Shruthi Prabhakara
Shruthi Prabhakara leads a team in Google Health whose mission is to research and develop state-of-the-art medical imaging products backed by Google's ML R&D technology. Prior to this, she has led teams in research (Perception, Augmented Reality) and personalized advertising. Her PhD. work at Pennsylvania State University's CSE department focused on problems at the intersection of machine learning and bioinformatics.
Authored Publications
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General Geospatial Inference with a Population Dynamics Foundation Model
Chaitanya Kamath
Shravya Shetty
David Schottlander
Yael Mayer
Joydeep Paul
Jamie McPike
Sheila de Guia
Niv Efron
(2024) (to appear)
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Understanding complex relationships between human behavior and local contexts is crucial for various applications in public health, social science, and environmental studies. Traditional approaches often make use of small sets of manually curated, domain-specific variables to represent human behavior, and struggle to capture these intricate connections, particularly when dealing with diverse data types. To address this challenge, this work introduces a novel approach that leverages the power of graph neural networks (GNNs). We first construct a large dataset encompassing human-centered variables aggregated at postal code and county levels across the United States. This dataset captures rich information on human behavior (internet search behavior and mobility patterns) along with environmental factors (local facility availability, temperature, and air quality). Next, we propose a GNN-based framework designed to encode the connections between these diverse features alongside the inherent spatial relationships between postal codes and their containing counties. We then demonstrate the effectiveness of our approach by benchmarking the model on 27 target variables spanning three distinct domains: health, socioeconomic factors, and environmental measurements. Through spatial interpolation, extrapolation, and super-resolution tasks, we show that the proposed method can effectively utilize the rich feature set to achieve accurate predictions across diverse geospatial domains.
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Assistive AI in Lung Cancer Screening: A Retrospective Multinational Study in the United States and Japan
Atilla Kiraly
Corbin Cunningham
Ryan Najafi
Jie Yang
Chuck Lau
Diego Ardila
Scott Mayer McKinney
Rory Pilgrim
Mozziyar Etemadi
Sunny Jansen
Lily Peng
Shravya Shetty
Neeral Beladia
Krish Eswaran
Radiology: Artificial Intelligence (2024)
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Lung cancer is the leading cause of cancer death world-wide with 1.8 million deaths in 20201. Studies have concluded that low-dose computed tomography lung cancer screening can reduce mortality by up to 61%2 and updated 2021 US guidelines expanded eligibility. As screening efforts rise, AI can play an important role, but must be unobtrusively integrated into existing clinical workflows. In this work, we introduce a state-of-the-art, cloud-based AI system providing lung cancer risk assessments without requiring any user input. We demonstrate its efficacy in assisting lung cancer screening under both US and Japanese screening settings using different patient populations and screening protocols. Technical improvements over a previously described system include a focus on earlier cancer detection for improved accuracy, introduction of an effective assistive user interface, and a system designed to integrate into typical clinical workflows. The stand-alone AI system was evaluated on 3085 individuals achieving area under the curve (AUC) scores of 91.7% (95%CI [89.6, 95.2]), 93.3% (95%CI [90.2, 95.7]), and 89.1% (95%CI [77.7, 97.3]) on three datasets (two from US and one from Japan), respectively. To evaluate the system’s assistive ability, we conducted two retrospective multi-reader multi-case studies on 627 cases read by experienced board certified radiologists (average 20 years of experience [7,40]) using local PACS systems in the respective US and Japanese screening settings. The studies measured the reader’s level of suspicion (LoS) and categorical responses for scores and management recommendations under country-specific screening protocols. The radiologists’ AUC for LoS increased with AI assistance by 2.3% (95%CI [0.1-4.5], p=0.022) for the US study and by 2.3% (95%CI [-3.5-8.1], p=0.179) for the Japan study. Specificity for recalls increased by 5.5% (95%CI [2.7-8.5], p<0.0001) for the US and 6.7% (95%CI [4.7-8.7], p<0.0001) for the Japan study. No significant reduction in other metrics occured. This work advances the state-of-the-art in lung cancer detection, introduces generalizable interface concepts that can be applicable to similar AI applications, and demonstrates its potential impact on diagnostic AI in global lung cancer screening with results suggesting a substantial drop in unnecessary follow-up procedures without impacting sensitivity.
