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On a dark night, away from city lights, the stars of the Milky Way can seem uncountable. Yet from any given location no more than 4,500 are visible to the naked eye. Meanwhile, our galaxy has 100–400 billion stars, and there are even more galaxies in the universe.
The numbers of the night sky are humbling. And they give us a deep perspective…on drugs.
Yes, this includes wow-the-stars-are-freaking-amazing-tonight drugs, but also the kinds of drugs that make us well again when we’re sick. The number of possible organic compounds with “drug-like” properties dwarfs the number of stars in the universe by over 30 orders of magnitude.
Next to this multiverse of possibility, the chemical configurations scientists have made into actual medicines are like the smattering of stars you’d glimpse downtown.
But for good reason.
Exploring all that potential drug-space is as humanly impossible as exploring all of physical space, and even if we could, most of what we’d find wouldn’t fit our purposes. Still, the idea that wonder drugs must surely lurk amid the multitudes is too tantalizing to ignore.
Which is why, Alex Zhavoronkov said at Singularity University’s Exponential Medicine in San Diego last week, we should use artificial intelligence to do more of the legwork and speed discovery. This, he said, could be one of the next big medical applications for AI.
Dogs, Diagnosis, and Drugs
Zhavoronkov is CEO of Insilico Medicine and CSO of the Biogerontology Research Foundation. Insilico is one of a number of AI startups aiming to accelerate drug discovery with AI.
In recent years, Zhavoronkov said, the now-famous machine learning technique, deep learning, has made progress on a number of fronts. Algorithms that can teach themselves to play games—like DeepMind’s AlphaGo Zero or Carnegie Mellon’s poker playing AI—are perhaps the most headline-grabbing of the bunch. But pattern recognition was the thing that kicked deep learning into overdrive early on, when machine learning algorithms went from struggling to tell dogs and cats apart to outperforming their peers and then their makers in quick succession.
[Watch this video for an AI update from Neil Jacobstein, chair of Artificial Intelligence and Robotics at Singularity University.]
In medicine, deep learning algorithms trained on databases of medical images can spot life-threatening disease with equal or greater accuracy than human professionals. There’s even speculation that AI, if we learn to trust it, could be invaluable in diagnosing disease. And, as Zhavoronkov noted, with more applications and a longer track record that trust is coming.
“Tesla is already putting cars on the street,” Zhavoronkov said. “Three-year, four-year-old technology is already carrying passengers from point A to point B, at 100 miles an hour, and one mistake and you’re dead. But people are trusting their lives to this technology.”
“So, why don’t we do it in pharma?”
Trial and Error and Try Again
AI wouldn’t drive the car in pharmaceutical research. It’d be an assistant that, when paired with a chemist or two, could fast-track discovery by screening more possibilities for better candidates.
There’s plenty of room to make things more efficient, according to Zhavoronkov.
Drug discovery is arduous and expensive. Chemists sift tens of thousands of candidate compounds for the most promising to synthesize. Of these, a handful will go on to further research, fewer will make it to human clinical trials, and a fraction of those will be approved.
The whole process can take many years and cost hundreds of millions of dollars.
This is a big data problem if ever there was one, and deep learning thrives on big data. Early applications have shown their worth unearthing subtle patterns in huge training databases. Although drug-makers already use software to sift compounds, such software requires explicit rules written by chemists. AI’s allure is its ability to learn and improve on its own.
“There are two strategies for AI-driven innovation in pharma to ensure you get better molecules and much faster approvals,” Zhavoronkov said. “One is looking for the needle in the haystack, and another one is creating a new needle.”
To find the needle in the haystack, algorithms are trained on large databases of molecules. Then they go looking for molecules with attractive properties. But creating a new needle? That’s a possibility enabled by the generative adversarial networks Zhavoronkov specializes in.
Such algorithms pit two neural networks against each other. One generates meaningful output while the other judges whether this output is true or false, Zhavoronkov said. Together, the networks generate new objects like text, images, or in this case, molecular structures.
