Highly Performing Automatic Detection of Structural Chromosomal Abnormalities Using Siamese Architecture.

The detection of structural chromosomal abnormalities (SCA) is crucial for diagnosis, prognosis and management of many genetic diseases and cancers. This detection, done by highly qualified medical experts, is tedious and time-consuming. We propose a highly performing and intelligent method to assist cytogeneticists to screen for SCA. Each chromosome is present in two copies that make up a pair of chromosomes. Usually, SCA are present in only one copy of the pair. Convolutional neural networks (CNN) with Siamese architecture are particularly relevant for evaluating similarities between two images, which is why we used this method to detect abnormalities between both chromosomes of a given pair. As a proof-of-concept, we first focused on a deletion occurring on chromosome 5 (del(5q)) observed in hematological malignancies. Using our dataset, we conducted several experiments without and with data augmentation on seven popular CNN models. Overall, performances obtained were very relevant for detecting deletions, particularly with Xception and InceptionResNetV2 models achieving 97.50% and 97.01% of F1-score, respectively. We additionally demonstrated that these models successfully recognized another SCA, inversion inv(3), which is one of the most difficult SCA to detect. The performance improved when the training was applied on inversion inv(3) dataset, achieving 94.82% of F1-score. The technique that we propose in this paper is the first highly performing method based on Siamese architecture that allows the detection of SCA. Our code is publicly available at: https://github.com/MEABECHAR/ChromosomeSiameseAD.

Influence of normalization and color features on super-pixel classification: application to cytological image segmentation.

Super-pixel feature extraction is a key problem to get an acceptable performance in color super-pixel classification. Given a color feature extraction problem, it is necessary to know which is the best approach to solve this problem. In the current work, we're interested in the challenge of nucleus and cytoplasm automatic recognition in the cytological image. We propose an automatic process for white blood cells (WBC) segmentation using super-pixel classification. The process is divided into five steps. In first step, the color normalization is calculated. The super-pixels generation by Simple Linear Iterative Clustering algorithm is performed in the second step. In third step, the color property is used to achieve illumination invariance. In fourth step, color features are calculated on each super-pixel. Finally, supervised learning is realized to classify each super-pixel into nucleus and cytoplasm region. The present work rallied an exhaustive statistical evaluation of a very wide variety of the color super-pixel classification, with height normalization methods, four-color spaces and four feature extraction techniques. Normalization and color spaces slightly increase the average accuracy of super-pixel classification. Our experiments based to statistical comparison allow to conclude that comprehensive gray world normalized normalization is better than without normalization for super-pixel classification achieving the first positions in the Friedman ranking. RGB space is the best color spaces to be used in super-pixel feature extraction for nucleus and cytoplasm segmentation. For feature extraction, the learning methods work better on the first order statistics features for the automatic WBC segmentation.