SinaInnovations 2019: A Close-up Look at Artificial Intelligence

Keynote speaker Michael Snyder, PhD

What is the role of artificial intelligence (AI) in medicine, and how is it changing the practice of health care as we know it? That was the subject of the eighth annual SinaInnovations Conference, held Tuesday, October 15, and Wednesday, October 16, in Stern Auditorium. The event featured leading physicians and scientists from academia and industry who spoke about their work in deploying AI—the most powerful technology under development—to augment discovery and clinical use.

Experts shared their experiences in using AI in a variety of ways, from medical imaging, to predicting disease, to keeping people healthy, and highlighted the massive transformation taking place in health care and medicine, where software is driving innovation.

Michael Snyder, PhD, Chair of the Department of Genetics, and Director of the Center for Genomics and Personalized Medicine at Stanford University, a keynote speaker, discussed the role of AI in advancing personalized medicine. “I see a world where, with genome sequencing and continuous monitoring using wearable devices, we can better manage people’s health and hopefully do this at an individual level, and have personal machine-learning algorithms that follow people and their health state,” Dr. Snyder said. “We’re very capable of measuring more things, and here’s an area where AI can make a big impact.”

Melissa A. Haendel, PhD, Director of Translational Data Science at Oregon State University, spoke about her work in leading the federally funded Monarch Initiative, which is building sophisticated algorithms that integrate a multitude of data about rare diseases in order to improve research and clinical care. “No one group is actually annotating a disease model that has all the same attributes,” Dr. Haendel said. “We can’t even count the number of rare diseases.” Her team’s goal, she said, is to pull all of the data together and use it to build models that help physicians make earlier diagnoses, identify biomarkers of disease, and find better treatments.

Conference participants Heather J. Lynch, PhD, Associate Professor of Ecology and Evolution, Stony Brook University, left, and Georgia D. Tourassi, PhD, Director, Health Data Sciences Institute, Oak Ridge National Laboratory.

David Sontag, PhD, Associate Professor of Electrical Engineering and Computer Science at Massachusetts Institute of Technology, discussed how AI can be used to redesign electronic medical records so they can yield more reliable information on the patient’s risk for various diseases. In one case, he said, his team developed a machine-learning algorithm to help an infectious disease clinician at Massachusetts General Hospital and Brigham and Women’s Hospital reduce the number of unnecessary prescriptions for antibiotics.

AI is already playing a role in augmenting radiology. Keith J. Dreyer, DO, PhD, Vice Chairman, Radiology, at Massachusetts General Hospital and Chief Science Officer of the American College of Radiology, told the audience that “AI has huge value” and will be increasingly useful over time as the field matures.

In his keynote address, Pieter Abbeel, PhD, an entrepreneur and Professor of Electrical Engineering and Computer Science at the University of California, Berkeley, showed how deep machine learning takes place through constant repetition. In one example, he illustrated how a robot learns to run. After 2,000 iterations, it will become proficient. By comparison, a healthy human child would learn to run proficiently after roughly two weeks of practice. In many cases, he said, machines have achieved human-level error rates.

Among the many algorithms Stanford University is working on is one that recognizes the photo of a radiological image taken with a mobile phone, according to Curtis Langlotz, MD, PhD, Director of Stanford’s Center for Artificial Intelligence in Medicine and Imaging. This technology would allow general practitioners and other health care professionals in remote areas to use their mobile phones to access an algorithm that would assist them in making medical decisions when a radiologist is not available. For example, they would be able to determine whether a patient with, say, tuberculosis, should be discharged from the hospital.

Speakers and attendees at the conference agreed that AI is both promising and challenging. Suresh Venkatasubramanian, PhD, Professor of Computing at the University of Utah, cautioned that inherent bias in the data will create bias in the algorithms. “Models are fragile,” he said. “The Achilles heel is that the more sophisticated a system gets, especially with deep learning, the more sensitive it gets to small perturbations, and this could wreak havoc on the system.”

