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Bryan He, Alan C. Kwan, Jae Hyung Cho, Neal Yuan, Charles Pollick, Takahiro Shiota, Joseph Ebinger, Natalie A. Bello, Janet Wei, Kiranbir Josan, Grant Duffy, Melvin Jujjavarapu, Robert Siegel, Susan Cheng, James Y. Zou, and David Ouyang
Nature, 2023.
Artificial intelligence (AI) has been developed for echocardiography, although it has not yet been tested with blinding and randomization. Here we designed a blinded, randomized non-inferiority clinical trial (ClinicalTrials.gov ID: NCT05140642; no outside funding) of AI versus sonographer initial assessment of left ventricular ejection fraction (LVEF) to evaluate the impact of AI in the interpretation workflow. The primary end point was the change in the LVEF between initial AI or sonographer assessment and final cardiologist assessment, evaluated by the proportion of studies with substantial change (more than 5% change). From 3,769 echocardiographic studies screened, 274 studies were excluded owing to poor image quality. The proportion of studies substantially changed was 16.8% in the AI group and 27.2% in the sonographer group (difference of −10.4%, 95% confidence interval: −13.2% to −7.7%, P < 0.001 for non-inferiority, P < 0.001 for superiority). The mean absolute difference between final cardiologist assessment and independent previous cardiologist assessment was 6.29% in the AI group and 7.23% in the sonographer group (difference of −0.96%, 95% confidence interval: −1.34% to −0.54%, P < 0.001 for superiority). The AI-guided workflow saved time for both sonographers and cardiologists, and cardiologists were not able to distinguish between the initial assessments by AI versus the sonographer (blinding index of 0.088). For patients undergoing echocardiographic quantification of cardiac function, initial assessment of LVEF by AI was non-inferior to assessment by sonographers.
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Bryan He, Ludvig Bergenstråhle, Linnea Stenbeck, Abubakar Abid, Alma Andersson, Åke Borg, Jonas Maaskola, Joakim Lundeberg, and James Zou
Nature Biomedical Engineering, 2020.
Spatial transcriptomics allows for the measurement of RNA abundance at a high spatial resolution, making it possible to systematically link the morphology of cellular neighbourhoods and spatially localized gene expression. Here, we report the development of a deep learning algorithm for the prediction of local gene expression from haematoxylin-and-eosin-stained histopathology images using a new dataset of 30,612 spatially resolved gene expression data matched to histopathology images from 23 patients with breast cancer. We identified over 100 genes, including known breast cancer biomarkers of intratumoral heterogeneity and the co-localization of tumour growth and immune activation, the expression of which can be predicted from the histopathology images at a resolution of 100 µm. We also show that the algorithm generalizes well to The Cancer Genome Atlas and to other breast cancer gene expression datasets without the need for re-training. Predicting the spatially resolved transcriptome of a tissue directly from tissue images may enable image-based screening for molecular biomarkers with spatial variation.
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David Ouyang, Bryan He, Amirata Ghorbani, Neal Yuan, Joseph Ebinger, Curt P. Langlotz, Paul A. Heidenreich, Robert A. Harrington, David H. Liang, Euan A. Ashley, and James Y. Zou
Nature, 2020.
Accurate assessment of cardiac function is crucial for the diagnosis of cardiovascular disease, screening for cardiotoxicity and decisions regarding the clinical management of patients with a critical illness. However, human assessment of cardiac function focuses on a limited sampling of cardiac cycles and has considerable inter-observer variability despite years of training. Here, to overcome this challenge, we present a video-based deep learning algorithm—EchoNet-Dynamic—that surpasses the performance of human experts in the critical tasks of segmenting the left ventricle, estimating ejection fraction and assessing cardiomyopathy. Trained on echocardiogram videos, our model accurately segments the left ventricle with a Dice similarity coefficient of 0.92, predicts ejection fraction with a mean absolute error of 4.1% and reliably classifies heart failure with reduced ejection fraction (area under the curve of 0.97). In an external dataset from another healthcare system, EchoNet-Dynamic predicts the ejection fraction with a mean absolute error of 6.0% and classifies heart failure with reduced ejection fraction with an area under the curve of 0.96. Prospective evaluation with repeated human measurements confirms that the model has variance that is comparable to or less than that of human experts. By leveraging information across multiple cardiac cycles, our model can rapidly identify subtle changes in ejection fraction, is more reproducible than human evaluation and lays the foundation for precise diagnosis of cardiovascular disease in real time. As a resource to promote further innovation, we also make publicly available a large dataset of 10,030 annotated echocardiogram videos.
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Bryan He, Milos Vukadinovic, Grant Duffy, James Zou, David Ouyang
Preprint, 2024
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Teaching
I was a teaching assistant at Stanford:
CS 221: Artificial Intelligence: Principles and Techniques
Spring 2018
CS 221: Artificial Intelligence: Principles and Techniques
Fall 2017
I was a teaching assistant for the following courses at Caltech:
CS 155: Machine Learning/Data Mining
Winter 2015
CS 156a: Learning Systems
Fall 2014
CS 156b: Learning Systems
Spring 2014
CS 2: Introduction to Programming Methods
Winter 2013
Open-source Contributions and Personal Projects
Replication of the supervised part of Alphago (learning to select moves and predict winner using human training data)
Alphazero implementation for Connect Four