Chromosome Cluster Identification Framework Based on Geometric Features and Machine Learning Algorithms

Abstract

In medicine, chromosome karyotype analysis is vital for genetic disease diagnoses, such as Edward syndrome, Patau syndrome, and Down syndrome. However, the chromosome karyotype analysis is usually manually done by extensive experienced clinical analysts, which is tedious and time-consuming. Consequently, automatic or partial automatic chromosome karyotyping is essential to alleviate clinical analysts’ jobs. This paper proposes a chromosome cluster identification framework based on geometric chromosome features and machine learning algorithms to identify chromosome clusters needed to further process in the automated instance segmentation task. In the proposed framework, we first collect multiple dimensions of chromosome geometric features into a feature tuple, including object area, bounding box area, convex area, extent, solidity, perimeter, equivalent diameter, eccentricity, major axis length, minor axis length, and minor-major axis ratio. Second, we classify these chromosome feature tuples utilizing different machine learning classification algorithms. The experiment results show that our proposed method yields 96.21 ± 0.91% classification accuracy and 0.9832 ± 0.0111AUC (Area Under The Curve) value in the clinical dataset. The highlight of this paper is that the performance of the proposed approach has exceeded the existing geometric features threshold-based methods and multiple end-to-end deep learning-based baselines. Moreover, our proposed method can be deployed on any devices and platforms with a Python running environment, which significantly improves application flexibility. To facilitate peers in reproducing and employing our work, we release the code and the corresponding clinical dataset on Github.