“We started employing this particular technology to make deep neural networks imagine new molecules, to make it perfect right from the start. So, to come up with really perfect needles,” Zhavoronkov said. “[You] can essentially go to this [generative adversarial network] and ask it to create molecules that inhibit protein X at concentration Y, with the highest viability, specific characteristics, and minimal side effects.”
Zhavoronkov believes AI can find or fabricate more needles from the array of molecular possibilities, freeing human chemists to focus on synthesizing only the most promising. If it works, he hopes we can increase hits, minimize misses, and generally speed the process up.
Proof’s in the Pudding
Insilico isn’t alone on its drug-discovery quest, nor is it a brand new area of interest.
Last year, a Harvard group published a paper on an AI that similarly suggests drug candidates. The software trained on 250,000 drug-like molecules and used its experience to generate new molecules that blended existing drugs and made suggestions based on desired properties.
An MIT Technology Review article on the subject highlighted a few of the challenges such systems may still face. The results returned aren’t always meaningful or easy to synthesize in the lab, and the quality of these results, as always, is only as good as the data dined upon.
Stanford chemistry professor and Andreesen Horowitz partner, Vijay Pande, said that images, speech, and text—three of the areas deep learning’s made quick strides in—have better, cleaner data. Chemical data, on the other hand, is still being optimized for deep learning. Also, while there are public databases, much data still lives behind closed doors at private companies.
To overcome the challenges and prove their worth, Zhavoronkov said, his company is very focused on validating the tech. But this year, skepticism in the pharmaceutical industry seems to be easing into interest and investment.
AI drug discovery startup Exscientia inked a deal with Sanofi for $280 million and GlaxoSmithKline for $42 million. Insilico is also partnering with GlaxoSmithKline, and Numerate is working with Takeda Pharmaceutical. Even Google may jump in. According to an article in Nature outlining the field, the firm’s deep learning project, Google Brain, is growing its biosciences team, and industry watchers wouldn’t be surprised to see them target drug discovery.
With AI and the hardware running it advancing rapidly, the greatest potential may yet be ahead. Perhaps, one day, all 1060 molecules in drug-space will be at our disposal. “You should take all the data you have, build n new models, and search as much of that 1060 as possible” before every decision you make, Brandon Allgood, CTO at Numerate, told Nature.
Today’s projects need to live up to their promises, of course, but Zhavoronkov believes AI will have a big impact in the coming years, and now’s the time to integrate it. “If you are working for a pharma company, and you’re still thinking, ‘Okay, where is the proof?’ Once there is a proof, and once you can see it to believe it—it’s going to be too late,” he said.
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Ask any neuroscientist to draw you a neuron, and it’ll probably look something like a star with two tails: one stubby with extensive tree-like branches, the other willowy, lengthy and dotted with spindly spikes.
While a decent abstraction, this cartoonish image hides the uncomfortable truth that scientists still don’t know much about what many neurons actually look like, not to mention the extent of their connections.
But without untangling the jumbled mess of neural wires that zigzag across the brain, scientists are stumped in trying to answer one of the most fundamental mysteries of the brain: how individual neuronal threads carry and assemble information, which forms the basis of our thoughts, memories, consciousness, and self.
What if there was a way to virtually trace and explore the brain’s serpentine fibers, much like the way Google Maps allows us to navigate the concrete tangles of our cities’ highways?
Thanks to an interdisciplinary team at Janelia Research Campus, we’re on our way. Meet MouseLight, the most extensive map of the mouse brain ever attempted. The ongoing project has an ambitious goal: reconstructing thousands—if not more—of the mouse’s 70 million neurons into a 3D map. (You can play with it here!)
With map in hand, neuroscientists around the world can begin to answer how neural circuits are organized in the brain, and how information flows from one neuron to another across brain regions and hemispheres.
