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      A foundation model for generalizable disease detection from retinal images

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          Abstract

          Medical artificial intelligence (AI) offers great potential for recognizing signs of health conditions in retinal images and expediting the diagnosis of eye diseases and systemic disorders 1 . However, the development of AI models requires substantial annotation and models are usually task-specific with limited generalizability to different clinical applications 2 . Here, we present RETFound, a foundation model for retinal images that learns generalizable representations from unlabelled retinal images and provides a basis for label-efficient model adaptation in several applications. Specifically, RETFound is trained on 1.6 million unlabelled retinal images by means of self-supervised learning and then adapted to disease detection tasks with explicit labels. We show that adapted RETFound consistently outperforms several comparison models in the diagnosis and prognosis of sight-threatening eye diseases, as well as incident prediction of complex systemic disorders such as heart failure and myocardial infarction with fewer labelled data. RETFound provides a generalizable solution to improve model performance and alleviate the annotation workload of experts to enable broad clinical AI applications from retinal imaging.

          Abstract

          RETFound, a foundation model for retinal images that learns generalizable representations from unlabelled images, is trained on 1.6 million unlabelled images by self-supervised learning and then adapted to disease detection tasks with explicit labels.

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          The UK Biobank resource with deep phenotyping and genomic data

          The UK Biobank project is a prospective cohort study with deep genetic and phenotypic data collected on approximately 500,000 individuals from across the United Kingdom, aged between 40 and 69 at recruitment. The open resource is unique in its size and scope. A rich variety of phenotypic and health-related information is available on each participant, including biological measurements, lifestyle indicators, biomarkers in blood and urine, and imaging of the body and brain. Follow-up information is provided by linking health and medical records. Genome-wide genotype data have been collected on all participants, providing many opportunities for the discovery of new genetic associations and the genetic bases of complex traits. Here we describe the centralized analysis of the genetic data, including genotype quality, properties of population structure and relatedness of the genetic data, and efficient phasing and genotype imputation that increases the number of testable variants to around 96 million. Classical allelic variation at 11 human leukocyte antigen genes was imputed, resulting in the recovery of signals with known associations between human leukocyte antigen alleles and many diseases.
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            Dermatologist-level classification of skin cancer with deep neural networks

            Skin cancer, the most common human malignancy, is primarily diagnosed visually, beginning with an initial clinical screening and followed potentially by dermoscopic analysis, a biopsy and histopathological examination. Automated classification of skin lesions using images is a challenging task owing to the fine-grained variability in the appearance of skin lesions. Deep convolutional neural networks (CNNs) show potential for general and highly variable tasks across many fine-grained object categories. Here we demonstrate classification of skin lesions using a single CNN, trained end-to-end from images directly, using only pixels and disease labels as inputs. We train a CNN using a dataset of 129,450 clinical images—two orders of magnitude larger than previous datasets—consisting of 2,032 different diseases. We test its performance against 21 board-certified dermatologists on biopsy-proven clinical images with two critical binary classification use cases: keratinocyte carcinomas versus benign seborrheic keratoses; and malignant melanomas versus benign nevi. The first case represents the identification of the most common cancers, the second represents the identification of the deadliest skin cancer. The CNN achieves performance on par with all tested experts across both tasks, demonstrating an artificial intelligence capable of classifying skin cancer with a level of competence comparable to dermatologists. Outfitted with deep neural networks, mobile devices can potentially extend the reach of dermatologists outside of the clinic. It is projected that 6.3 billion smartphone subscriptions will exist by the year 2021 (ref. 13) and can therefore potentially provide low-cost universal access to vital diagnostic care.
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              ImageNet: A large-scale hierarchical image database

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                Author and article information