Greg Zaharchuk, MD, PhD, Professor of Radiology (Neuroimaging and Neurointervention) at Stanford University, concluded his talk with a nod to the future. “I think we’re only scratching the surface. This is a moment of extreme creativity, and it’s a very exciting time to be in the field.” Rather than replacing radiologists and other medical specialists, he added, AI “is really going to extend our abilities as physicians.”

New Gift Supports Young Entrepreneurs at Mount Sinai

This year, for the first time, a nonprofit biotech accelerator company founded by five former postdocs at the Icahn School of Medicine at Mount Sinai presented the school with a five-year, $50,000 gift to support young entrepreneurs in the New York City area whose science is being used to create therapies, devices, and diagnostics that support human health. The gift from The Keystone for Incubating Innovation in Life Sciences (KiiLN) went to Raymond A. Alvarez, PhD, Assistant Professor of Medicine (Infectious Diseases) at the Icahn School of Medicine at Mount Sinai, who is working on a platform that identifies and studies the antibodies of individuals who are immune to hantaviruses, which are spread by rodents and have a 38 percent mortality rate. Currently, there are no vaccines or treatments for hantaviruses.

 

2019 Mount Sinai Health Hackathon Winners

The three team finalists were: George:  Katie Depue, David Koellhofer, and Brendan Reilly.  Deliberate: Marc Aafjes, Michael Balangue, Do Hyung Kwon, Hansaim Lim, and Paulo Serodio. Deep Brain Precision: John Di Capua, Taylor Miller, Ashley So, and Danielle Soldin.

One hundred eighty medical and graduate students, and others, formed 19 teams to participate in the fourth annual Mount Sinai Health Hackathon in October. The 48-hour competition, held over the weekend leading up to the SinaInnovations Conference, challenged the participants to create novel health care solutions that would expand the limits of human performance.

Three teams each received checks totaling $2,500 and will have the opportunity to pitch their ideas again in 2020 at Mount Sinai’s Innovation Showcase before a group of entrepreneurs and venture capitalists. They will be joined by a fourth wild-card team chosen from the non-finalists.

Scott L. Friedman, MD, Dean for Therapeutic Discovery, and Chief of the Division of Liver Diseases at the Icahn School of Medicine at Mount Sinai, told the participants, “We started this event four years ago as part of a larger effort to spur innovation. This is really the embodiment of our values about teamwork and doing great things.”

The three team finalists were:

Deliberate: Improving the quality of care in psychotherapy through confidential recording and analysis. Team members: Marc Aafjes, Michael Balangue, Do Hyung Kwon, Hansaim Lim, and Paulo Serodio.

George: An artificial intelligence application that allows dialysis providers to optimize scheduling and improve a clinic’s efficiency. Team members: Katie Depue, David Koellhofer, and Brendan Reilly.

 Deep Brain Precision: An app that would allow physicians to monitor a patient’s progress after receiving deep brain stimulation for Parkinson’s disease and other motor disorders. Team members: John Di Capua, Taylor Miller, Ashley So, and Danielle Soldin.

Sponsors and partners: Accenture; Altice Business; Cisco; Farmer’s Fridge; Kitware; PepsiCo; Persistent Systems; the National Center for Advancing Translational Sciences, National Institutes of Health; and the Christopher & Dana Reeve Foundation.

Joining Forces to Create a New Digital Health Institute

From left: Dennis S. Charney, MD, Anne and Joel Ehrenkranz Dean, Icahn School of Medicine at Mount Sinai, and President for Academic Affairs, Mount Sinai Health System; and Christoph Meinel, PhD, Chief Executive Officer, Hasso Plattner Institute, and Dean, Joint Digital Engineering Faculty, Hasso Plattner Institute and University of Potsdam.

The Mount Sinai Health System and the Hasso Plattner Institute (HPI), a leading data science research and educational institution in Germany, have formed an affiliation that will combine their expertise in health care delivery, biomedical and digital engineering, and artificial intelligence. The aim is to develop digital health tools with real-time predictive and preventive capabilities that empower patients and health care providers and improve health outcomes.