The first release, presented Monday at the Society for Neuroscience Annual Conference in Washington, DC, contains information about the shape and sizes of 300 neurons.
And that’s just the beginning.
“MouseLight’s new dataset is the largest of its kind,” says Dr. Wyatt Korff, director of project teams. “It’s going to change the textbook view of neurons.”
MouseLight is hardly the first rodent brain atlasing project.
The Mouse Brain Connectivity Atlas at the Allen Institute for Brain Science in Seattle tracks neuron activity across small circuits in an effort to trace a mouse’s connectome—a complete atlas of how the firing of one neuron links to the next.
MICrONS (Machine Intelligence from Cortical Networks), the $100 million government-funded “moonshot” hopes to distill brain computation into algorithms for more powerful artificial intelligence. Its first step? Brain mapping.
What makes MouseLight stand out is its scope and level of detail.
MICrONS, for example, is focused on dissecting a cubic millimeter of the mouse visual processing center. In contrast, MouseLight involves tracing individual neurons across the entire brain.
And while connectomics outlines the major connections between brain regions, the birds-eye view entirely misses the intricacies of each individual neuron. This is where MouseLight steps in.
Slice and Dice
With a width only a fraction of a human hair, neuron projections are hard to capture in their native state. Tug or squeeze the brain too hard, and the long, delicate branches distort or even shred into bits.
In fact, previous attempts at trying to reconstruct neurons at this level of detail topped out at just a dozen, stymied by technological hiccups and sky-high costs.
A few years ago, the MouseLight team set out to automate the entire process, with a few time-saving tweaks. Here’s how it works.
After injecting a mouse with a virus that causes a handful of neurons to produce a green-glowing protein, the team treated the brain with a sugar alcohol solution. This step “clears” the brain, transforming the beige-colored organ to translucent, making it easier for light to penetrate and boosting the signal-to-background noise ratio. The brain is then glued onto a small pedestal and ready for imaging.
Building upon an established method called “two-photon microscopy,” the team then tweaked several parameters to reduce imaging time from days (or weeks) down to a fraction of that. Endearingly known as “2P” by the experts, this type of laser microscope zaps the tissue with just enough photos to light up a single plane without damaging the tissue—sharper plane, better focus, crisper image.
After taking an image, the setup activates its vibrating razor and shaves off the imaged section of the brain—a waspy slice about 200 micrometers thick. The process is repeated until the whole brain is imaged.
This setup increased imaging speed by 16 to 48 times faster than conventional microscopy, writes team leader Dr. Jayaram Chandrashekar, who published a version of the method early last year in eLife.
The resulting images strikingly highlight every crook and cranny of a neuronal branch, popping out against a pitch-black background. But pretty pictures come at a hefty data cost: each image takes up a whopping 20 terabytes of data—roughly the storage space of 4,000 DVDs, or 10,000 hours of movies.
Stitching individual images back into 3D is an image-processing nightmare. The MouseLight team used a combination of computational power and human prowess to complete this final step.
The reconstructed images are handed off to a mighty team of seven trained neuron trackers. With the help of tracing algorithms developed in-house and a keen eye, each member can track roughly a neuron a day—significantly less time than the week or so previously needed.
A Numbers Game
Even with just 300 fully reconstructed neurons, MouseLight has already revealed new secrets of the brain.
While it’s widely accepted that axons, the neurons’ outgoing projection, can span the entire length of the brain, these extra-long connections were considered relatively rare. (In fact, one previously discovered “giant neuron” was thought to link to consciousness because of its expansive connections).
Images captured from two-photon microscopy show an axon and dendrites protruding from a neuron’s cell body (sphere in center). Image Credit: Janelia Research Center, MouseLight project team
MouseLight blows that theory out of the water.
The data clearly shows that “giant neurons” are far more common than previously thought. For example, four neurons normally associated with taste had wiry branches that stretched all the way into brain areas that control movement and process touch.
