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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
#437701 Robotics, AI, and Cloud Computing ...
IBM must be brimming with confidence about its new automated system for performing chemical synthesis because Big Blue just had twenty or so journalists demo the complex technology live in a virtual room.
IBM even had one of the journalists choose the molecule for the demo: a molecule in a potential Covid-19 treatment. And then we watched as the system synthesized and tested the molecule and provided its analysis in a PDF document that we all saw in the other journalist’s computer. It all worked; again, that’s confidence.
The complex system is based upon technology IBM started developing three years ago that uses artificial intelligence (AI) to predict chemical reactions. In August 2018, IBM made this service available via the Cloud and dubbed it RXN for Chemistry.
Now, the company has added a new wrinkle to its Cloud-based AI: robotics. This new and improved system is no longer named simply RXN for Chemistry, but RoboRXN for Chemistry.
All of the journalists assembled for this live demo of RoboRXN could watch as the robotic system executed various steps, such as moving the reactor to a small reagent and then moving the solvent to a small reagent. The robotic system carried out the entire set of procedures—completing the synthesis and analysis of the molecule—in eight steps.
Image: IBM Research
IBM RXN helps predict chemical reaction outcomes or design retrosynthesis in seconds.
In regular practice, a user will be able to suggest a combination of molecules they would like to test. The AI will pick up the order and task a robotic system to run the reactions necessary to produce and test the molecule. Users will be provided analyses of how well their molecules performed.
Back in March of this year, Silicon Valley-based startup Strateos demonstrated something similar that they had developed. That system also employed a robotic system to help researchers working from the Cloud create new chemical compounds. However, what distinguishes IBM’s system is its incorporation of a third element: the AI.
The backbone of IBM’s AI model is a machine learning translation method that treats chemistry like language translation. It translates the language of chemistry by converting reactants and reagents to products through the use of Statistical Machine Intelligence and Learning Engine (SMILE) representation to describe chemical entities.
IBM has also leveraged an automatic data driven strategy to ensure the quality of its data. Researchers there used millions of chemical reactions to teach the AI system chemistry, but contained within that data set were errors. So, how did IBM clean this so-called noisy data to eliminate the potential for bad models?
According to Alessandra Toniato, a researcher at IBM Zurichh, the team implemented what they dubbed the “forgetting experiment.”
Toniato explains that, in this approach, they asked the AI model how sure it was that the chemical examples it was given were examples of correct chemistry. When faced with this choice, the AI identified chemistry that it had “never learnt,” “forgotten six times,” or “never forgotten.” Those that were “never forgotten” were examples that were clean, and in this way they were able to clean the data that AI had been presented.
While the AI has always been part of the RXN for Chemistry, the robotics is the newest element. The main benefit that turning over the carrying out of the reactions to a robotic system is expected to yield is to free up chemists from doing the often tedious process of having to design a synthesis from scratch, says Matteo Manica, a research staff member in Cognitive Health Care and Life Sciences at IBM Research Zürich.
“In this demo, you could see how the system is synergistic between a human and AI,” said Manica. “Combine that with the fact that we can run all these processes with a robotic system 24/7 from anywhere in the world, and you can see how it will really help up to speed up the whole process.”
There appear to be two business models that IBM is pursuing with its latest technology. One is to deploy the entire system on the premises of a company. The other is to offer licenses to private Cloud installations.
Photo: Michael Buholzer
Teodoro Laino of IBM Research Europe.
“From a business perspective you can think of having a system like we demonstrated being replicated on the premise within companies or research groups that would like to have the technology available at their disposal,” says Teodoro Laino, distinguished RSM, manager at IBM Research Europe. “On the other hand, we are also pushing at bringing the entire system to a service level.”
Just as IBM is brimming with confidence about its new technology, the company also has grand aspirations for it.
Laino adds: “Our aim is to provide chemical services across the world, a sort of Amazon of chemistry, where instead of looking for chemistry already in stock, you are asking for chemistry on demand.”
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