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#436578 AI Just Discovered a New Antibiotic to ...
Penicillin, one of the greatest discoveries in the history of medicine, was a product of chance.
After returning from summer vacation in September 1928, bacteriologist Alexander Fleming found a colony of bacteria he’d left in his London lab had sprouted a fungus. Curiously, wherever the bacteria contacted the fungus, their cell walls broke down and they died. Fleming guessed the fungus was secreting something lethal to the bacteria—and the rest is history.
Fleming’s discovery of penicillin and its later isolation, synthesis, and scaling in the 1940s released a flood of antibiotic discoveries in the next few decades. Bacteria and fungi had been waging an ancient war against each other, and the weapons they’d evolved over eons turned out to be humanity’s best defense against bacterial infection and disease.
In recent decades, however, the flood of new antibiotics has slowed to a trickle.
Their development is uneconomical for drug companies, and the low-hanging fruit has long been picked. We’re now facing the emergence of strains of super bacteria resistant to one or more antibiotics and an aging arsenal to fight them with. Gone unchallenged, an estimated 700,000 deaths worldwide due to drug resistance could rise to as many as 10 million in 2050.
Increasingly, scientists warn the tide is turning, and we need a new strategy to keep pace with the remarkably quick and boundlessly creative tactics of bacterial evolution.
But where the golden age of antibiotics was sparked by serendipity, human intelligence, and natural molecular weapons, its sequel may lean on the uncanny eye of artificial intelligence to screen millions of compounds—and even design new ones—in search of the next penicillin.
Hal Discovers a Powerful Antibiotic
In a paper published this week in the journal, Cell, MIT researchers took a step in this direction. The team says their machine learning algorithm discovered a powerful new antibiotic.
Named for the AI in 2001: A Space Odyssey, the antibiotic, halicin, successfully wiped out dozens of bacterial strains, including some of the most dangerous drug-resistant bacteria on the World Health Organization’s most wanted list. The bacteria also failed to develop resistance to E. coli during a month of observation, in stark contrast to existing antibiotic ciprofloxacin.
“In terms of antibiotic discovery, this is absolutely a first,” Regina Barzilay, a senior author on the study and computer science professor at MIT, told The Guardian.
The algorithm that discovered halicin was trained on the molecular features of 2,500 compounds. Nearly half were FDA-approved drugs, and another 800 naturally occurring. The researchers specifically tuned the algorithm to look for molecules with antibiotic properties but whose structures would differ from existing antibiotics (as halicin’s does). Using another machine learning program, they screened the results for those likely to be safe for humans.
Early study suggests halicin attacks the bacteria’s cell membranes, disrupting their ability to produce energy. Protecting the cell membrane from halicin might take more than one or two genetic mutations, which could account for its impressive ability to prevent resistance.
“I think this is one of the more powerful antibiotics that has been discovered to date,” James Collins, an MIT professor of bioengineering and senior author told The Guardian. “It has remarkable activity against a broad range of antibiotic-resistant pathogens.”
Beyond tests in petri-dish bacterial colonies, the team also tested halicin in mice. The antibiotic cleared up infections of a strain of bacteria resistant to all known antibiotics in a day. The team plans further study in partnership with a pharmaceutical company or nonprofit, and they hope to eventually prove it safe and effective for use in humans.
This last bit remains the trickiest step, given the cost of getting a new drug approved. But Collins hopes algorithms like theirs will help. “We could dramatically reduce the cost required to get through clinical trials,” he told the Financial Times.
A Universe of Drugs Awaits
The bigger story may be what happens next.
How many novel antibiotics await discovery, and how far can AI screening take us? The initial 6,000 compounds scanned by Barzilay and Collins’s team is a drop in the bucket.
They’ve already begun digging deeper by setting the algorithm loose on 100 million molecules from an online library of 1.5 billion compounds called the ZINC15 database. This first search took three days and turned up 23 more candidates that, like halicin, differ structurally from existing antibiotics and may be safe for humans. Two of these—which the team will study further—appear to be especially powerful.
Even more ambitiously, Barzilay hopes the approach can find or even design novel antibiotics that kill bad bacteria with alacrity while sparing the good guys. In this way, a round of antibiotics would cure whatever ails you without taking out your whole gut microbiome in the process.
All this is part of a larger movement to use machine learning algorithms in the long, expensive process of drug discovery. Other players in the area are also training AI on the vast possibility space of drug-like compounds. Last fall, one of the leaders in the area, Insilico, was challenged by a partner to see just how fast their method could do the job. The company turned out a new a proof-of-concept drug candidate in only 46 days.
The field is still developing, however, and it has yet to be seen exactly how valuable these approaches will be in practice. Barzilay is optimistic though.
“There is still a question of whether machine-learning tools are really doing something intelligent in healthcare, and how we can develop them to be workhorses in the pharmaceuticals industry,” she said. “This shows how far you can adapt this tool.”
Image Credit: Halicin (top row) prevented the development of antibiotic resistance in E. coli, while ciprofloxacin (bottom row) did not. Collins Lab at MIT 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