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#431559 Drug Discovery AI to Scour a Universe of ...

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.
Image Credit: Klavdiya Krinichnaya / Shutterstock.com Continue reading

Posted in Human Robots

#431424 A ‘Google Maps’ for the Mouse Brain ...

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.”

http://mouselight.janelia.org/assets/carousel/ML-Movie.mp4
Brain Atlas
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

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#431203 Could We Build a Blade Runner-Style ...

The new Blade Runner sequel will return us to a world where sophisticated androids made with organic body parts can match the strength and emotions of their human creators. As someone who builds biologically inspired robots, I’m interested in whether our own technology will ever come close to matching the “replicants” of Blade Runner 2049.
The reality is that we’re a very long way from building robots with human-like abilities. But advances in so-called soft robotics show a promising way forward for technology that could be a new basis for the androids of the future.
From a scientific point of view, the real challenge is replicating the complexity of the human body. Each one of us is made up of millions and millions of cells, and we have no clue how we can build such a complex machine that is indistinguishable from us humans. The most complex machines today, for example the world’s largest airliner, the Airbus A380, are composed of millions of parts. But in order to match the complexity level of humans, we would need to scale this complexity up about a million times.
There are currently three different ways that engineering is making the border between humans and robots more ambiguous. Unfortunately, these approaches are only starting points and are not yet even close to the world of Blade Runner.
There are human-like robots built from scratch by assembling artificial sensors, motors, and computers to resemble the human body and motion. However, extending the current human-like robot would not bring Blade Runner-style androids closer to humans, because every artificial component, such as sensors and motors, are still hopelessly primitive compared to their biological counterparts.
There is also cyborg technology, where the human body is enhanced with machines such as robotic limbs and wearable and implantable devices. This technology is similarly very far away from matching our own body parts.
Finally, there is the technology of genetic manipulation, where an organism’s genetic code is altered to modify that organism’s body. Although we have been able to identify and manipulate individual genes, we still have a limited understanding of how an entire human emerges from genetic code. As such, we don’t know the degree to which we can actually program code to design everything we wish.
Soft robotics: a way forward?
But we might be able to move robotics closer to the world of Blade Runner by pursuing other technologies and, in particular, by turning to nature for inspiration. The field of soft robotics is a good example. In the last decade or so, robotics researchers have been making considerable efforts to make robots soft, deformable, squishable, and flexible.
This technology is inspired by the fact that 90% of the human body is made from soft substances such as skin, hair, and tissues. This is because most of the fundamental functions in our body rely on soft parts that can change shape, from the heart and lungs pumping fluid around our body to the eye lenses generating signals from their movement. Cells even change shape to trigger division, self-healing and, ultimately, the evolution of the body.
The softness of our bodies is the origin of all their functionality needed to stay alive. So being able to build soft machines would at least bring us a step closer to the robotic world of Blade Runner. Some of the recent technological advances include artificial hearts made out of soft functional materials that are pumping fluid through deformation. Similarly, soft, wearable gloves can help make hand grasping stronger. And “epidermal electronics” has enabled us to tattoo electronic circuits onto our biological skins.
Softness is the keyword that brings humans and technologies closer together. Sensors, motors, and computers are all of a sudden integrated into human bodies once they became soft, and the border between us and external devices becomes ambiguous, just like soft contact lenses became part of our eyes.
Nevertheless, the hardest challenge is how to make individual parts of a soft robot body physically adaptable by self-healing, growing, and differentiating. After all, every part of a living organism is also alive in biological systems in order to make our bodies totally adaptable and evolvable, the function of which could make machines totally indistinguishable from ourselves.
It is impossible to predict when the robotic world of Blade Runner might arrive, and if it does, it will probably be very far in the future. But as long as the desire to build machines indistinguishable from humans is there, the current trends of robotic revolution could make it possible to achieve that dream.
This article was originally published on The Conversation. Read the original article.
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#431171 SceneScan: Real-Time 3D Depth Sensing ...