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An intentional approach to managing bias in embedding models
Atilla P. Kiraly
Jungyeon Park
Rory Pilgrim
Charles Lau
Heather Cole-Lewis
Shravya Shetty
Krish Eswaran
Leo Anthony Celi
The Lancet Digital Health, 6 (2024), E126-E130
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Advances in machine learning for health care have brought concerns about bias from the research community; specifically, the introduction, perpetuation, or exacerbation of care disparities. Reinforcing these concerns is the finding that medical images often reveal signals about sensitive attributes in ways that are hard to pinpoint by both algorithms and people. This finding raises a question about how to best design general purpose pretrained embeddings (GPPEs, defined as embeddings meant to support a broad array of use cases) for building downstream models that are free from particular types of bias. The downstream model should be carefully evaluated for bias, and audited and improved as appropriate. However, in our view, well intentioned attempts to prevent the upstream components—GPPEs—from learning sensitive attributes can have unintended consequences on the downstream models. Despite producing a veneer of technical neutrality, the resultant end-to-end system might still be biased or poorly performing. We present reasons, by building on previously published data, to support the reasoning that GPPEs should ideally contain as much information as the original data contain, and highlight the perils of trying to remove sensitive attributes from a GPPE. We also emphasise that downstream prediction models trained for specific tasks and settings, whether developed using GPPEs or not, should be carefully designed and evaluated to avoid bias that makes models vulnerable to issues such as distributional shift. These evaluations should be done by a diverse team, including social scientists, on a diverse cohort representing the full breadth of the patient population for which the final model is intended.
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Predicting Cardiovascular Disease Risk using Photoplethysmography and Deep Learning
Sebastien Baur
Christina Chen
Mariam Jabara
Babak Behsaz
Shravya Shetty
Goodarz Danaei
Diego Ardila
PLOS Glob Public Health, 4(6) (2024), e0003204
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Cardiovascular diseases (CVDs) are responsible for a large proportion of premature deaths in low- and middle-income countries. Early CVD detection and intervention is critical in these populations, yet many existing CVD risk scores require a physical examination or lab measurements, which can be challenging in such health systems due to limited accessibility. We investigated the potential to use photoplethysmography (PPG), a sensing technology available on most smartphones that can potentially enable large-scale screening at low cost, for CVD risk prediction. We developed a deep learning PPG-based CVD risk score (DLS) to predict the probability of having major adverse cardiovascular events (MACE: non-fatal myocardial infarction, stroke, and cardiovascular death) within ten years, given only age, sex, smoking status and PPG as predictors. We compare the DLS with the office-based refit-WHO score, which adopts the shared predictors from WHO and Globorisk scores (age, sex, smoking status, height, weight and systolic blood pressure) but refitted on the UK Biobank (UKB) cohort. All models were trained on a development dataset (141,509 participants) and evaluated on a geographically separate test (54,856 participants) dataset, both from UKB. DLS’s C-statistic (71.1%, 95% CI 69.9–72.4) is non-inferior to office-based refit-WHO score (70.9%, 95% CI 69.7–72.2; non-inferiority margin of 2.5%, p<0.01) in the test dataset. The calibration of the DLS is satisfactory, with a 1.8% mean absolute calibration error. Adding DLS features to the office-based score increases the C-statistic by 1.0% (95% CI 0.6–1.4). DLS predicts ten-year MACE risk comparable with the office-based refit-WHO score. Interpretability analyses suggest that the DLS-extracted features are related to PPG waveform morphology and are independent of heart rate. Our study provides a proof-of-concept and suggests the potential of a PPG-based approach strategies for community-based primary prevention in resource-limited regions.
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ELIXR: Towards a general purpose X-ray artificial intelligence system through alignment of large language models and radiology vision encoders
Shawn Xu
Lin Yang
Christopher Kelly
Timo Kohlberger
Martin Ma
Atilla Kiraly
Sahar Kazemzadeh
Zakkai Melamed
Jungyeon Park
Patricia MacWilliams
Chuck Lau
Christina Chen
Mozziyar Etemadi
Sreenivasa Raju Kalidindi
Kat Chou
Shravya Shetty
Daniel Golden
Rory Pilgrim
Krish Eswaran
arxiv (2023)
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Our approach, which we call Embeddings for Language/Image-aligned X-Rays, or ELIXR, leverages a language-aligned image encoder combined or grafted onto a fixed LLM, PaLM 2, to perform a broad range of tasks. We train this lightweight adapter architecture using images paired with corresponding free-text radiology reports from the MIMIC-CXR dataset. ELIXR achieved state-of-the-art performance on zero-shot chest X-ray (CXR) classification (mean AUC of 0.850 across 13 findings), data-efficient CXR classification (mean AUCs of 0.893 and 0.898 across five findings (atelectasis, cardiomegaly, consolidation, pleural effusion, and pulmonary edema) for 1% (~2,200 images) and 10% (~22,000 images) training data), and semantic search (0.76 normalized discounted cumulative gain (NDCG) across nineteen queries, including perfect retrieval on twelve of them). Compared to existing data-efficient methods including supervised contrastive learning (SupCon), ELIXR required two orders of magnitude less data to reach similar performance. ELIXR also showed promise on CXR vision-language tasks, demonstrating overall accuracies of 58.7% and 62.5% on visual question answering and report quality assurance tasks, respectively. These results suggest that ELIXR is a robust and versatile approach to CXR AI.
