AUTHOR=Abousamra Shahira , Gupta Rajarsi , Hou Le , Batiste Rebecca , Zhao Tianhao , Shankar Anand , Rao Arvind , Chen Chao , Samaras Dimitris , Kurc Tahsin , Saltz Joel TITLE=Deep Learning-Based Mapping of Tumor Infiltrating Lymphocytes in Whole Slide Images of 23 Types of Cancer JOURNAL=Frontiers in Oncology VOLUME=11 YEAR=2022 URL=https://www.frontiersin.org/journals/oncology/articles/10.3389/fonc.2021.806603 DOI=10.3389/fonc.2021.806603 ISSN=2234-943X ABSTRACT=
The role of tumor infiltrating lymphocytes (TILs) as a biomarker to predict disease progression and clinical outcomes has generated tremendous interest in translational cancer research. We present an updated and enhanced deep learning workflow to classify 50x50 um tiled image patches (100x100 pixels at 20x magnification) as TIL positive or negative based on the presence of 2 or more TILs in gigapixel whole slide images (WSIs) from the Cancer Genome Atlas (TCGA). This workflow generates TIL maps to study the abundance and spatial distribution of TILs in 23 different types of cancer. We trained three state-of-the-art, popular convolutional neural network (CNN) architectures (namely VGG16, Inception-V4, and ResNet-34) with a large volume of training data, which combined manual annotations from pathologists (strong annotations) and computer-generated labels from our previously reported first-generation TIL model for 13 cancer types (model-generated annotations). Specifically, this training dataset contains TIL positive and negative patches from cancers in additional organ sites and curated data to help improve algorithmic performance by decreasing known false positives and false negatives. Our new TIL workflow also incorporates automated thresholding to convert model predictions into binary classifications to generate TIL maps. The new TIL models all achieve better performance with improvements of up to 13% in accuracy and 15% in F-score. We report these new TIL models and a curated dataset of TIL maps, referred to as