Clinically Labeled Contrastive Learning for OCT Biomarker Classification

Kiran Kokilepersaud, Stephanie Trejo Corona, Mohit Prabhushankar, Ghassan AlRegib, Charles Wykoff

Research output: Contribution to journalArticlepeer-review


This paper presents a novel positive and negative set selection strategy for contrastive learning of medical images based on labels that can be extracted from clinical data. In the medical field, there exists a variety of labels for data that serve different purposes at different stages of a diagnostic and treatment process. Clinical labels and biomarker labels are two examples. In general, clinical labels are easier to obtain in larger quantities because they are regularly collected during routine clinical care, while biomarker labels require expert analysis and interpretation to obtain. Within the field of ophthalmology, previous work has shown that clinical values exhibit correlations with biomarker structures that manifest within optical coherence tomography (OCT) scans. We exploit this relationship by using the clinical data as pseudo-labels for our data without biomarker labels in order to choose positive and negative instances for training a backbone network with a supervised contrastive loss. In this way, a backbone network learns a representation space that aligns with the clinical data distribution available. Afterwards, we fine-tune the network trained in this manner with the smaller amount of biomarker labeled data with a cross-entropy loss in order to classify these key indicators of disease directly from OCT scans. We also expand on this concept by proposing a method that uses a linear combination of clinical contrastive losses. We benchmark our methods against state of the art self-supervised methods in a novel setting with biomarkers of varying granularity. We show performance improvements by as much as 5% in total biomarker detection AUROC.

Original languageEnglish (US)
Pages (from-to)1-13
Number of pages13
JournalIEEE Journal of Biomedical and Health Informatics
Early online dateMay 22 2023
StateE-pub ahead of print - May 22 2023


  • AI for Ophthalmology
  • Biological system modeling
  • Biomarkers
  • Biomedical imaging
  • Clinical Labels
  • Clinical diagnosis
  • Contrastive Learning
  • Diseases
  • Histograms
  • Medical Data
  • Medical Imaging
  • OCT
  • Optical coherence tomography
  • Training

ASJC Scopus subject areas

  • Computer Science Applications
  • Health Informatics
  • Electrical and Electronic Engineering
  • Health Information Management


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