Dealing with Small Datasets for Deep Learning in Medical Imaging: An Evaluation of Self-Supervised Pre-Training on CT Scans Comparing Contrastive and Masked Autoencoder Methods for Convolutional Models

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 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 CT classification tasks. Due to the challenge of obtaining sufficient annotated training data in medical imaging, it is of particular interest to evaluate how the self-supervised pre-training methods perform when fine-tuning on small datasets. By experimenting with gradually reducing the training dataset size for fine-tuning, 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 imaging tasks with only small annotated datasets.

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 Autoencoder Methods for Convolutional Models

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.

Where to look first? Behaviour control for fetch-and-carry missions of service robots

This paper presents the behaviour control of a service robot for intelligent object search in a domestic environment. A major challenge in service robotics is to enable fetch-and-carry missions that are satisfying for the user in terms of efficiency and human-oriented perception. The proposed behaviour controller provides an informed intelligent search based on a semantic segmentation framework for indoor scenes and integrates it with object recognition and grasping. Instead of manually annotating search positions in the environment, the framework automatically suggests likely locations to search for an object based on contextual information, e.g. next to tables and shelves. In a preliminary set of experiments we demonstrate that this behaviour control is as efficient as using manually annotated locations. Moreover, we argue that our approach will reduce the intensity of labour associated with programming fetch-and-carry tasks for service robots and that it will be perceived as more human-oriented.

Find my mug: Efficient object search with a mobile robot using semantic segmentation

In this paper, we propose an efficient semantic segmentation framework for indoor scenes, tailored to the application on a mobile robot. Semantic segmentation can help robots to gain a reasonable understanding of their environment, but to reach this goal, the algorithms not only need to be accurate, but also fast and robust. Therefore, we developed an optimized 3D point cloud processing framework based on a Randomized Decision Forest, achieving competitive results at sufficiently high frame rates. We evaluate the capabilities of our method on the popular NYU depth dataset and our own data and demonstrate its feasibility by deploying it on a mobile service robot, for which we could optimize an object search procedure using our results.