OMT and tensor SVD-based deep learning model for segmentation and predicting genetic markers of glioma: A multicenter study.

Journal: Proceedings of the National Academy of Sciences of the United States of America
Published Date:

Abstract

Glioma is the most common primary malignant brain tumor and preoperative genetic profiling is essential for the management of glioma patients. Our study focused on tumor regions segmentation and predicting the World Health Organization (WHO) grade, isocitrate dehydrogenase (IDH) mutation, and 1p/19q codeletion status using deep learning models on preoperative MRI. To achieve accurate tumor segmentation, we developed an optimal mass transport (OMT) approach to transform irregular MRI brain images into tensors. In addition, we proposed an algebraic preclassification (APC) model utilizing multimode OMT tensor singular value decomposition (SVD) to estimate preclassification probabilities. The fully automated deep learning model named OMT-APC was used for multitask classification. Our study incorporated preoperative brain MRI data from 3,565 glioma patients across 16 datasets spanning Asia, Europe, and America. Among these, 2,551 patients from 5 datasets were used for training and internal validation. In comparison, 1,014 patients from 11 datasets, including 242 patients from The Cancer Genome Atlas (TCGA), were used as independent external test. The OMT segmentation model achieved mean lesion-wise Dice scores of 0.880. The OMT-APC model was evaluated on the TCGA dataset, achieving accuracies of 0.855, 0.917, and 0.809, with AUC scores of 0.845, 0.908, and 0.769 for WHO grade, IDH mutation, and 1p/19q codeletion, respectively, which outperformed the four radiologists in all tasks. These results highlighted the effectiveness of our OMT and tensor SVD-based methods in brain tumor genetic profiling, suggesting promising applications for algebraic and geometric methods in medical image analysis.

Authors

  • Zhengyang Zhu
    Department of Forensic Pathology, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, People's Republic of China.
  • Han Wang
    Saw Swee Hock School of Public Health, National University Health System, National University of Singapore, Singapore.
  • Tiexiang Li
    School of Mathematics and Shing-Tung Yau Center, Southeast University, Nanjing 210096, China.
  • Tsung-Ming Huang
    Department of Mathematics, National Taiwan Normal University, Taipei, Taiwan.
  • Huiquan Yang
    Department of Radiology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China.
  • Zhennan Tao
    Department of Neurosurgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China.
  • Zhong-Heng Tan
    School of Mathematics and Shing-Tung Yau Center, Southeast University, Nanjing 210096, China.
  • Jianan Zhou
    Department of Radiology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China.
  • Sixuan Chen
    Department of Diagnostic Radiology, Jinling Hospital, Medical School of Nanjing University, Nanjing 210002, China.
  • Meiping Ye
    Department of Radiology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China.
  • Zhiqiang Zhang
    Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China.
  • Feng Li
    Department of General Surgery, Shanghai Traditional Chinese Medicine (TCM)-INTEGRATED Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai, China.
  • Dongming Liu
    School of Materials Science and Engineering, Key Lab of Efficient Conversion and Solid-State Storage of Hydrogen & Electricity, Anhui University of Technology, Maanshan, 243002, China.
  • Maoxue Wang
    Department of Radiology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China.
  • Jiaming Lu
    Department of Radiology, The Affiliated Drum Tower Hospital, Nanjing University Medical School, Nanjing, 210000, Jiangsu, China.
  • Wen Zhang
    Oil Crops Research Institute, Chinese Academy of Agricultural Sciences Wuhan 430062 China peiwuli@oilcrops.cn zhangqi521x@126.com +86-27-8681-2943 +86-27-8671-1839.
  • Xin Li
    Veterinary Diagnostic Center, Shanghai Animal Disease Control Center, Shanghai, China.
  • Qian Chen
    Department of Pain Medicine Guizhou Provincial Orthopedics Hospital Guiyang Guizhou China.
  • Zhuoru Jiang
    Department of Radiology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China.
  • Futao Chen
    Department of Radiology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China.
  • Xin Zhang
    First Department of Infectious Diseases, The First Affiliated Hospital of China Medical University, Shenyang, China.
  • Wen-Wei Lin
    Institute of Biomedical Sciences, National Sun Yat-sen University , Kaohsiung, Taiwan.
  • Shing-Tung Yau
    Yau Mathematical Sciences Center, Jingzhai, Tsinghua University, Beijing 100084, China.
  • Bing Zhang
    School of Information Science and Engineering, Yanshan University, Hebei Avenue, Qinhuangdao, 066004, China.