Feb 14 2024 King Abdullah University of Science & Technology (KAUST)
A new artificial intelligence (AI) tool that draws logical inferences about the function of unknown proteins promises to help scientists unravel the inner workings of the cell.
Developed by KAUST bioinformatics researcher Maxat Kulmanov and colleagues, the tool outperforms existing analytical methods for forecasting protein functions and is even able to analyze proteins with no clear matches in existing datasets.
The model, termed DeepGO-SE, takes advantage of large language models similar to those used by generative AI tools such as Chat-GPT. It then employs logical entailment to draw meaningful conclusions about molecular functions based on general biological principles about the way proteins work.
It essentially empowers computers to logically process outcomes by constructing models of part of the world -; in this case, protein function -; and inferring the most plausible scenario based on common sense and reasoning about what should happen in these world models.
"This method has many applications," says Robert Hoehndorf, head of the KAUST Bio-Ontology Research Group, who supervised this research, "especially when it is necessary to reason over data and hypotheses generated by a neural network or another machine learning model," he adds.
Kulmanov and Hoehndorf collaborated with KAUST's Stefan Arold, as well as researchers at the Swiss Institute of Bioinformatics, to assess the model's ability to decipher the functions of proteins whose role in the body are unknown. Related StoriesStudy pinpoints a protein linked to metastatic pancreatic cancerUnlocking Alzheimer's secrets: Study pinpoints APOE4's harmful effect on lipidsImmune protein Ku70 key in fighting bowel cancer
The tool successfully used data regarding the amino acid sequence of a poorly understood protein and its known interactions with other proteins and precisely predicted its molecular functions. The model was so accurate that DeepGO-SE was ranked in the top 20 of more than 1,600 algorithms in an international competition of function prediction tools.
The KAUST team is now using the tool to investigate the functions of enigmatic proteins discovered in plants that thrive in the extreme environment of the Saudi Arabian desert. They hope that the findings will be useful for identifying novel proteins for biotechnological applications and would like other researchers to embrace the tool. DeepGO-SE's ability to analyze uncharacterized proteins can facilitate tasks such as drug discovery, metabolic pathway analysis, disease associations, protein engineering, screening for specific proteins of interest and more."
Robert Hoehndorf, Head of the KAUST Bio-Ontology Research Group Source:
King Abdullah University of Science & Technology (KAUST)Journal reference:
Kulmanov, M., et al. (2024). Protein function prediction as approximate semantic entailment. Nature Machine Intelligence. doi.org/10.1038/s42256-024-00795-w.
Sir Keir Starmer has called for a tougher approach to policing Europe’s borders ahead of a meeting between leaders to discuss a potential shake-up of the European Convention on Human Rights (ECHR).
The prime minister said the way in which the ECHR is interpreted in courts must be modernised, with critics long claiming the charter is a major barrier to deportations of illegal migrants.
His deputy, David Lammy, will today be in Strasbourg, France, with fellow European ministers to discuss reforms of how the agreement is interpreted in law across the continent.
In an opinion piece for The Guardian, Sir Keir and his Danish counterpart, Mette Frederiksen, said the change was necessary to prevent voters from turning to populist political opponents.
Image: Small boat crossings have risen this year. File pic: PA
What’s the issue with the ECHR?
The ECHR, which is the foundation of Britain’s Human Rights Act, includes the right to family life in its Article 8.
That is often used as grounds to prevent deportations of illegal migrants from the UK.
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There has also been a rise in cases where Article 3 rights, prohibiting torture, were used to halt deportations over claims migrants’ healthcare needs could not be met in their home country, according to the Home Office.
The Conservatives and Reform UK have both said they would leave the ECHR if in power, while the Labour government has insisted it will remain a member of the treaty.
But Sir Keir admitted in his joint op-ed that the “current asylum framework was created for another era”.
“In a world with mass mobility, yesterday’s answers do not work. We will always protect those fleeing war and terror – but the world has changed, and asylum systems must change with it,” the two prime ministers wrote, as they push for a “modernisation of the interpretation” of the ECHR.
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What is happening today?
Mr Lammy is attending an informal summit of the Council of Europe.
He is expected to say: “We must strike a careful balance between individual rights and the public’s interest.
“The definition of ‘family life’ can’t be stretched to prevent the removal of people with no right to remain in the country [and] the threshold of ‘inhuman and degrading treatment’ must be constrained to the most serious issues.”
It is understood that a political declaration signed by the gathered ministers could carry enough weight to directly influence how the European Court of Human Rights interprets the treaty.
The UK government is expected to bring forward its own legislation to change how Article 8 is interpreted in UK courts, and is also considering a re-evaluation of the threshold for Article 3 rights.
