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Are AI Foundation Models Efficient for Segmentation of Echocardiograms?

Journal of the American Society of Echocardiography 2025年

作者： Ferreira, Danielle L. Arnaout, Rima Division of Cardiology Department of Medicine University of California San Francisco San Francisco California United States Bakar Computational Health Sciences Institute University of California San Francisco San Francisco California United States UCSF-UC Berkeley Joint Program in Computational Precision Health University of California San Francisco San Francisco California United States Center for Intelligent Imaging Department of Radiology University of California San Francisco San Francisco California United States

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Self-supervised learning for label-free segmentation in cardiac ultrasound

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Nature Communications 2025年第1期16卷 1-13页

作者： Ferreira, Danielle L. Lau, Connor Salaymang, Zaynaf Arnaout, Rima Department of Medicine Division of Cardiology University of California San Francisco 521 Parnassus Avenue San Francisco CA United States Bakar Computational Health Sciences Institute University of California San Francisco 490 Illinois St San Francisco CA United States Department of Radiology Center for Intelligent Imaging 505 Parnassus Avenue San Francisco CA United States UCSF-UC Berkeley Joint Program in Computational Precision Health 505 Parnassus Avenue San Francisco CA United States

Segmentation and measurement of cardiac chambers from ultrasound is critical, but laborious and poorly reproducible. Neural networks can assist, but supervised approaches require the same problematic manual annotations. We build a pipeline for self-supervised segmentation combining computer vision, clinical knowledge, and deep learning. We train on 450 echocardiograms and test on 18,423 echocardiograms (including external data), using the resulting segmentations to calculate measurements. Coefficient of determination (r²) between clinically measured and pipeline-predicted measurements (0.55-0.84) are comparable to inter-clinician variation and to supervised learning. Average accuracy for detecting abnormal chambers is 0.85 (0.71-0.97). A subset of test echocardiograms (n = 553) have corresponding cardiac MRIs (the gold standard). Correlation between pipeline and MRI measurements is similar to that of clinical echocardiogram. Finally, the pipeline segments the left ventricle with an average Dice score of 0.89 (95% CI [0.89]). Our results demonstrate a manual-label free, clinically valid, and scalable method for segmentation from ultrasound. © The Author(s) 2025.

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Artificial intelligence for modelling infectious disease epidemics

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Nature 2025年第8051期638卷 623-635页

作者： Kraemer, Moritz U. G. Tsui, Joseph L.-H. Chang, Serina Y. Lytras, Spyros Khurana, Mark P. Vanderslott, Samantha Bajaj, Sumali Scheidwasser, Neil Curran-Sebastian, Jacob Liam Semenova, Elizaveta Zhang, Mengyan Unwin, H. Juliette T. Watson, Oliver J. Mills, Cathal Dasgupta, Abhishek Ferretti, Luca Scarpino, Samuel V. Koua, Etien Morgan, Oliver Tegally, Houriiyah Paquet, Ulrich Moutsianas, Loukas Fraser, Christophe Ferguson, Neil M. Topol, Eric J. Duchêne, David A. Stadler, Tanja Kingori, Patricia Parker, Michael J. Dominici, Francesca Shadbolt, Nigel Suchard, Marc A. Ratmann, Oliver Flaxman, Seth Holmes, Edward C. Gomez-Rodriguez, Manuel Schölkopf, Bernhard Donnelly, Christl A. Pybus, Oliver G. Cauchemez, Simon Bhatt, Samir Pandemic Sciences Institute University of Oxford Oxford United Kingdom Department of Biology University of Oxford Oxford United Kingdom Department of Electrical Engineering and Computer Science University of California Berkeley Berkeley CA United States UCSF UC Berkeley Joint Program in Computational Precision Health Berkeley CA United States Division of Systems Virology Department of Microbiology and Immunology The Institute of Medical Science The University of Tokyo Tokyo Japan Section of Epidemiology Department of Public Health University of Copenhagen Copenhagen Denmark Oxford Vaccine Group University of Oxford and NIHR Oxford Biomedical Research Centre Oxford United Kingdom Department of Epidemiology and Biostatistics Imperial College London London United Kingdom Department of Computer Science University of Oxford Oxford United Kingdom School of Mathematics University of Bristol Bristol United Kingdom MRC Centre for Global Infectious Disease Analysis School of Public Health Imperial College London London United Kingdom Department of Statistics University of Oxford Oxford United Kingdom Doctoral Training Centre University of Oxford Oxford United Kingdom Institute for Experiential AI Northeastern University MA Boston Thailand Santa Fe Institute Santa Fe NM United States World Health Organization Regional Office for Africa Brazzaville Congo WHO Hub for Pandemic and Epidemic Intelligence Health Emergencies Programme World Health Organization Berlin Germany Centre for Epidemic Response and Innovation (CERI) School for Data Science and Computational Thinking Stellenbosch University Stellenbosch South Africa African Institute for Mathematical Sciences (AIMS) South Africa Muizenberg Cape Town South Africa Genomics England London United Kingdom Scripps Research La Jolla CA United States Department of Biosystems Science and Engineering ETH Zürich Basel Switzerland Swiss Institute of Bioinformatics Lausanne Switzerland The Ethox Centre Nuffield

