Tag Archives: Simulation
#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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#436911 Scientists Linked Artificial and ...
Scientists have linked up two silicon-based artificial neurons with a biological one across multiple countries into a fully-functional network. Using standard internet protocols, they established a chain of communication whereby an artificial neuron controls a living, biological one, and passes on the info to another artificial one.
Whoa.
We’ve talked plenty about brain-computer interfaces and novel computer chips that resemble the brain. We’ve covered how those “neuromorphic” chips could link up into tremendously powerful computing entities, using engineered communication nodes called artificial synapses.
As Moore’s law is dying, we even said that neuromorphic computing is one path towards the future of extremely powerful, low energy consumption artificial neural network-based computing—in hardware—that could in theory better link up with the brain. Because the chips “speak” the brain’s language, in theory they could become neuroprosthesis hubs far more advanced and “natural” than anything currently possible.
This month, an international team put all of those ingredients together, turning theory into reality.
The three labs, scattered across Padova, Italy, Zurich, Switzerland, and Southampton, England, collaborated to create a fully self-controlled, hybrid artificial-biological neural network that communicated using biological principles, but over the internet.
The three-neuron network, linked through artificial synapses that emulate the real thing, was able to reproduce a classic neuroscience experiment that’s considered the basis of learning and memory in the brain. In other words, artificial neuron and synapse “chips” have progressed to the point where they can actually use a biological neuron intermediary to form a circuit that, at least partially, behaves like the real thing.
That’s not to say cyborg brains are coming soon. The simulation only recreated a small network that supports excitatory transmission in the hippocampus—a critical region that supports memory—and most brain functions require enormous cross-talk between numerous neurons and circuits. Nevertheless, the study is a jaw-dropping demonstration of how far we’ve come in recreating biological neurons and synapses in artificial hardware.
And perhaps one day, the currently “experimental” neuromorphic hardware will be integrated into broken biological neural circuits as bridges to restore movement, memory, personality, and even a sense of self.
The Artificial Brain Boom
One important thing: this study relies heavily on a decade of research into neuromorphic computing, or the implementation of brain functions inside computer chips.
The best-known example is perhaps IBM’s TrueNorth, which leveraged the brain’s computational principles to build a completely different computer than what we have today. Today’s computers run on a von Neumann architecture, in which memory and processing modules are physically separate. In contrast, the brain’s computing and memory are simultaneously achieved at synapses, small “hubs” on individual neurons that talk to adjacent ones.
Because memory and processing occur on the same site, biological neurons don’t have to shuttle data back and forth between processing and storage compartments, massively reducing processing time and energy use. What’s more, a neuron’s history will also influence how it behaves in the future, increasing flexibility and adaptability compared to computers. With the rise of deep learning, which loosely mimics neural processing as the prima donna of AI, the need to reduce power while boosting speed and flexible learning is becoming ever more tantamount in the AI community.
Neuromorphic computing was partially born out of this need. Most chips utilize special ingredients that change their resistance (or other physical characteristics) to mimic how a neuron might adapt to stimulation. Some chips emulate a whole neuron, that is, how it responds to a history of stimulation—does it get easier or harder to fire? Others imitate synapses themselves, that is, how easily they will pass on the information to another neuron.
Although single neuromorphic chips have proven to be far more efficient and powerful than current computer chips running machine learning algorithms in toy problems, so far few people have tried putting the artificial components together with biological ones in the ultimate test.
That’s what this study did.
A Hybrid Network
Still with me? Let’s talk network.
It’s gonna sound complicated, but remember: learning is the formation of neural networks, and neurons that fire together wire together. To rephrase: when learning, neurons will spontaneously organize into networks so that future instances will re-trigger the entire network. To “wire” together, downstream neurons will become more responsive to their upstream neural partners, so that even a whisper will cause them to activate. In contrast, some types of stimulation will cause the downstream neuron to “chill out” so that only an upstream “shout” will trigger downstream activation.
Both these properties—easier or harder to activate downstream neurons—are essentially how the brain forms connections. The “amping up,” in neuroscience jargon, is long-term potentiation (LTP), whereas the down-tuning is LTD (long-term depression). These two phenomena were first discovered in the rodent hippocampus more than half a century ago, and ever since have been considered as the biological basis of how the brain learns and remembers, and implicated in neurological problems such as addition (seriously, you can’t pass Neuro 101 without learning about LTP and LTD!).
So it’s perhaps especially salient that one of the first artificial-brain hybrid networks recapitulated this classic result.
To visualize: the three-neuron network began in Switzerland, with an artificial neuron with the badass name of “silicon spiking neuron.” That neuron is linked to an artificial synapse, a “memristor” located in the UK, which is then linked to a biological rat neuron cultured in Italy. The rat neuron has a “smart” microelectrode, controlled by the artificial synapse, to stimulate it. This is the artificial-to-biological pathway.
