Classification in Histopathology: A unique deep embeddings extractor for multiple classification tasks

TL;DR

This paper presents a method using a pre-trained deep embeddings extractor combined with task-specific classifiers to improve histopathology image classification, reducing data needs and training time while boosting accuracy.

Contribution

It introduces a novel approach for selecting optimal feature extractors and a feature space augmentation strategy for histopathology classification tasks.

Findings

Significant F1-score improvements across tasks

Effective backbone selection method for domain-specific features

Enhanced classification performance with feature space augmentation

Abstract

In biomedical imaging, deep learning-based methods are state-of-the-art for every modality (virtual slides, MRI, etc.) In histopathology, these methods can be used to detect certain biomarkers or classify lesions. However, such techniques require large amounts of data to train high-performing models which can be intrinsically difficult to acquire, especially when it comes to scarce biomarkers. To address this challenge, we use a single, pre-trained, deep embeddings extractor to convert images into deep features and train small, dedicated classification head on these embeddings for each classification task. This approach offers several benefits such as the ability to reuse a single pre-trained deep network for various tasks; reducing the amount of labeled data needed as classification heads have fewer parameters; and accelerating training time by up to 1000 times, which allows for much more tuning of the classification head. In this work, we perform an extensive comparison of various open-source backbones and assess their fit to the target histological image domain. This is achieved using a novel method based on a proxy classification task. We demonstrate that thanks to this selection method, an optimal feature extractor can be selected for different tasks on the target domain. We also introduce a feature space augmentation strategy which proves to substantially improve the final metrics computed for the different tasks considered. To demonstrate the benefit of such backbone selection and feature-space augmentation, our experiments are carried out on three separate classification tasks and show a clear improvement on each of them: microcalcifications (29.1% F1-score increase), lymph nodes metastasis (12.5% F1-score increase), mitosis (15.0% F1-score increase).