                Contributors
                yukun.zhou.19@ucl.ac.uk
                p.keane@ucl.ac.uk
                Journal
                Nature
                Nature
                Nature
                Nature Publishing Group UK (London )
                0028-0836
                1476-4687
                13 September 2023
                13 September 2023
                2023
                : 622
                : 7981
                : 156-163
                Affiliations
                [1 ]Centre for Medical Image Computing, University College London, ( https://ror.org/02jx3x895) London, UK
                [2 ]GRID grid.436474.6, ISNI 0000 0000 9168 0080, NIHR Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust, ; London, UK
                [3 ]Department of Medical Physics and Biomedical Engineering, University College London, ( https://ror.org/02jx3x895) London, UK
                [4 ]Institute of Ophthalmology, University College London, ( https://ror.org/02jx3x895) London, UK
                [5 ]Department of Computer Science, University of Coruña, ( https://ror.org/01qckj285) A Coruña, Spain
                [6 ]Institute of Health Informatics, University College London, ( https://ror.org/02jx3x895) London, UK
                [7 ]Department of Ophthalmology, University of Washington, ( https://ror.org/00cvxb145) Seattle, WA USA
                [8 ]Roger and Angie Karalis Johnson Retina Center, University of Washington, ( https://ror.org/00cvxb145) Seattle, WA USA
                [9 ]GRID grid.214007.0, ISNI 0000000122199231, Department of Molecular Medicine, , Scripps Research, ; La Jolla, CA USA
                [10 ]Academic Unit of Ophthalmology, University of Birmingham, ( https://ror.org/03angcq70) Birmingham, UK
                [11 ]University Hospitals Birmingham NHS Foundation Trust, ( https://ror.org/014ja3n03) Birmingham, UK
                [12 ]Department of Computer Science, University College London, ( https://ror.org/02jx3x895) London, UK
                [13 ]University of Oxford, ( https://ror.org/052gg0110) Oxford, UK
                [14 ]University of Manchester, ( https://ror.org/027m9bs27) Manchester, UK
                [15 ]University of Bristol, ( https://ror.org/0524sp257) Bristol, UK
                [16 ]Kingston University, ( https://ror.org/05bbqza97) London, UK
                [17 ]University of Leeds, ( https://ror.org/024mrxd33) Leeds, UK
                [18 ]St Thomas’ Hospital, ( https://ror.org/054gk2851) London, UK
                [19 ]University of Southampton, ( https://ror.org/01ryk1543) Southampton, UK
                [20 ]Queens University Belfast, ( https://ror.org/00hswnk62) Belfast, UK
                [21 ]University of Edinburgh, ( https://ror.org/01nrxwf90) Edinburgh, UK
                [22 ]University of Dundee, ( https://ror.org/03h2bxq36) Dundee, UK
                [23 ]Cardiff University, ( https://ror.org/03kk7td41) Cardiff, UK
                [24 ]King’s College London, ( https://ror.org/0220mzb33) London, UK
                [25 ]University of Liverpool, ( https://ror.org/04xs57h96) Liverpool, UK
                [26 ]Leeds Teaching Hospitals NHS Trust, ( https://ror.org/00v4dac24) Leeds, UK
                [27 ]King’s College Hospital NHS Foundation Trust, ( https://ror.org/01n0k5m85) London, UK
                [28 ]University of Exeter, ( https://ror.org/03yghzc09) Exeter, UK
                [29 ]University of London, ( https://ror.org/04cw6st05) London, UK
                [30 ]University of Glasgow, ( https://ror.org/00vtgdb53) Glasgow, UK
                [31 ]Newcastle University, ( https://ror.org/01kj2bm70) Newcastle, UK
                [32 ]Gloucestershire Hospitals NHS Foundation Trust, ( https://ror.org/04mw34986) Gloucester, UK
                [33 ]GRID grid.264200.2, ISNI 0000 0000 8546 682X, St George’s University of London, ; London, UK
                [34 ]University of East Anglia, ( https://ror.org/026k5mg93) Norwich, UK
                [35 ]GRID grid.83440.3b, ISNI 0000000121901201, UCL Institute of Neurology, ; London, UK
                [36 ]Royal Liverpool University Hospital, ( https://ror.org/01ycr6b80) Liverpool, UK
                Author information
                http://orcid.org/0000-0002-0840-6422
                http://orcid.org/0000-0002-3184-2353
                http://orcid.org/0000-0001-5219-9312
                http://orcid.org/0000-0002-2201-859X
                http://orcid.org/0000-0003-2834-3040
                http://orcid.org/0000-0003-1686-7189
                http://orcid.org/0000-0002-7913-1403
                http://orcid.org/0000-0002-9265-2393
                http://orcid.org/0000-0002-1478-4729
                http://orcid.org/0000-0001-7849-0087
                http://orcid.org/0000-0003-2439-350X
                Article
                6555
                10.1038/s41586-023-06555-x
                10550819
                37704728
                a24bd657-257b-4fe7-8787-59e01bbd48c9
                © The Author(s) 2023

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 5 December 2022
                : 18 August 2023
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                © Springer Nature Limited 2023

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                medical imaging,prognosis,translational research,retinal diseases,cardiovascular diseases

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