Assessing Foundation Models for Computational Pathology in Endometrial Cancer
Modern Pathology, vol. 39, pp. 101070
Abstract
Computational pathology leverages deep learning to extract clinically relevant information from digitized tumor slides, predicting histopathological subtypes, molecular alterations, and patient outcomes. Recent pipelines increasingly rely on foundation models trained on large pan-cancer data sets to generate generalizable features. In endometrial cancer (EC), their comparative performance for clinical diagnostic tasks remains unexplored. This study evaluates the performance of 7 state-of-the-art foundation models across morphological, molecular, and prognostic tasks using a large EC data set of 3293 patients from randomized trials and clinical cohorts. In addition, their performance was compared with 2 versions of an EC-specific feature extractor (EsVIT) exclusively trained on EC. The foundation models H-OPTIMUS-0, CONCH, and VIRCHOW2 achieved the highest mean performance, but the best-performing foundation model varied by task. The top-performing foundation model outperformed EsVIT across all tasks, which highlights the superiority of foundation models over the domain-specific feature extractor EsVIT in EC. Selecting the optimal foundation model for novel tasks remains challenging due to performance plateaus and limited information on the training data sets, requiring rigorous benchmarking and domain insights to reach maximum potential.
Authors 21
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Leiden University Medical Center
Affiliation as printed
Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
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Leiden University Medical Center
Affiliation as printed
Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
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Leiden University Medical Center
Affiliation as printed
Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
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University of Basel · University Hospital of Basel
Affiliation as printed
Computational and Translational Pathology Lab, Department of Biomedical Engineering, University of Basel, Basel, Switzerland; Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
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SIB Swiss Institute of Bioinformatics · University of Basel · University Hospital of Basel · ETH Zurich
Affiliation as printed
Computational and Translational Pathology Lab, Department of Biomedical Engineering, University of Basel, Basel, Switzerland; Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland; Department of Computer Science, ETH Zurich, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
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Copenhagen University Hospital · Rigshospitalet
Affiliation as printed
Department of Gynecology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
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Affiliation as printed
Department of Radiation Oncology, Medisch Spectrum Twente, Enschede, The Netherlands
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Affiliation as printed
Maastricht Radiation Oncology, MAASTRO, Maastricht, The Netherlands
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National Health Service · Barts Health NHS Trust
Affiliation as printed
Department of Clinical Oncology, Barts Health National Health Service Trust, London, United Kingdom
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Affiliation as printed
Department of Medical Oncology, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia
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Sunnybrook Health Science Centre · Sunnybrook Hospital · Odette Cancer Centre
Affiliation as printed
Department of Medical Oncology and Hematology, Odette Cancer center, Sunnybrook Health Sciences Center, Toronto, Ontario, Canada
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Affiliation as printed
Department Medical Oncology, Gustave Roussy Institute, Villejuif, France
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Affiliation as printed
Department of Gynecology, Tygerberg Academic Hospital, Cape Town, South Africa
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University Medical Center Groningen · University of Groningen
Affiliation as printed
Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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Leiden University Medical Center
Affiliation as printed
Department of Radiation Oncology, Leiden University Medical Center, Leiden, The Netherlands
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Erasmus MC · Erasmus MC Cancer Institute
Affiliation as printed
Department of Radiotherapy, Erasmus Medical Center Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
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Leiden University Medical Center
Affiliation as printed
Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
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Leiden University Medical Center
Affiliation as printed
Department of Radiation Oncology, Leiden University Medical Center, Leiden, The Netherlands
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University of Basel · University Hospital of Basel
Affiliation as printed
Computational and Translational Pathology Lab, Department of Biomedical Engineering, University of Basel, Basel, Switzerland; Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
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Leiden University Medical Center
Affiliation as printed
Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands. Electronic address: t.bosse@lumc.nl
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Leiden University Medical Center
Affiliation as printed
Department of Radiation Oncology, Leiden University Medical Center, Leiden, The Netherlands
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