Erwin P. Bottinger, MD, left, and Joel Dudley, PhD, are co-directors of the new Hasso Plattner Institute for Digital Health at Mount Sinai.

The newly formed Hasso Plattner Institute for Digital Health at Mount Sinai will be led by Joel Dudley, PhD, Executive Vice President for Precision Health, Mount Sinai Health System, Mount Sinai Professor in Biomedical Data Science, and Director of the Institute for Next Generation Healthcare, Icahn School of Medicine at Mount Sinai; and Erwin P. Bottinger, MD, Professor of Digital Health-Personalized Medicine, Hasso Plattner Institute, University of Potsdam, Germany, and Head of HPI’s Digital Health Center. A $15 million gift from the Hasso Plattner Foundation will establish the new Institute, which was announced in March at the Icahn School of Medicine.

“This endeavor will usher in a new era of digital health at Mount Sinai that advances the field of precision medicine,” says Dennis S. Charney, MD, Anne and Joel Ehrenkranz Dean, Icahn School of Medicine at Mount Sinai, and President for Academic Affairs, Mount Sinai Health System. “By leveraging our shared knowledge and academic excellence, Mount Sinai and HPI are positioned to find solutions that will revolutionize health care and science, and improve health nationally and globally.”

The Hasso Plattner Institute for Digital Health at Mount Sinai joins more than 20 institutes launched at the Icahn School of Medicine. Its goals include building a digital health population of engaged participants to collect comprehensive and longitudinal health data from wearable devices, genetic sequencing, and electronic health records; creating a cloud-based health data platform for research and care using machine learning and artificial intelligence; and researching and testing prototype digital health solutions for patients, providers, and health systems. Mount Sinai’s expertise in genomics, big data, supercomputing, and bioinformatics—along with a large and diverse patient population and an ability to translate from the lab directly to the clinic—provides a foundation for the Institute.

For example, the Institute for Next Generation Healthcare (INGH), under the leadership of Dr. Dudley, has developed a translational biomedical research model using advances in clinical medicine, digital health, and artificial intelligence, and INGH’s Lab 100 is leveraging data and technology to redesign the way health is measured and health care is delivered. In another innovative effort, the BioMe™ BioBank Program, housed at The Charles Bronfman Institute for Personalized Medicine at Mount Sinai, is enabling researchers to conduct genetic, epidemiologic, molecular, and genomic studies on large collections of research specimens linked with electronic health records. Until 2015, Dr. Bottinger was Professor of Medicine (Nephrology), and Pharmacological Sciences at the Icahn School of Medicine, and he helped lay the groundwork for the BioBank Program and The Institute for Personalized Medicine.

“Investigators at the Icahn School of Medicine at Mount Sinai and the Hasso Plattner Institute have been publishing groundbreaking work in the areas of genome diagnostics, precision medicine, digital health, biomedical data science, artificial intelligence, and information technology,” says Dr. Dudley. “We believe the new Institute will help turn the promise of digital health into reality at the front lines of next generation health care.”

Dr. Bottinger says, “We know we can save lives, prevent disease, and improve the health of patients with artificial intelligence in real-time analysis of health data from electronic health records, genetic information, and mobile sensor technologies.”

Two Studies Point to the Quality of Neoantigens in Determining Long-Term Cancer Survival

Benjamin Greenbaum, PhD

The quality, not quantity, of tumor neoantigens may best predict a patient’s response to cancer immunotherapy and his or her chance of long-term survival. That finding was based on two groundbreaking studies co-authored by Benjamin Greenbaum, PhD, Assistant Professor, Medicine (Hematology and Medical Oncology), and Pathology, Icahn School of Medicine at Mount Sinai. Now, it is being further explored by Dr. Greenbaum and Vinod Balachandran, MD, Memorial Sloan Kettering Cancer Center, through a Stand Up to Cancer Convergence 2.0 Grant and funding from the Lustgarten Foundation.

Their goal is to understand the underpinnings of pancreatic cancer survivorship, and their team is one of seven research groups that comprise Stand Up to Cancer’s broad $11 million initiative that was announced in January 2018. Neoantigens, or peptides found on the surface of cancer cells, are considered promising targets for cancer immunotherapy.

