Synthetic DOmain-Targeted Augmentation (S-DOTA) Improves Model Generalization in Digital Pathology

• URL: http://arxiv.org/abs/2305.02401v1
• Date: Wed, 3 May 2023 19:53:30 GMT
• Title: Synthetic DOmain-Targeted Augmentation (S-DOTA) Improves Model Generalization in Digital Pathology
• Authors: Sai Chowdary Gullapally, Yibo Zhang, Nitin Kumar Mittal, Deeksha Kartik, Sandhya Srinivasan, Kevin Rose, Daniel Shenker, Dinkar Juyal, Harshith Padigela, Raymond Biju, Victor Minden, Chirag Maheshwari, Marc Thibault, Zvi Goldstein, Luke Novak, Nidhi Chandra, Justin Lee, Aaditya Prakash, Chintan Shah, John Abel, Darren Fahy, Amaro Taylor-Weiner, Anand Sampat
• Abstract summary: Machine learning algorithms have the potential to improve patient outcomes in digital pathology. generalization is limited by sensitivity to variations in tissue preparation, staining procedures and scanning equipment. We studied the effectiveness of two Synthetic DOmain-Targeted Augmentation (S-DOTA) methods, namely CycleGAN-enabled Scanner Transform (ST) and targeted Stain Vector Augmentation (SVA) We evaluated the ability of these techniques to improve model generalization to various tasks and settings.
• Score: 1.488519799639108
• License: http://creativecommons.org/licenses/by-nc-nd/4.0/
• Abstract: Machine learning algorithms have the potential to improve patient outcomes in digital pathology. However, generalization of these tools is currently limited by sensitivity to variations in tissue preparation, staining procedures and scanning equipment that lead to domain shift in digitized slides. To overcome this limitation and improve model generalization, we studied the effectiveness of two Synthetic DOmain-Targeted Augmentation (S-DOTA) methods, namely CycleGAN-enabled Scanner Transform (ST) and targeted Stain Vector Augmentation (SVA), and compared them against the International Color Consortium (ICC) profile-based color calibration (ICC Cal) method and a baseline method using traditional brightness, color and noise augmentations. We evaluated the ability of these techniques to improve model generalization to various tasks and settings: four models, two model types (tissue segmentation and cell classification), two loss functions, six labs, six scanners, and three indications (hepatocellular carcinoma (HCC), nonalcoholic steatohepatitis (NASH), prostate adenocarcinoma). We compared these methods based on the macro-averaged F1 scores on in-distribution (ID) and out-of-distribution (OOD) test sets across multiple domains, and found that S-DOTA methods (i.e., ST and SVA) led to significant improvements over ICC Cal and baseline on OOD data while maintaining comparable performance on ID data. Thus, we demonstrate that S-DOTA may help address generalization due to domain shift in real world applications.

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