AlphaFold developers win US$3-million Breakthrough Prize

Demis Hassabis (left) and John Jumper (right) of DeepMind developed AlphaFold, an AI that can predict the structure of proteins.Credit: Breakthrough Price

The researchers behind the AlphaFold artificial intelligence (AI) system have won one of the breakthrough prizes of $3 million this year — the most lucrative in science. Demis Hassabis and John Jumper, both of DeepMind in London, were credited with creating the tool that predicted the 3D structures of nearly every known protein on the planet.

“Few discoveries change a field so dramatically, so quickly,” said Mohammed AlQuraishi, a computer biologist at Columbia University in New York City. “It has really changed the practice of structural biology, both computationally and experimentally.”

The award was one of five Breakthrough awards – awarded for achievements in life sciences, physics and mathematics – announced September 22.

Award-winning AI

AlphaFold grew out of the success of DeepMind’s AlphaGo. This was the AI ​​that defeated Lee Sedol, a master of the strategy game Go, in Seoul in 2016. “That was the pinnacle of gaming AI, but it should never have been an end in itself,” Hassabis says. “I wanted to build AI to accelerate scientific discoveries.” The day after returning from Seoul, the team turned their attention to protein folding.

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The system caused a stir in November 2020 by winning the biannual CASP (Critical Assessment of Structure Prediction) competition and beating some 100 other software programs. An earlier version of AlphaFold had won in 2018, but not convincingly, forcing the team back to the drawing board. “Machine learning is about striking the right balance between the architecture – the constraints imposed by the known underlying science – and the data,” Jumper says.

Since DeepMind released an open source version of AlphaFold in July 20211, more than half a million researchers have used the machine learning system and generated thousands of papers. In July of this year, DeepMind released 200 million protein structures that were predicted from amino acid sequences. So far, the data has been used to address issues ranging from antibiotic resistance to crop resilience.

“This is a major breakthrough, not only because they developed the algorithm, but also because they made it available and provided all those structures,” said Christine Orengo, a computer biologist at University College London. She adds that the achievement was made possible by a wealth of protein sequence data collected by the global community.

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Hassabis says he was “stunned” when he learned he had won a Breakthrough award, and Jumper says he “couldn’t believe it was real”. Hassabis plans to donate a portion of its profits to educational programs aimed at increasing diversity, as well as initiatives to support schools in rural Nepal.

Sleep Science and Cellular Systems

Another Life-sciences Breakthrough award was jointly awarded to sleep scientists Masashi Yanagisawa of the University of Tsukuba, Japan, and Emmanuel Mignot of Stanford University in Palo Alto, California, for their independent discovery that narcolepsy is caused by a deficiency of the chemical. substance orexin in the brain.

Both researchers are “giants of the field” who have made it possible to definitively diagnose the condition, says Birgitte Rahbek Kornum, a neurophysiologist at the University of Copenhagen. “Narcolepsy seriously affects quality of life, and because of this, patients knew exactly what was going on, rather than being told to ‘hold on and stay awake,'” she says. The findings have also led to the development of drug treatments that are currently in clinical trials.

Yanagisawa says he is “deeply honored” by the award and plans to use the money to set up an endowment to fund research. “Stable support for young scientists to do exploratory work in Japan is problematic,” he says, noting that his own discovery was only possible because he was free to “go on a ‘fishing expedition’ with no guarantee of success.”

A third prize in life sciences is shared by Clifford Brangwynne of Princeton University in New Jersey and Anthony Hyman of the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden, Germany, for discovering a mechanism by which cell contents can self-organize by separating in drops.

Quantum pioneers

This year’s Breakthrough Prize in Fundamental Physics is shared by four founding fathers of quantum information: Peter Shor of the Massachusetts Institute of Technology in Cambridge; David Deutsch at the University of Oxford, UK; Charles Bennett at IBM in Yorktown, New York; and Gilles Brassard at the University of Montreal in Quebec. Their research laid the foundation for the development of ultra-secure communications and computers that could one day outperform standard machines at some tasks.

“I was really surprised to hear that I got the award,” says Shor. “There’s so much that others have done.” In the 1990s, Shor developed the first potentially useful quantum algorithm, which could one day enable quantum computers to quickly split large numbers into their prime factors.2. This increases the ability to crack encryption codes used to secure much of today’s Internet traffic based on large prime numbers. “This huge result proved that quantum computers were more than just an academic curiosity,” said Nikita Gourianov, a quantum physicist at the University of Oxford.

The Breakthrough Prize in Mathematics goes to Daniel Spielman, a mathematician at Yale University in New Haven, Connecticut. Spielman was recognized for several advancements, including the development of error-correcting codes to filter out noise in high-definition television broadcasts.

The Breakthrough Prizes were founded in 2012 by Yuri Milner, a Russian-Israeli billionaire. They are now sponsored by Milner and other internet entrepreneurs, including Mark Zuckerberg, the chief executive of Meta (formerly Facebook).

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