Yun Liu
Yun is a senior staff research scientist in Google Research. In this role he focuses on developing and validating machine learning for medical applications across multiple fields: pathology, ophthalmology, radiology, dermatology, and more. Yun completed his PhD at Harvard-MIT Health Sciences and Technology, where he worked on predictive risk modeling using biomedical signals, medical text, and billing codes. He has previously also worked on predictive modeling for nucleic acid sequences and protein structures. Yun completed a B.S. in Molecular and Cellular Biology and Computer Science at Johns Hopkins University.
Research Areas
Authored Publications
Sort By
Prospective Multi-Site Validation of AI to Detect Tuberculosis and Chest X-Ray Abnormalities
Sahar Kazemzadeh
Atilla Kiraly
Nsala Sanjase
Minyoi Maimbolwa
Brian Shuma
Shahar Jamshy
Christina Chen
Arnav Agharwal
Chuck Lau
Daniel Golden
Jin Yu
Eric Wu
Kat Chou
Shravya Shetty
Krish Eswaran
Rory Pilgrim
Monde Muyoyeta
NEJM AI (2024)
Preview abstract
Background
Using artificial intelligence (AI) to interpret chest X-rays (CXRs) could support accessible triage tests for active pulmonary tuberculosis (TB) in resource-constrained settings.
Methods
The performance of two cloud-based CXR AI systems — one to detect TB and the other to detect CXR abnormalities — in a population with a high TB and human immunodeficiency virus (HIV) burden was evaluated. We recruited 1978 adults who had TB symptoms, were close contacts of known TB patients, or were newly diagnosed with HIV at three clinical sites. The TB-detecting AI (TB AI) scores were converted to binary using two thresholds: a high-sensitivity threshold and an exploratory threshold designed to resemble radiologist performance. Ten radiologists reviewed images for signs of TB, blinded to the reference standard. Primary analysis measured AI detection noninferiority to radiologist performance. Secondary analysis evaluated AI detection as compared with the World Health Organization (WHO) targets (90% sensitivity, 70% specificity). Both used an absolute margin of 5%. The abnormality-detecting AI (abnormality AI) was evaluated for noninferiority to a high-sensitivity target suitable for triaging (90% sensitivity, 50% specificity).
Results
Of the 1910 patients analyzed, 1827 (96%) had conclusive TB status, of which 649 (36%) were HIV positive and 192 (11%) were TB positive. The TB AI’s sensitivity and specificity were 87% and 70%, respectively, at the high-sensitivity threshold and 78% and 82%, respectively, at the balanced threshold. Radiologists’ mean sensitivity was 76% and mean specificity was 82%. At the high-sensitivity threshold, the TB AI was noninferior to average radiologist sensitivity (P<0.001) but not to average radiologist specificity (P=0.99) and was higher than the WHO target for specificity but not sensitivity. At the balanced threshold, the TB AI was comparable to radiologists. The abnormality AI’s sensitivity and specificity were 97% and 79%, respectively, with both meeting the prespecified targets.
Conclusions
The CXR TB AI was noninferior to radiologists for active pulmonary TB triaging in a population with a high TB and HIV burden. Neither the TB AI nor the radiologists met WHO recommendations for sensitivity in the study population. AI can also be used to detect other CXR abnormalities in the same population.
View details
Searching for Dermatology Information Online using Images vs Text: a Randomized Study
Jay Hartford
Natalie Salaets
Kimberley Raiford
Jay Nayar
Dounia Berrada
Harsh Kharbanda
Lou Wang
Peggy Bui
medRxiv (2024)
Preview abstract
Background Skin conditions are extremely common worldwide, and are an important cause of both anxiety and morbidity. Since the advent of the internet, individuals have used text-based search (eg, “red rash on arm”) to learn more about concerns on their skin, but this process is often hindered by the inability to accurately describe the lesion’s morphology. In the study, we surveyed respondents’ experiences with an image-based search, compared to the traditional text-based search experience.
Methods An internet-based survey was conducted to evaluate the experience of text-based vs image-based search for skin conditions. We recruited respondents from an existing cohort of volunteers in a commercial survey panel; survey respondents that met inclusion/exclusion criteria, including willingness to take photos of a visible concern on their body, were enrolled. Respondents were asked to use the Google mobile app to conduct both regular text-based search (Google Search) and image-based search (Google Lens) for their concern, with the order of text vs. image search randomized. Satisfaction for each search experience along six different dimensions were recorded and compared, and respondents’ preferences for the different search types along these same six dimensions were recorded.