“We knew that different regions of the brain talked to each other, but seeing it in 3D is different,” says Dr. Eve Marder at Brandeis University.
“The results are so stunning because they give you a really clear view of how the whole brain is connected.”
With a tested and true system in place, the team is now aiming to add 700 neurons to their collection within a year.
But appearance is only part of the story.
We can’t tell everything about a person simply by how they look. Neurons are the same: scientists can only infer so much about a neuron’s function by looking at their shape and positions. The team also hopes to profile the gene expression patterns of each neuron, which could provide more hints to their roles in the brain.
MouseLight essentially dissects the neural infrastructure that allows information traffic to flow through the brain. These anatomical highways are just the foundation. Just like Google Maps, roads form only the critical first layer of the map. Street view, traffic information and other add-ons come later for a complete look at cities in flux.
The same will happen for understanding our ever-changing brain.
Image Credit: Janelia Research Campus, MouseLight project team Continue reading
Swarms of drones buzz overhead, while robotic vehicles crawl across the landscape. Orbiting satellites snap high-resolution images of the scene far below. Not one human being can be seen in the pre-dawn glow spreading across the land.
This isn’t some post-apocalyptic vision of the future à la The Terminator. This is a snapshot of the farm of the future. Every phase of the operation—from seed to harvest—may someday be automated, without the need to ever get one’s fingernails dirty.
In fact, it’s science fiction already being engineered into reality. Today, robots empowered with artificial intelligence can zap weeds with preternatural precision, while autonomous tractors move with tireless efficiency across the farmland. Satellites can assess crop health from outer space, providing gobs of data to help produce the sort of business intelligence once accessible only to Fortune 500 companies.
“Precision agriculture is on the brink of a new phase of development involving smart machines that can operate by themselves, which will allow production agriculture to become significantly more efficient. Precision agriculture is becoming robotic agriculture,” said professor Simon Blackmore last year during a conference in Asia on the latest developments in robotic agriculture. Blackmore is head of engineering at Harper Adams University and head of the National Centre for Precision Farming in the UK.
It’s Blackmore’s university that recently showcased what may someday be possible. The project, dubbed Hands Free Hectare and led by researchers from Harper Adams and private industry, farmed one hectare (about 2.5 acres) of spring barley without one person ever setting foot in the field.
The team re-purposed, re-wired and roboticized farm equipment ranging from a Japanese tractor to a 25-year-old combine. Drones served as scouts to survey the operation and collect samples to help the team monitor the progress of the barley. At the end of the season, the robo farmers harvested about 4.5 tons of barley at a price tag of £200,000.
“This project aimed to prove that there’s no technological reason why a field can’t be farmed without humans working the land directly now, and we’ve done that,” said Martin Abell, mechatronics researcher for Precision Decisions, which partnered with Harper Adams, in a press release.
I, Robot Farmer
The Harper Adams experiment is the latest example of how machines are disrupting the agricultural industry. Around the same time that the Hands Free Hectare combine was harvesting barley, Deere & Company announced it would acquire a startup called Blue River Technology for a reported $305 million.
Blue River has developed a “see-and-spray” system that combines computer vision and artificial intelligence to discriminate between crops and weeds. It hits the former with fertilizer and blasts the latter with herbicides with such precision that it can eliminate 90 percent of the chemicals used in conventional agriculture.
It’s not just farmland that’s getting a helping hand from robots. A California company called Abundant Robotics, spun out of the nonprofit research institute SRI International, is developing robots capable of picking apples with vacuum-like arms that suck the fruit straight off the trees in the orchards.
“Traditional robots were designed to perform very specific tasks over and over again. But the robots that will be used in food and agricultural applications will have to be much more flexible than what we’ve seen in automotive manufacturing plants in order to deal with natural variation in food products or the outdoor environment,” Dan Harburg, an associate at venture capital firm Anterra Capital who previously worked at a Massachusetts-based startup making a robotic arm capable of grabbing fruit, told AgFunder News.