Nerian Introduces a High-Performance Successor for the Proven SP1 System
Stereo vision, which is the three-dimensional perception of our environment with two sensors likeour eyes, is a well-known technology. As a passive method – there is no need to emit light in thevisible or invisible spectral range – this technology can open up new possibilities for three dimensional perception, even under difficult conditions.
But as often, the devil is in the details: for most applications, the software implementation withstandard PCs, but also with graphics processors, is too slow. Another complicating factor is thatthese hardware platforms are expensive and not energy-efficient. The solution is to instead usespecialized hardware for image processing. A programmable logic device – a so-called FPGA – cangreatly accelerate the image processing.
As a technology leader, Nerian Vision Technologies has been following this path successfully forthe past two years with the SP1 stereo vision system, which has enabled completely newapplications in the fields of robotics, automation technology, medical technology, autonomousdriving and other domains. Now the company introduces two successors:
SceneScan and SceneScan Pro. Real eye-catchers in a double sense: stereo vision in an elegant design!But more important is, of course, the significantly improved inner workings of the two new modelsin comparison to their predecessor. The new hardware allows processing rates of up to 100 framesper second at resolutions of up to 3 megapixels, which leaves the SP1 far behind:
Photo Credit: Nerian Vision Technologies – www.nerian.com

The table illustrates the difference: while SceneScan Pro has the highest possible computing powerand is designed for the most demanding applications, SceneScan has been cost-reduced forapplications with lower requirements. The customer can thus optimize his embedded vision solution both in terms of costs and technology.
The new duo is completed by Nerian’s proven Karmin stereo cameras. Of course, industrialUSB3Vision cameras by other manufacturers are also supported.This combination not only supports the above-mentioned applications even better, but alsofacilitates completely new and innovative ones. If required, customer-specific adaptations are alsopossible.
ContactNerian Vision TechnologiesOwner: Dr. Konstantin SchauweckerGotenstr. 970771 Leinfelden-EchterdingenGermanyPhone: +49 711 / 2195 9414Email: service@nerian.comWebsite: http://nerian.com
Press Release Authored By: Nerian Vision Technologies
Photo Credit: Nerian Vision Technologies – www.nerian.com
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#430761 How Robots Are Getting Better at Making ...

