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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
#436126 Quantum Computing Gets a Boost From AI ...
Illustration: Greg Mably
Anyone of a certain age who has even a passing interest in computers will remember the remarkable breakthrough that IBM made in 1997 when its Deep Blue chess-playing computer defeated Garry Kasparov, then the world chess champion. Computer scientists passed another such milestone in March 2016, when DeepMind (a subsidiary of Alphabet, Google’s parent company) announced that its AlphaGo program had defeated world-champion player Lee Sedol in the game of Go, a board game that had vexed AI researchers for decades. Recently, DeepMind’s algorithms have also bested human players in the computer games StarCraft IIand Quake Arena III.
Some believe that the cognitive capacities of machines will overtake those of human beings in many spheres within a few decades. Others are more cautious and point out that our inability to understand the source of our own cognitive powers presents a daunting hurdle. How can we make thinking machines if we don’t fully understand our own thought processes?
Citizen science, which enlists masses of people to tackle research problems, holds promise here, in no small part because it can be used effectively to explore the boundary between human and artificial intelligence.
Some citizen-science projects ask the public to collect data from their surroundings (as eButterfly does for butterflies) or to monitor delicate ecosystems (as Eye on the Reef does for Australia’s Great Barrier Reef). Other projects rely on online platforms on which people help to categorize obscure phenomena in the night sky (Zooniverse) or add to the understanding of the structure of proteins (Foldit). Typically, people can contribute to such projects without any prior knowledge of the subject. Their fundamental cognitive skills, like the ability to quickly recognize patterns, are sufficient.
In order to design and develop video games that can allow citizen scientists to tackle scientific problems in a variety of fields, professor and group leader Jacob Sherson founded ScienceAtHome (SAH), at Aarhus University, in Denmark. The group began by considering topics in quantum physics, but today SAH hosts games covering other areas of physics, math, psychology, cognitive science, and behavioral economics. We at SAH search for innovative solutions to real research challenges while providing insight into how people think, both alone and when working in groups.
It is computationally intractable to completely map out a higher-dimensional landscape: It is called the curse of high dimensionality, and it plagues many optimization problems.
We believe that the design of new AI algorithms would benefit greatly from a better understanding of how people solve problems. This surmise has led us to establish the Center for Hybrid Intelligence within SAH, which tries to combine human and artificial intelligence, taking advantage of the particular strengths of each. The center’s focus is on the gamification of scientific research problems and the development of interfaces that allow people to understand and work together with AI.
Our first game, Quantum Moves, was inspired by our group’s research into quantum computers. Such computers can in principle solve certain problems that would take a classical computer billions of years. Quantum computers could challenge current cryptographic protocols, aid in the design of new materials, and give insight into natural processes that require an exact solution of the equations of quantum mechanics—something normal computers are inherently bad at doing.
One candidate system for building such a computer would capture individual atoms by “freezing” them, as it were, in the interference pattern produced when a laser beam is reflected back on itself. The captured atoms can thus be organized like eggs in a carton, forming a periodic crystal of atoms and light. Using these atoms to perform quantum calculations requires that we use tightly focused laser beams, called optical tweezers, to transport the atoms from site to site in the light crystal. This is a tricky business because individual atoms do not behave like particles; instead, they resemble a wavelike liquid governed by the laws of quantum mechanics.
In Quantum Moves, a player manipulates a touch screen or mouse to move a simulated laser tweezer and pick up a trapped atom, represented by a liquidlike substance in a bowl. Then the player must bring the atom back to the tweezer’s initial position while trying to minimize the sloshing of the liquid. Such sloshing would increase the energy of the atom and ultimately introduce errors into the operations of the quantum computer. Therefore, at the end of a move, the liquid should be at a complete standstill.
To understand how people and computers might approach such a task differently, you need to know something about how computerized optimization algorithms work. The countless ways of moving a glass of water without spilling may be regarded as constituting a “solution landscape.” One solution is represented by a single point in that landscape, and the height of that point represents the quality of the solution—how smoothly and quickly the glass of water was moved. This landscape might resemble a mountain range, where the top of each mountain represents a local optimum and where the challenge is to find the highest peak in the range—the global optimum.
Illustration: Greg Mably
Researchers must compromise between searching the landscape for taller mountains (“exploration”) and climbing to the top of the nearest mountain (“exploitation”). Making such a trade-off may seem easy when exploring an actual physical landscape: Merely hike around a bit to get at least the general lay of the land before surveying in greater detail what seems to be the tallest peak. But because each possible way of changing the solution defines a new dimension, a realistic problem can have thousands of dimensions. It is computationally intractable to completely map out such a higher-dimensional landscape. We call this the curse of high dimensionality, and it plagues many optimization problems.
