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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.
Image credit: NIH/NIAID Continue reading
Posted in Human Robots
#436426 Video Friday: This Robot Refuses to Fall ...
Video Friday is your weekly selection of awesome robotics videos, collected by your Automaton bloggers. We’ll also be posting a weekly calendar of upcoming robotics events for the next few months; here’s what we have so far (send us your events!):
Robotic Arena – January 25, 2020 – Wrocław, Poland
DARPA SubT Urban Circuit – February 18-27, 2020 – Olympia, Wash., USA
Let us know if you have suggestions for next week, and enjoy today’s videos.
In case you somehow missed the massive Skydio 2 review we posted earlier this week, the first batches of the drone are now shipping. Each drone gets a lot of attention before it goes out the door, and here’s a behind-the-scenes clip of the process.
[ Skydio ]
Sphero RVR is one of the 15 robots on our robot gift guide this year. Here’s a new video Sphero just released showing some of the things you can do with the robot.
[ RVR ]
NimbRo-OP2 has some impressive recovery skills from the obligatory research-motivated robot abuse.
[ NimbRo ]
Teams seeking to qualify for the Virtual Urban Circuit of the Subterranean Challenge can access practice worlds to test their approaches prior to submitting solutions for the competition. This video previews three of the practice environments.
[ DARPA SubT ]
Stretchable skin-like robots that can be rolled up and put in your pocket have been developed by a University of Bristol team using a new way of embedding artificial muscles and electrical adhesion into soft materials.
[ Bristol ]
Happy Holidays from ABB!
Helping New York celebrate the festive season, twelve ABB robots are interacting with visitors to Bloomingdale’s iconic holiday celebration at their 59th Street flagship store. ABB’s robots are the main attraction in three of Bloomingdale’s twelve-holiday window displays at Lexington and Third Avenue, as ABB demonstrates the potential for its robotics and automation technology to revolutionize visual merchandising and make the retail experience more dynamic and whimsical.
[ ABB ]
We introduce pelican eel–inspired dual-morphing architectures that embody quasi-sequential behaviors of origami unfolding and skin stretching in response to fluid pressure. In the proposed system, fluid paths were enclosed and guided by a set of entirely stretchable origami units that imitate the morphing principle of the pelican eel’s stretchable and foldable frames. This geometric and elastomeric design of fluid networks, in which fluid pressure acts in the direction that the whole body deploys first, resulted in a quasi-sequential dual-morphing response. To verify the effectiveness of our design rule, we built an artificial creature mimicking a pelican eel and reproduced biomimetic dual-morphing behavior.
And here’s a real pelican eel:
[ Science Robotics ]
Delft Dynamics’ updated anti-drone system involves a tether, mid-air net gun, and even a parachute.
[ Delft Dynamics ]
Teleoperation is a great way of helping robots with complex tasks, especially if you can do it through motion capture. But what if you’re teleoperating a non-anthropomorphic robot? Columbia’s ROAM Lab is working on it.
[ Paper ] via [ ROAM Lab ]
I don’t know how I missed this video last year because it’s got a steely robot hand squeezing a cute lil’ chick.
[ MotionLib ] via [ RobotStart ]
In this video we present results of a trajectory generation method for autonomous overtaking of unexpected obstacles in a dynamic urban environment. In these settings, blind spots can arise from perception limitations. For example when overtaking unexpected objects on the vehicle’s ego lane on a two-way street. In this case, a human driver would first make sure that the opposite lane is free and that there is enough room to successfully execute the maneuver, and then it would cut into the opposite lane in order to execute the maneuver successfully. We consider the practical problem of autonomous overtaking when the coverage of the perception system is impaired due to occlusion.
[ Paper ]
New weirdness from Toio!
[ Toio ]
Palo Alto City Library won a technology innovation award! Watch to see how Senior Librarian Dan Lou is using Misty to enhance their technology programs to inspire and educate customers.
[ Misty Robotics ]
We consider the problem of reorienting a rigid object with arbitrary known shape on a table using a two-finger pinch gripper. Reorienting problem is challenging because of its non-smoothness and high dimensionality. In this work, we focus on solving reorienting using pivoting, in which we allow the grasped object to rotate between fingers. Pivoting decouples the gripper rotation from the object motion, making it possible to reorient an object under strict robot workspace constraints.
[ CMU ]
How can a mobile robot be a good pedestrian without bumping into you on the sidewalk? It must be hard for a robot to navigate in crowded environments since the flow of traffic follows implied social rules. But researchers from MIT developed an algorithm that teaches mobile robots to maneuver in crowds of people, respecting their natural behaviour.
