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#437673 Can AI and Automation Deliver a COVID-19 ...
Illustration: Marysia Machulska
Within moments of meeting each other at a conference last year, Nathan Collins and Yann Gaston-Mathé began devising a plan to work together. Gaston-Mathé runs a startup that applies automated software to the design of new drug candidates. Collins leads a team that uses an automated chemistry platform to synthesize new drug candidates.
“There was an obvious synergy between their technology and ours,” recalls Gaston-Mathé, CEO and cofounder of Paris-based Iktos.
In late 2019, the pair launched a project to create a brand-new antiviral drug that would block a specific protein exploited by influenza viruses. Then the COVID-19 pandemic erupted across the world stage, and Gaston-Mathé and Collins learned that the viral culprit, SARS-CoV-2, relied on a protein that was 97 percent similar to their influenza protein. The partners pivoted.
Their companies are just two of hundreds of biotech firms eager to overhaul the drug-discovery process, often with the aid of artificial intelligence (AI) tools. The first set of antiviral drugs to treat COVID-19 will likely come from sifting through existing drugs. Remdesivir, for example, was originally developed to treat Ebola, and it has been shown to speed the recovery of hospitalized COVID-19 patients. But a drug made for one condition often has side effects and limited potency when applied to another. If researchers can produce an antiviral that specifically targets SARS-CoV-2, the drug would likely be safer and more effective than a repurposed drug.
There’s one big problem: Traditional drug discovery is far too slow to react to a pandemic. Designing a drug from scratch typically takes three to five years—and that’s before human clinical trials. “Our goal, with the combination of AI and automation, is to reduce that down to six months or less,” says Collins, who is chief strategy officer at SRI Biosciences, a division of the Silicon Valley research nonprofit SRI International. “We want to get this to be very, very fast.”
That sentiment is shared by small biotech firms and big pharmaceutical companies alike, many of which are now ramping up automated technologies backed by supercomputing power to predict, design, and test new antivirals—for this pandemic as well as the next—with unprecedented speed and scope.
“The entire industry is embracing these tools,” says Kara Carter, president of the International Society for Antiviral Research and executive vice president of infectious disease at Evotec, a drug-discovery company in Hamburg. “Not only do we need [new antivirals] to treat the SARS-CoV-2 infection in the population, which is probably here to stay, but we’ll also need them to treat future agents that arrive.”
There are currentlyabout 200 known viruses that infect humans. Although viruses represent less than 14 percent of all known human pathogens, they make up two-thirds of all new human pathogens discovered since 1980.
Antiviral drugs are fundamentally different from vaccines, which teach a person’s immune system to mount a defense against a viral invader, and antibody treatments, which enhance the body’s immune response. By contrast, antivirals are chemical compounds that directly block a virus after a person has become infected. They do this by binding to specific proteins and preventing them from functioning, so that the virus cannot copy itself or enter or exit a cell.
The SARS-CoV-2 virus has an estimated 25 to 29 proteins, but not all of them are suitable drug targets. Researchers are investigating, among other targets, the virus’s exterior spike protein, which binds to a receptor on a human cell; two scissorlike enzymes, called proteases, that cut up long strings of viral proteins into functional pieces inside the cell; and a polymerase complex that makes the cell churn out copies of the virus’s genetic material, in the form of single-stranded RNA.
But it’s not enough for a drug candidate to simply attach to a target protein. Chemists also consider how tightly the compound binds to its target, whether it binds to other things as well, how quickly it metabolizes in the body, and so on. A drug candidate may have 10 to 20 such objectives. “Very often those objectives can appear to be anticorrelated or contradictory with each other,” says Gaston-Mathé.
Compared with antibiotics, antiviral drug discovery has proceeded at a snail’s pace. Scientists advanced from isolating the first antibacterial molecules in 1910 to developing an arsenal of powerful antibiotics by 1944. By contrast, it took until 1951 for researchers to be able to routinely grow large amounts of virus particles in cells in a dish, a breakthrough that earned the inventors a Nobel Prize in Medicine in 1954.