Although algorithms are wonderfully efficient at crawling to the top of a given mountain, finding good ways of searching through the broader landscape poses quite a challenge, one that is at the forefront of AI research into such control problems. The conventional approach is to come up with clever ways of reducing the search space, either through insights generated by researchers or with machine-learning algorithms trained on large data sets.
At SAH, we attacked certain quantum-optimization problems by turning them into a game. Our goal was not to show that people can beat computers in this arena but rather to understand the process of generating insights into such problems. We addressed two core questions: whether allowing players to explore the infinite space of possibilities will help them find good solutions and whether we can learn something by studying their behavior.
Today, more than 250,000 people have played Quantum Moves, and to our surprise, they did in fact search the space of possible moves differently from the algorithm we had put to the task. Specifically, we found that although players could not solve the optimization problem on their own, they were good at searching the broad landscape. The computer algorithms could then take those rough ideas and refine them.
Herbert A. Simon said that “solving a problem simply means representing it so as to make the solution transparent.” Apparently, that’s what our games can do with their novel user interfaces.
Perhaps even more interesting was our discovery that players had two distinct ways of solving the problem, each with a clear physical interpretation. One set of players started by placing the tweezer close to the atom while keeping a barrier between the atom trap and the tweezer. In classical physics, a barrier is an impenetrable obstacle, but because the atom liquid is a quantum-mechanical object, it can tunnel through the barrier into the tweezer, after which the player simply moved the tweezer to the target area. Another set of players moved the tweezer directly into the atom trap, picked up the atom liquid, and brought it back. We called these two strategies the “tunneling” and “shoveling” strategies, respectively.
Such clear strategies are extremely valuable because they are very difficult to obtain directly from an optimization algorithm. Involving humans in the optimization loop can thus help us gain insight into the underlying physical phenomena that are at play, knowledge that may then be transferred to other types of problems.
Quantum Moves raised several obvious issues. First, because generating an exceptional solution required further computer-based optimization, players were unable to get immediate feedback to help them improve their scores, and this often left them feeling frustrated. Second, we had tested this approach on only one scientific challenge with a clear classical analogue, that of the sloshing liquid. We wanted to know whether such gamification could be applied more generally, to a variety of scientific challenges that do not offer such immediately applicable visual analogies.
We address these two concerns in Quantum Moves 2. Here, the player first generates a number of candidate solutions by playing the original game. Then the player chooses which solutions to optimize using a built-in algorithm. As the algorithm improves a player’s solution, it modifies the solution path—the movement of the tweezer—to represent the optimized solution. Guided by this feedback, players can then improve their strategy, come up with a new solution, and iteratively feed it back into this process. This gameplay provides high-level heuristics and adds human intuition to the algorithm. The person and the machine work in tandem—a step toward true hybrid intelligence.
In parallel with the development of Quantum Moves 2, we also studied how people collaboratively solve complex problems. To that end, we opened our atomic physics laboratory to the general public—virtually. We let people from around the world dictate the experiments we would run to see if they would find ways to improve the results we were getting. What results? That’s a little tricky to explain, so we need to pause for a moment and provide a little background on the relevant physics.
One of the essential steps in building the quantum computer along the lines described above is to create the coldest state of matter in the universe, known as a Bose-Einstein condensate. Here millions of atoms oscillate in synchrony to form a wavelike substance, one of the largest purely quantum phenomena known. To create this ultracool state of matter, researchers typically use a combination of laser light and magnetic fields. There is no familiar physical analogy between such a strange state of matter and the phenomena of everyday life.
The result we were seeking in our lab was to create as much of this enigmatic substance as was possible given the equipment available. The sequence of steps to accomplish that was unknown. We hoped that gamification could help to solve this problem, even though it had no classical analogy to present to game players.
Images: ScienceAtHome
Fun and Games: The
Quantum Moves game evolved over time, from a relatively crude early version [top] to its current form [second from top] and then a major revision,
Quantum Moves 2 [third from top].
Skill Lab: Science Detective games [bottom] test players’ cognitive skills.
In October 2016, we released a game that, for two weeks, guided how we created Bose-Einstein condensates in our laboratory. By manipulating simple curves in the game interface, players generated experimental sequences for us to use in producing these condensates—and they did so without needing to know anything about the underlying physics. A player would generate such a solution, and a few minutes later we would run the sequence in our laboratory. The number of ultracold atoms in the resulting Bose-Einstein condensate was measured and fed back to the player as a score. Players could then decide either to try to improve their previous solution or to copy and modify other players’ solutions. About 600 people from all over the world participated, submitting 7,577 solutions in total. Many of them yielded bigger condensates than we had previously produced in the lab.
