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#437872 AlphaFold Proves That AI Can Crack ...
Any successful implementation of artificial intelligence hinges on asking the right questions in the right way. That’s what the British AI company DeepMind (a subsidiary of Alphabet) accomplished when it used its neural network to tackle one of biology’s grand challenges, the protein-folding problem. Its neural net, known as AlphaFold, was able to predict the 3D structures of proteins based on their amino acid sequences with unprecedented accuracy.
AlphaFold’s predictions at the 14th Critical Assessment of protein Structure Prediction (CASP14) were accurate to within an atom’s width for most of the proteins. The competition consisted of blindly predicting the structure of proteins that have only recently been experimentally determined—with some still awaiting determination.
Called the building blocks of life, proteins consist of 20 different amino acids in various combinations and sequences. A protein's biological function is tied to its 3D structure. Therefore, knowledge of the final folded shape is essential to understanding how a specific protein works—such as how they interact with other biomolecules, how they may be controlled or modified, and so on. “Being able to predict structure from sequence is the first real step towards protein design,” says Janet M. Thornton, director emeritus of the European Bioinformatics Institute. It also has enormous benefits in understanding disease-causing pathogens. For instance, at the moment only about 18 of the 26 proteins in the SARS-CoV-2 virus are known.
Predicting a protein’s 3D structure is a computational nightmare. In 1969 Cyrus Levinthal estimated that there are 10300 possible conformational combinations for a single protein, which would take longer than the age of the known universe to evaluate by brute force calculation. AlphaFold can do it in a few days.
As scientific breakthroughs go, AlphaFold’s discovery is right up there with the likes of James Watson and Francis Crick’s DNA double-helix model, or, more recently, Jennifer Doudna and Emmanuelle Charpentier’s CRISPR-Cas9 genome editing technique.
How did a team that just a few years ago was teaching an AI to master a 3,000-year-old game end up training one to answer a question plaguing biologists for five decades? That, says Briana Brownell, data scientist and founder of the AI company PureStrategy, is the beauty of artificial intelligence: The same kind of algorithm can be used for very different things.
“Whenever you have a problem that you want to solve with AI,” she says, “you need to figure out how to get the right data into the model—and then the right sort of output that you can translate back into the real world.”
DeepMind’s success, she says, wasn’t so much a function of picking the right neural nets but rather “how they set up the problem in a sophisticated enough way that the neural network-based modeling [could] actually answer the question.”
AlphaFold showed promise in 2018, when DeepMind introduced a previous iteration of their AI at CASP13, achieving the highest accuracy among all participants. The team had trained its to model target shapes from scratch, without using previously solved proteins as templates.
For 2020 they deployed new deep learning architectures into the AI, using an attention-based model that was trained end-to-end. Attention in a deep learning network refers to a component that manages and quantifies the interdependence between the input and output elements, as well as between the input elements themselves.
The system was trained on public datasets of the approximately 170,000 known experimental protein structures in addition to databases with protein sequences of unknown structures.
“If you look at the difference between their entry two years ago and this one, the structure of the AI system was different,” says Brownell. “This time, they’ve figured out how to translate the real world into data … [and] created an output that could be translated back into the real world.”
Like any AI system, AlphaFold may need to contend with biases in the training data. For instance, Brownell says, AlphaFold is using available information about protein structure that has been measured in other ways. However, there are also many proteins with as yet unknown 3D structures. Therefore, she says, a bias could conceivably creep in toward those kinds of proteins that we have more structural data for.
Thornton says it’s difficult to predict how long it will take for AlphaFold’s breakthrough to translate into real-world applications.
“We only have experimental structures for about 10 per cent of the 20,000 proteins [in] the human body,” she says. “A powerful AI model could unveil the structures of the other 90 per cent.”
Apart from increasing our understanding of human biology and health, she adds, “it is the first real step toward… building proteins that fulfill a specific function. From protein therapeutics to biofuels or enzymes that eat plastic, the possibilities are endless.” Continue reading
Posted in Human Robots
#437820 In-Shoe Sensors and Mobile Robots Keep ...