And the lag between the discovery of a virus and the creation of a treatment can be heartbreaking. According to the World Health Organization, 71 million people worldwide have chronic hepatitis C, a major cause of liver cancer. The virus that causes the infection was discovered in 1989, but effective antiviral drugs didn’t hit the market until 2014.
While many antibiotics work on a range of microbes, most antivirals are highly specific to a single virus—what those in the business call “one bug, one drug.” It takes a detailed understanding of a virus to develop an antiviral against it, says Che Colpitts, a virologist at Queen’s University, in Canada, who works on antivirals against RNA viruses. “When a new virus emerges, like SARS-CoV-2, we’re at a big disadvantage.”
Making drugs to stop viruses is hard for three main reasons. First, viruses are the Spartans of the pathogen world: They’re frugal, brutal, and expert at evading the human immune system. About 20 to 250 nanometers in diameter, viruses rely on just a few parts to operate, hijacking host cells to reproduce and often destroying those cells upon departure. They employ tricks to camouflage their presence from the host’s immune system, including preventing infected cells from sending out molecular distress beacons. “Viruses are really small, so they only have a few components, so there’s not that many drug targets available to start with,” says Colpitts.
Second, viruses replicate quickly, typically doubling in number in hours or days. This constant copying of their genetic material enables viruses to evolve quickly, producing mutations able to sidestep drug effects. The virus that causes AIDS soon develops resistance when exposed to a single drug. That’s why a cocktail of antiviral drugs is used to treat HIV infection.
Finally, unlike bacteria, which can exist independently outside human cells, viruses invade human cells to propagate, so any drug designed to eliminate a virus needs to spare the host cell. A drug that fails to distinguish between a virus and a cell can cause serious side effects. “Discriminating between the two is really quite difficult,” says Evotec’s Carter, who has worked in antiviral drug discovery for over three decades.
And then there’s the money barrier. Developing antivirals is rarely profitable. Health-policy researchers at the London School of Economics recently estimated that the average cost of developing a new drug is US $1 billion, and up to $2.8 billion for cancer and other specialty drugs. Because antivirals are usually taken for only short periods of time or during short outbreaks of disease, companies rarely recoup what they spent developing the drug, much less turn a profit, says Carter.
To change the status quo, drug discovery needs fresh approaches that leverage new technologies, rather than incremental improvements, says Christian Tidona, managing director of BioMed X, an independent research institute in Heidelberg, Germany. “We need breakthroughs.”
Putting Drug Development on Autopilot
Earlier this year, SRI Biosciences and Iktos began collaborating on a way to use artificial intelligence and automated chemistry to rapidly identify new drugs to target the COVID-19 virus. Within four months, they had designed and synthesized a first round of antiviral candidates. Here’s how they’re doing it.
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STEP 1: Iktos’s AI platform uses deep-learning algorithms in an iterative process to come up with new molecular structures likely to bind to and disable a specific coronavirus protein. Illustrations: Chris Philpot
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STEP 2: SRI Biosciences’s SynFini system is a three-part automated chemistry suite for producing new compounds. Starting with a target compound from Iktos, SynRoute uses machine learning to analyze and optimize routes for creating that compound, with results in about 10 seconds. It prioritizes routes based on cost, likelihood of success, and ease of implementation.
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STEP 3: SynJet, an automated inkjet printer platform, tests the routes by printing out tiny quantities of chemical ingredients to see how they react. If the right compound is produced, the platform tests it.
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STEP 4: AutoSyn, an automated tabletop chemical plant, synthesizes milligrams to grams of the desired compound for further testing. Computer-selected “maps” dictate paths through the plant’s modular components.
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STEP 5: The most promising compounds are tested against live virus samples.
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Iktos’s AI platform was created by a medicinal chemist and an AI expert. To tackle SARS-CoV-2, the company used generative models—deep-learning algorithms that generate new data—to “imagine” molecular structures with a good chance of disabling a key coronavirus protein.