Results 372 respondents were enrolled in the study, with 44% self-identifying as women, 86% as White and 41% over age 45. The rate of respondents who were at least moderately familiar with searching for skin conditions using text-based search versus image-based search were 81.5% and 63.5%, respectively. After using both search modalities, respondents were highly satisfied with both image-based and text-based search, with >90% at least somewhat satisfied in each dimension and no significant differences seen between text-based and image-based search when examining the responses on an absolute scale per search modality. When asked to directly rate their preferences in a comparative way, survey respondents preferred image-based search over text-based search in 5 out of 6 dimensions, with an absolute 9.9% more preferring image-based search over text-based search overall (p=0.004). 82.5% (95% CI 78.2 - 86.3) reported a preference to leverage image-based search (alone or in combination with text-based search) in future searches. Of those who would prefer to use a combination of both, 64% indicated they would like to start with image-based search, indicating that image-based search may be the preferred entry point for skin-related searches.
Conclusion Despite being less familiar with image-based search upon study inception, survey respondents generally preferred image-based search to text-based search and overwhelmingly wanted to include this in future searches. These results suggest the potential for image-based search to play a key role in people searching for information regarding skin concerns.
View details
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
Preview abstract
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.
View details
Health equity assessment of machine learning performance (HEAL): a framework and dermatology AI model case study
Terry Spitz
Malcolm Chelliah
Heather Cole-Lewis
Stephanie Farquhar
Qinghan Xue
Jenna Lester
Cían Hughes
Patricia Strachan
Fraser Tan
Peggy Bui
Craig Mermel
Lily Peng
Sunny Virmani
Ivor Horn
Cameron Chen
The Lancet eClinicalMedicine (2024)
Preview abstract
Background
Artificial intelligence (AI) has repeatedly been shown to encode historical inequities in healthcare. We aimed to develop a framework to quantitatively assess the performance equity of health AI technologies and to illustrate its utility via a case study.
Methods
Here, we propose a methodology to assess whether health AI technologies prioritise performance for patient populations experiencing worse outcomes, that is complementary to existing fairness metrics. We developed the Health Equity Assessment of machine Learning performance (HEAL) framework designed to quantitatively assess the performance equity of health AI technologies via a four-step interdisciplinary process to understand and quantify domain-specific criteria, and the resulting HEAL metric. As an illustrative case study (analysis conducted between October 2022 and January 2023), we applied the HEAL framework to a dermatology AI model. A set of 5420 teledermatology cases (store-and-forward cases from patients of 20 years or older, submitted from primary care providers in the USA and skin cancer clinics in Australia), enriched for diversity in age, sex and race/ethnicity, was used to retrospectively evaluate the AI model's HEAL metric, defined as the likelihood that the AI model performs better for subpopulations with worse average health outcomes as compared to others. The likelihood that AI performance was anticorrelated to pre-existing health outcomes was estimated using bootstrap methods as the probability that the negated Spearman's rank correlation coefficient (i.e., “R”) was greater than zero. Positive values of R suggest that subpopulations with poorer health outcomes have better AI model performance. Thus, the HEAL metric, defined as p (R >0), measures how likely the AI technology is to prioritise performance for subpopulations with worse average health outcomes as compared to others (presented as a percentage below). Health outcomes were quantified as disability-adjusted life years (DALYs) when grouping by sex and age, and years of life lost (YLLs) when grouping by race/ethnicity. AI performance was measured as top-3 agreement with the reference diagnosis from a panel of 3 dermatologists per case.
Findings
Across all dermatologic conditions, the HEAL metric was 80.5% for prioritizing AI performance of racial/ethnic subpopulations based on YLLs, and 92.1% and 0.0% respectively for prioritizing AI performance of sex and age subpopulations based on DALYs. Certain dermatologic conditions were significantly associated with greater AI model performance compared to a reference category of less common conditions. For skin cancer conditions, the HEAL metric was 73.8% for prioritizing AI performance of age subpopulations based on DALYs.
Interpretation
Analysis using the proposed HEAL framework showed that the dermatology AI model prioritised performance for race/ethnicity, sex (all conditions) and age (cancer conditions) subpopulations with respect to pre-existing health disparities. More work is needed to investigate ways of promoting equitable AI performance across age for non-cancer conditions and to better understand how AI models can contribute towards improving equity in health outcomes.
