Connecting biology with machine learning

Broad Institute launches the Eric and Wendy Schmidt Center for better understanding programs of life

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Connecting biology with machine learning

CAMBRIDGE, Mass.—The Broad Institute of MIT and Harvard recently announced the launch of the Eric and Wendy Schmidt Center, an initiative funded by a $150-million endowment gift from the Schmidts that will catalyze a new scientific discipline at the intersection of biology and machine learning.

Based in Cambridge at the Broad Institute, the center will bring together a global and collaborative network across academia and industry to promote interdisciplinary research between the data and life sciences to transform biology and ultimately improve human health. In recognition of the Schmidts’ gift, The Broad Foundation announced an additional $150-million endowment gift to the Broad Institute. To date, The Broad Foundation has pledged more than $1 billion to establish and endow the Broad Institute.

Two recent revolutions inspired the creation of the Schmidt Center: the exponential growth and widespread adaptation of data technologies like machine learning and cloud computing, and the dramatic advances in generating massive amounts of data about living systems through next-generation DNA sequencing, single-cell genomics, and advanced medical imaging.

Until now, these fields have largely developed in parallel. Their convergence will create a new era of biology, one that is expected to yield a deep understanding of biological processes, with the ultimate aim of improving human health through more powerful disease prevention, diagnosis, and treatment. This will require creating centers of excellence that can identify problems of fundamental biological importance, translate them into the language of machine learning, and then convene leading researchers from around the world to solve them collaboratively.

This approach advances Eric and Wendy Schmidt’s work through Schmidt Futures, a philanthropic initiative they founded to bet early on exceptional people making the world better, particularly through innovative breakthroughs in science and technology. The Schmidt Center represents the initiative’s largest philanthropic gift to date.

The Schmidt Center will be co-directed by Caroline Uhler—an associate professor of electrical engineering and computer science and part of the Institute for Data, Systems, and Society at MIT, as well as an associate member of the Broad Institute—and Anthony Philippakis, Broad’s chief data officer.

“The pandemic has shown us that prioritizing science, innovation, and research is one of the greatest investments we can make in our future,” said Eric Schmidt, a member of the Broad Institute board and co-founder with his wife Wendy of Schmidt Futures, The Schmidt Family Foundation, and Schmidt Ocean Institute. “Much like Eli and Edye Broad saw the potential in creating the Broad Institute, Wendy and I believe this center has the promise to create a new field of science that could benefit human health in ways we can't even begin to imagine. The Broad Institute is uniquely fertile ground for cultivating a center of excellence in this new field. Beginning with its origins in the human genome project and its extension into statistical genetics and single-cell genomics, the Broad Institute has excelled at connecting the world’s best scientists and software engineers and equipping them with the right tools to seek answers to questions previously thought impossible.”

“Biology is now producing data at previously unimaginable scales—but our ability to understand and interpret that data hasn't kept pace,” said Todd Golub, director of the Broad Institute. “Adapting the methods of machine learning for biology will give scientists the chance to understand the programs of life, and the Eric and Wendy Schmidt Center will enable new partnerships between academia and industry that can greatly accelerate our progress.”

“Eli and Edye Broad made a big bet 15 years ago, joining with MIT and Harvard to advance the promise of genomic medicine,” said Gerun Riley, president of The Broad Foundation and member of the Broad Institute board. “We are thrilled to partner with the Schmidts to realize this exciting evolution of the Broad Institute by building on its foundational ethos to create a new scientific discipline that will further propel life-changing research and discovery.”

Creating a collaborative ecosystem

The Eric and Wendy Schmidt Center will draw talent from across the Broad community, including MIT, Harvard, and the Harvard teaching hospitals. It will benefit from and partner with the pioneering work already underway at Broad, such as the Models, Inference & Algorithms (MIA) Initiative at the Broad and the cross-institutional Machine Learning for Health (ML4H) effort, with the shared goal of enabling a global and collaborative ecosystem to catalyze this new field. The center is organized around principles of ethics and equity, with researchers focused on engaging underrepresented groups, anticipating outcomes for vulnerable populations, and developing open-source tools that will maximize benefit to all, inclusive of ethnicity, gender, socioeconomic status, and more.

