an automated algorithm for identifying large earthen and shell mounds built by native populations long before Europeans arrived with far-off visions of skyscrapers and superhighways in their eyes. The sites still hidden in places like the South Carolina wilderness contain a wealth of information about how people lived, even what they ate, and the ways they interacted with the local environment and other cultures.
In this particular case, the imagery comes from LiDAR, which uses light pulses that can penetrate tree canopies to map forest floors. The team taught the computer the shape, size, and texture characteristics of the mounds so it could identify potential sites from the digital 3D datasets that it analyzed.
“The process resulted in several thousand possible features that my colleagues and I checked by hand,” Davis told Singularity Hub. “While not entirely automated, this saved the equivalent of years of manual labor that would have been required for analyzing the whole LiDAR image by hand.”
In Madagascar—where Davis is studying human settlement history across the world’s fourth largest island over a timescale of millennia—he developed a predictive algorithm to help locate archaeological sites using freely available satellite imagery. His team was able to survey and identify more than 70 new archaeological sites—and potentially hundreds more—across an area of more than 1,000 square kilometers during the course of about a year.
Machines Learning From the Past Prepare Us for the Future
One impetus behind the rapid identification of archaeological sites is that many are under threat from climate change, such as coastal erosion from sea level rise, or other human impacts. Meanwhile, traditional archaeological approaches are expensive and laborious—serious handicaps in a race against time.
“It is imperative to record as many archaeological sites as we can in a short period of time. That is why AI and machine learning are useful for my research,” Davis said.
Studying the rise and fall of past civilizations can also teach modern humans a thing or two about how to grapple with these current challenges.
Researchers at the Institut Català d’Arqueologia Clàssica (ICAC) turned to machine-learning algorithms to reconstruct more than 20,000 kilometers of paleo-rivers along the Indus Valley civilization of what is now part of modern Pakistan and India. Such AI-powered mapping techniques wouldn’t be possible using satellite images alone.
That effort helped locate many previously unknown archaeological sites and unlocked new insights into those Bronze Age cultures. However, the analytics can also assist governments with important water resource management today, according to Hèctor A. Orengo Romeu, co-director of the Landscape Archaeology Research Group at ICAC.
“Our analyses can contribute to the forecasts of the evolution of aquifers in the area and provide valuable information on aspects such as the variability of agricultural productivity or the influence of climate change on the expansion of the Thar desert, in addition to providing cultural management tools to the government,” he said.
Leveraging AI for Language and Lots More
While landscape archaeology is one major application of AI in archaeology, it’s far from the only one. In 2000, only about a half-dozen scientific papers referred to the use of AI, according to the Web of Science, reputedly the world’s largest global citation database. Last year, more than 65 papers were published concerning the use of machine intelligence technologies in archaeology, with a significant uptick beginning in 2015.
AI methods, for instance, are being used to understand the chemical makeup of artifacts like pottery and ceramics, according to Davis. “This can help identify where these materials were made and how far they were transported. It can also help us to understand the extent of past trading networks.”
Linguistic anthropologists have also used machine intelligence methods to trace the evolution of different languages, Davis said. “Using AI, we can learn when and where languages emerged around the world.”
In other cases, AI has helped reconstruct or decipher ancient texts. Last year, researchers at Google’s DeepMind used a deep neural network called PYTHIA to recreate missing inscriptions in ancient Greek from damaged surfaces of objects made of stone or ceramics.
Named after the Oracle at Delphi, PYTHIA “takes a sequence of damaged text as input, and is trained to predict character sequences comprising hypothesised restorations of ancient Greek inscriptions,” the researchers reported.
In a similar fashion, Chinese scientists applied a convolutional neural network (CNN) to untangle another ancient tongue once found on turtle shells and ox bones. The CNN managed to classify oracle bone morphology in order to piece together fragments of these divination objects, some with inscriptions that represent the earliest evidence of China’s recorded history.
“Differentiating the materials of oracle bones is one of the most basic steps for oracle bone morphology—we need to first make sure we don’t assemble pieces of ox bones with tortoise shells,” lead author of the study, associate professor Shanxiong Chen at China’s Southwest University, told Synced, an online tech publication in China.
AI Helps Archaeologists Get the Scoop…
And then there are applications of AI in archaeology that are simply … interesting. Just last month, researchers published a paper about a machine learning method trained to differentiate between human and canine paleofeces.
The algorithm, dubbed CoproID, compares the gut microbiome DNA found in the ancient material with DNA found in modern feces, enabling it to get the scoop on the origin of the poop.
Also known as coprolites, paleo-feces from humans and dogs are often found in the same archaeological sites. Scientists need to know which is which if they’re trying to understand something like past diets or disease.
“CoproID is the first line of identification in coprolite analysis to confirm that what we’re looking for is actually human, or a dog if we’re interested in dogs,” Maxime Borry, a bioinformatics PhD student at the Max Planck Institute for the Science of Human History, told Vice.
…But Machine Intelligence Is Just Another Tool
There is obviously quite a bit of work that can be automated through AI. But there’s no reason for archaeologists to hit the unemployment line any time soon. There are also plenty of instances where machines can’t yet match humans in identifying objects or patterns. At other times, it’s just faster doing the analysis yourself, Davis noted.
“For ‘big data’ tasks like detecting archaeological materials over a continental scale, AI is useful,” he said. “But for some tasks, it is sometimes more time-consuming to train an entire computer algorithm to complete a task that you can do on your own in an hour.”