So this exercise succeeded in achieving our primary goal, but it also allowed us to learn something about human behavior. We learned, for example, that players behave differently based on where they sit on the leaderboard. High-performing players make small changes to their successful solutions (exploitation), while poorly performing players are willing to make more dramatic changes (exploration). As a collective, the players nicely balance exploration and exploitation. How they do so provides valuable inspiration to researchers trying to understand human problem solving in social science as well as to those designing new AI algorithms.
How could mere amateurs outperform experienced experimental physicists? The players certainly weren’t better at physics than the experts—but they could do better because of the way in which the problem was posed. By turning the research challenge into a game, we gave players the chance to explore solutions that had previously required complex programming to study. Indeed, even expert experimentalists improved their solutions dramatically by using this interface.
Insight into why that’s possible can probably be found in the words of the late economics Nobel laureate Herbert A. Simon: “Solving a problem simply means representing it so as to make the solution transparent [PDF].” Apparently, that’s what our games can do with their novel user interfaces. We believe that such interfaces might be a key to using human creativity to solve other complex research problems.
Eventually, we’d like to get a better understanding of why this kind of gamification works as well as it does. A first step would be to collect more data on what the players do while they are playing. But even with massive amounts of data, detecting the subtle patterns underlying human intuition is an overwhelming challenge. To advance, we need a deeper insight into the cognition of the individual players.
As a step forward toward this goal, ScienceAtHome created Skill Lab: Science Detective, a suite of minigames exploring visuospatial reasoning, response inhibition, reaction times, and other basic cognitive skills. Then we compare players’ performance in the games with how well these same people did on established psychological tests of those abilities. The point is to allow players to assess their own cognitive strengths and weaknesses while donating their data for further public research.
In the fall of 2018 we launched a prototype of this large-scale profiling in collaboration with the Danish Broadcasting Corp. Since then more than 20,000 people have participated, and in part because of the publicity granted by the public-service channel, participation has been very evenly distributed across ages and by gender. Such broad appeal is rare in social science, where the test population is typically drawn from a very narrow demographic, such as college students.
Never before has such a large academic experiment in human cognition been conducted. We expect to gain new insights into many things, among them how combinations of cognitive abilities sharpen or decline with age, what characteristics may be used to prescreen for mental illnesses, and how to optimize the building of teams in our work lives.
And so what started as a fun exercise in the weird world of quantum mechanics has now become an exercise in understanding the nuances of what makes us human. While we still seek to understand atoms, we can now aspire to understand people’s minds as well.
This article appears in the November 2019 print issue as “A Man-Machine Mind Meld for Quantum Computing.”
About the Authors
Ottó Elíasson, Carrie Weidner, Janet Rafner, and Shaeema Zaman Ahmed work with the ScienceAtHome project at Aarhus University in Denmark. Continue reading
Posted in Human Robots
#436119 How 3D Printing, Vertical Farming, and ...
Food. What we eat, and how we grow it, will be fundamentally transformed in the next decade.
Already, indoor farming is projected to be a US$40.25 billion industry by 2022, with a compound annual growth rate of 9.65 percent. Meanwhile, the food 3D printing industry is expected to grow at an even higher rate, averaging 50 percent annual growth.
And converging exponential technologies—from materials science to AI-driven digital agriculture—are not slowing down. Today’s breakthroughs will soon allow our planet to boost its food production by nearly 70 percent, using a fraction of the real estate and resources, to feed 9 billion by mid-century.
What you consume, how it was grown, and how it will end up in your stomach will all ride the wave of converging exponentials, revolutionizing the most basic of human needs.
Printing Food
3D printing has already had a profound impact on the manufacturing sector. We are now able to print in hundreds of different materials, making anything from toys to houses to organs. However, we are finally seeing the emergence of 3D printers that can print food itself.
Redefine Meat, an Israeli startup, wants to tackle industrial meat production using 3D printers that can generate meat, no animals required. The printer takes in fat, water, and three different plant protein sources, using these ingredients to print a meat fiber matrix with trapped fat and water, thus mimicking the texture and flavor of real meat.
Slated for release in 2020 at a cost of $100,000, their machines are rapidly demonetizing and will begin by targeting clients in industrial-scale meat production.
Anrich3D aims to take this process a step further, 3D printing meals that are customized to your medical records, heath data from your smart wearables, and patterns detected by your sleep trackers. The company plans to use multiple extruders for multi-material printing, allowing them to dispense each ingredient precisely for nutritionally optimized meals. Currently in an R&D phase at the Nanyang Technological University in Singapore, the company hopes to have its first taste tests in 2020.