The multiverse of science fiction is populated by robots that are indistinguishable from humans. They are usually smarter, faster, and stronger than us. They seem capable of doing any job imaginable, from piloting a starship and battling alien invaders to taking out the trash and cooking a gourmet meal.
The reality, of course, is far from fantasy. Aside from industrial settings, robots have yet to meet The Jetsons. The robots the public are exposed to seem little more than over-sized plastic toys, pre-programmed to perform a set of tasks without the ability to interact meaningfully with their environment or their creators.
To paraphrase PayPal co-founder and tech entrepreneur Peter Thiel, we wanted cool robots, instead we got 140 characters and Flippy the burger bot. But scientists are making progress to empower robots with the ability to see and respond to their surroundings just like humans.
Some of the latest developments in that arena were presented this month at the annual Robotics: Science and Systems Conference in Cambridge, Massachusetts. The papers drilled down into topics that ranged from how to make robots more conversational and help them understand language ambiguities to helping them see and navigate through complex spaces.
Improved Vision
Ben Burchfiel, a graduate student at Duke University, and his thesis advisor George Konidaris, an assistant professor of computer science at Brown University, developed an algorithm to enable machines to see the world more like humans.
In the paper, Burchfiel and Konidaris demonstrate how they can teach robots to identify and possibly manipulate three-dimensional objects even when they might be obscured or sitting in unfamiliar positions, such as a teapot that has been tipped over.
The researchers trained their algorithm by feeding it 3D scans of about 4,000 common household items such as beds, chairs, tables, and even toilets. They then tested its ability to identify about 900 new 3D objects just from a bird’s eye view. The algorithm made the right guess 75 percent of the time versus a success rate of about 50 percent for other computer vision techniques.
In an email interview with Singularity Hub, Burchfiel notes his research is not the first to train machines on 3D object classification. How their approach differs is that they confine the space in which the robot learns to classify the objects.
“Imagine the space of all possible objects,” Burchfiel explains. “That is to say, imagine you had tiny Legos, and I told you [that] you could stick them together any way you wanted, just build me an object. You have a huge number of objects you could make!”
The infinite possibilities could result in an object no human or machine might recognize.
To address that problem, the researchers had their algorithm find a more restricted space that would host the objects it wants to classify. “By working in this restricted space—mathematically we call it a subspace—we greatly simplify our task of classification. It is the finding of this space that sets us apart from previous approaches.”
Following Directions
Meanwhile, a pair of undergraduate students at Brown University figured out a way to teach robots to understand directions better, even at varying degrees of abstraction.
The research, led by Dilip Arumugam and Siddharth Karamcheti, addressed how to train a robot to understand nuances of natural language and then follow instructions correctly and efficiently.
“The problem is that commands can have different levels of abstraction, and that can cause a robot to plan its actions inefficiently or fail to complete the task at all,” says Arumugam in a press release.
In this project, the young researchers crowdsourced instructions for moving a virtual robot through an online domain. The space consisted of several rooms and a chair, which the robot was told to manipulate from one place to another. The volunteers gave various commands to the robot, ranging from general (“take the chair to the blue room”) to step-by-step instructions.
The researchers then used the database of spoken instructions to teach their system to understand the kinds of words used in different levels of language. The machine learned to not only follow instructions but to recognize the level of abstraction. That was key to kickstart its problem-solving abilities to tackle the job in the most appropriate way.
The research eventually moved from virtual pixels to a real place, using a Roomba-like robot that was able to respond to instructions within one second 90 percent of the time. Conversely, when unable to identify the specificity of the task, it took the robot 20 or more seconds to plan a task about 50 percent of the time.
One application of this new machine-learning technique referenced in the paper is a robot worker in a warehouse setting, but there are many fields that could benefit from a more versatile machine capable of moving seamlessly between small-scale operations and generalized tasks.
“Other areas that could possibly benefit from such a system include things from autonomous vehicles… to assistive robotics, all the way to medical robotics,” says Karamcheti, responding to a question by email from Singularity Hub.
More to Come
These achievements are yet another step toward creating robots that see, listen, and act more like humans. But don’t expect Disney to build a real-life Westworld next to Toon Town anytime soon.
“I think we’re a long way off from human-level communication,” Karamcheti says. “There are so many problems preventing our learning models from getting to that point, from seemingly simple questions like how to deal with words never seen before, to harder, more complicated questions like how to resolve the ambiguities inherent in language, including idiomatic or metaphorical speech.”
Even relatively verbose chatbots can run out of things to say, Karamcheti notes, as the conversation becomes more complex.
The same goes for human vision, according to Burchfiel.
While deep learning techniques have dramatically improved pattern matching—Google can find just about any picture of a cat—there’s more to human eyesight than, well, meets the eye.
“There are two big areas where I think perception has a long way to go: inductive bias and formal reasoning,” Burchfiel says.
The former is essentially all of the contextual knowledge people use to help them reason, he explains. Burchfiel uses the example of a puddle in the street. People are conditioned or biased to assume it’s a puddle of water rather than a patch of glass, for instance.
“This sort of bias is why we see faces in clouds; we have strong inductive bias helping us identify faces,” he says. “While it sounds simple at first, it powers much of what we do. Humans have a very intuitive understanding of what they expect to see, [and] it makes perception much easier.”
Formal reasoning is equally important. A machine can use deep learning, in Burchfiel’s example, to figure out the direction any river flows once it understands that water runs downhill. But it’s not yet capable of applying the sort of human reasoning that would allow us to transfer that knowledge to an alien setting, such as figuring out how water moves through a plumbing system on Mars.
“Much work was done in decades past on this sort of formal reasoning… but we have yet to figure out how to merge it with standard machine-learning methods to create a seamless system that is useful in the actual physical world.”
Robots still have a lot to learn about being human, which should make us feel good that we’re still by far the most complex machines on the planet.
Image Credit: Alex Knight via Unsplash Continue reading

Posted in Human Robots