Infectious disease threats to individual and public health are numerous, varied and frequently unexpected. Artificial intelligence (AI) and related technologies, which are already supporting human decision making in economics, medicine and social science, have the potential to transform the scope and power of infectious disease epidemiology. Here we consider the application to infectious disease modelling of AI systems that combine machine learning, computational statistics, information retrieval and data science. We first outline how recent advances in AI can accelerate breakthroughs in answering key epidemiological questions and we discuss specific AI methods that can be applied to routinely collected infectious disease surveillance data. Second, we elaborate on the social context of AI for infectious disease epidemiology, including issues such as explainability, safety, accountability and ethics. Finally, we summarize some limitations of AI applications in this field and provide recommendations for how infectious disease epidemiology can harness most effectively current and future developments in AI. © Springer Nature Limited 2025.

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A Narrative Review on the Application of Large Language Models to Support Cancer Care and Research

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Yearbook of medical informatics 2024年第1期33卷 90-98页

作者： Benson, Ryzen Elia, Marianna Hyams, Benjamin Chang, Ji Hyun Hong, Julian C. Department of Radiation Oncology University of California San Francisco CA United States Bakar Computational Health Sciences Institute University of California San Francisco CA United States School of Medicine University of California San Francisco CA United States Department of Radiation Oncology Seoul National University Hospital Seoul National University College of Medicine Seoul South Korea UCSF UC Berkeley Joint Program in Computational Precision Health (CPH) San Francisco CA United States

OBJECTIVES: The emergence of large language models has resulted in a significant shift in informatics research and carries promise in clinical cancer care. Here we provide a narrative review of the recent use of large language models (LLMs) to support cancer care, prevention, and research. METHODS: We performed a search of the Scopus database for studies on the application of bidirectional encoder representations from transformers (BERT) and generative-pretrained transformer (GPT) LLMs in cancer care published between the start of 2021 and the end of 2023. We present salient and impactful papers related to each of these themes. RESULTS: Studies identified focused on aspects of clinical decision support (CDS), cancer education, and support for research activities. The use of LLMs for CDS primarily focused on aspects of treatment and screening planning, treatment response, and the management of adverse events. Studies using LLMs for cancer education typically focused on question-answering, assessing cancer myths and misconceptions, and text summarization and simplification. Finally, studies using LLMs to support research activities focused on scientific writing and idea generation, cohort identification and extraction, clinical data processing, and NLP-centric tasks. CONCLUSIONS: The application of LLMs in cancer care has shown promise across a variety of diverse use cases. Future research should utilize quantitative metrics, qualitative insights, and user insights in the development and evaluation of LLM-based cancer care tools. The development of open-source LLMs for use in cancer care research and activities should also be a priority. The Author(s). This is an open access article published by Thieme under the terms of the Creative Commons Attribution License, permitting unrestricted use, distribution, and reproduction so long as the original work is properly cited. (https://***/licenses/by/4.0/).