View details
Health AI Developer Foundations
Atilla Kiraly
Sebastien Baur
Kenneth Philbrick
Fereshteh Mahvar
Liron Yatziv
Tiffany Chen
Bram Sterling
Nick George
Fayaz Jamil
Jing Tang
Kai Bailey
Faruk Ahmed
Akshay Goel
Abbi Ward
Lin Yang
Shravya Shetty
Daniel Golden
Tim Thelin
Rory Pilgrim
Can "John" Kirmizi
arXiv (2024)
Preview abstract
Robust medical Machine Learning (ML) models have the potential to revolutionize healthcare by accelerating clinical research, improving workflows and outcomes, and producing novel insights or capabilities. Developing such ML models from scratch is cost prohibitive and requires substantial compute, data, and time (e.g., expert labeling). To address these challenges, we introduce Health AI Developer Foundations (HAI-DEF), a suite of pre-trained, domain-specific foundation models, tools, and recipes to accelerate building ML for health applications. The models cover various modalities and domains, including radiology (X-rays and computed tomography), histopathology, dermatological imaging, and audio. These models provide domain specific embeddings that facilitate AI development with less labeled data, shorter training times, and reduced computational costs compared to traditional approaches. In addition, we utilize a common interface and style across these models, and prioritize usability to enable developers to integrate HAI-DEF efficiently. We present model evaluations across various tasks and conclude with a discussion of their application and evaluation, covering the importance of ensuring efficacy, fairness, and equity. Finally, while HAI-DEF and specifically the foundation models lower the barrier to entry for ML in healthcare, we emphasize the importance of validation with problem- and population-specific data for each desired usage setting. This technical report will be updated over time as more modalities and features are added.
View details
Differences between Patient and Clinician Submitted Images: Implications for Virtual Care of Skin Conditions
Rajeev Rikhye
Grace Eunhae Hong
Margaret Ann Smith
Aaron Loh
Vijaytha Muralidharan
Doris Wong
Michelle Phung
Nicolas Betancourt
Bradley Fong
Rachna Sahasrabudhe
Khoban Nasim
Alec Eschholz
Kat Chou
Peggy Bui
Justin Ko
Steven Lin
Mayo Clinic Proceedings: Digital Health (2024)
Preview abstract
Objective: To understand and highlight the differences in clinical, demographic, and image quality characteristics between patient-taken (PAT) and clinic-taken (CLIN) photographs of skin conditions.
Patients and Methods: This retrospective study applied logistic regression to data from 2500 deidentified cases in Stanford Health Care’s eConsult system, from November 2015 to January 2021. Cases with undiagnosable or multiple conditions or cases with both patient and clinician image sources were excluded, leaving 628 PAT cases and 1719 CLIN cases. Demographic characteristic factors, such as age and sex were self-reported, whereas anatomic location, estimated skin type, clinical signs and symptoms, condition duration, and condition frequency were summarized from patient health records. Image quality variables such as blur, lighting issues and whether the image contained skin, hair, or nails were estimated through a deep learning model.
Results: Factors that were positively associated with CLIN photographs, post-2020 were as follows: age 60 years or older, darker skin types (eFST V/VI), and presence of skin growths. By contrast, factors that were positively associated with PAT photographs include conditions appearing intermittently, cases with blurry photographs, photographs with substantial nonskin (or nail/hair) regions and cases with more than 3 photographs. Within the PAT cohort, older age was associated with blurry photographs.
Conclusion: There are various demographic, clinical, and image quality characteristic differences between PAT and CLIN photographs of skin concerns. The demographic characteristic differences present important considerations for improving digital literacy or access, whereas the image quality differences point to the need for improved patient education and better image capture workflows, particularly among elderly patients.
View details
A Toolbox for Surfacing Health Equity Harms and Biases in Large Language Models
Heather Cole-Lewis
Nenad Tomašev
Liam McCoy
Leo Anthony Celi
Alanna Walton
Akeiylah DeWitt
Philip Mansfield
Sushant Prakash
Joelle Barral
Ivor Horn
Karan Singhal
Nature Medicine (2024)
Preview abstract
Large language models (LLMs) hold promise to serve complex health information needs but also have the potential to introduce harm and exacerbate health disparities. Reliably evaluating equity-related model failures is a critical step toward developing systems that promote health equity. We present resources and methodologies for surfacing biases with potential to precipitate equity-related harms in long-form, LLM-generated answers to medical questions and conduct a large-scale empirical case study with the Med-PaLM 2 LLM. Our contributions include a multifactorial framework for human assessment of LLM-generated answers for biases and EquityMedQA, a collection of seven datasets enriched for adversarial queries. Both our human assessment framework and our dataset design process are grounded in an iterative participatory approach and review of Med-PaLM 2 answers. Through our empirical study, we find that our approach surfaces biases that may be missed by narrower evaluation approaches. Our experience underscores the importance of using diverse assessment methodologies and involving raters of varying backgrounds and expertise. While our approach is not sufficient to holistically assess whether the deployment of an artificial intelligence (AI) system promotes equitable health outcomes, we hope that it can be leveraged and built upon toward a shared goal of LLMs that promote accessible and equitable healthcare.
