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Outlier Guided Optimization of Abdominal Segmentation

Posted by on Wednesday, February 12, 2020 in Abdomen Imaging, News.

Yuchen Xu*, Olivia Tang*, Yucheng Tang, Ho Hin Lee, Yunqiang Chen, Dashan Gao, Shizhong Han, Riqiang Gao, Michael R. Savona, Richard G. Abramson, Yuankai Huo, Bennett A. Landman, “Outlier Guided Optimization of Abdomen Segmentation”, SPIE IP:MI 2020. Houston, TX

https://arxiv.org/abs/2002.04098

Abstract

Abdominal multi-organ segmentation of computed tomography (CT) images has been the subject of extensive research interest. It presents a substantial challenge in medical image processing, as the shape and distribution of abdominal organs can vary greatly among the population and within an individual over time. While continuous integration of novel datasets into the training set provides potential for better segmentation performance, collection of data at scale is not only costly, but also impractical in some contexts. Moreover, it remains unclear what marginal value additional data have to offer. Herein, we propose a single-pass active learning method through human quality assurance (QA). We built on a pre-trained 3D U-Net model for abdominal multi-organ segmentation and augmented the dataset either with outlier data (e.g., exemplars for which the baseline algorithm failed) or inliers (e.g., exemplars for which the baseline algorithm worked). The new models were trained using the augmented datasets with 5-fold cross-validation (for outlier data) and withheld outlier samples (for inlier data). Manual labeling of outliers increased Dice scores with outliers by 0.130, compared to an increase of 0.067 with inliers (p<0.001, two-tailed paired t-test). By adding 5 to 37 inliers or outliers to training, we find that the marginal value of adding outliers is higher than that of adding inliers. In summary, improvement on single-organ performance was obtained without diminishing multi-organ performance or significantly increasing training time. Hence, identification and correction of baseline failure cases present an effective and efficient method of selecting training data to improve algorithm performance.

Examples of segmentations generated by the baseline algorithm. A. An inlier, where the algorithm correctly predicted larger organs, like the liver (on the left side of image in purple) and spleen (on the right side of image in red- pink) and suggested mostly accurate areas of smaller organs. B. An outlier (global failure), where the liver (purple) and spleen (red-pink) were largely correct but major inconsistencies are visible with other organs.
Examples of segmentations generated by the baseline algorithm. A. An inlier, where the algorithm correctly predicted larger organs, like the liver (on the left side of image in purple) and spleen (on the right side of image in red- pink) and suggested mostly accurate areas of smaller organs. B. An outlier (global failure), where the liver (purple) and spleen (red-pink) were largely correct but major inconsistencies are visible with other organs.

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