In shoe sensor
Researchers at Stevens Institute of Technology are leveraging some of the newest mechanical and robotic technologies to help some of our oldest populations stay healthy, active, and independent.
Yi Guo, professor of electrical and computer engineering and director of the Robotics and Automation Laboratory, and Damiano Zanotto, assistant professor of mechanical engineering, and director of the Wearable Robotic Systems Laboratory, are collaborating with Ashley Lytle, assistant professor in Stevens’ College of Arts and Letters, and Ashwini K. Rao of Columbia University Medical Center, to combine an assistive mobile robot companion with wearable in-shoe sensors in a system designed to help elderly individuals maintain the balance and motion they need to thrive.
“Balance and motion can be significant issues for this population, and if elderly people fall and experience an injury, they are less likely to stay fit and exercise,” Guo said. “As a consequence, their level of fitness and performance decreases. Our mobile robot companion can help decrease the chances of falling and contribute to a healthy lifestyle by keeping their walking function at a good level.”
The mobile robots are designed to lead walking sessions and using the in-shoe sensors, monitor the user’s gait, indicate issues, and adjust the exercise speed and pace. The initiative is part of a four-year National Science Foundation research project.
“For the first time, we’re integrating our wearable sensing technology with an autonomous mobile robot,” said Zanotto, who worked with elderly people at Columbia University Medical Center for three years before coming to Stevens in 2016. “It’s exciting to be combining these different areas of expertise to leverage the strong points of wearable sensing technology, such as accurately capturing human movement, with the advantages of mobile robotics, such as much larger computational powers.”
The team is developing algorithms that fuse real-time data from smart, unobtrusive, in-shoe sensors and advanced on-board sensors to inform the robot’s navigation protocols and control the way the robot interacts with elderly individuals. It’s a promising way to assist seniors in safely doing walking exercises and maintaining their quality of life.
Bringing the benefits of the lab to life
Guo and Zanotto are working with Lytle, an expert in social and health psychology, to implement a social connectivity capability and make the bi-directional interaction between human and robot even more intuitive, engaging, and meaningful for seniors.
“Especially during COVID, it’s important for elderly people living on their own to connect socially with family and friends,” Zanotto said, “and the robot companion will also offer teleconferencing tools to provide that interaction in an intuitive and transparent way.”
“We want to use the robot for social connectedness, perhaps integrating it with a conversation agent such as Alexa,” Guo added. “The goal is to make it a companion robot that can sense, for example, that you are cooking, or you’re in the living room, and help with things you would do there.”
It’s a powerful example of how abstract concepts can have meaningful real-life benefits.
“As engineers, we tend to work in the lab, trying to optimize our algorithms and devices and technologies,” Zanotto noted, “but at the end of the day, what we do has limited value unless it has impact on real life. It’s fascinating to see how the devices and technologies we’re developing in the lab can be applied to make a difference for real people.”
Maintaining balance in a global pandemic
Although COVID-19 has delayed the planned testing at a senior center in New York City, it has not stopped the team’s progress.
“Although we can’t test on elderly populations yet, our students are still testing in the lab,” Guo said. “This summer and fall, for the first time, the students validated the system’s real-time ability to monitor and assess the dynamic margin of stability during walking—in other words, to evaluate whether the person following the robot is walking normally or has a risk of falling. They’re also designing parameters for the robot to give early warnings and feedback that help the human subjects correct posture and gait issues while walking.”
Those warnings would be literally underfoot, as the in-shoe sensors would pulse like a vibrating cell phone to deliver immediate directional information to the subject.
“We’re not the first to use this vibrotactile stimuli technology, but this application is new,” Zanotto said.
So far, the team has published papers in top robotics publication venues including IEEE Transactions on Neural Systems and Rehabilitation Engineering and the 2020 IEEE International Conference on Robotics and Automation (ICRA). It’s a big step toward realizing the synergies of bringing the technical expertise of engineers to bear on the clinical focus on biometrics—and the real lives of seniors everywhere. Continue reading
Posted in Human Robots