Funding
National Cancer Institute (NCI)
United States Department of Health and Human Services
Find out more...National Institute of Environmental Health Sciences (DEHS)
National Institute of General Medical Sciences (NIGMS)
United States Department of Health and Human Services
Find out more...National Institute of Allergy and Infectious Diseases (NIAID)
United States Department of Health and Human Services
Find out more...Chan Zuckerberg Initiative (CZI)
ARTICLE ABSTRACT
Early and precise diagnosis is vital to improving patient outcomes and reducing morbidity. In resource-limited settings, cancer diagnosis is often challenging due to shortages of expert pathologists. We assess the effectiveness of general-purpose pathology foundation models (FM) for the diagnosis and annotation of nonmelanoma skin cancer (NMSC) in resource-limited settings.
We evaluated three pathology FMs (UNI, PRISM, and Prov-GigaPath) using deidentified NMSC histology images from the Bangladesh Vitamin E and Selenium Trial to predict cancer subtype based on zero-shot whole-slide embeddings. In addition, we evaluated tile aggregation methods and machine learning models for prediction. Lastly, we employed few-shot learning of PRISM tile embeddings to perform whole-slide annotation.
We found that the best model used PRISM’s aggregated tile embeddings to train a multilayer perceptron model to predict NMSC subtype [mean area under the receiver operating characteristic curve (AUROC) = 0.925, P < 0.001]. Within the other FMs, we found that using attention-based multi-instance learning to aggregate tile embeddings to train a multilayer perceptron model was optimal (UNI: mean AUROC = 0.913, P < 0.001; Prov-GigaPath: mean AUROC = 0.908, P < 0.001). We finally exemplify the utility of few-shot annotation in computation- and expertise-limited settings.
Our study highlights the important role FMs may play in confronting public health challenges and exhibits a real-world potential for machine learning–aided cancer diagnosis.
Pathology FMs offer a promising pathway to improve early and precise NMSC diagnosis, especially in resource-limited environments. These tools could also facilitate patient stratification and recruitment for prospective clinical trials aimed at improving NMSC management.