关键词： large language models clinical decision support artificial intelligence natural language processing generative AI

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Grade Inflation in Generative Models

arXiv

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arXiv 2024年

作者： Nguyen, Phuc Li, Miao Morgan, Alexandra Arnaout, Rima Arnaout, Ramy BostonMA02215 United States The Department of Medicine The Bakar Computational Health Sciences Institute The UCSF UC Berkeley Joint Program for Computational Precision Health The University of California San Francisco San FranciscoCA94143 United States The Department of Pathology The Division of Clinical Informatics Department of Medicine BIDMC Harvard Medical School BostonMA02215 United States

Generative models hold great potential, but only if one can trust the evaluation of the data they generate. We show that many commonly used quality scores for comparing two-dimensional distributions of synthetic vs. ground-truth data give better results than they should, a phenomenon we call the "grade inflation problem." We show that the correlation score, Jaccard score, earth-mover's score, and Kullback-Leibler (relative-entropy) score all suffer grade inflation. We propose that any score that values all datapoints equally, as these do, will also exhibit grade inflation;we refer to such scores as "equipoint" scores. We introduce the concept of "equidensity" scores, and present the Eden score, to our knowledge the first example of such a score. We find that Eden avoids grade inflation and agrees better with human perception of goodness-of-fit than the equipoint scores above. We propose that any reasonable equidensity score will avoid grade inflation. We identify a connection between equidensity scores and Rényi entropy of negative order. We conclude that equidensity scores are likely to outperform equipoint scores for generative models, and for comparing low-dimensional distributions more generally. © 2024, CC BY-NC-SA.

关键词： Inflation

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Are foundation models efficient for medical image segmentation?

arXiv

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arXiv 2023年

作者： Ferreira, Danielle L. Arnaout, Rima Department of Medicine Division of Cardiology Bakar Computational Health Sciences Institute University of California San Francisco 521 Parnassus Avenue San FranciscoCA94143 United States Department of Medicine Division of Cardiology Bakar Computational Health Sciences Institute UCSF-UC Berkeley Joint Program in Computational Precision Health Department of Radiology Center for Intelligent Imaging University of California San Francisco 521 Parnassus Ave Box 0124 San FranciscoCA94143 United States

Foundation models are experiencing a surge in popularity. The Segment Anything model (SAM) asserts an ability to segment a wide spectrum of objects but required supervised training at unprecedented scale. We compared SAM’s performance (against clinical ground truth) and resources (labeling time, compute) to a modality-specific, label-free self-supervised learning (SSL) method on 25 measurements for 100 cardiac ultrasounds. SAM performed poorly and required significantly more labeling and computing resources, demonstrating worse efficiency than SSL. © 2023, CC BY-NC-ND.

关键词： Image segmentation

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When exposure affects subgroup membership: Framing relevant causal questions in perinatal epidemiology and beyond

arXiv

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arXiv 2024年

作者： Gupta, Shalika Balzer, Laura B. Kamya, Moses R. Havlir, Diane V. Petersen, Maya L. Division of Epidemiology University of California Berkeley United States Division of Biostatistics University of California Berkeley United States Department of Medicine Makerere University College of Health Sciences Uganda Division of HIV Infectious Diseases and Global Medicine Department of Medicine University of California San Francisco United States UCSF-UC Berkeley Program in Computational Precision Health United States

Perinatal epidemiology often aims to evaluate exposures on infant outcomes. When the exposure affects the composition of people who give birth to live infants (e.g., by affecting fertility, behavior, or birth outcomes), this "live birth process" mediates the exposure effect on infant outcomes. Causal estimands previously proposed for this setting include the total exposure effect on composite birth and infant outcomes, controlled direct effects (e.g., enforcing birth), and principal stratum direct effects. Using perinatal HIV transmission in the SEARCH Study as a motivating example, we present two alternative causal estimands: 1) conditional total effects;and 2) conditional stochastic direct effects, formulated under a hypothetical intervention to draw mediator values from some distribution (possibly conditional on covariates). The proposed conditional total effect includes impacts of an intervention that operate by changing the types of people who have a live birth and the timing of births. The proposed conditional stochastic direct effects isolate the effect of an exposure on infant outcomes excluding any impacts through this live birth process. In SEARCH, this approach quantifies the impact of a universal testing and treatment intervention on infant HIV-free survival absent any effect of the intervention on the live birth process, within a clearly defined target population of women of reproductive age with HIV at study baseline. Our approach has implications for the evaluation of intervention effects in perinatal epidemiology broadly, and whenever causal effects within a subgroup are of interest and exposure affects membership in the subgroup. © 2024, CC BY.

