Automatic Cancer Cell Taxonomy Using an Ensemble of Deep Neural Networks

SIMPLE SUMMARY: As of recently, cancer is considered a major cause of death in developed and developing countries. Therefore, there is an urgent need for improvements in existing diagnostic methods for effective early diagnosis. However, cross-contamination of cancer cell lines results in the development of inappropriate treatments that cannot be administered to patients. To address this issue, we propose an automatic cancer cell taxonomy with high accuracy using optical images of cells obtained through low-scale benchtop optical microscopy. Specifically, we built a deep-learning-based framework to classify cervical, hepatocellular, breast, and lung cancer cells. The experimental results demonstrated that the proposed deep-learning-based approach facilitates the automatic identification of cancer cells. Moreover, our findings provide important insights into the design of convolutional neural networks for various clinical tasks that utilize microscopic images. ABSTRACT: Microscopic image-based analysis has been intensively performed for pathological studies and diagnosis of diseases. However, mis-authentication of cell lines due to misjudgments by pathologists has been recognized as a serious problem. To address this problem, we propose a deep-learning-based approach for the automatic taxonomy of cancer cell types. A total of 889 bright-field microscopic images of four cancer cell lines were acquired using a benchtop microscope. Individual cells were further segmented and augmented to increase the image dataset. Afterward, deep transfer learning was adopted to accelerate the classification of cancer types. Experiments revealed that the deep-learning-based methods outperformed traditional machine-learning-based methods. Moreover, the Wilcoxon signed-rank test showed that deep ensemble approaches outperformed individual deep-learning-based models (p < 0.001) and were in effect to achieve the classification accuracy up to 97.735%. Additional investigation with the Wilcoxon signed-rank test was conducted to consider various network design choices, such as the type of optimizer, type of learning rate scheduler, degree of fine-tuning, and use of data augmentation. Finally, it was found that the using data augmentation and updating all the weights of a network during fine-tuning improve the overall performance of individual convolutional neural network models.