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.
All 14 children arrested on suspicion of manslaughter after a boy died in a fire have been released on police bail, officers said.
Layton Carr, 14, was found dead near the site of a fire at Fairfield industrial park in the Bill Quay area of Gateshead on Friday.
Northumbria Police said on Saturday that they had arrested 11 boys and three girls in connection with the incident.
In an update on Sunday, a Northumbria Police spokesman said: “All those arrested have since been released on police bail pending further inquiries.”
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Teenager dies in industrial estate fire
Firefighters raced to the industrial site shortly after 8pm on Friday, putting out the blaze a short time later.
Police then issued an appeal for Carr, who was believed to be in the area at that time.
In a statement on Saturday, the force said that “sadly, following searches, a body believed to be that of 14-year-old Layton Carr was located deceased inside the building”.
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David Thompson, headteacher of Hebburn Comprehensive School, where Layton was a pupil, said the school community was “heartbroken”.
Mr Thompson described him as a “valued and much-loved member of Year 9” and said he would be “greatly missed by everyone”.
He added that the school’s “sincere condolences” were with Layton’s family and that the community would “rally together to support one another through this tragedy”.
A fundraising page on GoFundMe has been set up to help Layton’s mother pay for funeral costs.
Image: Pic: Gofundme
Organiser Stephanie Simpson said: “The last thing Georgia needs to stress trying to pay for a funeral for her Boy Any donations will help thank you.”
One tribute in a Facebook post read: “Can’t believe I’m writing this my nephew RIP Layton 💔 forever 14 you’ll be a massive miss, thinking of my sister and 2 beautiful nieces right now.”
Detective Chief Inspector Louise Jenkins, of Northumbria Police, also said: “This is an extremely tragic incident where a boy has sadly lost his life.”
She added that the force’s “thoughts are with Layton’s family as they begin to attempt to process the loss of their loved one”.
They are working to establish “the full circumstances surrounding the incident” and officers will be in the area to “offer reassurance to the public”, she added.
A cordon remains in place at the site while police carry out enquiries.
Football bodies could be forced to pay towards the care costs of ex-players who have been diagnosed with brain conditions, under proposals set to be considered by MPs.
Campaigners are drafting amendments to the Football Governance Bill, which would treat conditions caused by heading balls as an “industrial injuries issue”.
The proposals seek to require the football industry to provide the necessary financial support.
Campaigners say existing support is not fit for purpose, including the Brain Health Fund which was set up with an initial £1m by the Professional Footballers’ Association (PFA), supported by the Premier League.
But the Premier League said the fund has supported 121 families with at-home adaptations and care home fees.
From England‘s 1966 World Cup-winning team, both Jack and Bobby Charlton died with dementia, as did Martin Peters, Ray Wilson and Nobby Stiles.
Image: Neil Ruddock speaks to Sky’s Rob Harris outside parliament
Ex-players, including former Liverpool defender Neil Ruddock, went to parliament last week to lobby MPs.
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Ruddock told Sky News he had joined campaigners “for the families who’ve gone through hell”.
“A professional footballer, greatest job in the world, but no one knew the dangers, and that’s scary,” he said.
“Every time someone heads a ball it’s got to be dangerous to you. You know, I used to head 100 balls a day in training. I didn’t realise that might affect my future.”
A study co-funded by the PFA and the Football Association (FA) in 2019 found footballers were three and a half times more likely to die of a neurodegenerative disease than members of the public of the same age.
‘In denial’
Among those calling on football authorities to contribute towards the care costs of ex-players who have gone on to develop conditions such as Alzheimer’s and dementia is Labour MP Chris Evans.
Mr Evans, who represents Caerphilly in South Wales, hopes to amend the Bill to establish a care and financial support scheme for ex-footballers and told a recent event in parliament that affected ex-players “deserve to be compensated”.
Greater Manchester Mayor Andy Burnham, who helped to draft the amendment, said the game was “in denial about the whole thing”.
Mr Burnham called for it to be seen as “an industrial injuries issue in the same way with mining”.
A spokesperson for the FA said it was taking a “leading role in reviewing and improving the safety of our game” and that it had “already taken many proactive steps to review and address potential risk factors”.
An English Football League spokesperson said it was “working closely with other football bodies” to ensure both professional and grassroots football are “as safe as it can be”.
And that comes in the context of increased warnings from government and the security services about Iranian activity on British soil.
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Last year, the director general of MI5, Ken McCallum, said his organisation and police had responded to 20 Iran-backed plots presenting potentially lethal threats to British citizens and UK residents since January 2022.
He linked that increase to the ongoing situation in Iran’s own backyard.
“As events unfold in the Middle East, we will give our fullest attention to the risk of an increase in – or a broadening of – Iranian state aggression in the UK,” he said.
The implication is that even as Iran grapples with a rapidly changing situation in its own region, having seen its proxies, Hezbollahin Lebanon and Hamas in Gaza, decimated and itself coming under Israeli attack, it may seek avenues further abroad.
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The government reiterated this warning only a few weeks ago, with security minister Dan Jarvis addressing parliament.
“The threat from Iran sits in a wider context of the growing, diversifying and evolving threat that the UK faces from malign activity by a number of states,” Jarvis said.
“The threat from states has become increasingly interconnected in nature, blurring the lines between: domestic and international; online and offline; and states and their proxies.
“Turning specifically to Iran, the regime has become increasingly emboldened, asserting itself more aggressively to advance their objectives and undermine ours.”
As part of that address, Jarvis highlighted the National Security Act 2023, which “criminalises assisting a foreign intelligence service”, among other things.
So it was notable that this was the act used in one of this weekend’s investigations.
The suspects were detained under section 27 of the same act, which allows police to arrest those suspected of being “involved in foreign power threat activity”.