StainNet: A Special Staining Self-Supervised Vision Transformer for Computational Pathology

Jiawen Li, Jiali Hu, Xitong Ling, Yongqiang Lv, Yuxuan Chen, Yizhi Wang, Tian Guan, Yifei Liu, Yonghong He

Keywords: Special Staining, foundation model, computational pathology.

Abstract: Foundation models trained with self-supervised learning (SSL) on large-scale histological images have significantly accelerated the development of computational pathology. These models can serve as backbones for region-of-interest (ROI) image analysis or patch-level feature extractors in whole-slide images (WSIs) based on multiple instance learning (MIL). Existing pathology foundation models (PFMs) are typically pre-trained on Hematoxylin-Eosin (H\&E) stained pathology images. However, images with special stains, such as immunohistochemistry, are also frequently used in clinical practice. PFMs pre-trained mainly on H\&E-stained images may be limited in clinical applications involving special stains. To address this issue, we propose StainNet, a specialized foundation model for special stains based on the vision transformer (ViT) architecture. StainNet adopts a self-distillation SSL approach and is trained on over 1.4 million patch images cropping from 20,231 publicly available special staining WSIs in the HISTAI database. To evaluate StainNet, we conduct experiments on an in-house slide-level liver malignancy classification task and two public ROI-level datasets to demonstrate its strong ability. We also perform few-ratio learning and retrieval evaluations, and compare StainNet with recently larger PFMs to further highlight its strengths. We have released the StainNet model weights at: https://huggingface.co/JWonderLand/StainNet.

Primary Subject Area: Foundation Models

Secondary Subject Area: Application: Histopathology

Registration Requirement: Yes

Reproducibility: https://huggingface.co/JWonderLand/StainNet

Visa & Travel: Yes

Read CFP & Author Instructions: Yes

Originality Policy: Yes

Single-blind & Not Under Review Elsewhere: Yes

LLM Policy: Yes

Submission Number: 45