A Comprehensive Evaluation of Histopathology Foundation Models for Ovarian Cancer Subtype Classification
<|reference_start|>A Comprehensive Evaluation of Histopathology Foundation Models for Ovarian Cancer Subtype Classification: Large pretrained transformers are increasingly being developed as generalised foundation models which can underpin powerful task-specific artificial intelligence models. Histopathology foundation models show great promise across many tasks, but analyses have typically been limited by arbitrary hyperparameters that were not tuned to the specific task. We report the most rigorous single-task validation of histopathology foundation models to date, specifically in ovarian cancer morphological subtyping. Attention-based multiple instance learning classifiers were compared using three ImageNet-pretrained feature extractors and fourteen histopathology foundation models. The training set consisted of 1864 whole slide images from 434 ovarian carcinoma cases at Leeds Teaching Hospitals NHS Trust. Five-class classification performance was evaluated through five-fold cross-validation, and these cross-validation models were ensembled for hold-out testing and external validation on the Transcanadian Study and OCEAN Challenge datasets. The best-performing model used the H-optimus-0 foundation model, with five-class balanced accuracies of 89%, 97%, and 74% in the test sets. Normalisations and augmentations aided the performance of the ImageNet-pretrained ResNets, but these were still outperformed by 13 of the 14 foundation models. Hyperparameter tuning the downstream classifiers improved performance by a median 1.9% balanced accuracy, with many improvements being statistically significant. Histopathology foundation models offer a clear benefit to ovarian cancer subtyping, improving classification performance to a degree where clinical utility is tangible, albeit with an increased computational burden. Such models could provide a second opinion to histopathologists diagnosing challenging cases and may improve the accuracy, objectivity, and efficiency of pathological diagnoses overall.<|reference_end|>
@article{breen2024a,
    title={A Comprehensive Evaluation of Histopathology Foundation Models for
  Ovarian Cancer Subtype Classification},
    author={Jack Breen, Katie Allen, Kieran Zucker, Lucy Godson, Nicolas M. Orsi,
  Nishant Ravikumar},
    journal={arXiv preprint arXiv:2405.09990},
    year={2024},
    archivePrefix={arXiv},
    eprint={2405.09990},
    primaryClass={eess.IV cs.AI cs.CV}
}