For a new drug target, the software proposes and evaluates roughly 1 million compounds, says Gaston-Mathé. It’s an iterative process: At each step, the system generates 100 virtual compounds, which are tested in silico with predictive models to see how closely they meet the objectives. The test results are then used to design the next batch of compounds. “It’s like we have a very, very fast chemist who is designing compounds, testing compounds, getting back the data, then designing another batch of compounds,” he says.
The computer isn’t as smart as a human chemist, Gaston-Mathé notes, but it’s much faster, so it can explore far more of what people in the field call “chemical space”—the set of all possible organic compounds. Unexplored chemical space is huge: Biochemists estimate that there are at least 1063 possible druglike molecules, and that 99.9 percent of all possible small molecules or compounds have never been synthesized.
Still, designing a chemical compound isn’t the hardest part of creating a new drug. After a drug candidate is designed, it must be synthesized, and the highly manual process for synthesizing a new chemical hasn’t changed much in 200 years. It can take days to plan a synthesis process and then months to years to optimize it for manufacture.
That’s why Gaston-Mathé was eager to send Iktos’s AI-generated designs to Collins’s team at SRI Biosciences. With $13.8 million from the Defense Advanced Research Projects Agency, SRI Biosciences spent the last four years automating the synthesis process. The company’s automated suite of three technologies, called SynFini, can produce new chemical compounds in just hours or days, says Collins.
First, machine-learning software devises possible routes for making a desired molecule. Next, an inkjet printer platform tests the routes by printing out and mixing tiny quantities of chemical ingredients to see how they react with one another; if the right compound is produced, the platform runs tests on it. Finally, a tabletop chemical plant synthesizes milligrams to grams of the desired compound.
Less than four months after Iktos and SRI Biosciences announced their collaboration, they had designed and synthesized a first round of antiviral candidates for SARS-CoV-2. Now they’re testing how well the compounds work on actual samples of the virus.
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63 possible druglike molecules, 99.9 percent have never been synthesized.
Theirs isn’t the only collaborationapplying new tools to drug discovery. In late March, Alex Zhavoronkov, CEO of Hong Kong–based Insilico Medicine, came across a YouTube video showing three virtual-reality avatars positioning colorful, sticklike fragments in the side of a bulbous blue protein. The three researchers were using VR to explore how compounds might bind to a SARS-CoV-2 enzyme. Zhavoronkov contacted the startup that created the simulation—Nanome, in San Diego—and invited it to examine Insilico’s AI-generated molecules in virtual reality.
Insilico runs an AI platform that uses biological data to train deep-learning algorithms, then uses those algorithms to identify molecules with druglike features that will likely bind to a protein target. A four-day training sprint in late January yielded 100 molecules that appear to bind to an important SARS-CoV-2 protease. The company recently began synthesizing some of those molecules for laboratory testing.
Nanome’s VR software, meanwhile, allows researchers to import a molecular structure, then view and manipulate it on the scale of individual atoms. Like human chess players who use computer programs to explore potential moves, chemists can use VR to predict how to make molecules more druglike, says Nanome CEO Steve McCloskey. “The tighter the interface between the human and the computer, the more information goes both ways,” he says.
Zhavoronkov sent data about several of Insilico’s compounds to Nanome, which re-created them in VR. Nanome’s chemist demonstrated chemical tweaks to potentially improve each compound. “It was a very good experience,” says Zhavoronkov.
Meanwhile, in March, Takeda Pharmaceutical Co., of Japan, invited Schrödinger, a New York–based company that develops chemical-simulation software, to join an alliance working on antivirals. Schrödinger’s AI focuses on the physics of how proteins interact with small molecules and one another.
The software sifts through billions of molecules per week to predict a compound’s properties, and it optimizes for multiple desired properties simultaneously, says Karen Akinsanya, chief biomedical scientist and head of discovery R&D at Schrödinger. “There’s a huge sense of urgency here to come up with a potent molecule, but also to come up with molecules that are going to be well tolerated” by the body, she says. Drug developers are seeking compounds that can be broadly used and easily administered, such as an oral drug rather than an intravenous drug, she adds.
