Deep Learning based Staging of Bone Lesions from Computed Tomography Scans (January 2021)

Samira Masoudi, Sherif Mehralivand, Stephanie A. Harmon, Nathan Lay, Liza Lindenberg, Esther Mena, Peter A. Pinto, Deborah E. Citrin, James L. Gulley, Bradford J. Wood, William L. Dahut, Ravi A. Madan, Ulas Bagci, Peter L. Choyke, Baris Turkbey

Research output: Contribution to journalArticlepeer-review


In this study, we formulated an efficient deep learning-based classification strategy for characterizing metastatic bone lesions using computed tomography scans (CTs) of prostate cancer patients. For this purpose, 2,880 annotated bone lesions from CT scans of 114 patients diagnosed with prostate cancer were used for training, validation, and final evaluation. These annotations were in the form of lesion full segmentation, lesion type and labels of either benign or malignant. In this work, we present our approach in developing the state-of-the-art model to classify bone lesions as benign or malignant, where (1) we introduce a valuable dataset to address a clinically important problem, (2) we increase the reliability of our model by patient-level stratification of our dataset following lesion-aware distribution at each of the training, validation, and test splits, (3) we explore the impact of lesion texture, morphology, size, location, and volumetric information on the classification performance, (4) we investigate the functionality of lesion classification using different algorithms including lesion-based average 2D ResNet-50, lesion-based average 2D ResNeXt-50, 3D ResNet-18, 3D ResNet-50, as well as the ensemble of 2D ResNet-50 and 3D ResNet-18. For this purpose, we employed a train/validation/test split equal to 75%/12%/13% with several data augmentation methods applied to the training dataset to avoid overfitting and to increase reliability. We achieved an accuracy of 92.2% for correct classification of benign vs. malignant bone lesions in the test set using an ensemble of lesion-based average 2D ResNet-50 and 3D ResNet-18 with texture, volumetric information, and morphology having the greatest discriminative power respectively. To the best of our knowledge, this is the highest ever achieved lesion-level accuracy having a very comprehensive data set for such a clinically important problem. This level of classification performance in the early stages of metastasis development bodes well for clinical translation of this strategy.

Original languageEnglish (US)
JournalIEEE Access
StateAccepted/In press - 2021


  • Bone lesion
  • Bones
  • CT scan
  • Computed tomography
  • Imaging
  • Lesions
  • Metastasis
  • Prostate cancer
  • Three-dimensional displays
  • classification
  • deep learning
  • lesion-aware data stratification

ASJC Scopus subject areas

  • Computer Science(all)
  • Materials Science(all)
  • Engineering(all)


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