“It’s crucial that we develop an inclusive network of partners from across the biomedical and clinical communities, as well as academia and industry,” said Schmidt Center co-executive director Uhler. “By connecting clinicians with biotechnologists and data scientists trained in diverse areas—from mathematics to computer science, electrical engineering and computational biology—we can begin to gain unprecedented insights into the biology of cells, tissues and organisms.”

In addition to continuing to work closely with MIT, Harvard, and the Harvard-affiliated hospitals, as well as through existing technology partnerships the Broad has already established with Bayer, IBM, Intel, and Verily, the Eric and Wendy Schmidt Center will bring a new set of collaborators. They include:

  •     Mila (Quebec AI Institute), led by Yoshua Bengio
  •     European Laboratory for Learning and Intelligent Systems, Tuebingen, led by Bernhard Schoelkopf
  •     Oxford Big Data Institute, directed by Cecilia Lindgren (incoming director)
  •     The Alan Turing Institute, directed by Sir Adrian Smith
  •     Clinicians and researchers at Mayo Clinic and Geisinger
  •     Biopharmaceutical companies, including Genentech (a member of the Roche Group), AstraZeneca, and Novartis
        Technology and research companies focused on scientific inquiry, including DeepMind, Google Research, and Microsoft

“Learning the programs of life will require new and collaborative approaches to creating data platforms, analytical tools and biotechnologies,” said Schmidt Center co-executive director Philippakis, who trained as a cardiologist at Brigham and Women’s Hospital and as a computational biologist. “By bringing them together, we can nucleate discoveries at the interface of biology and machine learning, discoveries that may ultimately transform medicine and impact the lives of many suffering from disease.”

“Having been part of this center from its inception, I am deeply and personally grateful to Eric and Wendy Schmidt for their vision and generosity,” said Aviv Regev, head of Genentech Research and Early Development and former chair of the caculty and first recruited core member at the Broad Institute. During her time at the Broad Institute, Regev helped lay the foundation for what is now the Schmidt Center by steering scientific strategy around the interface of artificial intelligence, machine learning, and biology, and by driving early discussions that led to the Center’s formation. “The convergence of biology and machine learning is a powerful catalyst that will not only impact both fields but also transform our ability to develop medicines for patients. Advancing this convergence is at the forefront of our work in research and development at Genentech, and we’re delighted to participate in this interdisciplinary initiative and to grow collaborative networks across these communities.”

The interface of biology and machine learning

The Eric and Wendy Schmidt Center will pursue foundational discoveries in both the life sciences and the data sciences.

Currently, representing data in a way that makes underlying biological principles or causal mechanisms clear is tremendously challenging. Therefore, two machine learning fields that are particularly significant to biology are “representation learning,” which extracts underlying structure from troves of data, and “causal inference,” which helps predict how changing particular variables impacts a whole dataset.

“In biology, we don’t just want to make predictions, we want to understand the underlying mechanisms,” said Uhler. “One of the amazing things about biology is our ability to perform perturbations on a scale that is unimaginable in most other fields. This opens the door to bridging the gap between predictive and causal modeling, enabling us to understand the mechanisms of disease.”

“The life sciences are in the midst of a data revolution,” said Philippakis. “This is a unique moment in time, one where we can bring the modern tools of machine learning to bear on questions of fundamental importance to biology and medicine.”

“The time is now ripe for biology to not only benefit from advances in machine learning, but to also drive the next generation of foundational mathematical insights. Biology and medicine are presenting deep and important questions, and generating vast datasets. These represent the substrate for a new era of discovery at the interface of the life sciences and machine learning.” said Yoshua Bengio, scientific director of Mila and 2018 ACM A.M. Turing Award recipient for his pioneering work on deep learning.