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Optimizing Audio Augmentations for Contrastive Learning of Health-Related Acoustic Signals
Louis Blankemeier
Sebastien Baur
Diego Ardila
arXiv (2023)
Deep Learning Detection of Active Pulmonary Tuberculosis at Chest Radiography Matched the Clinical Performance of Radiologists
Sahar Kazemzadeh
Jin Yu
Shahar Jamshy
Rory Pilgrim
Christina Chen
Neeral Beladia
Chuck Lau
Scott Mayer McKinney
Thad Hughes
Atilla Peter Kiraly
Sreenivasa Raju Kalidindi
Monde Muyoyeta
Jameson Malemela
Ting Shih
Lily Hao Yi Peng
Kat Chou
Cameron Chen
Krish Eswaran
Shravya Ramesh Shetty
Radiology (2022)
Preview abstract
Background: The World Health Organization (WHO) recommends chest radiography to facilitate tuberculosis (TB) screening. However, chest radiograph interpretation expertise remains limited in many regions. Purpose: To develop a deep learning system (DLS) to detect active pulmonary TB on chest radiographs and compare its performance to that of radiologists. Materials and Methods: A DLS was trained and tested using retrospective chest radiographs (acquired between 1996 and 2020) from 10 countries. To improve generalization, large-scale chest radiograph pretraining, attention pooling, and semisupervised learning (“noisy-student”) were incorporated. The DLS was evaluated in a four-country test set (China, India, the United States, and Zambia) and in a mining population in South Africa, with positive TB confirmed with microbiological tests or nucleic acid amplification testing (NAAT). The performance of the DLS was compared with that of 14 radiologists. The authors studied the efficacy of the DLS compared with that of nine radiologists using the Obuchowski-Rockette-Hillis procedure. Given WHO targets of 90% sensitivity and 70% specificity, the operating point of the DLS (0.45) was prespecified to favor sensitivity. Results: A total of 165 754 images in 22 284 subjects (mean age, 45 years; 21% female) were used for model development and testing. In the four-country test set (1236 subjects, 17% with active TB), the receiver operating characteristic (ROC) curve of the DLS was higher than those for all nine India-based radiologists, with an area under the ROC curve of 0.89 (95% CI: 0.87, 0.91). Compared with these radiologists, at the prespecified operating point, the DLS sensitivity was higher (88% vs 75%, P < .001) and specificity was noninferior (79% vs 84%, P = .004). Trends were similar within other patient subgroups, in the South Africa data set, and across various TB-specific chest radiograph findings. In simulations, the use of the DLS to identify likely TB-positive chest radiographs for NAAT confirmation reduced the cost by 40%–80% per TB-positive patient detected. Conclusion: A deep learning method was found to be noninferior to radiologists for the determination of active tuberculosis on digital chest radiographs.
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Supervised Transfer Learning at Scale for Medical Imaging
Aaron Loh
Basil Mustafa
Jan Freyberg
Neil Houlsby
Patricia MacWilliams
Megan Wilson
Scott Mayer McKinney
Jim Winkens
Peggy Bui
Umesh Telang
ArXiV (2021)
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Transfer learning is a standard building block of successful medical imaging models, yet previous efforts suggest that at limited scale of pre-training data and model capacity, benefits of transfer learning to medical imaging are insubstantial. In this work, we explore whether scaling up pre-training can help improve transfer to medical tasks. In particular, we show that when using the Big Transfer recipe to further scale up pre-training, we can indeed considerably improve transfer performance across three popular yet diverse medical imaging tasks - interpretation of chest radiographs, breast cancer detection from mammograms and skin condition detection from smartphone images. Despite pre-training on unrelated source domains, we show that scaling up the model capacity and pre-training data yields performance improvements regardless of how much downstream medical data is available. In particular, we show suprisingly large improvements to zero-shot generalisation under distribution shift. Probing and quantifying other aspects of model performance relevant to medical imaging and healthcare, we demonstrate that these gains do not come at the expense of model calibration or fairness.
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