These are only a few of the many 3D food printing startups springing into existence. The benefits from such innovations are boundless.
Not only will food 3D printing grant consumers control over the ingredients and mixtures they consume, but it is already beginning to enable new innovations in flavor itself, democratizing far healthier meal options in newly customizable cuisine categories.
Vertical Farming
Vertical farming, whereby food is grown in vertical stacks (in skyscrapers and buildings rather than outside in fields), marks a classic case of converging exponential technologies. Over just the past decade, the technology has surged from a handful of early-stage pilots to a full-grown industry.
Today, the average American meal travels 1,500-2,500 miles to get to your plate. As summed up by Worldwatch Institute researcher Brian Halweil, “We are spending far more energy to get food to the table than the energy we get from eating the food.” Additionally, the longer foods are out of the soil, the less nutritious they become, losing on average 45 percent of their nutrition before being consumed.
Yet beyond cutting down on time and transportation losses, vertical farming eliminates a whole host of issues in food production. Relying on hydroponics and aeroponics, vertical farms allows us to grow crops with 90 percent less water than traditional agriculture—which is critical for our increasingly thirsty planet.
Currently, the largest player around is Bay Area-based Plenty Inc. With over $200 million in funding from Softbank, Plenty is taking a smart tech approach to indoor agriculture. Plants grow on 20-foot-high towers, monitored by tens of thousands of cameras and sensors, optimized by big data and machine learning.
This allows the company to pack 40 plants in the space previously occupied by 1. The process also produces yields 350 times greater than outdoor farmland, using less than 1 percent as much water.
And rather than bespoke veggies for the wealthy few, Plenty’s processes allow them to knock 20-35 percent off the costs of traditional grocery stores. To date, Plenty has their home base in South San Francisco, a 100,000 square-foot farm in Kent, Washington, an indoor farm in the United Arab Emirates, and recently started construction on over 300 farms in China.
Another major player is New Jersey-based Aerofarms, which can now grow two million pounds of leafy greens without sunlight or soil.
To do this, Aerofarms leverages AI-controlled LEDs to provide optimized wavelengths of light for each plant. Using aeroponics, the company delivers nutrients by misting them directly onto the plants’ roots—no soil required. Rather, plants are suspended in a growth mesh fabric made from recycled water bottles. And here too, sensors, cameras, and machine learning govern the entire process.
While 50-80 percent of the cost of vertical farming is human labor, autonomous robotics promises to solve that problem. Enter contenders like Iron Ox, a firm that has developed the Angus robot, capable of moving around plant-growing containers.
The writing is on the wall, and traditional agriculture is fast being turned on its head.
Materials Science
In an era where materials science, nanotechnology, and biotechnology are rapidly becoming the same field of study, key advances are enabling us to create healthier, more nutritious, more efficient, and longer-lasting food.
For starters, we are now able to boost the photosynthetic abilities of plants. Using novel techniques to improve a micro-step in the photosynthesis process chain, researchers at UCLA were able to boost tobacco crop yield by 14-20 percent. Meanwhile, the RIPE Project, backed by Bill Gates and run out of the University of Illinois, has matched and improved those numbers.
And to top things off, The University of Essex was even able to improve tobacco yield by 27-47 percent by increasing the levels of protein involved in photo-respiration.
In yet another win for food-related materials science, Santa Barbara-based Apeel Sciences is further tackling the vexing challenge of food waste. Now approaching commercialization, Apeel uses lipids and glycerolipids found in the peels, seeds, and pulps of all fruits and vegetables to create “cutin”—the fatty substance that composes the skin of fruits and prevents them from rapidly spoiling by trapping moisture.
By then spraying fruits with this generated substance, Apeel can preserve foods 60 percent longer using an odorless, tasteless, colorless organic substance.
And stores across the US are already using this method. By leveraging our advancing knowledge of plants and chemistry, materials science is allowing us to produce more food with far longer-lasting freshness and more nutritious value than ever before.
Convergence
With advances in 3D printing, vertical farming, and materials sciences, we can now make food smarter, more productive, and far more resilient.
By the end of the next decade, you should be able to 3D print a fusion cuisine dish from the comfort of your home, using ingredients harvested from vertical farms, with nutritional value optimized by AI and materials science. However, even this picture doesn’t account for all the rapid changes underway in the food industry.
Join me next week for Part 2 of the Future of Food for a discussion on how food production will be transformed, quite literally, from the bottom up.
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Image Credit: Vanessa Bates Ramirez Continue reading
Posted in Human Robots