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Explainable AI for Rational Antibiotic Discovery

Researchers now employ artificial intelligence (AI) models based on deep learning to make functional predictions about big datasets. While the concepts behind these networks are well established, their inner workings are often invisible to the user. The emerging area of explainable AI (xAI) provides model interpretation techniques that empower life science researchers to uncover the underlying basis on which AI models make such predictions.

In this month’s episode, Deanna MacNeil from The Scientist spoke with Jim Collins from the Massachusetts Institute of Technology to learn how researchers are using explainable AI and artificial neural networks to gain mechanistic insights for large scale antibiotic discovery. Learn more
Portrait of Hammaad Adam

Growing our donated organ supply

For those in need of one, an organ transplant is a matter of life and death.

Every year, the medical procedure gives thousands of people with advanced or end-stage diseases extended life. This “second chance” is heavily dependent on the availability, compatibility, and proximity of a precious resource that can’t be simply bought, grown, or manufactured — at least not yet.

Instead, organs must be given — cut from one body and implanted into another. And because living organ donation is only viable in certain cases, many organs are only available for donation after the donor’s death.

Unsurprisingly, the logistical and ethical complexity of distributing a limited number of transplant organs to a growing wait list of patients has received much attention. There’s an important part of the process that has received less focus, however, and which may hold significant untapped potential: organ procurement itself. Learn more
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When an antibiotic fails: MIT scientists are using AI to target “sleeper” bacteria

Since the 1970s, modern antibiotic discovery has been experiencing a lull. Now the World Health Organization has declared the antimicrobial resistance crisis as one of the top 10 global public health threats.

When an infection is treated repeatedly, clinicians run the risk of bacteria becoming resistant to the antibiotics. But why would an infection return after proper antibiotic treatment? One well-documented possibility is that the bacteria are becoming metabolically inert, escaping detection of traditional antibiotics that only respond to metabolic activity. When the danger has passed, the bacteria return to life and the infection reappears.

“Resistance is happening more over time, and recurring infections are due to this dormancy,” says Jackie Valeri, a former MIT-Takeda Fellow (centered within the MIT Abdul Latif Jameel Clinic for Machine Learning in Health) who recently earned her PhD in biological engineering from the Collins Lab. Valeri is the first author of a new paper published in this month’s print issue of Cell Chemical Biology that demonstrates how machine learning could help screen compounds that are lethal to dormant bacteria. Learn more

A new computational technique could make it easier to engineer useful proteins

To engineer proteins with useful functions, researchers usually begin with a natural protein that has a desirable function, such as emitting fluorescent light, and put it through many rounds of random mutation that eventually generate an optimized version of the protein.

This process has yielded optimized versions of many important proteins, including green fluorescent protein (GFP). However, for other proteins, it has proven difficult to generate an optimized version. MIT researchers have now developed a computational approach that makes it easier to predict mutations that will lead to better proteins, based on a relatively small amount of data.

Using this model, the researchers generated proteins with mutations that were predicted to lead to improved versions of GFP and a protein from adeno-associated virus (AAV), which is used to deliver DNA for gene therapy. They hope it could also be used to develop additional tools for neuroscience research and medical applications.

“Protein design is a hard problem because the mapping from DNA sequence to protein structure and function is really complex. There might be a great protein 10 changes away in the sequence, but each intermediate change might correspond to a totally nonfunctional protein. It’s like trying to find your way to the river basin in a mountain range, when there are craggy peaks along the way that block your view. The current work tries to make the riverbed easier to find,” says Ila Fiete, a professor of brain and cognitive sciences at MIT, a member of MIT’s McGovern Institute for Brain Research, director of the K. Lisa Yang Integrative Computational Neuroscience Center, and one of the senior authors of the study.

Regina Barzilay, the School of Engineering Distinguished Professor for AI and Health at MIT, and Tommi Jaakkola, the Thomas Siebel Professor of Electrical Engineering and Computer Science at MIT, are also senior authors of an open-access paper on the work, which will be presented at the International Conference on Learning Representations in May. MIT graduate students Andrew Kirjner and Jason Yim are the lead authors of the study. Other authors include Shahar Bracha, an MIT postdoc, and Raman Samusevich, a graduate student at Czech Technical University. Learn more

