Deep Learning‑Based Framework for Slide‑Based Histopathological Image Analysis

Authors

Sai Kosaraju, University of Nevada, Las Vegas
Jeongyeon Park, Sun Moon University
Hyun Lee, Sun Moon UniversityFollow
Jung Wook Yang, Gyeongsang National University College of MedicineFollow
Mingon Kang, University of Nevada, Las Vegas, Las VegasFollow

Document Type

Article

Publication Date

11-9-2022

Publication Title

Scientific Reports

Volume

12

First page number:

1

Last page number:

15

Abstract

Digital pathology coupled with advanced machine learning (e.g., deep learning) has been changing the paradigm of whole-slide histopathological images (WSIs) analysis. Major applications in digital pathology using machine learning include automatic cancer classification, survival analysis, and subtyping from pathological images. While most pathological image analyses are based on patch-wise processing due to the extremely large size of histopathology images, there are several applications that predict a single clinical outcome or perform pathological diagnosis per slide (e.g., cancer classification, survival analysis). However, current slide-based analyses are task-dependent, and a general framework of slide-based analysis in WSI has been seldom investigated. We propose a novel slide-based histopathology analysis framework that creates a WSI representation map, called HipoMap, that can be applied to any slide-based problems, coupled with convolutional neural networks. HipoMap converts a WSI of various shapes and sizes to structured image-type representation. Our proposed HipoMap outperformed existing methods in intensive experiments with various settings and datasets. HipoMap showed the Area Under the Curve (AUC) of 0.96±0.026 (5% improved) in the experiments for lung cancer classification, and c-index of 0.787±0.013 (3.5% improved) and coefficient of determination (R²) of 0.978±0.032 (24% improved) in survival analysis and survival prediction with TCGA lung cancer data respectively, as a general framework of slide-based analysis with a flexible capability. The results showed significant improvement comparing to the current state-of-the-art methods on each task. We further discussed experimental results of HipoMap as pathological viewpoints and verified the performance using publicly available TCGA datasets. A Python package is available at https://pypi.org/project/hipomap, and the package can be easily installed using Python PIP. The open-source codes in Python are available at: https://github.com/datax-lab/HipoMap.

Controlled Subject

Cancer; Cancer--Histopathology; Lungs--Cancer

Disciplines

Computer Sciences

File Format

PDF

File Size

5100 KB

Language

English

Rights

IN COPYRIGHT. For more information about this rights statement, please visit http://rightsstatements.org/vocab/InC/1.0/

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 License.

Repository Citation

Kosaraju, S., Park, J., Lee, H., Yang, J. W., Kang, M. (2022). Deep Learning‑Based Framework for Slide‑Based Histopathological Image Analysis. Scientific Reports, 12 1-15.
http://dx.doi.org/10.1038/s41598-022-23166-0