Author Interviews, Nature, Technology, University of Pittsburgh / 26.02.2024
SLIDE: Machine Learning Technique Can Infer Hidden States Underlying/Driving Disease Processes
MedicalResearch.com Interview with:
[caption id="attachment_61350" align="alignleft" width="150"]
Dr. Das[/caption]
Jishnu Das, Ph.D.
Center for Systems Immunology
Departments of Immunology and Computational & Systems Biology,
Assistant Professor School of Medicine
University of Pittsburgh
MedicalResearch.com: What is the background for this study? How does this new AI model work? How is it different from other models?
Response: Modern multi-omic technologies generate an enormous amount of data across scales of organization, and with differing resolution. While recent machine learning methods have harnessed these to predict clinical/physiological outcomes, they are often black boxes that do not provide meaningful inference beyond prediction. Differences in data generation modalities, redundancy in the data, as well as large numbers of irrelevant features make inference of biological mechanisms from high-dimensional omic datasets challenging.
To address these challenges, we developed a machine learning technique called SLIDE (Significant Latent Factor Interaction Discovery and Exploration). We reasoned that features that are directly measured by current technologies are constrained by strengths and weaknesses of current platforms. So, while some observed features may be excellent correlates of outcomes of interest, inferring biological mechanisms from these multi-omic datasets requires us to delve beyond the observable into the hidden states, i.e., latent factors. These hidden states encapsulate the true drivers of underlying biological processes and capture a complex multi-scale interplay between entities measured by these datasets. Our method moves beyond simple biomarkers/correlates (“the what”) to hidden states that actually explain clinical/physiological outcomes (“the how” and “the why”).
Dr. Das[/caption]
Jishnu Das, Ph.D.
Center for Systems Immunology
Departments of Immunology and Computational & Systems Biology,
Assistant Professor School of Medicine
University of Pittsburgh
MedicalResearch.com: What is the background for this study? How does this new AI model work? How is it different from other models?
Response: Modern multi-omic technologies generate an enormous amount of data across scales of organization, and with differing resolution. While recent machine learning methods have harnessed these to predict clinical/physiological outcomes, they are often black boxes that do not provide meaningful inference beyond prediction. Differences in data generation modalities, redundancy in the data, as well as large numbers of irrelevant features make inference of biological mechanisms from high-dimensional omic datasets challenging.
To address these challenges, we developed a machine learning technique called SLIDE (Significant Latent Factor Interaction Discovery and Exploration). We reasoned that features that are directly measured by current technologies are constrained by strengths and weaknesses of current platforms. So, while some observed features may be excellent correlates of outcomes of interest, inferring biological mechanisms from these multi-omic datasets requires us to delve beyond the observable into the hidden states, i.e., latent factors. These hidden states encapsulate the true drivers of underlying biological processes and capture a complex multi-scale interplay between entities measured by these datasets. Our method moves beyond simple biomarkers/correlates (“the what”) to hidden states that actually explain clinical/physiological outcomes (“the how” and “the why”).
Dr. Traverso[/caption]
Giovanni Traverso MD PhD
Karl Van Tassel (1925) Career Development Professor
Department of Mechanical Engineering
Koch Institute of Integrative Cancer Research
Division of Gastroenterology
Brigham and Women’s Hospital
Harvard Medical School, Boston, MA, USA
MedicalResearch.com: What is the background for this study?
Response: I think its always important to acknowledge that this is a big team effort. We have the teams from MIT, Celero Systems, West Virgnia University (WVU) and Brigham and Women’s Hospital (BWH) all working together on this. For this study, Celero prototyped the devices that we tested in pre-clinical (Swine) models and in a first-in-human study with the team at WVU.
Our lab focuses on the development of ingestible devices for drug delivery and sensing and these have informed the development of these efforts as you can see.