关键词： Epidemiology

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Label-free segmentation from cardiac ultrasound using self-supervised learning

arXiv

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arXiv 2022年

作者： Ferreira, Danielle L. Lau, Connor Salaymang, Zaynaf Arnaout, Rima Department of Medicine Division of Cardiology Bakar Computational Health Sciences Institute University of California San Francisco 521 Parnassus Avenue San FranciscoCA94143 United States Department of Medicine Division of Cardiology 505 Parnassus Avenue San FranciscoCA94143 United States Department of Medicine Division of Cardiology Bakar Computational Health Sciences Institute UCSF-UC Berkeley Joint Program in Computational Precision Health Department of Radiology Center for Intelligent Imaging University of California San Francisco 521 Parnassus Ave Box 0124 San FranciscoCA94143 United States

Segmentation and measurement of cardiac chambers is critical in cardiac ultrasound but is laborious and poorly reproducible. Neural networks can assist, but supervised approaches require the same laborious manual annotations. We built a pipeline for self-supervised (no manual labels) segmentation combining computer vision, clinical domain knowledge, and deep learning. We trained on 450 echocardiograms (93,000 images) and tested on 8,393 echocardiograms (4,476,266 images;mean 61 years, 51% female), using the resulting segmentations to calculate biometrics. We also tested against external images from an additional 10,030 patients with available manual tracings of the left ventricle. r2 between clinically measured and pipeline-predicted measurements were similar to reported inter-clinician variation and comparable to supervised learning across several different measurements (r2 0.56-0.84). Average accuracy for detecting abnormal chamber size and function was 0.85 (range 0.71-0.97) compared to clinical measurements. A subset of test echocardiograms (n=553) had corresponding cardiac MRIs, where MRI is the gold standard. Correlation between pipeline and MRI measurements was similar to that between clinical echocardiogram and MRI. Finally, the pipeline accurately segments the left ventricle with an average Dice score of 0.89 (95% CI [0.89]) in the external, manually labeled dataset. Our results demonstrate a manual-label free, clinically valid, and highly scalable method for segmentation from ultrasound, a noisy but globally important imaging modality. © 2022, CC BY-NC-ND.

关键词： Self-supervised learning

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The Minimum Information about CLinical Artificial Intelligence Checklist for Generative Modeling Research (MI-CLAIM-GEN)

arXiv

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arXiv 2024年

作者： Miao, Brenda Y. Chen, Irene Y. Williams, Christopher Y.K. Davidson, Jaysón Garcia-Agundez, Augusto Sun, Shenghuan Zack, Travis Saria, Suchi Arnaout, Rima Quer, Giorgio Sadaei, Hossein J. Torkamani, Ali Beaulieu-Jones, Brett Yu, Bin Gianfrancesco, Milena Butte, Atul J. Norgeot, Beau Sushil, Madhumita Bakar Computational Health Sciences Institute University of California San Francisco San FranciscoCA United States UCSF-UC Berkeley Joint Program in Computational Precision Health University of California Berkeley University of California San Francisco BerkeleyCA United States Department of Electrical Engineering and Computer Sciences University of California Berkeley BerkeleyCA United States Berkeley AI Research University of California Berkeley BerkeleyCA United States Department of Medicine Division of Rheumatology University of California San Francisco San FranciscoCA United States Helen Diller Family Comprehensive Cancer Center University of California San Francisco San FranciscoCA United States Center for Data-driven Insights and Innovation University of California Office of the President OaklandCA United States Bayesian Health New YorkNY10282 United States Department of Computer Science Johns Hopkins University Whiting School of Engineering BaltimoreMD United States Department of Health Policy & Management Johns Hopkins University Bloomberg School of Public Health BaltimoreMD United States Department of Medicine Johns Hopkins Medicine BaltimoreMD21205 United States Departments of Medicine Radiology and Pediatrics University of California San Francisco San FranciscoCA United States Scripps Research Translational Institute La Jolla CA United States Department of Integrative Structural and Computational Biology Scripps Research La Jolla CA92037 United States Department of Medicine University of Chicago ChicagoIL United States Department of Statistics University of California Berkeley BerkeleyCA United States Center for Computational Biology University of California Berkeley BerkeleyCA United States Qualified Health PBC Palo AltoCA United States

