Compound Figure Separation of Biomedical Images: Mining Large Datasets for Self-supervised Learning

TL;DR

This paper introduces SimCFS, a novel framework for separating compound biomedical images into individual images without bounding box annotations, enhancing large-scale data collection for self-supervised learning in medical imaging.

Contribution

The study presents a resource-efficient, annotation-free method for compound figure separation, enabling better utilization of large unannotated biomedical image datasets for self-supervised learning.

Findings

Achieved state-of-the-art performance on ImageCLEF 2016 dataset.

Pretrained models improved downstream image classification accuracy.

Proposed method reduces reliance on extensive bounding box annotations.

Abstract

With the rapid development of self-supervised learning (e.g., contrastive learning), the importance of having large-scale images (even without annotations) for training a more generalizable AI model has been widely recognized in medical image analysis. However, collecting large-scale task-specific unannotated data at scale can be challenging for individual labs. Existing online resources, such as digital books, publications, and search engines, provide a new resource for obtaining large-scale images. However, published images in healthcare (e.g., radiology and pathology) consist of a considerable amount of compound figures with subplots. In order to extract and separate compound figures into usable individual images for downstream learning, we propose a simple compound figure separation (SimCFS) framework without using the traditionally required detection bounding box annotations, with a new loss function and a hard case simulation. Our technical contribution is four-fold: (1) we introduce a simulation-based training framework that minimizes the need for resource extensive bounding box annotations; (2) we propose a new side loss that is optimized for compound figure separation; (3) we propose an intra-class image augmentation method to simulate hard cases; and (4) to the best of our knowledge, this is the first study that evaluates the efficacy of leveraging self-supervised learning with compound image separation. From the results, the proposed SimCFS achieved state-of-the-art performance on the ImageCLEF 2016 Compound Figure Separation Database. The pretrained self-supervised learning model using large-scale mined figures improved the accuracy of downstream image classification tasks with a contrastive learning algorithm. The source code of SimCFS is made publicly available at https://github.com/hrlblab/ImageSeperation.