J. Imaging, Vol. 9, Pages 25: Human Hepatocellular Carcinoma Classification from H&E Stained Histopathology Images with 3D Convolutional Neural Networks and Focal Loss Function

J. Imaging, Vol. 9, Pages 25: Human Hepatocellular Carcinoma Classification from H&E Stained Histopathology Images with 3D Convolutional Neural Networks and Focal Loss Function

Journal of Imaging doi: 10.3390/jimaging9020025

Authors: Umut Cinar Rengul Cetin Atalay Yasemin Yardimci Cetin

This paper proposes a new Hepatocellular Carcinoma (HCC) classification method utilizing a hyperspectral imaging system (HSI) integrated with a light microscope. Using our custom imaging system, we have captured 270 bands of hyperspectral images of healthy and cancer tissue samples with HCC diagnosis from a liver microarray slide. Convolutional Neural Networks with 3D convolutions (3D-CNN) have been used to build an accurate classification model. With the help of 3D convolutions, spectral and spatial features within the hyperspectral cube are incorporated to train a strong classifier. Unlike 2D convolutions, 3D convolutions take the spectral dimension into account while automatically collecting distinctive features during the CNN training stage. As a result, we have avoided manual feature engineering on hyperspectral data and proposed a compact method for HSI medical applications. Moreover, the focal loss function, utilized as a CNN cost function, enables our model to tackle the class imbalance problem residing in the dataset effectively. The focal loss function emphasizes the hard examples to learn and prevents overfitting due to the lack of inter-class balancing. Our empirical results demonstrate the superiority of hyperspectral data over RGB data for liver cancer tissue classification. We have observed that increased spectral dimension results in higher classification accuracy. Both spectral and spatial features are essential in training an accurate learner for cancer tissue classification.