Image: David Lammy will swap Westminster for Strasbourg today
The plans have been criticised by Amnesty International UK, which described them as weakening protections.
“Human rights were never meant to be optional or reserved for comfortable and secure times. They were designed to be a compass, our conscience, when the politics of fear and division try to steer us wrong,” Steve Valdez-Symonds, the organisation’s refugee and migrant rights programme director, said.
Sir Keir’s government has already adopted several hardline immigration measures – modelled on those introduced by Ms Federiksen’s Danish government – to decrease the number of migrants crossing the Channel via small boats.
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Starmer-Macron deal ‘a sticking plaster’
Meanwhile, French far-right leader Jordan Bardella told The Daily Telegraph he would rewrite his country’s border policy to allow British patrol boats to push back small vessels carrying migrants into France’s waters if he were elected.
The National Rally leader called Sir Keir’s “one-in, one-out” agreement with Emmanuel Macron, which includes Britain returning illegal arrivals in exchange for accepting a matching number of legitimate asylum seekers, a “sticking plaster” and “smokescreen”.
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Far-right, 30, and France’s most popular politician
He said that only a complete overhaul of French immigration policy would stop the Channel crossings.
Mr Bardella is currently leading in opinion polls to win the first round of France’s next presidential election, expected to happen in 2027, to replace Mr Macron.
Employees stand near an The Amazon Inc. logo is displayed above the reception counter at the company’s campus in Hyderabad, India, on Friday, Sept. 6, 2019.
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Amazon on Wednesday committed to investing over $35 billion in India’s cloud and artificial intelligence space by 2030, as hyperscalers race to get a foothold in the market.
The commitment, unveiled at the Amazon Smbhav Summit in New Delhi, builds on nearly $40 billion already invested in the country.
In a press release, Amazon said the new funds will target AI-driven digitization, export growth and job creation, aligning with India’s national priorities to build up its local AI environment.
By 2030, Amazon said the plan is expected to generate an additional 1 million direct, indirect, induced and seasonal jobs in India, quadruple exports to $80 billion and deliver AI benefits to 15 million small businesses.
The investment highlights Amazon’s bet on India’s booming digital economy, where it has been building fulfillment centers, data centers and payments infrastructure.
It also comes soon after Microsoft announced plans to invest $17.5 billion in India’s AI infrastructure as Big Tech players accelerate their push into the market.
“We are humbled to have been a part of India’s digital transformation journey over the past 15 years,” said Amit Agarwal, senior vice president for emerging markets at Amazon.
“Looking ahead, we’re excited to continue being a catalyst for India’s growth, as we democratize access to AI for millions of Indians.”
The race for the new US Federal Reserve chair is nearing the finish line, with US President Donald Trump reportedly set to begin interviewing finalists for the top job this week.
According to a report from the Financial Times on Tuesday, Treasury Secretary Scott Bessent has presented a list of four names to the White House.
One of these is former Fed governor Kevin Warsh, whom Bessent is scheduled to meet with on Wednesday. Another is National Economic Council director Kevin Hassett, who is seen as the frontrunner for the role.
Another two names would be picked from a list of other finalists, which includes Fed governors Christopher Waller and Michelle Bowman, and BlackRock chief investment officer Rick Rieder.
Trump and Bessent are expected to hold at least one interview next week, as a decision looks likely to be announced in January.
However, Trump has revealed he already has his eye on one particular candidate.
“We’re going to be looking at a couple different people, but I have a pretty good idea of who I want,” Trump said to journalists on Air Force One on Tuesday.
Kevin Hassett is a frontrunner for Fed chair role
The upcoming round of interviews suggests that Hassett may not be the clear lock in for the role as previously thought, though he is seen as the favorite.
Earlier this month, prediction market odds on Kalshi and Polymarket shot up for Hassett significantly following comments from Trump at the White House on Dec. 2.
While welcoming guests, Trump labeled Hassett as “potential Fed chair” leading many to assume the president had let a major hint slip.
With Hassett’s odds spiking to 85% after Trump’s comments last week, they have since declined to around 73% for Hassett, while Warsh’s odds sit at 13% on Kalshi at the time of writing, which has floated around this range over December.
Regardless of who ends up taking over as chair, the move is bound to impact crypto markets under the new leadership.
If elected, Hassett has asserted that he will be apolitical in terms of running the Fed, despite his close ties to Trump. Speaking with The Wall Street Journal this week, Hassett said that “You just do the right thing” when asked if he would blindly follow orders from Trump.
“Suppose that inflation has gotten from, say, 2.5% to 4%. You can’t cut,” Hassett said, adding that he would rely on his own “judgment, which I think the president trusts.”