Weakly supervised 3D classification of chest CT using aggregated multi-resolution deep segmentation features

Anindo Saha, Fakrul I. Tushar, Khrystyna Faryna, Vincent M. D'Anniballe, Rui Hou, MacIej A. Mazurowski, Geoffrey D. Rubin, Joseph Y. Lo

Research output: Chapter in Book/Report/Conference proceedingConference contribution

3 Scopus citations


Weakly supervised disease classification of CT imaging suffers from poor localization owing to case-level annotations, where even a positive scan can hold hundreds to thousands of negative slices along multiple planes. Furthermore, although deep learning segmentation and classification models extract distinctly unique combinations of anatomical features from the same target class(es), they are typically seen as two independent processes in a computer-aided diagnosis (CAD) pipeline, with little to no feature reuse. In this research, we propose a medical classifier that leverages the semantic structural concepts learned via multi-resolution segmentation feature maps, to guide weakly supervised 3D classification of chest CT volumes. Additionally, a comparative analysis is drawn across two different types of feature aggregation to explore the vast possibilities surrounding feature fusion. Using a dataset of 1593 scans labeled on a case-level basis via rule-based model, we train a dual-stage convolutional neural network (CNN) to perform organ segmentation and binary classification of four representative diseases (emphysema, pneumonia/atelectasis, mass and nodules) in lungs. The baseline model, with separate stages for segmentation and classification, results in AUC of 0.791. Using identical hyperparameters, the connected architecture using static and dynamic feature aggregation improves performance to AUC of 0.832 and 0.851, respectively. This study advances the field in two key ways. First, case-level report data is used to weakly supervise a 3D CT classifier of multiple, simultaneous diseases for an organ. Second, segmentation and classification models are connected with two different feature aggregation strategies to enhance the classification performance.

Original languageEnglish (US)
Title of host publicationMedical Imaging 2020
Subtitle of host publicationComputer-Aided Diagnosis
EditorsHorst K. Hahn, Maciej A. Mazurowski
ISBN (Electronic)9781510633957
StatePublished - 2020
Externally publishedYes
EventMedical Imaging 2020: Computer-Aided Diagnosis - Houston, United States
Duration: Feb 16 2020Feb 19 2020

Publication series

NameProgress in Biomedical Optics and Imaging - Proceedings of SPIE
ISSN (Print)1605-7422


ConferenceMedical Imaging 2020: Computer-Aided Diagnosis
Country/TerritoryUnited States


  • 3d classification
  • convolutional neural network
  • ct
  • feature aggregation
  • lungs
  • weak supervision

ASJC Scopus subject areas

  • Electronic, Optical and Magnetic Materials
  • Atomic and Molecular Physics, and Optics
  • Biomaterials
  • Radiology Nuclear Medicine and imaging


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