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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.
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Posted in Human Robots
#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
#430743 Teaching Machines to Understand, and ...
We humans are swamped with text. It’s not just news and other timely information: Regular people are drowning in legal documents. The problem is so bad we mostly ignore it. Every time a person uses a store’s loyalty rewards card or connects to an online service, his or her activities are governed by the equivalent of hundreds of pages of legalese. Most people pay no attention to these massive documents, often labeled “terms of service,” “user agreement,” or “privacy policy.”
These are just part of a much wider societal problem of information overload. There is so much data stored—exabytes of it, as much stored as has ever been spoken by people in all of human history—that it’s humanly impossible to read and interpret everything. Often, we narrow down our pool of information by choosing particular topics or issues to pay attention to. But it’s important to actually know the meaning and contents of the legal documents that govern how our data is stored and who can see it.
As computer science researchers, we are working on ways artificial intelligence algorithms could digest these massive texts and extract their meaning, presenting it in terms regular people can understand.
Can computers understand text?
Computers store data as 0s and 1s—data that cannot be directly understood by humans. They interpret these data as instructions for displaying text, sound, images, or videos that are meaningful to people. But can computers actually understand the language, not only presenting the words but also their meaning?
One way to find out is to ask computers to summarize their knowledge in ways that people can understand and find useful. It would be best if AI systems could process text quickly enough to help people make decisions as they are needed—for example, when you’re signing up for a new online service and are asked to agree with the site’s privacy policy.
What if a computerized assistant could digest all that legal jargon in a few seconds and highlight key points? Perhaps a user could even tell the automated assistant to pay particular attention to certain issues, like when an email address is shared, or whether search engines can index personal posts. Companies could use this capability, too, to analyze contracts or other lengthy documents.
To do this sort of work, we need to combine a range of AI technologies, including machine learning algorithms that take in large amounts of data and independently identify connections among them; knowledge representation techniques to express and interpret facts and rules about the world; speech recognition systems to convert spoken language to text; and human language comprehension programs that process the text and its context to determine what the user is telling the system to do.
Examining privacy policies
A modern internet-enabled life today more or less requires trusting for-profit companies with private information (like physical and email addresses, credit card numbers and bank account details) and personal data (photos and videos, email messages and location information).
These companies’ cloud-based systems typically keep multiple copies of users’ data as part of backup plans to prevent service outages. That means there are more potential targets—each data center must be securely protected both physically and electronically. Of course, internet companies recognize customers’ concerns and employ security teams to protect users’ data. But the specific and detailed legal obligations they undertake to do that are found in their impenetrable privacy policies. No regular human—and perhaps even no single attorney—can truly understand them.
In our study, we ask computers to summarize the terms and conditions regular users say they agree to when they click “Accept” or “Agree” buttons for online services. We downloaded the publicly available privacy policies of various internet companies, including Amazon AWS, Facebook, Google, HP, Oracle, PayPal, Salesforce, Snapchat, Twitter, and WhatsApp.
Summarizing meaning
Our software examines the text and uses information extraction techniques to identify key information specifying the legal rights, obligations and prohibitions identified in the document. It also uses linguistic analysis to identify whether each rule applies to the service provider, the user or a third-party entity, such as advertisers and marketing companies. Then it presents that information in clear, direct, human-readable statements.
For example, our system identified one aspect of Amazon’s privacy policy as telling a user, “You can choose not to provide certain information, but then you might not be able to take advantage of many of our features.” Another aspect of that policy was described as “We may also collect technical information to help us identify your device for fraud prevention and diagnostic purposes.”
We also found, with the help of the summarizing system, that privacy policies often include rules for third parties—companies that aren’t the service provider or the user—that people might not even know are involved in data storage and retrieval.
The largest number of rules in privacy policies—43 percent—apply to the company providing the service. Just under a quarter of the rules—24 percent—create obligations for users and customers. The rest of the rules govern behavior by third-party services or corporate partners, or could not be categorized by our system.
The next time you click the “I Agree” button, be aware that you may be agreeing to share your data with other hidden companies who will be analyzing it.
We are continuing to improve our ability to succinctly and accurately summarize complex privacy policy documents in ways that people can understand and use to access the risks associated with using a service.
This article was originally published on The Conversation. Read the original article. Continue reading
Posted in Human Robots