Discriminative bag-of-cells for imaging-genomics

Benjamin Chidester, Minh N. Do, Jian Ma

Research output: Contribution to journalConference articlepeer-review


Connecting genotypes to image phenotypes is crucial for a comprehensive understanding of cancer. To learn such connections, new machine learning approaches must be developed for the better integration of imaging and genomic data. Here we propose a novel approach called Discriminative Bag-of-Cells (DBC) for predicting genomic markers using imaging features, which addresses the challenge of summarizing histopathological images by representing cells with learned discriminative types, or codewords. We also developed a reliable and efficient patch-based nuclear segmentation scheme using convolutional neural networks from which nuclear and cellular features are extracted. Applying DBC on TCGA breast cancer samples to predict basal subtype status yielded a class-balanced accuracy of 70% on a separate test partition of 213 patients. As data sets of imaging and genomic data become increasingly available, we believe DBC will be a useful approach for screening histopathological images for genomic markers. Source code of nuclear segmentation and DBC are available at: https://github.com/bchidest/DBC.

Original languageEnglish (US)
Pages (from-to)319-330
Number of pages12
JournalPacific Symposium on Biocomputing
Issue number212669
StatePublished - 2018
Event23rd Pacific Symposium on Biocomputing, PSB 2018 - Kohala Coast, United States
Duration: Jan 3 2018Jan 7 2018


  • Computational pathology
  • Histopathological image analysis
  • Imaging-genomics

ASJC Scopus subject areas

  • Biomedical Engineering
  • Computational Theory and Mathematics


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