Meanwhile, the rat neuron in Italy also has electrodes that listen in on its electrical signaling. This signaling is passed back to another artificial synapse in the UK, which is then used to control a second artificial neuron back in Switzerland. This is the biological-to-artificial pathway back. As a testimony in how far we’ve come in digitizing neural signaling, all of the biological neural responses are digitized and sent over the internet to control its far-out artificial partner.
Here’s the crux: to demonstrate a functional neural network, just having the biological neuron passively “pass on” electrical stimulation isn’t enough. It has to show the capacity to learn, that is, to be able to mimic the amping up and down-tuning that are LTP and LTD, respectively.
You’ve probably guessed the results: certain stimulation patterns to the first artificial neuron in Switzerland changed how the artificial synapse in the UK operated. This, in turn, changed the stimulation to the biological neuron, so that it either amped up or toned down depending on the input.
Similarly, the response of the biological neuron altered the second artificial synapse, which then controlled the output of the second artificial neuron. Altogether, the biological and artificial components seamlessly linked up, over thousands of miles, into a functional neural circuit.
Cyborg Mind-Meld
So…I’m still picking my jaw up off the floor.
It’s utterly insane seeing a classic neuroscience learning experiment repeated with an integrated network with artificial components. That said, a three-neuron network is far from the thousands of synapses (if not more) needed to truly re-establish a broken neural circuit in the hippocampus, which DARPA has been aiming to do. And LTP/LTD has come under fire recently as the de facto brain mechanism for learning, though so far they remain cemented as neuroscience dogma.
However, this is one of the few studies where you see fields coming together. As Richard Feynman famously said, “What I cannot recreate, I cannot understand.” Even though neuromorphic chips were built on a high-level rather than molecular-level understanding of how neurons work, the study shows that artificial versions can still synapse with their biological counterparts. We’re not just on the right path towards understanding the brain, we’re recreating it, in hardware—if just a little.
While the study doesn’t have immediate use cases, practically it does boost both the neuromorphic computing and neuroprosthetic fields.
“We are very excited with this new development,” said study author Dr. Themis Prodromakis at the University of Southampton. “On one side it sets the basis for a novel scenario that was never encountered during natural evolution, where biological and artificial neurons are linked together and communicate across global networks; laying the foundations for the Internet of Neuro-electronics. On the other hand, it brings new prospects to neuroprosthetic technologies, paving the way towards research into replacing dysfunctional parts of the brain with AI chips.”
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#436256 Alphabet Is Developing a Robot to Take ...
Robots excel at carrying out specialized tasks in controlled environments, but put them in your average office and they’d be lost. Alphabet wants to change that by developing what they call the Everyday Robot, which could learn to help us out with our daily chores.
For a long time most robots were painstakingly hand-coded to carry out their functions, but since the deep learning revolution earlier this decade there’s been a growing effort to imbue them with AI that lets them learn new tasks through experience.
That’s led to some impressive breakthroughs, like a robotic hand nimble enough to solve a Rubik’s cube and a robotic arm that can accurately toss bananas across a room.
And it turns out Alphabet’s early-stage research and development division, Alphabet X, has also secretly been using similar machine learning techniques to develop robots adaptable enough to carry out a range of tasks in cluttered and unpredictable human environments like homes and offices.
The robots they’ve built combine a wheeled base with a single arm and a head full of sensors (including LIDAR) for 3D scanning, borrowed from Alphabet’s self-driving car division, Waymo.
At the minute, though, they’re largely restricted to sorting trash for recycling, project leader Hans Peter Brondmo writes in a blog post. While that might sound mundane, identifying different kinds of trash, grasping it, and moving it to the correct bin is still a difficult thing for a robot to do consistently. Some of the robots also have to navigate around the office to sort trash at various recycling stations.
Alphabet says even its human staff were getting it wrong 20 percent of the time, but after several months of training the robots have managed to get that down to 3.5 percent.
Every day, 30 robots toil away in what’s been dubbed the “playpen” sorting trash, and then every night thousands of virtual robots continue to practice in a simulation. This experience is then used to update the robots’ control algorithms each night. All the robots also share their experiences with the others through a process called collaborative learning.
The process isn’t flawless, though. Simonite notes that while the robots exhibit some uncannily smart behaviors, like stirring piles of rubbish to make it easier to grab specific items, they also frequently miss or fumble the objects they’re trying to grasp.
Nonetheless, the project’s leaders are happy with their progress so far. And the hope is that creating robots that are able to learn from little more than experience in complex environments like an office should be a first step towards general-purpose robots that can pick up a variety of useful skills to assist humans.
Taking that next step will be the major test of the project. So far there’s been limited evidence that experience gained by robots in one task can be transferred to learning another. That’s something the group hopes to demonstrate next year.
And it seems there may be more robot news coming out of Alphabet X soon. The group has several other robotics “moonshots” in the pipeline, built on technology and talent transferred over in 2016 from the remains of a broadly unsuccessful splurge on robotics startups by former Google executive Andy Rubin.
Whether this robotics renaissance at Alphabet will finally help robots break into our homes and offices remains to be seen, but with the resources they have at hand, they just may be able to make it happen.
Image Credit: Everyday Robot, Alphabet X Continue reading
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