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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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#431189 Researchers Develop New Tech to Predict ...
It is one of the top 10 deadliest diseases in the United States, and it cannot be cured or prevented. But new studies are finding ways to diagnose Alzheimer’s disease in its earliest stages, while some of the latest research says technologies like artificial intelligence can detect dementia years before the first symptoms occur.
These advances, in turn, will help bolster clinical trials seeking a cure or therapies to slow or prevent the disease. Catching Alzheimer’s disease or other forms of dementia early in their progression can help ease symptoms in some cases.
“Often neurodegeneration is diagnosed late when massive brain damage has already occurred,” says professor Francis L Martin at the University of Central Lancashire in the UK, in an email to Singularity Hub. “As we know more about the molecular basis of the disease, there is the possibility of clinical interventions that might slow or halt the progress of the disease, i.e., before brain damage. Extending cognitive ability for even a number of years would have huge benefit.”
Blood Diamond
Martin is the principal investigator on a project that has developed a technique to analyze blood samples to diagnose Alzheimer’s disease and distinguish between other forms of dementia.
The researchers used sensor-based technology with a diamond core to analyze about 550 blood samples. They identified specific chemical bonds within the blood after passing light through the diamond core and recording its interaction with the sample. The results were then compared against blood samples from cases of Alzheimer’s disease and other neurodegenerative diseases, along with those from healthy individuals.
“From a small drop of blood, we derive a fingerprint spectrum. That fingerprint spectrum contains numerical data, which can be inputted into a computational algorithm we have developed,” Martin explains. “This algorithm is validated for prediction of unknown samples. From this we determine sensitivity and specificity. Although not perfect, my clinical colleagues reliably tell me our results are far better than anything else they have seen.”
Martin says the breakthrough is the result of more than 10 years developing sensor-based technologies for routine screening, monitoring, or diagnosing neurodegenerative diseases and cancers.
“My vision was to develop something low-cost that could be readily applied in a typical clinical setting to handle thousands of samples potentially per day or per week,” he says, adding that the technology also has applications in environmental science and food security.
The new test can also distinguish accurately between Alzheimer’s disease and other forms of neurodegeneration, such as Lewy body dementia, which is one of the most common causes of dementia after Alzheimer’s.
“To this point, other than at post-mortem, there has been no single approach towards classifying these pathologies,” Martin notes. “MRI scanning is often used but is labor-intensive, costly, difficult to apply to dementia patients, and not a routine point-of-care test.”
Crystal Ball
Canadian researchers at McGill University believe they can predict Alzheimer’s disease up to two years before its onset using big data and artificial intelligence. They developed an algorithm capable of recognizing the signatures of dementia using a single amyloid PET scan of the brain of patients at risk of developing the disease.
Alzheimer’s is caused by the accumulation of two proteins—amyloid beta and tau. The latest research suggests that amyloid beta leads to the buildup of tau, which is responsible for damaging nerve cells and connections between cells called synapses.
The work was recently published in the journal Neurobiology of Aging.
“Despite the availability of biomarkers capable of identifying the proteins causative of Alzheimer’s disease in living individuals, the current technologies cannot predict whether carriers of AD pathology in the brain will progress to dementia,” Sulantha Mathotaarachchi, lead author on the paper and an expert in artificial neural networks, tells Singularity Hub by email.
The algorithm, trained on a population with amnestic mild cognitive impairment observed over 24 months, proved accurate 84.5 percent of the time. Mathotaarachchi says the algorithm can be trained on different populations for different observational periods, meaning the system can grow more comprehensive with more data.
“The more biomarkers we incorporate, the more accurate the prediction could be,” Mathotaarachchi adds. “However, right now, acquiring [the] required amount of training data is the biggest challenge. … In Alzheimer’s disease, it is known that the amyloid protein deposition occurs decades before symptoms onset.”
Unfortunately, the same process occurs in normal aging as well. “The challenge is to identify the abnormal patterns of deposition that lead to the disease later on,” he says
One of the key goals of the project is to improve the research in Alzheimer’s disease by ensuring those patients with the highest probability to develop dementia are enrolled in clinical trials. That will increase the efficiency of clinical programs, according to Mathotaarachchi.
“One of the most important outcomes from our study was the pilot, online, real-time prediction tool,” he says. “This can be used as a framework for patient screening before recruiting for clinical trials. … If a disease-modifying therapy becomes available for patients, a predictive tool might have clinical applications as well, by providing to the physician information regarding clinical progression.”
Pixel by Pixel Prediction
Private industry is also working toward improving science’s predictive powers when it comes to detecting dementia early. One startup called Darmiyan out of San Francisco claims its proprietary software can pick up signals before the onset of Alzheimer’s disease by up to 15 years.
Darmiyan didn’t respond to a request for comment for this article. Venture Beat reported that the company’s MRI-analyzing software “detects cell abnormalities at a microscopic level to reveal what a standard MRI scan cannot” and that the “software measures and highlights subtle microscopic changes in the brain tissue represented in every pixel of the MRI image long before any symptoms arise.”
Darmiyan claims to have a 90 percent accuracy rate and says its software has been vetted by top academic institutions like New York University, Rockefeller University, and Stanford, according to Venture Beat. The startup is awaiting FDA approval to proceed further but is reportedly working with pharmaceutical companies like Amgen, Johnson & Johnson, and Pfizer on pilot programs.
“Our technology enables smarter drug selection in preclinical animal studies, better patient selection for clinical trials, and much better drug-effect monitoring,” Darmiyan cofounder and CEO Padideh Kamali-Zare told Venture Beat.
Conclusions
An estimated 5.5 million Americans have Alzheimer’s, and one in 10 people over age 65 have been diagnosed with the disease. By mid-century, the number of Alzheimer’s patients could rise to 16 million. Health care costs in 2017 alone are estimated to be $259 billion, and by 2050 the annual price tag could be more than $1 trillion.
In sum, it’s a disease that cripples people and the economy.
Researchers are always after more data as they look to improve outcomes, with the hope of one day developing a cure or preventing the onset of neurodegeneration altogether. If interested in seeing this medical research progress, you can help by signing up on the Brain Health Registry to improve the quality of clinical trials.
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#430158 Stanford Robots Load a Hovering Drone, ...
Students in Stanford’s experimental robotics class teach industrial robots new tricks Continue reading
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