Tag Archives: Artificial intelligence
#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
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#437816 As Algorithms Take Over More of the ...
Algorithms play an increasingly prominent part in our lives, governing everything from the news we see to the products we buy. As they proliferate, experts say, we need to make sure they don’t collude against us in damaging ways.
Fears of malevolent artificial intelligence plotting humanity’s downfall are a staple of science fiction. But there are plenty of nearer-term situations in which relatively dumb algorithms could do serious harm unintentionally, particularly when they are interlocked in complex networks of relationships.
In the economic sphere a high proportion of decision-making is already being offloaded to machines, and there have been warning signs of where that could lead if we’re not careful. The 2010 “Flash Crash,” where algorithmic traders helped wipe nearly $1 trillion off the stock market in minutes, is a textbook example, and widespread use of automated trading software has been blamed for the increasing fragility of markets.
But another important place where algorithms could undermine our economic system is in price-setting. Competitive markets are essential for the smooth functioning of the capitalist system that underpins Western society, which is why countries like the US have strict anti-trust laws that prevent companies from creating monopolies or colluding to build cartels that artificially inflate prices.
These regulations were built for an era when pricing decisions could always be traced back to a human, though. As self-adapting pricing algorithms increasingly decide the value of products and commodities, those laws are starting to look unfit for purpose, say the authors of a paper in Science.
Using algorithms to quickly adjust prices in a dynamic market is not a new idea—airlines have been using them for decades—but previously these algorithms operated based on rules that were hard-coded into them by programmers.
Today the pricing algorithms that underpin many marketplaces, especially online ones, rely on machine learning instead. After being set an overarching goal like maximizing profit, they develop their own strategies based on experience of the market, often with little human oversight. The most advanced also use forms of AI whose workings are opaque even if humans wanted to peer inside.
In addition, the public nature of online markets means that competitors’ prices are available in real time. It’s well-documented that major retailers like Amazon and Walmart are engaged in a never-ending bot war, using automated software to constantly snoop on their rivals’ pricing and inventory.
This combination of factors sets the stage perfectly for AI-powered pricing algorithms to adopt collusive pricing strategies, say the authors. If given free reign to develop their own strategies, multiple pricing algorithms with real-time access to each other’s prices could quickly learn that cooperating with each other is the best way to maximize profits.
The authors note that researchers have already found evidence that pricing algorithms will spontaneously develop collusive strategies in computer-simulated markets, and a recent study found evidence that suggests pricing algorithms may be colluding in Germany’s retail gasoline market. And that’s a problem, because today’s anti-trust laws are ill-suited to prosecuting this kind of behavior.
Collusion among humans typically involves companies communicating with each other to agree on a strategy that pushes prices above the true market value. They then develop rules to determine how they maintain this markup in a dynamic market that also incorporates the threat of retaliatory pricing to spark a price war if another cartel member tries to undercut the agreed pricing strategy.
Because of the complexity of working out whether specific pricing strategies or prices are the result of collusion, prosecutions have instead relied on communication between companies to establish guilt. That’s a problem because algorithms don’t need to communicate to collude, and as a result there are few legal mechanisms to prosecute this kind of collusion.
That means legal scholars, computer scientists, economists, and policymakers must come together to find new ways to uncover, prohibit, and prosecute the collusive rules that underpin this behavior, say the authors. Key to this will be auditing and testing pricing algorithms, looking for things like retaliatory pricing, price matching, and aggressive responses to price drops but not price rises.
Once collusive pricing rules are uncovered, computer scientists need to come up with ways to constrain algorithms from adopting them without sacrificing their clear efficiency benefits. It could also be helpful to make preventing this kind of collusive behavior the responsibility of the companies deploying them, with stiff penalties for those who don’t keep their algorithms in check.
One problem, though, is that algorithms may evolve strategies that humans would never think of, which could make spotting this behavior tricky. Imbuing courts with the technical knowledge and capacity to investigate this kind of evidence will also prove difficult, but getting to grips with these problems is an even more pressing challenge than it might seem at first.
While anti-competitive pricing algorithms could wreak havoc, there are plenty of other arenas where collusive AI could have even more insidious effects, from military applications to healthcare and insurance. Developing the capacity to predict and prevent AI scheming against us will likely be crucial going forward.
Image Credit: Pexels from Pixabay Continue reading
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