Recent advances in generative models, including large language models (LLMs), vision language models (VLMs), and diffusion models, have accelerated the field of natural language and image processing in medicine and marked a significant paradigm shift in how biomedical models can be developed and deployed. While these models are highly adaptable to new tasks, scaling and evaluating their usage presents new challenges not addressed in previous frameworks. In particular, the ability of these models to produce useful outputs with little to no specialized training data ("zero-" or "few-shot" approaches), as well as the open-ended nature of their outputs, necessitate the development of new guidelines for robust reporting of clinical generative model research. In response to gaps in standards and best practices for the development of clinical AI tools identified by US Executive Order 141103 and several emerging national networks for clinical AI evaluation, we begin to formalize some of these guidelines by building on the original MI-CLAIM checklist. The new checklist, MI-CLAIM-GEN (Table 1), aims to address differences in training, evaluation, interpretability, and reproducibility of new generative models compared to non-generative ("predictive") AI models. This MI-CLAIM-GEN checklist also seeks to clarify cohort selection reporting with unstructured clinical data and adds additional items on alignment with ethical standards for clinical AI research. © 2024, CC BY.

关键词： Generative adversarial networks

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The Science of precision Prevention: Research Opportunities and Clinical Applications to Reduce Cardiovascular health Disparities

JACC: Advances

引用

JACC: Advances 2024年第1期3卷 100759-100759页

作者： Pearson, Thomas A. Vitalis, Debbie Pratt, Charlotte Campo, Rebecca Armoundas, Antonis A. Au, David Beech, Bettina Brazhnik, Olga Chute, Christopher G. Davidson, Karina W. Diez-Roux, Ana V. Fine, Lawrence J. Gabriel, Davera Groenveld, Peter Hall, Jaclyn Hamilton, Alison B. Hu, Hui Ji, Heng Kind, Amy Kraus, William E. Krumholz, Harlan Mensah, George A. Merchant, Raina M. Mozaffarian, Dariush Murray, David M. Neumark-Sztainer, Dianne Petersen, Maya Goff, David College of Medicine and College of Public Health and Health Professions University of Florida Health Science Center Gainesville FL United States Division of Cardiovascular Sciences National Heart Lung and Blood Institute National Institutes of Health Bethesda MD United States Cardiovascular Research Center Massachusetts General Hospital and Broad Institute Massachusetts Institute of Technology Cambridge MA United States Center of Innovation for Veteran-Centered and Value-Driven Care University of Washington Seattle WA United States UH Population Health University of Houston Houston TX United States Johns Hopkins Medicine Institute for Clinical and Translational Research Baltimore MD United States Institute of Health System Science Feinstein Institutes for Medical Research Northwell Health New Hyde Park NY United States Feinstein Institutes for Medical Research Northwell Health Manhasset NY United States Urban Health Collaborative Drexel Dornsife School of Public Health Philadelphia PA United States Biomedical Informatics and Data Science Section Johns Hopkins University School of Medicine Baltimore MD United States Center for Health Care Transformation and Innovation University of Pennsylvania Perelman School of Medicine Philadelphia PA United States Department of Health Outcomes and Biomedical Informatics Institute for Child Health Policy College of Medicine University of Florida Gainesville FL United States Center for the Study of Healthcare Innovation Implementation & Policy VA Greater Los Angeles Healthcare System Los Angeles CA United States Channing Division of Network Medicine Department of Medicine Brigham and Women's Hospital and Harvard Medical School Boston MA United States Department of Computer Science University of Illinois Urbana-Champaign Champaign IL United States Center for Health Disparities Research (CHDR) University of Wisconsin School of Medicine and Public Health Madison WI United States Duke Molecular Physiology Insti

precision prevention embraces personalized prevention but includes broader factors such as social determinants of health to improve cardiovascular health. The quality, quantity, precision, and diversity of data relatable to individuals and communities continue to expand. New analytical methods can be applied to these data to create tools to attribute risk, which may allow a better understanding of cardiovascular health disparities. Interventions using these analytic tools should be evaluated to establish feasibility and efficacy for addressing cardiovascular disease disparities in diverse individuals and communities. Training in these approaches is important to create the next generation of scientists and practitioners in precision prevention. This state-of-the-art review is based on a workshop convened to identify current gaps in knowledge and methods used in precision prevention intervention research, discuss opportunities to expand trials of implementation science to close the health equity gaps, and expand the education and training of a diverse precision prevention workforce. © 2023 The Authors

关键词： data science health equity health promotion implementation science personalized medicine precision analytics

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