[ Roboy Research Reviews ]
What happens when humans and robots make art together? In this awe-inspiring talk, artist Sougwen Chung shows how she “taught” her artistic style to a machine — and shares the results of their collaboration after making an unexpected discovery: robots make mistakes, too. “Part of the beauty of human and machine systems is their inherent, shared fallibility,” she says.
[ TED ]
Last month at the Cooper Union in New York City, IEEE TechEthics hosted a public panel session on the facts and misperceptions of autonomous vehicles, part of the IEEE TechEthics Conversations Series. The speakers were: Jason Borenstein from Georgia Tech; Missy Cummings from Duke University; Jack Pokrzywa from SAE; and Heather M. Roff from Johns Hopkins Applied Physics Laboratory. The panel was moderated by Mark A. Vasquez, program manager for IEEE TechEthics.
[ IEEE TechEthics ]
Two videos this week from Lex Fridman’s AI podcast: Noam Chomsky, and Whitney Cummings.
[ AI Podcast ]
This week’s CMU RI Seminar comes from Jeff Clune at the University of Wyoming, on “Improving Robot and Deep Reinforcement Learning via Quality Diversity and Open-Ended Algorithms.”
Quality Diversity (QD) algorithms are those that seek to produce a diverse set of high-performing solutions to problems. I will describe them and a number of their positive attributes. I will then summarize our Nature paper on how they, when combined with Bayesian Optimization, produce a learning algorithm that enables robots, after being damaged, to adapt in 1-2 minutes in order to continue performing their mission, yielding state-of-the-art robot damage recovery. I will next describe our QD-based Go-Explore algorithm, which dramatically improves the ability of deep reinforcement learning algorithms to solve previously unsolvable problems wherein reward signals are sparse, meaning that intelligent exploration is required. Go-Explore solves Montezuma’s Revenge, considered by many to be a major AI research challenge. Finally, I will motivate research into open-ended algorithms, which seek to innovate endlessly, and introduce our POET algorithm, which generates its own training challenges while learning to solve them, automatically creating a curricula for robots to learn an expanding set of diverse skills. POET creates and solves challenges that are unsolvable with traditional deep reinforcement learning techniques.
[ CMU RI ] Continue reading
Posted in Human Robots
#436234 Robot Gift Guide 2019
Welcome to the eighth edition of IEEE Spectrum’s Robot Gift Guide!
This year we’re featuring 15 robotic products that we think will make fantastic holiday gifts. As always, we tried to include a broad range of robot types and prices, focusing mostly on items released this year. (A reminder: While we provide links to places where you can buy these items, we’re not endorsing any in particular, and a little bit of research may result in better deals.)
If you need even more robot gift ideas, take a look at our past guides: 2018, 2017, 2016, 2015, 2014, 2013, and 2012. Some of those robots are still great choices and might be way cheaper now than when we first posted about them. And if you have suggestions that you’d like to share, post a comment below to help the rest of us find the perfect robot gift.
Skydio 2
Image: Skydio
What makes robots so compelling is their autonomy, and the Skydio 2 is one of the most autonomous robots we’ve ever seen. It uses an array of cameras to map its environment and avoid obstacles in real-time, making flight safe and effortless and enabling the kinds of shots that would be impossible otherwise. Seriously, this thing is magical, and it’s amazing that you can actually buy one.
$1,000
Skydio
UBTECH Jimu MeeBot 2
Image: UBTECH
The Jimu MeeBot 2.0 from UBTECH is a STEM education robot designed to be easy to build and program. It includes six servo motors, a color sensor, and LED lights. An app for iPhone or iPad provides step-by-step 3D instructions, and helps you code different behaviors for the robot. It’s available exclusively from Apple.
$130
Apple
iRobot Roomba s9+
Image: iRobot
We know that $1,400 is a crazy amount of money to spend on a robot vacuum, but the Roomba s9+ is a crazy robot vacuum. As if all of its sensors and mapping intelligence wasn’t enough, it empties itself, which means that you can have your floors vacuumed every single day for a month and you don’t have to even think about it. This is what home robots are supposed to be.
$1,400
iRobot
PFF Gita
Photo: Piaggio Fast Forward
Nobody likes carrying things, which is why Gita is perfect for everyone with an extra $3,000 lying around. Developed by Piaggio Fast Forward, this autonomous robot will follow you around with a cargo hold full of your most important stuff, and do it in a way guaranteed to attract as much attention as possible.