Schrödinger evaluated four protein targets and performed virtual screens for two of them, a computing-intensive process. In June, Google Cloud donated the equivalent of 16 million hours of Nvidia GPU time for the company’s calculations. Next, the alliance’s drug companies will synthesize and test the most promising compounds identified by the virtual screens.
Other companies, including Amazon Web Services, IBM, and Intel, as well as several U.S. national labs are also donating time and resources to the Covid-19 High Performance Computing Consortium. The consortium is supporting 87 projects, which now have access to 6.8 million CPU cores, 50,000 GPUs, and 600 petaflops of computational resources.
While advanced technologies could transform early drug discovery, any new drug candidate still has a long road after that. It must be tested in animals, manufactured in large batches for clinical trials, then tested in a series of trials that, for antivirals, lasts an average of seven years.
In May, the BioMed X Institute in Germany launched a five-year project to build a Rapid Antiviral Response Platform, which would speed drug discovery all the way through manufacturing for clinical trials. The €40 million ($47 million) project, backed by drug companies, will identify outside-the-box proposals from young scientists, then provide space and funding to develop their ideas.
“We’ll focus on technologies that allow us to go from identification of a new virus to 10,000 doses of a novel potential therapeutic ready for trials in less than six months,” says BioMed X’s Tidona, who leads the project.
While a vaccine will likely arrive long before a bespoke antiviral does, experts expect COVID-19 to be with us for a long time, so the effort to develop a direct-acting, potent antiviral continues. Plus, having new antivirals—and tools to rapidly create more—can only help us prepare for the next pandemic, whether it comes next month or in another 102 years.
“We’ve got to start thinking differently about how to be more responsive to these kinds of threats,” says Collins. “It’s pushing us out of our comfort zones.”
This article appears in the October 2020 print issue as “Automating Antivirals.” Continue reading
Posted in Human Robots
#437630 How Toyota Research Envisions the Future ...
Yesterday, the Toyota Research Institute (TRI) showed off some of the projects that it’s been working on recently, including a ceiling-mounted robot that could one day help us with household chores. That system is just one example of how TRI envisions the future of robotics and artificial intelligence. As TRI CEO Gill Pratt told us, the company is focusing on robotics and AI technology for “amplifying, rather than replacing, human beings.” In other words, Toyota wants to develop robots not for convenience or to do our jobs for us, but rather to allow people to continue to live and work independently even as we age.
To better understand Toyota’s vision of robotics 15 to 20 years from now, it’s worth watching the 20-minute video below, which depicts various scenarios “where the application of robotic capabilities is enabling members of an aging society to live full and independent lives in spite of the challenges that getting older brings.” It’s a long video, but it helps explains TRI’s perspective on how robots will collaborate with humans in our daily lives over the next couple of decades.
Those are some interesting conceptual telepresence-controlled bipeds they’ve got running around in that video, right?
For more details, we sent TRI some questions on how it plans to go from concepts like the ones shown in the video to real products that can be deployed in human environments. Below are answers from TRI CEO Gill Pratt, who is also chief scientist for Toyota Motor Corp.; Steffi Paepcke, senior UX designer at TRI; and Max Bajracharya, VP of robotics at TRI.
IEEE Spectrum: TRI seems to have a more explicit focus on eventual commercialization than most of the robotics research that we cover. At what point TRI starts to think about things like reliability and cost?
Photo: TRI
Toyota is exploring robots capable of manipulating dishes in a sink and a dishwasher, performing experiments and simulations to make sure that the robots can handle a wide range of conditions.
Gill Pratt: It’s a really interesting question, because the normal way to think about this would be to say, well, both reliability and cost are product development tasks. But actually, we need to think about it at the earliest possible stage with research as well. The hardware that we use in the laboratory for doing experiments, we don’t worry about cost there, or not nearly as much as you’d worry about for a product. However, in terms of what research we do, we very much have to think about, is it possible (if the research is successful) for it to end up in a product that has a reasonable cost. Because if a customer can’t afford what we come up with, maybe it has some academic value but it’s not actually going to make a difference in their quality of life in the real world. So we think about cost very much from the beginning.
