Benchmarking foundation models as feature extractors for weakly supervised computational pathology
Nature Biomedical Engineering, vol. 10, pp. 1113–1123
Abstract
Numerous pathology foundation models have been developed to extract clinically relevant information. There is currently limited literature independently evaluating these foundation models on external cohorts and clinically relevant tasks to uncover adjustments for future improvements. Here we benchmark 19 histopathology foundation models on 13 patient cohorts with 6,818 patients and 9,528 slides from lung, colorectal, gastric and breast cancers. The models were evaluated on weakly supervised tasks related to biomarkers, morphological properties and prognostic outcomes. We show that a vision-language foundation model, CONCH, yielded the highest overall performance when compared with vision-only foundation models, with Virchow2 as close second, although its superior performance was less pronounced in low-data scenarios and low-prevalence tasks. The experiments reveal that foundation models trained on distinct cohorts learn complementary features to predict the same label, and can be fused to outperform the current state of the art. An ensemble combining CONCH and Virchow2 predictions outperformed individual models in 55% of tasks, leveraging their complementary strengths in classification scenarios. Moreover, our findings suggest that data diversity outweighs data volume for foundation models.
Authors 16
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Technische Universität Dresden · Else Kröner Fresenius Center for Digital Health · University Hospital Carl Gustav Carus
Affiliation as printed
Else Kroener Fresenius Center for Digital Health, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
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Technische Universität Dresden · Else Kröner Fresenius Center for Digital Health · University Hospital Carl Gustav Carus
Affiliation as printed
Else Kroener Fresenius Center for Digital Health, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
StratifAI GmbH, Dresden, Germany
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Technische Universität Dresden · Else Kröner Fresenius Center for Digital Health · University Hospital Carl Gustav Carus · Helmholtz-Zentrum Dresden-Rossendorf · Nationales Centrum für Tumorerkrankungen Dresden
Affiliation as printed
Department for Visceral, Thoracic and Vascular Surgery, University Hospital and Faculty of Medicine Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
Else Kroener Fresenius Center for Digital Health, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
National Center for Tumor Diseases Dresden (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
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Technische Universität Dresden · Else Kröner Fresenius Center for Digital Health · University Hospital Carl Gustav Carus
Affiliation as printed
Else Kroener Fresenius Center for Digital Health, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
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Affiliation as printed
Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
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German Cancer Research Center · National Center for Tumor Diseases · Deutsches Konsortium für Translationale Krebsforschung
Affiliation as printed
Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
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Technische Universität Dresden · Else Kröner Fresenius Center for Digital Health · University Hospital Carl Gustav Carus
Affiliation as printed
Else Kroener Fresenius Center for Digital Health, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
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Johannes Kepler University of Linz · Kepler Universitätsklinikum
Affiliation as printed
Institute of Pathology and Molecular Pathology, Kepler University Hospital, Johannes Kepler University Linz, Linz, Austria
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Affiliation as printed
Institute of Tissue Medicine and Pathology, University of Bern, Bern, Switzerland
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University Hospital Schleswig-Holstein
Affiliation as printed
Department of Pathology, University Hospital Schleswig-Holstein, Kiel, Germany
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University Hospital Schleswig-Holstein
Affiliation as printed
Department of Pathology, University Hospital Schleswig-Holstein, Kiel, Germany
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University Medical Center of the Johannes Gutenberg University Mainz
Affiliation as printed
Institute of Pathology, University Medical Center Mainz, Mainz, Germany
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Affiliation as printed
Department of Diagnostic and Interventional Radiology, University Hospital Aachen, Aachen, Germany
StratifAI GmbH, Dresden, Germany
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European Institute of Oncology
Affiliation as printed
Division of New Drugs and Early Drug Development, European Institute of Oncology IRCCS, Milan, Italy
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Technische Universität Dresden · Else Kröner Fresenius Center for Digital Health · University Hospital Carl Gustav Carus
Affiliation as printed
Else Kroener Fresenius Center for Digital Health, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
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Jakob Nikolas Kather corresponding
Heidelberg University · Technische Universität Dresden · University Hospital Heidelberg · Else Kröner Fresenius Center for Digital Health · University Hospital Carl Gustav Carus · National Center for Tumor Diseases
Affiliation as printed
Department of Medicine I, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany. jakob-nikolas.kather@alumni.dkfz.de
Else Kroener Fresenius Center for Digital Health, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany. jakob-nikolas.kather@alumni.dkfz.de
Medical Oncology, National Center for Tumor Diseases (NCT), University Hospital Heidelberg, Heidelberg, Germany. jakob-nikolas.kather@alumni.dkfz.de
Department of Medicine I, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
Medical Oncology, National Center for Tumor Diseases (NCT), University Hospital Heidelberg, Heidelberg, Germany
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