Dr. Hidde ten Berg[/caption]
Dr. Hidde ten Berg
Department Emergency Medicine and
[caption id="attachment_60847" align="alignleft" width="125"]
Dr. Steef Kurstjens[/caption]
Dr. Steef Kurstjens
Department of Clinical cChemistry and Haematology
Jeroen Bosch Hospital, 's-Hertogenbosch, The Netherlands
MedicalResearch.com: What is the background for this study?
Response: At this moment we are still in the exploratory phase, and therefore, there is no widespread or routine usage of ChatGPT in Emergency Medicine. That said, there are instances where individual physicians have used ChatGPT for specific purposes. These may include facilitating bureaucratic tasks that can often be time-consuming, aiding in writing e-mails or texts, and serving as a brainstorming tool when dealing with complex medical cases and questions. Though not yet a standardized practice, these isolated examples demonstrate a growing interest for the potential application of this novel technology.
Mr. Londoner[/caption]
Ken Londoner, MBA
Founder, Chief Executive Officer, Chairman, and Director
Ali M. Fazlollahi[/caption]
Ali M. Fazlollahi, MSc, McGill Medicine Class of 2025
Neurosurgical Simulation and Artificial Intelligence Learning Centre
Department of Neurology and Neurosurgery, Montreal Neurological Institute and Hospital
Faculty of Medicine and Health Sciences
McGill University, Montreal, Canada
MedicalResearch.com: What is the background for this study?
Response: COVID-19 disrupted hands on surgical exposure of medical students and academic centres around the world had to quickly adapt to teaching technical skills remotely. At the same time, advances in artificial intelligence (AI) allowed researchers at the Neurosurgical Simulation and Artificial Intelligence Learning Centre to develop an intelligent tutoring system that evaluates performance and provides high-quality personalized feedback to students. Because this is the first AI system capable of providing surgical instructions in simulation, we sought to evaluate its effectiveness compared with learning from expert human instructors who provided coaching remotely.
Dr. Torkamani[/caption]
Ali Torkamani, Ph.D.
Director of Genomics and Genome Informatics
Scripps Research Translational Institute
Professor, Integrative Structural and Computational Biology
Scripps Research
La Jolla, CA 92037
MedicalResearch.com: What is the background for this study?
Response: Prior research has shown that people with higher polygenic risk for coronary artery disease achieve greater risk reduction with statin or other lipid lowering therapy. In general, adherence to standard guidelines for lipid lowering therapy is low - about 30% of people who should be on lipid lowering therapy are, with no correlation to their genetic risk. We set out to see whether communicating personalized risk, including polygenic risk, for coronary artery disease would drive the adoption of lipid lowering therapy.
Dr. Pollitt[/caption]
Krystal Pollitt, PhD, P.Eng.
Assistant Professor of Epidemiology (Environmental Health Sciences)
Assistant Professor in Chemical and Environmental Engineering
Affiliated Faculty, Yale Institute for Global Health
Yale School of Public Health
MedicalResearch.com: What is the background for this study?
Response: People infected with COVID-19 can release SARS-CoV-2 virus in aerosol and droplets when they exhale. This can be from coughing or sneezing but also when they speaker or just breathe. While the larger droplets can settle to the ground quickly (seconds to minutes), smaller aerosol can remain in the air in longer periods (minutes to hours). SARS-CoV-2 can be transmitted by inhaling aerosol or droplets containing infectious virus. The Fresh Air Clip enables detection of droplet and aerosol containing virus.
Response: Point-of-care ultrasound is one of the most significant advances in bedside patient care, and its use is expanding across nearly all fields of medicine. In order to best prepare medical students for residency and beyond, it is imperative to begin POCUS training as early as possible. At the Lewis Katz School of Medicine at Temple University, we introduced POCUS education over a decade ago and have expanded it since then.
By providing each student with a Butterfly iQ device, we can augment our curriculum significantly. In addition to our robust pre-clinical sessions, now we will expand into the clinical years highlighting the utility of POCUS with actual patients.
