Unsupervised machine learning for identifying important visual features through bag-of-words using histopathology data from chronic kidney disease

Autor: Joonsang Lee, Elisa Warner, Salma Shaikhouni, Markus Bitzer, Matthias Kretzler, Debbie Gipson, Subramaniam Pennathur, Keith Bellovich, Zeenat Bhat, Crystal Gadegbeku, Susan Massengill, Kalyani Perumal, Jharna Saha, Yingbao Yang, Jinghui Luo, Xin Zhang, Laura Mariani, Jeffrey B. Hodgin, Arvind Rao, the C-PROBE Study
Jazyk: angličtina
Rok vydání: 2022
Předmět:
Zdroj: Scientific Reports, Vol 12, Iss 1, Pp 1-13 (2022)
Druh dokumentu: article
ISSN: 2045-2322
DOI: 10.1038/s41598-022-08974-8
Popis: Abstract Pathologists use visual classification to assess patient kidney biopsy samples when diagnosing the underlying cause of kidney disease. However, the assessment is qualitative, or semi-quantitative at best, and reproducibility is challenging. To discover previously unknown features which predict patient outcomes and overcome substantial interobserver variability, we developed an unsupervised bag-of-words model. Our study applied to the C-PROBE cohort of patients with chronic kidney disease (CKD). 107,471 histopathology images were obtained from 161 biopsy cores and identified important morphological features in biopsy tissue that are highly predictive of the presence of CKD both at the time of biopsy and in one year. To evaluate the performance of our model, we estimated the AUC and its 95% confidence interval. We show that this method is reliable and reproducible and can achieve 0.93 AUC at predicting glomerular filtration rate at the time of biopsy as well as predicting a loss of function at one year. Additionally, with this method, we ranked the identified morphological features according to their importance as diagnostic markers for chronic kidney disease. In this study, we have demonstrated the feasibility of using an unsupervised machine learning method without human input in order to predict the level of kidney function in CKD. The results from our study indicate that the visual dictionary, or visual image pattern, obtained from unsupervised machine learning can predict outcomes using machine-derived values that correspond to both known and unknown clinically relevant features.
Databáze: Directory of Open Access Journals
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