‘A.I. Revolution’ Review: A Cause for Cautious Hope

There are no representatives of the United Auto Workers or Teamsters weighing in on how smart robots might be threatening their workers in a more immediate fashion, but the medical advancements explored are exhilarating. MIT computer scientist Regina Barzilay, along with Massachusetts General Hospital, has developed a way of reading mammograms and detecting suspicious growths long before the human eye could spot any abnormalities. The development of pharmaceuticals has leapt into the future. The program also takes pains, effectively, in laying out how AI differs from, say, the way algorithms work, by reading patterns in Big Data and drawing conclusions from them. The processes of machine learning and artificial intelligence—which continue to advance—are made quite plain, while perhaps still being beyond summarization by those of us who only recently have learned how to spell algorithm. Learn more
Still of Regina Barzilay from AI Revolution

A.I. Revolution

Can we harness the power of artificial intelligence to solve the world’s most challenging problems without creating an uncontrollable force that ultimately destroys us? ChatGPT and other new A.I. tools can now answer complex questions, write essays, and generate realistic-looking images in a matter of seconds. They can even pass a lawyer’s bar exam. Should we celebrate? Or worry? Or both? Correspondent Miles O’Brien investigates how researchers are trying to transform the world using A.I., hunting for big solutions in fields from medicine to climate change. (Premiering March 27 at 9 pm on PBS) Learn more
Antibodies (pink) bind to influenza virus proteins (yellow) (artist’s conception)

‘A landmark moment’: scientists use AI to design antibodies from scratch

Researchers have used generative artificial intelligence (AI) to help them make completely new antibodies for the first time.

The proof-of-principle work, reported this week in a preprint on bioRxiv, raises the possibility of bringing AI-guided protein design to the therapeutic antibody market, which is worth hundreds of billions of dollars.

Antibodies — immune molecules that strongly attach to proteins implicated in disease — have conventionally been made using brute-force approaches that involve immunizing animals or screening vast numbers of molecules.

AI tools that can shortcut those costly efforts have the potential to “democratize the ability to design antibodies”, says study co-author Nathaniel Bennett, a computational biochemist at the University of Washington in Seattle. “Ten years from now, this is how we’re going to be designing antibodies.”

“It’s a really promising piece of research” that represents an important step in applying AI protein-design tools to making new antibodies, says Charlotte Deane, an immuno-informatician at the University of Oxford, UK. Learn more
Ernest Fraenkel portrait in a wet lab.

Deciphering the cellular mechanisms behind ALS

At a time in which scientific research is increasingly cross-disciplinary, Ernest Fraenkel, the Grover M. Hermann Professor in Health Sciences and Technology in MIT’s Department of Biological Engineering, stands out as both a very early adopter of drawing from different scientific fields and a great advocate of the practice today.

When Fraenkel’s students find themselves at an impasse in their work, he suggests they approach their problem from a different angle or look for inspiration in a completely unrelated field.

“I think the thing that I always come back to is try going around it from the side,” Fraenkel says. “Everyone in the field is working in exactly the same way. Maybe you’ll come up with a solution by doing something different.” Learn more
Dimitris Bertismas standing at a podium speaking.

Hartford HealthCare launches new center to use artificial intelligence in hospitals

HARTFORD — Hartford HealthCare is launching a new center dedicated to using artificial intelligence in healthcare, which officials said is the first in New England and one of a few in the United States.

The goal of using AI in a hospital system is to create more equitable and affordable healthcare, Jeffrey Flaks, president and chief executive officer of Hartford HealthCare, said at a press conference announcing the launch this week.

"Artificial intelligence is ubiquitous in healthcare," Flaks said. "It has the potential to impact all aspects of our operations, but our focus is to make healthcare more accessible, more affordable, to make it more equitable and to make it better."

Some of the research initiatives using AI include predicting COVID-19 spikes, how long someone might stay at the hospital, how a patient's condition might worsen, if a secondary stroke might happen and the outcomes of different surgeries. It can also be used in scheduling to make the hospital more efficient, officials said.

The Center for AI Innovation in Healthcare comes from a nearly decade-long, ongoing international collaboration between Hartford HealthCare, the Massachusetts Institute of Technology and the University of Oxford.

"To advance ourselves from being one of the earliest early adapters, to now being a co-developer, inventor and creator, and to be a pioneer in artificial intelligence, gives us the opportunity to truly impact how we deliver healthcare," Flaks said.

Through the collaborations, Hartford HealthCare Innovation developed Holistic Hospital Optimization, nicknamed H2O, which uses AI to help make hospital operations more efficient, including scheduling staff and operating rooms, as well as predicting how long a patient will stay, officials said.

The AI system follows a Holistic AI in Medicine framework, Dimitris Bertsimas, associate dean of analytics at MIT-Sloan, said at the press conference. It analyzes data hospitals collect, such as tabular data and images, which can then be applied "in a real-world environment in high-quality healthcare."

Flaks said that by minimizing administrative tasks, the medical staff can feel supported and have their attention be on patients. Learn more
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