Benchmarking foundation models as feature extractors for weakly-supervised computational pathology

• URL: http://arxiv.org/abs/2408.15823v1
• Date: Wed, 28 Aug 2024 14:34:45 GMT
• Title: Benchmarking foundation models as feature extractors for weakly-supervised computational pathology
• Authors: Peter Neidlinger, Omar S. M. El Nahhas, Hannah Sophie Muti, Tim Lenz, Michael Hoffmeister, Hermann Brenner, Marko van Treeck, Rupert Langer, Bastian Dislich, Hans Michael Behrens, Christoph Röcken, Sebastian Foersch, Daniel Truhn, Antonio Marra, Oliver Lester Saldanha, Jakob Nikolas Kather,
• Abstract summary: We benchmarked ten histopathology foundation models on 13 patient cohorts with 6,791 patients and 9,493 slides from lung, colorectal, gastric, and breast cancers. We show that a vision-language foundation model, CONCH, yielded the highest performance in 42% of tasks when compared to vision-only foundation models.
• Score: 0.6151041580858937
• License: http://creativecommons.org/licenses/by/4.0/
• Abstract: Advancements in artificial intelligence have driven the development of numerous pathology foundation models capable of extracting clinically relevant information. However, there is currently limited literature independently evaluating these foundation models on truly external cohorts and clinically-relevant tasks to uncover adjustments for future improvements. In this study, we benchmarked ten histopathology foundation models on 13 patient cohorts with 6,791 patients and 9,493 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 performance in 42% of tasks when compared to vision-only foundation models. 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. Creating an ensemble of complementary foundation models outperformed CONCH in 66% of tasks. Moreover, our findings suggest that data diversity outweighs data volume for foundation models. Our work highlights actionable adjustments to improve pathology foundation models.

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