The same is true with reliability. Right now, we’re working very hard to make our control techniques robust to wide variations in the environment. For instance, in work that Russ Tedrake is doing with manipulating dishes in a sink and a dishwasher, both in physical testing and in simulation, we’re doing thousands and now millions of different experiments to make sure that we can handle the edge cases and it works over a very wide range of conditions.
A tremendous amount of work that we do is trying to bring robotics out of the age of doing demonstrations. There’s been a history of robotics where for some time, things have not been reliable, so we’d catch the robot succeeding just once and then show that video to the world, and people would get the mis-impression that it worked all of the time. Some researchers have been very good about showing the blooper reel too, to show that some of the time, robots don’t work.
“A tremendous amount of work that we do is trying to bring robotics out of the age of doing demonstrations. There’s been a history of robotics where for some time, things have not been reliable, so we’d catch the robot succeeding just once and then show that video to the world, and people would get the mis-impression that it worked all of the time.”
—Gill Pratt, TRI
In the spirit of sharing things that didn’t work, can you tell us a bit about some of the robots that TRI has had under development that didn’t make it into the demo yesterday because they were abandoned along the way?
Steffi Paepcke: We’re really looking at how we can connect people; it can be hard to stay in touch and see our loved ones as much as we would like to. There have been a few prototypes that we’ve worked on that had to be put on the shelf, at least for the time being. We were exploring how to use light so that people could be ambiently aware of one another across distances. I was very excited about that—the internal name was “glowing orb.” For a variety of reasons, it didn’t work out, but it was really fascinating to investigate different modalities for keeping in touch.
Another prototype we worked on—we found through our research that grocery shopping is obviously an important part of life, and for a lot of older adults, it’s not necessarily the right answer to always have groceries delivered. Getting up and getting out of the house keeps you physically active, and a lot of people prefer to continue doing it themselves. But it can be challenging, especially if you’re purchasing heavy items that you need to transport. We had a prototype that assisted with grocery shopping, but when we pivoted our focus to Japan, we found that the inside of a Japanese home really needs to stay inside, and the outside needs to stay outside, so a robot that traverses both domains is probably not the right fit for a Japanese audience, and those were some really valuable lessons for us.
Photo: TRI
Toyota recently demonstrated a gantry robot that would hang from the ceiling to perform tasks like wiping surfaces and clearing clutter.
I love that TRI is exploring things like the gantry robot both in terms of near-term research and as part of its long-term vision, but is a robot like this actually worth pursuing? Or more generally, what’s the right way to compromise between making an environment robot friendly, and asking humans to make changes to their homes?
Max Bajracharya: We think a lot about the problems that we’re trying to address in a holistic way. We don’t want to just give people a robot, and assume that they’re not going to change anything about their lifestyle. We have a lot of evidence from people who use automated vacuum cleaners that people will adapt to the tools you give them, and they’ll change their lifestyle. So we want to think about what is that trade between changing the environment, and giving people robotic assistance and tools.
We certainly think that there are ways to make the gantry system plausible. The one you saw today is obviously a prototype and does require significant infrastructure. If we’re going to retrofit a home, that isn’t going to be the way to do it. But we still feel like we’re very much in the prototype phase, where we’re trying to understand whether this is worth it to be able to bypass navigation challenges, and coming up with the pros and cons of the gantry system. We’re evaluating whether we think this is the right approach to solving the problem.
To what extent do you think humans should be either directly or indirectly in the loop with home and service robots?
Bajracharya: Our goal is to amplify people, so achieving this is going to require robots to be in a loop with people in some form. One thing we have learned is that using people in a slow loop with robots, such as teaching them or helping them when they make mistakes, gives a robot an important advantage over one that has to do everything perfectly 100 percent of the time. In unstructured human environments, robots are going to encounter corner cases, and are going to need to learn to adapt. People will likely play an important role in helping the robots learn. Continue reading
Posted in Human Robots
#437373 Microsoft’s New Deepfake Detector Puts ...
The upcoming US presidential election seems set to be something of a mess—to put it lightly. Covid-19 will likely deter millions from voting in person, and mail-in voting isn’t shaping up to be much more promising. This all comes at a time when political tensions are running higher than they have in decades, issues that shouldn’t be political (like mask-wearing) have become highly politicized, and Americans are dramatically divided along party lines.
