WeakSTIL: Weak whole-slide image level stromal tumor infiltrating lymphocyte scores are all you need

TL;DR

WeakSTIL is a weakly supervised deep learning method that accurately predicts stromal tumor infiltrating lymphocyte percentages in breast cancer tissue slides, reducing annotation effort and providing interpretable results for clinical use.

Contribution

It introduces a two-stage weak label pipeline for sTIL% scoring in WSIs, achieving comparable accuracy to expert annotations with less annotation effort.

Findings

Achieves a coefficient of determination of 0.45 with expert scores.

Reaches an AUC of 0.89 for sTIL-high vs sTIL-low classification.

Provides highly interpretable tile-level predictions.

Abstract

We present WeakSTIL, an interpretable two-stage weak label deep learning pipeline for scoring the percentage of stromal tumor infiltrating lymphocytes (sTIL%) in H&E-stained whole-slide images (WSIs) of breast cancer tissue. The sTIL% score is a prognostic and predictive biomarker for many solid tumor types. However, due to the high labeling efforts and high intra- and interobserver variability within and between expert annotators, this biomarker is currently not used in routine clinical decision making. WeakSTIL compresses tiles of a WSI using a feature extractor pre-trained with self-supervised learning on unlabeled histopathology data and learns to predict precise sTIL% scores for each tile in the tumor bed by using a multiple instance learning regressor that only requires a weak WSI-level label. By requiring only a weak label, we overcome the large annotation efforts required to train currently existing TIL detection methods. We show that WeakSTIL is at least as good as other TIL detection methods when predicting the WSI-level sTIL% score, reaching a coefficient of determination of $0.45\pm0.15$ when compared to scores generated by an expert pathologist, and an AUC of $0.89\pm0.05$ when treating it as the clinically interesting sTIL-high vs sTIL-low classification task. Additionally, we show that the intermediate tile-level predictions of WeakSTIL are highly interpretable, which suggests that WeakSTIL pays attention to latent features related to the number of TILs and the tissue type. In the future, WeakSTIL may be used to provide consistent and interpretable sTIL% predictions to stratify breast cancer patients into targeted therapy arms.