“This means ag-focused robotics startups have to design systems from the ground up, which can take time and money, and their robots have to be able to complete multiple tasks to avoid sitting on the shelf for a significant portion of the year,” he noted.
Eyes in the Sky
It will take more than an army of robotic tractors to grow a successful crop. The farm of the future will rely on drones, satellites, and other airborne instruments to provide data about their crops on the ground.
Companies like Descartes Labs, for instance, employ machine learning to analyze satellite imagery to forecast soy and corn yields. The Los Alamos, New Mexico startup collects five terabytes of data every day from multiple satellite constellations, including NASA and the European Space Agency. Combined with weather readings and other real-time inputs, Descartes Labs can predict cornfield yields with 99 percent accuracy. Its AI platform can even assess crop health from infrared readings.
The US agency DARPA recently granted Descartes Labs $1.5 million to monitor and analyze wheat yields in the Middle East and Africa. The idea is that accurate forecasts may help identify regions at risk of crop failure, which could lead to famine and political unrest. Another company called TellusLabs out of Somerville, Massachusetts also employs machine learning algorithms to predict corn and soy yields with similar accuracy from satellite imagery.
Farmers don’t have to reach orbit to get insights on their cropland. A startup in Oakland, Ceres Imaging, produces high-resolution imagery from multispectral cameras flown across fields aboard small planes. The snapshots capture the landscape at different wavelengths, identifying insights into problems like water stress, as well as providing estimates of chlorophyll and nitrogen levels. The geo-tagged images mean farmers can easily locate areas that need to be addressed.
Growing From the Inside
Even the best intelligence—whether from drones, satellites, or machine learning algorithms—will be challenged to predict the unpredictable issues posed by climate change. That’s one reason more and more companies are betting the farm on what’s called controlled environment agriculture. Today, that doesn’t just mean fancy greenhouses, but everything from warehouse-sized, automated vertical farms to grow rooms run by robots, located not in the emptiness of Kansas or Nebraska but smack dab in the middle of the main streets of America.
Proponents of these new concepts argue these high-tech indoor farms can produce much higher yields while drastically reducing water usage and synthetic inputs like fertilizer and herbicides.
Iron Ox, out of San Francisco, is developing one-acre urban greenhouses that will be operated by robots and reportedly capable of producing the equivalent of 30 acres of farmland. Powered by artificial intelligence, a team of three robots will run the entire operation of planting, nurturing, and harvesting the crops.
Vertical farming startup Plenty, also based in San Francisco, uses AI to automate its operations, and got a $200 million vote of confidence from the SoftBank Vision Fund earlier this year. The company claims its system uses only 1 percent of the water consumed in conventional agriculture while producing 350 times as much produce. Plenty is part of a new crop of urban-oriented farms, including Bowery Farming and AeroFarms.
“What I can envision is locating a larger scale indoor farm in the economically disadvantaged food desert, in order to stimulate a broader economic impact that could create jobs and generate income for that area,” said Dr. Gary Stutte, an expert in space agriculture and controlled environment agriculture, in an interview with AgFunder News. “The indoor agriculture model is adaptable to becoming an engine for economic growth and food security in both rural and urban food deserts.”
Still, the model is not without its own challenges and criticisms. Most of what these farms can produce falls into the “leafy greens” category and often comes with a premium price, which seems antithetical to the proposed mission of creating oases in the food deserts of cities. While water usage may be minimized, the electricity required to power the operation, especially the LEDs (which played a huge part in revolutionizing indoor agriculture), are not cheap.
Still, all of these advances, from robo farmers to automated greenhouses, may need to be part of a future where nearly 10 billion people will inhabit the planet by 2050. An oft-quoted statistic from the Food and Agriculture Organization of the United Nations says the world must boost food production by 70 percent to meet the needs of the population. Technology may not save the world, but it will help feed it.
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