“This is the beginning of a journey that will unfold over many decades,” said Stuart Feldman, chief scientist at Schmidt Futures, the philanthropic initiative co-founded by Eric and Wendy Schmidt. “Scientists are close to cataloguing the components of life—genes, proteins, and cells. Our mission here is to understand, analyze, and model the entire cell taking a fresh perspective inspired by discrete mathematics and computer science, as well as three-dimensional time-varying physical models. These models will lead to new ways to manipulate cells and their internal structures and pathways.”

The gift for the Schmidt Center will be made to the Broad Institute from the Schwab Charitable Fund, made possible through the generosity of Eric and Wendy Schmidt at the recommendation of Schmidt Futures.

Launching with partnerships across academia and industry

“Machine learning is transforming scientific discovery, presenting tremendous opportunities in the biological sciences,” said Dan Huttenlocher, dean of the MIT Schwarzman College of Computing. “This new center is emblematic of Eric and Wendy Schmidt’s visionary support of scientific and technological advances to benefit humanity. We look forward to dynamic new collaborations with the center and life-changing results.”

“Medicine is experiencing a data revolution. Now, more than ever, technology, policy, and culture are converging, enabling us to unlock the full potential of real-world data for medical innovation,” said Dr. John Halamka, president of Mayo Clinic Platform. “We are excited to join forces with the Eric and Wendy Schmidt Center to solve some of the most complex medical problems.”

“Broad and Oxford have a long tradition of deep collaboration in human genetics and biomedical research,” said Cecilia Lindgren, incoming Director of the Oxford Big Data Institute, UK. “We are excited to enter a new phase of our partnership, one where we will work together to understand the programs of life through research at the interface of biology and machine learning.”

“The Turing is delighted to be working collaboratively with the Broad Institute, alongside the other outstanding institutes, and we look forward to the future knowledge exchange and research activity,” said Chris Holmes, program director for Health and Medical Sciences at The Alan Turing Institute. “Together, and with our partners at Health Data Research UK, we recognize the incredible potential that combining machine learning with biology presents and the considerable opportunities that lie ahead in improved understanding of biological systems that underlie diseases currently affecting people in all walks of society.”

“We’re on the cusp of a revolutionary period in which the digitization of human biology and the power of cloud computing and AI will yield previously unimaginable breakthroughs in human health and well-being,” said Kevin Scott, chief technology officer of Microsoft. “We’re thrilled to collaborate with the Schmidt Center and the Broad Institute and bring Microsoft’s technologies and global network of more than 168,000 health and life sciences partners to help drive that progress.”

“It is a privilege to be amongst the founding collaborators of the Schmidt Center, which fuses life-science research with modern machine learning and encourages partnership between industry and academic partners,” said Lindsay Edwards, vice president and head of AI, Respiratory and Immunology at AstraZeneca. “Research and innovation conducted at the Schmidt Center will deliver new insights into fundamental biology and could help us accelerate the discovery of life-changing medicines.”

“To solve the most pressing challenges in human health as efficiently and equitably as possible, it is essential that we build bridges across sectors and disciplines,” said Jay Bradner, president of the Novartis Institutes for BioMedical Research. “Wielding the full power of data science and AI within the life sciences could have profound implications for discovery and medicine. I commend Eric and Wendy Schmidt, The Broad Foundation, and the Broad Institute for their bold commitment and support for vital collaboration in this space.”

“Taking the rich interface between biology and machine learning and moving toward a genuine fusion of the two disciplines will require an engaged and fully bilingual research and learning community,” said Alex Bloemendal, co-chair of the Models, Inference and Algorithms initiative (MIA) at the Broad Institute. “We are thrilled about the potential for the Schmidt Center to accelerate and enable such transformation, and look forward to new partnerships as we continue building our community together,” added Aleks Goeva, also co-chair of MIA.

“The impact of this can reach beyond biomedicine and inspire efforts in other scientific disciplines,” said Golub. “The learnings from the fusion of biology with data science has the potential for massive impact, informing the fields of climate science, chemistry, materials science, and beyond.”

IMAGE CREDIT: The Broad Institute

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