So the last thing we need right now is yet another wrench in the spokes of democracy, in the form of disinformation; we all saw how that played out in 2016, and it wasn’t pretty. For the record, disinformation purposely misleads people, while misinformation is simply inaccurate, but without malicious intent. While there’s not a ton tech can do to make people feel safe at crowded polling stations or up the Postal Service’s budget, tech can help with disinformation, and Microsoft is trying to do so.
On Tuesday the company released two new tools designed to combat disinformation, described in a blog post by VP of Customer Security and Trust Tom Burt and Chief Scientific Officer Eric Horvitz.
The first is Microsoft Video Authenticator, which is made to detect deepfakes. In case you’re not familiar with this wicked byproduct of AI progress, “deepfakes” refers to audio or visual files made using artificial intelligence that can manipulate peoples’ voices or likenesses to make it look like they said things they didn’t. Editing a video to string together words and form a sentence someone didn’t say doesn’t count as a deepfake; though there’s manipulation involved, you don’t need a neural network and you’re not generating any original content or footage.
The Authenticator analyzes videos or images and tells users the percentage chance that they’ve been artificially manipulated. For videos, the tool can even analyze individual frames in real time.
Deepfake videos are made by feeding hundreds of hours of video of someone into a neural network, “teaching” the network the minutiae of the person’s voice, pronunciation, mannerisms, gestures, etc. It’s like when you do an imitation of your annoying coworker from accounting, complete with mimicking the way he makes every sentence sound like a question and his eyes widen when he talks about complex spreadsheets. You’ve spent hours—no, months—in his presence and have his personality quirks down pat. An AI algorithm that produces deepfakes needs to learn those same quirks, and more, about whoever the creator’s target is.
Given enough real information and examples, the algorithm can then generate its own fake footage, with deepfake creators using computer graphics and manually tweaking the output to make it as realistic as possible.
The scariest part? To make a deepfake, you don’t need a fancy computer or even a ton of knowledge about software. There are open-source programs people can access for free online, and as far as finding video footage of famous people—well, we’ve got YouTube to thank for how easy that is.
Microsoft’s Video Authenticator can detect the blending boundary of a deepfake and subtle fading or greyscale elements that the human eye may not be able to see.
In the blog post, Burt and Horvitz point out that as time goes by, deepfakes are only going to get better and become harder to detect; after all, they’re generated by neural networks that are continuously learning from and improving themselves.
Microsoft’s counter-tactic is to come in from the opposite angle, that is, being able to confirm beyond doubt that a video, image, or piece of news is real (I mean, can McDonald’s fries cure baldness? Did a seal slap a kayaker in the face with an octopus? Never has it been so imperative that the world know the truth).
A tool built into Microsoft Azure, the company’s cloud computing service, lets content producers add digital hashes and certificates to their content, and a reader (which can be used as a browser extension) checks the certificates and matches the hashes to indicate the content is authentic.
Finally, Microsoft also launched an interactive “Spot the Deepfake” quiz it developed in collaboration with the University of Washington’s Center for an Informed Public, deepfake detection company Sensity, and USA Today. The quiz is intended to help people “learn about synthetic media, develop critical media literacy skills, and gain awareness of the impact of synthetic media on democracy.”
The impact Microsoft’s new tools will have remains to be seen—but hey, we’re glad they’re trying. And they’re not alone; Facebook, Twitter, and YouTube have all taken steps to ban and remove deepfakes from their sites. The AI Foundation’s Reality Defender uses synthetic media detection algorithms to identify fake content. There’s even a coalition of big tech companies teaming up to try to fight election interference.
One thing is for sure: between a global pandemic, widespread protests and riots, mass unemployment, a hobbled economy, and the disinformation that’s remained rife through it all, we’re going to need all the help we can get to make it through not just the election, but the rest of the conga-line-of-catastrophes year that is 2020.
Image Credit: Darius Bashar on Unsplash Continue reading
Posted in Human Robots