$3,250
Gita
DJI Mavic Mini
Photo: DJI
It’s tiny, it’s cheap, and it takes good pictures—what more could you ask for from a drone? And for $400, this is an excellent drone to get if you’re on a budget and comfortable with manual flight. Keep in mind that while the Mavic Mini is small enough that you don’t need to register it with the FAA, you do still need to follow all the same rules and regulations.
$400
DJI
LEGO Star Wars Droid Commander
Image: LEGO
Designed for kids ages 8+, this LEGO set includes more than 1,000 pieces, enough to build three different droids: R2-D2, Gonk Droid, and Mouse Droid. Using a Bluetooth-controlled robotic brick called Move Hub, which connects to the LEGO BOOST Star Wars app, kids can change how the robots behave and solve challenges, learning basic robotics and coding skills.
$200
LEGO
Sony Aibo
Photo: Sony
Robot pets don’t get much more sophisticated (or expensive) than Sony’s Aibo. Strictly speaking, it’s one of the most complex consumer robots you can buy, and Sony continues to add to Aibo’s software. Recent new features include user programmability, and the ability to “feed” it.
$2,900 (free aibone and paw pads until 12/29/2019)
Sony
Neato Botvac D4 Connected
Photo: Neato
The Neato Botvac D4 may not have all of the features of its fancier and more expensive siblings, but it does have the features that you probably care the most about: The ability to make maps of its environment for intelligent cleaning (using lasers!), along with user-defined no-go lines that keep it where you want it. And it cleans quite well, too.
$530 $350 (sale)
Neato Robotics
Cubelets Curiosity Set
Photo: Modular Robotics
Cubelets are magnetic blocks that you can snap together to make an endless variety of robots with no programming and no wires. The newest set, called Curiosity, is designed for kids ages 4+ and comes with 10 robotic cubes. These include light and distance sensors, motors, and a Bluetooth module, which connects the robot constructions to the Cubelets app.
$250
Modular Robotics
Tertill
Photo: Franklin Robotics
Tertill does one simple job: It weeds your garden. It’s waterproof, dirt proof, solar powered, and fully autonomous, meaning that you can leave it out in your garden all summer and just enjoy eating your plants rather than taking care of them.
$350
Tertill
iRobot Root
Photo: iRobot
Root was originally developed by Harvard University as a tool to help kids progressively learn to code. iRobot has taken over Root and is now supporting the curriculum, which starts for kids before they even know how to read and should keep them busy for years afterwards.
$200
iRobot
LOVOT
Image: Lovot
Let’s be honest: Nobody is really quite sure what LOVOT is. We can all agree that it’s kinda cute, though. And kinda weird. But cute. Created by Japanese robotics startup Groove X, LOVOT does have a whole bunch of tech packed into its bizarre little body and it will do its best to get you to love it.
$2,750 (¥300,000)
LOVOT
Sphero RVR
Photo: Sphero
RVR is a rugged, versatile, easy to program mobile robot. It’s a development platform designed to be a bridge between educational robots like Sphero and more sophisticated and expensive systems like Misty. It’s mostly affordable, very expandable, and comes from a company with a lot of experience making robots.
$250
Sphero
“How to Train Your Robot”
Image: Lawrence Hall of Science
Aimed at 4th and 5th graders, “How to Train Your Robot,” written by Blooma Goldberg, Ken Goldberg, and Ashley Chase, and illustrated by Dave Clegg, is a perfect introduction to robotics for kids who want to get started with designing and building robots. But the book isn’t just for beginners: It’s also a fun, inspiring read for kids who are already into robotics and want to go further—it even introduces concepts like computer simulations and deep learning. You can download a free digital copy or request hardcopies here.
Free
UC Berkeley
MIT Mini Cheetah
Photo: MIT
Yes, Boston Dynamics’ Spot, now available for lease, is probably the world’s most famous quadruped, but MIT is starting to pump out Mini Cheetahs en masse for researchers, and while we’re not exactly sure how you’d manage to get one of these things short of stealing one directly for MIT, a Mini Cheetah is our fantasy robotics gift this year. Mini Cheetah looks like a ton of fun—it’s portable, highly dynamic, super rugged, and easy to control. We want one!
Price N/A
MIT Biomimetic Robotics Lab
For more tech gift ideas, see also IEEE Spectrum’s annual Gift Guide. Continue reading
Posted in Human Robots