“Previous research has shown that T cell immunity is linked to exceptional outcomes for the few long-term survivors of pancreatic cancer, but it wasn’t clear if neoantigens played a role,” says Dr. Greenbaum. “Our newest research shows there are particular neoantigens that seem to be driving this long-term response in patients with pancreatic cancer, and further suggests that targeting those neoantigens might be a viable therapeutic strategy.”

According to Dr. Greenbaum, who was trained as a physicist and quantitative biologist, “One of the most exciting aspects of our work is collaborating with academic teams that can combine the tools and knowledge from diverse fields like theoretical physics, structural biology, mathematics, computer science, and translational genomics. We never lose sight of the fact that our combined efforts could one day result in clinical breakthroughs that benefit countless numbers of people.”

Earlier research formed the basis of the team’s efforts. In the first of two back-to-back studies published in Nature (November 2017), researchers described a mathematical model they developed—the first of its kind—to predict how a cancer patient would benefit from certain immunotherapies. Dr. Greenbaum was the senior author on this work with first author Marta Luksza, PhD, Assistant Professor of Oncological Sciences, Icahn School of Medicine at Mount Sinai.

By capturing aspects of a tumor’s evolution and ways in which it interacted with the underlying immune system, the new model appeared to offer an approach beyond previous biomarkers. Going forward, it also has the potential to uncover new therapeutic targets within the immune system, and help in the design of vaccines for patients who do not respond to immunotherapy.

The second study, whose first author was Dr. Balachandran, applied the modeling framework in order to better understand immune response in patients with pancreatic cancer and, more specifically, the unique role of neoantigens.

As part of the broad initiative, the Mount Sinai researchers are focused on better understanding what makes a neoantigen a good immune target, and the role of the microbiome in neoantigen recognition. By advancing the core science behind developing a vaccine for pancreatic cancer, the research could eventually improve treatment prospects for patients with this deadly form of the disease.

As they investigate the immune system’s response to cancers, the Convergence 2.0 team will be encouraged to draw upon the knowledge of Microsoft Research experts in machine learning and artificial intelligence. In addition to Dr. Luksza, the research team includes Nina Bhardwaj, MD, PhD, from the Icahn School of Medicine at Mount Sinai; and Eileen M. O’Reilly, MD; Taha Merghoub, PhD; and Jedd D. Wolchok, MD, PhD, from Memorial Sloan Kettering Cancer Center.

Machine Learning Techniques Generate Clinical Labels of Medical Scans


Researchers used machine learning techniques, including natural language processing algorithms, to identify clinical concepts in radiologist reports for CT scans, according to a study conducted at the Icahn School of Medicine at Mount Sinai and published in the journal Radiology.  The technology is an important first step in the development of artificial intelligence that could interpret scans and diagnose conditions.

Read the press release

Researchers Studying More Precise Methods for Prostate Cancer Screening

On the heels of new recommendations for prostate cancer screening, researchers at Mount Sinai are studying how to more precisely diagnose the disease.

“In prostate cancer, the primary method that clinicians use to characterize a cancer and decide on a treatment protocol is the Gleason grade, or the Gleason score, of the patient,” says Gerardo Fernandez, MD, the Medical Director of Pathology at Mount Sinai St. Luke’s  in New York. “Over the years, though, it turns out that we have over-treated prostate cancer by quite a bit. So the idea of having cancer leads a lot of patients to decide on radical treatments, namely surgery. What we’re trying to do is characterize prostate cancer more effectively than just by using the Gleason score.”

He adds: “Google might use similar techniques to characterize facial properties that allows them to do facial recognition software. We apply similar computer and engineering technology to images of cancer — how separated are the nuclei from one another, how bigger the nuclei, what protein markers do those nuclei contain. So we characterize these images with complex methods, and we extract these features out of them. Now, once we have the features, we use artificial intelligence-type approaches to take all of that data and figure out what combinations of features do a better job of predicting the behavior of the cancer than Gleason alone.”

 

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