CIR-Net: Automatic Classification of Human Chromosome Based on Inception-ResNet Architecture

Chengchuang Lin, Gansen Zhao*, Zhirong Yang, Aihua Yin, Xinming Wang, Li Guo, Hanbiao Chen, Zhaohui Ma, Lei Zhao, Haoyu Luo, Tianxing Wang, Bichao Ding, Xiongwen Pang, Qiren Chen

*Corresponding author for this work

Research output: Contribution to journalArticleScientificpeer-review

8 Citations (Scopus)


Background: In medicine, karyotyping chromosomes is important for medical diagnostics, drug development, and biomedical research. Unfortunately, chromosome karyotyping is usually done by skilled cytologists manually, which requires experience, domain expertise, and considerable manual efforts. Therefore, automating the karyotyping process is a significant and meaningful task. Method: This paper focuses on chromosome classification because it is critical for chromosome karyotyping. In recent years, deep learning-based methods are the most promising methods for solving the tasks of chromosome classification. Although the deep learning-based Inception architecture has yielded state-of-the-art performance in the 2015 ILSVRC challenge, it has not been used in chromosome classification tasks so far. Therefore, we develop an automatic chromosome classification approach named CIR-Net based on Inception-ResNet which is an optimized version of Inception. However, the classification performance of origin Inception-ResNet on the insufficient chromosome dataset still has a lot of capacity for improvement. Further, we propose a simple but effective augmentation method called CDA for improving the performance of CIR-Net. Results: The experimental results show that our proposed method achieves 95.98 percent classification accuracy on the clinical G-band chromosome dataset whose training dataset is insufficient. Moreover, the proposed augmentation method CDA improves more than 8.5 percent (from 87.46 to 95.98 percent) classification accuracy comparing to other methods. In this paper, the experimental results demonstrate that our proposed method is recent the most effective solution for solving clinical chromosome classification problems in chromosome auto-karyotyping on the condition of the insufficient training dataset. Code and Dataset are available at

Original languageEnglish
Pages (from-to)1285-1293
Number of pages9
JournalIEEE/ACM Transactions on Computational Biology and Bioinformatics
Issue number3
Publication statusPublished - 2022
MoE publication typeA1 Journal article-refereed


  • biomedical image analysis
  • Chromosome classification
  • chromosome image augmentation
  • inception-ResNet


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