Dealing with Small Annotated Datasets for Deep Learning in Medical Imaging: An Evaluation of Self-Supervised Pre-Training on CT Scans Comparing Contrastive and Masked Autoencod
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Deep learning in medical imaging has the potential to minimize the risk of diagnostic errors, reduce radiologist workload, and accelerate diagnosis. Training such deep learning models requires large and accurate datasets, with annotations for all training samples. However, in the medical imaging domain, annotated datasets for specific tasks are often small due to the high complexity of annotations, limited access, or the rarity of diseases. To address this challenge, deep learning models can be pre-trained on large image datasets without annotations using methods from the field of self-supervised learning. After pre-training, small annotated datasets are sufficient to fine-tune the models for a specific task, the so-called “downstream task". The most popular self-supervised pre-training approaches in medical imaging are based on contrastive learning. However, recent studies in natural image processing indicate a strong potential for masked autoencoder approaches. Our work compares state-of-the-art contrastive learning methods with the recently introduced masked autoencoder approach "SparK" for convolutional neural networks (CNNs) on medical images. Therefore we pre-train on a large unannotated CT image dataset and fine-tune on several downstream CT classification tasks. Due to the challenge of obtaining sufficient annotated training data in the medical imaging domain, it is of particular interest to evaluate how the self-supervised pre-training methods perform on small downstream datasets. By experimenting with gradually reducing the training dataset size of our downstream tasks, we find that the reduction has different effects depending on the type of pre-training chosen. The SparK pre-training method is more robust to the training dataset size than the contrastive methods. Based on our results, we propose the SparK pre-training for medical downstream tasks with small datasets.
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