Whitehead Innovation Initiative gains momentum after a year of successes

In April 2024, Whitehead Institute announced that, through a generous gift from the Centurion Foundation, Michael and Victoria Chambers provided $10 million in funding to seed new research at the intersection of biology and artificial intelligence (AI). This generous gift established the Whitehead Innovation Initiative, a comprehensive program that explores the power of AI tools in biological research, while establishing Whitehead Institute as a leader in applying AI tools to biological questions.

Under the Whitehead Innovation Initiative, the Institute has funded eleven research projects and organized seminars, a symposium, and other community events. The Initiative also supports the Institute’s inaugural AI Fellow, Na Sun.

Valhalla Fellow Allison Hamilos, a member of the Initiative advisory committee, sees untapped potential in bringing biologists and computer scientists together. "Part of this is learning how to talk to each other, learning how to break down barriers that normally separate people coming from different disciplines," she says. "It can be intimidating on both sides. We want to make AI and machine learning tools accessible to everyone in the Whitehead community."

Whitehead Institute's strength lies in its emphasis on foundational biology — a commitment to pursuing a deep understanding of biological processes. "The question is, in foundational biology, how can we augment what we're doing with AI? We're trying to explore how these computational tools can be useful in ways that maybe other people haven't considered," says Matteo Di Bernardo, a graduate student and one of the Initiative's community leaders. "You can make use of some of these tools in your workflow without having to rethink who you are as a scientist."

So far, the Whitehead Innovation Initiative has funded eleven projects that use AI tools to answer important questions in foundational biology. Two of these projects have already resulted in published work, including ProtGPS, an AI model that can accurately predict where proteins localize in the cell based on particular stretches of their amino acid sequences, like a zip code indicating a specific neighborhood. The model was developed by researchers in Whitehead Institute Member Richard Young's lab, along with collaborator Regina Barzilay, the School of Engineering Distinguished Professor for AI and Health at MIT’s Computer Science and Artificial Intelligence Laboratory. "I think these published works are an important validation of the initiative," says Young, who is the Initiative's committee chair.

Some of the other projects supported by this funding come from the labs of Whitehead Institute Member Jonathan Weissman and Whitehead Institute Member Olivia Corradin. Researchers in the Weissman lab developed a tool, called PEtracer, that examines cell lineages and spatial patterns in tissues, providing a detailed view of how genetic and environmental factors influence cancer growth. The tool produces a wealth of data — data that researchers hope to apply towards training AI models to predict the behavior of cells. In the Corradin lab, researchers used machine learning to investigate how gene expression varies across patients with opioid use disorder. In a second project, the group employed machine learning to identify previously-overlooked genes implicated in a wide variety of diseases.

The initiative's first year culminated in AI: Advancing Foundational Biology, a symposium held at Whitehead Institute on April 8, drawing an audience of over 400 researchers and students to attend talks on computational biology and cutting-edge AI. The symposium's keynote speaker was Caroline Uhler, director of the Eric and Wendy Schmidt Center at the Broad Institute of MIT and Harvard. Among the speakers was Whitehead Institute's inaugural AI Fellow, Na Sun, who develops machine learning models to study how cells communicate with one another in the context of Alzheimer's disease. The talks that afternoon spanned a wide range of topics — from applying AI to studying neurodegeneration and cancer, to how to understand and interpret predictions generated from AI models.

Organizers of the Whitehead Innovation Initiative are looking forward to next year's symposium, as well as another rich line-up of seminars. Funding from the program also supports a growing number of labs pursuing AI projects. "We've been able to plan a program of events that we think is really impactful," Di Bernardo says. "We're learning what's useful to people, and that is very valuable."

"Reflecting on the past year, what strikes me is how much excitement has grown and community has been rallied around this idea of integrating biology with cutting-edge AI," Hamilos says. "The outcomes of events from the past year speak for themselves."