View details
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)
Preview abstract
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.
View details
General Geospatial Inference with a Population Dynamics Foundation Model
Chaitanya Kamath
Prithul Sarker
Joydeep Paul
Yael Mayer
Sheila de Guia
Jamie McPike
Adam Boulanger
David Schottlander
Yao Xiao
Manjit Chakravarthy Manukonda
Monica Bharel
Von Nguyen
Luke Barrington
Niv Efron
Krish Eswaran
Shravya Shetty
(2024) (to appear)
Preview abstract
Supporting the health and well-being of dynamic populations around the world requires governmental agencies, organizations, and researchers to understand and reason over complex relationships between human behavior and local contexts. This support includes identifying populations at elevated risk and gauging where to target limited aid resources. Traditional approaches to these classes of problems often entail developing manually curated, task-specific features and models to represent human behavior and the natural and built environment, which can be challenging to adapt to new, or even related tasks. To address this, we introduce the Population Dynamics Foundation Model (PDFM), which aims to capture the relationships between diverse data modalities and is applicable to a broad range of geospatial tasks. We first construct a geo-indexed dataset for postal codes and counties across the United States, capturing rich aggregated information on human behavior from maps, busyness, and aggregated search trends, and environmental factors such as weather and air quality. We then model this data and the complex relationships between locations using a graph neural network, producing embeddings that can be adapted to a wide range of downstream tasks using relatively simple models. We evaluate the effectiveness of our approach by benchmarking it on 27 downstream tasks spanning three distinct domains: health indicators, socioeconomic factors, and environmental measurements. The approach achieves state-of-the-art performance on geospatial interpolation across all tasks, surpassing existing satellite and geotagged image based location encoders. In addition, it achieves state-of-the-art performance in extrapolation and super-resolution for 25 of the 27 tasks. We also show that the PDFM can be combined with a state-of-the-art forecasting foundation model, TimesFM, to predict unemployment and poverty, achieving performance that surpasses fully supervised forecasting. The full set of embeddings and sample code are publicly available for researchers. In conclusion, we have demonstrated a general purpose approach to geospatial modeling tasks critical to understanding population dynamics by leveraging a rich set of complementary globally available datasets that can be readily adapted to previously unseen machine learning tasks.
View details
Searching for Dermatology Information Online using Images vs Text: a Randomized Study
Jay Hartford
Natalie Salaets
Kimberley Raiford
Jay Nayar
Dounia Berrada
Harsh Kharbanda
Lou Wang
Peggy Bui
medRxiv (2024)
Preview abstract
Background: Skin conditions are extremely common worldwide, and are an important cause of both anxiety and morbidity. Since the advent of the internet, individuals have used text-based search (eg, “red rash on arm”) to learn more about concerns on their skin, but this process is often hindered by the inability to accurately describe the lesion’s morphology. In the study, we surveyed respondents’ experiences with an image-based search, compared to the traditional text-based search experience.
Methods: An internet-based survey was conducted to evaluate the experience of text-based vs image-based search for skin conditions. We recruited respondents from an existing cohort of volunteers in a commercial survey panel; survey respondents that met inclusion/exclusion criteria, including willingness to take photos of a visible concern on their body, were enrolled. Respondents were asked to use the Google mobile app to conduct both regular text-based search (Google Search) and image-based search (Google Lens) for their concern, with the order of text vs. image search randomized. Satisfaction for each search experience along six different dimensions were recorded and compared, and respondents’ preferences for the different search types along these same six dimensions were recorded.
Results: 372 respondents were enrolled in the study, with 44% self-identifying as women, 86% as White and 41% over age 45. The rate of respondents who were at least moderately familiar with searching for skin conditions using text-based search versus image-based search were 81.5% and 63.5%, respectively. After using both search modalities, respondents were highly satisfied with both image-based and text-based search, with >90% at least somewhat satisfied in each dimension and no significant differences seen between text-based and image-based search when examining the responses on an absolute scale per search modality. When asked to directly rate their preferences in a comparative way, survey respondents preferred image-based search over text-based search in 5 out of 6 dimensions, with an absolute 9.9% more preferring image-based search over text-based search overall (p=0.004). 82.5% (95% CI 78.2 - 86.3) reported a preference to leverage image-based search (alone or in combination with text-based search) in future searches. Of those who would prefer to use a combination of both, 64% indicated they would like to start with image-based search, indicating that image-based search may be the preferred entry point for skin-related searches.
Conclusion: Despite being less familiar with image-based search upon study inception, survey respondents generally preferred image-based search to text-based search and overwhelmingly wanted to include this in future searches. These results suggest the potential for image-based search to play a key role in people searching for information regarding skin concerns.
View details