Still, there’s no telling what the future will hold for studying the past using artificial intelligence.
“We have already started to see real improvements in the accuracy and reliability of these approaches, but there is a lot more to do,” Davis said. “Hopefully, we start to see these methods being directly applied to a variety of interesting questions around the world, as these methods can produce datasets that would have been impossible a few decades ago.”
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#436944 Is Digital Learning Still Second Best?
As Covid-19 continues to spread, the world has gone digital on an unprecedented scale. Tens of thousands of employees are working from home, and huge conferences, like the Google I/O and Apple WWDC software extravaganzas, plan to experiment with digital events.
Universities too are sending students home. This might have meant an extended break from school not too long ago. But no more. As lecture halls go empty, an experiment into digital learning at scale is ramping up. In the US alone, over 100 universities, from Harvard to Duke, are offering online classes to students to keep the semester going.
While digital learning has been improving for some time, Covid-19 may not only tip us further into a more digitally connected reality, but also help us better appreciate its benefits. This is important because historically, digital learning has been viewed as inferior to traditional learning. But that may be changing.
The Inversion
We often think about digital technologies as ways to reach people without access to traditional services—online learning for children who don’t have schools nearby or telemedicine for patients with no access to doctors. And while these solutions have helped millions of people, they’re often viewed as “second best” and “better than nothing.” Even in more resource-rich environments, there’s an assumption one should pay more to attend an event in person—a concert, a football game, an exercise class—while digital equivalents are extremely cheap or free. Why is this? And is the situation about to change?
Take the case of Dr. Sanjeev Arora, a professor of medicine at the University of New Mexico. Arora started Project Echo because he was frustrated by how many late-stage cases of hepatitis C he encountered in rural New Mexico. He realized that if he had reached patients sooner, he could have prevented needless deaths. The solution? Digital learning for local health workers.
Project Echo connects rural healthcare practitioners to specialists at top health centers by video. The approach is collaborative: Specialists share best practices and work through cases with participants to apply them in the real world and learn from edge cases. Added to expert presentations, there are lots of opportunities to ask questions and interact with specialists.
The method forms a digital loop of learning, practice, assessment, and adjustment.
Since 2003, Project Echo has scaled to 800 locations in 39 countries and trained over 90,000 healthcare providers. Most notably, a study in The New England Journal of Medicine found that the outcomes of hepatitis C treatment given by Project Echo trained healthcare workers in rural and underserved areas were similar to outcomes at university medical centers. That is, digital learning in this context was equivalent to high quality in-person learning.
If that is possible today, with simple tools, will they surpass traditional medical centers and schools in the future? Can digital learning more generally follow suit and have the same success? Perhaps. Going digital brings its own special toolset to the table too.
The Benefits of Digital
If you’re training people online, you can record the session to better understand their engagement levels—or even add artificial intelligence to analyze it in real time. Ahura AI, for example, founded by Bryan Talebi, aims to upskill workers through online training. Early study of their method suggests they can significantly speed up learning by analyzing users’ real-time emotions—like frustration or distraction—and adjusting the lesson plan or difficulty on the fly.
Other benefits of digital learning include the near-instantaneous download of course materials—rather than printing and shipping books—and being able to more easily report grades and other results, a requirement for many schools and social services organizations. And of course, as other digitized industries show, digital learning can grow and scale further at much lower costs.
To that last point, 360ed, a digital learning startup founded in 2016 by Hla Hla Win, now serves millions of children in Myanmar with augmented reality lesson plans. And Global Startup Ecosystem, founded by Christine Souffrant Ntim and Einstein Kofi Ntim in 2015, is the world’s first and largest digital accelerator program. Their entirely online programs support over 1,000 companies in 90 countries. It’s astonishing how fast both of these organizations have grown.
Notably, both examples include offline experiences too. Many of the 360ed lesson plans come with paper flashcards children use with their smartphones because the online-offline interaction improves learning. The Global Startup Ecosystem also hosts about 10 additional in-person tech summits around the world on various topics through a related initiative.
Looking further ahead, probably the most important benefit of online learning will be its potential to integrate with other digital systems in the workplace.
Imagine a medical center that has perfect information about every patient and treatment in real time and that this information is (anonymously and privately) centralized, analyzed, and shared with medical centers, research labs, pharmaceutical companies, clinical trials, policy makers, and medical students around the world. Just as self-driving cars can learn to drive better by having access to the experiences of other self-driving cars, so too can any group working to solve complex, time-sensitive challenges learn from and build on each other’s experiences.
Why This Matters
While in the long term the world will likely end up combining the best aspects of traditional and digital learning, it’s important in the near term to be more aware of the assumptions we make about digital technologies. Some of the most pioneering work in education, healthcare, and other industries may not be highly visible right now because it is in a virtual setting. Most people are unaware, for example, that the busiest emergency room in rural America is already virtual.
Once they start converging with other digital technologies, these innovations will likely become the mainstream system for all of us. Which raises more questions: What is the best business model for these virtual services? If they start delivering better healthcare and educational outcomes than traditional institutions, should they charge more? Hopefully, we will see an even bigger shift occurring, in which technology allows us to provide high quality education, healthcare, and other services to everyone at more affordable prices than today.
These are some of the topics we can consider as Covid-19 forces us into uncharted territory.
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