Publications

Successful Identification of Nasopharyngeal Carcinoma in Nasopharyngeal Biopsies Using Deep Learning

Published in Cancers, 2020

Pathologic diagnosis of nasopharyngeal carcinoma (NPC) can be challenging since most cases are nonkeratinizing carcinoma with little differentiation and many admixed lymphocytes. Our aim was to evaluate the possibility to identify NPC in nasopharyngeal biopsies using deep learning. A total of 726 nasopharyngeal biopsies were included. Among them, 100 cases were randomly selected as the testing set, 20 cases as the validation set, and all other 606 cases as the training set. All three datasets had equal numbers of NPC cases and benign cases. Manual annotation was performed. Cropped square image patches of 256 × 256 pixels were used for patch-level training, validation, and testing. The final patch-level algorithm effectively identified NPC patches, with an area under the receiver operator characteristic curve (AUC) of 0.9900. Using gradient-weighted class activation mapping, we demonstrated that the identification of NPC patches was based on morphologic features of tumor cells. At the second stage, whole-slide images were sequentially cropped into patches, inferred with the patch-level algorithm, and reconstructed into images with a smaller size for training, validation, and testing. Finally, the AUC was 0.9848 for slide-level identification of NPC. Our result shows for the first time that deep learning algorithms can identify NPC.

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A Multi-Organ Nucleus Segmentation Challenge

Published in IEEE Transactions on Medical Imaging, 2019

Generalized nucleus segmentation techniques can contribute greatly to reducing the time to develop and validate visual biomarkers for new digital pathology datasets. We summarize the results of MoNuSeg 2018 Challenge whose objective was to develop generalizable nuclei segmentation techniques in digital pathology. The challenge was an official satellite event of the MICCAI 2018 conference in which 32 teams with more than 80 participants from geographically diverse institutes participated. Contestants were given a training set with 30 images from seven organs with annotations of 21,623 individual nuclei. A test dataset with 14 images taken from seven organs, including two organs that did not appear in the training set was released without annotations. Entries were evaluated based on average aggregated Jaccard index (AJI) on the test set to prioritize accurate instance segmentation as opposed to mere semantic segmentation. More than half the teams that completed the challenge outperformed a previous baseline. Among the trends observed that contributed to increased accuracy were the use of color normalization as well as heavy data augmentation. Additionally, fully convolutional networks inspired by variants of U-Net, FCN, and Mask-RCNN were popularly used, typically based on ResNet or VGG base architectures. Watershed segmentation on predicted semantic segmentation maps was a popular post-processing strategy. Several of the top techniques compared favorably to an individual human annotator and can be used with confidence for nuclear morphometrics.

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Training Deep Neural Networks Directly on Hundred-million-pixel Histopathology Images on a Large-scale GPU Cluster

Published in The International Conference for High Performance Computing, 2019

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Deep Convolutional Neural Network-Based Positron Emission Tomography Analysis Predicts Esophageal Cancer Outcome.

Published in Journal of clinical medicine, 2019

In esophageal cancer, few prediction tools can be confidently used in current clinical practice. We developed a deep convolutional neural network (CNN) with 798 positron emission tomography (PET) scans of esophageal squamous cell carcinoma and 309 PET scans of stage I lung cancer. In the first stage, we pretrained a 3D-CNN with all PET scans for a task to classify the scans into esophageal cancer or lung cancer. Overall, 548 of 798 PET scans of esophageal cancer patients were included in the second stage with an aim to classify patients who expired within or survived more than one year after diagnosis. The area under the receiver operating characteristic curve (AUC) was used to evaluate model performance. In the pretrain model, the deep CNN attained an AUC of 0.738 in identifying patients who expired within one year after diagnosis. In the survival analysis, patients who were predicted to be expired but were alive at one year after diagnosis had a 5-year survival rate of 32.6%, which was significantly worse than the 5-year survival rate of the patients who were predicted to survive and were alive at one year after diagnosis (50.5%, p < 0.001). These results suggest that the prediction model could identify tumors with more aggressive behavior. In the multivariable analysis, the prediction result remained an independent prognostic factor (hazard ratio: 2.830; 95% confidence interval: 2.252-3.555, p < 0.001). We conclude that a 3D-CNN can be trained with PET image datasets to predict esophageal cancer outcome with acceptable accuracy.

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