This gift was made possible by the incredible generosity of Dr. Ronald Salvitti, MD ’63.
Dr. Ferrara[/caption]
Michele Ferrara, PhD.
Professor of Psychobiology and Physiological Psychology
Chair of the Psychology Didactic Council
Department of Biotechnological and Applied Clinical Sciences
University of L'Aquila
MedicalResearch.com: What is the background for this study?
Response: During the current period of social distancing, the pervasive increase in the use of electronic devices (smartphones, computers, tablets and televisions) is an indisputable fact. Especially during the long lockdown period of Spring 2020, technologies played a pivotal role in coping with the unprecedented and stressful isolation phase. However, exposure to backlit screens in the hours before falling asleep can have serious repercussions on sleep health: on the one hand, by mimicking the effects of exposure to sunlight, and thus interfering with the circadian rhythm of the hormone melatonin, and on the other hand, counteracting the evening sleepiness due to the emotionally and psycho-physiologically activating contents.
In light of this assumption, we decided to test longitudinally during the third and the seventh week of lockdown a large Italian sample (2123 subjects) through a web-based survey. We assessed sleep disturbances/habits and the occurring changes of electronic device usage in the 2 hours before the sleep onset.
Dani Clode[/caption]
Dani Clode
Designer & Senior Research Technician
Plasticity Laboratory
Institute of Cognitive Neuroscience
University College London
MedicalResearch.com: What was the inspiration behind creating the Third Thumb?
[caption id="attachment_57498" align="alignleft" width="145"]
Dr. Navlakha[/caption]
Saket Navlakha PhD
Simons Center for Quantitative Biology
Cold Spring Harbor Laboratory
Cold Spring Harbor, NY
MedicalResearch.com: What is the background for this algorithm? How does it aide in patient care?
Response: The machine learning algorithm helps to predict if and when a patient will develop severe COVID symptoms, based on information on how the patient presents on the day of infection. This could lead to improved patient outcomes, by getting a “heads up” on what may happen in the near future.
Dr. Peruvemba[/caption]
Ramani “Ram” Peruvemba, MD, FASA
Co-founder and CMO of HSR.health
MedicalResearch.com: Would you tell us about your background?
Response: I am a dual-board certified Anesthesiologist and Pain Management physician, currently serving as the co-founder and CMO of
Dr. Yun Liu[/caption]
Yun Liu, PhD
Google Health
Palo Alto, California
MedicalResearch.com: What is the background for this study? Would you describe the system? Does it use dermatoscopic images?
Response: Dermatologic conditions are extremely common and a leading cause of morbidity worldwide. Due to limited access to dermatologists, patients often first seek help from non-specialists. However, non-specialists have been reported to have lower diagnostic accuracies compared to dermatologists, which may impact the quality of care.
In this study, we built upon prior work published in
Dr. Traverso[/caption]
Carlo Giovanni Traverso, MB, BChir, PhD
Associate Physician, Brigham and Women's Hospital
Assistant Professor,
[caption id="attachment_56823" align="alignleft" width="150"]
Dr. Chai[/caption]
Peter R. Chai, MD, MMS
Emergency Medicine Physician and Medical Toxicologist
Harvard Medical School
Brigham and Women's Hospital
Department of Medicine
MedicalResearch.com: What is the background for this study? What are some of the functions that Dr. Spot can facilitate?
Response: During the COVID-19 pandemic, we wanted to consider innovative methods to provide additional social distance for physicians evaluating low acuity individuals who may have COVID-19 disease in the emergency department. While other health systems had instituted processes like evaluating patients from outside of emergency department rooms or calling patients to obtain a history, we considered the use of a mobile robotic system in collaboration with Boston Dynamics to provide telemedicine triage on an agile platform that could be navigated around a busy emergency department. Dr. Spot was built with a camera system to help an operator navigate it through an emergency department into a patient room where an on-board tablet would permit face-to-face triage and assessment of individuals.