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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
#437807 Why We Need Robot Sloths
An inherent characteristic of a robot (I would argue) is embodied motion. We tend to focus on motion rather a lot with robots, and the most dynamic robots get the most attention. This isn’t to say that highly dynamic robots don’t deserve our attention, but there are other robotic philosophies that, while perhaps less visually exciting, are equally valuable under the right circumstances. Magnus Egerstedt, a robotics professor at Georgia Tech, was inspired by some sloths he met in Costa Rica to explore the idea of “slowness as a design paradigm” through an arboreal robot called SlothBot.
Since the robot moves so slowly, why use a robot at all? It may be very energy-efficient, but it’s definitely not more energy efficient than a static sensing system that’s just bolted to a tree or whatever. The robot moves, of course, but it’s also going to be much more expensive (and likely much less reliable) than a handful of static sensors that could cover a similar area. The problem with static sensors, though, is that they’re constrained by power availability, and in environments like under a dense tree canopy, you’re not going to be able to augment their lifetime with solar panels. If your goal is a long-duration study of a small area (over weeks or months or more), SlothBot is uniquely useful in this context because it can crawl out from beneath a tree to find some sun to recharge itself, sunbathe for a while, and then crawl right back again to resume collecting data.
SlothBot is such an interesting concept that we had to check in with Egerstedt with a few more questions.
IEEE Spectrum: Tell us what you find so amazing about sloths!
Magnus Egerstedt: Apart from being kind of cute, the amazing thing about sloths is that they have carved out a successful ecological niche for themselves where being slow is not only acceptable but actually beneficial. Despite their pretty extreme low-energy lifestyle, they exhibit a number of interesting and sometimes outright strange behaviors. And, behaviors having to do with territoriality, foraging, or mating look rather different when you are that slow.
Are you leveraging the slothiness of the design for this robot somehow?
Sadly, the sloth design serves no technical purpose. But we are also viewing the SlothBot as an outreach platform to get kids excited about robotics and/or conservation biology. And having the robot look like a sloth certainly cannot hurt.
“Slowness is ideal for use cases that require a long-term, persistent presence in an environment, like for monitoring tasks. I can imagine slow robots being out on farm fields for entire growing cycles, or suspended on the ocean floor keeping track of pollutants or temperature variations.”
—Magnus Egerstedt, Georgia Tech
Can you talk more about slowness as a design paradigm?
The SlothBot is part of a broader design philosophy that I have started calling “Robot Ecology.” In ecology, the connections between individuals and their environments/habitats play a central role. And the same should hold true in robotics. The robot design must be understood in the environmental context in which it is to be deployed. And, if your task is to be present in a slowly varying environment over a long time scale, being slow seems like the right way to go. Slowness is ideal for use cases that require a long-term, persistent presence in an environment, like for monitoring tasks, where the environment itself is slowly varying. I can imagine slow robots being out on farm fields for entire growing cycles, or suspended on the ocean floor keeping track of pollutants or temperature variations.
How do sloths inspire SlothBot’s functionality?
Its motions are governed by what we call survival constraints. These constraints ensure that the SlothBot is always able to get to a sunny spot to recharge. The actual performance objective that we have given to the robot is to minimize energy consumption, i.e., to simply do nothing subject to the survival constraints. The majority of the time, the robot simply sits there under the trees, measuring various things, seemingly doing absolutely nothing and being rather sloth-like. Whenever the SlothBot does move, it does not move according to some fixed schedule. Instead, it moves because it has to in order to “survive.”
How would you like to improve SlothBot?
I have a few directions I would like to take the SlothBot. One is to make the sensor suites richer to make sure that it can become a versatile and useful science instrument. Another direction involves miniaturization – I would love to see a bunch of small SlothBots “living” among the trees somewhere in a rainforest for years, providing real-time data as to what is happening to the ecosystem. Continue reading