Deep learning has become the mainstream technology in computer vision, and it has received extensive research interest in developing new medical image processing algorithms to support disease detection and diagnosis. As compared to conventional machine learning technologies, the major advantage of deep learning is that models can automatically identify and recognize representative features through the hierarchal model architecture, while avoiding the laborious development of hand-crafted features. In this paper, we reviewed and summarized more than 200 recently published papers to provide a comprehensive overview of applying deep learning methods in various medical image analysis tasks. Especially, we emphasize the latest progress and contributions of state-of-the-art unsupervised and semi-supervised deep learning in medical images, which are summarized based on different application scenarios, including lesion classification, segmentation, detection, and image registration. Additionally, we also discussed the major technical challenges and suggested the possible solutions in future research efforts.

Recent advances and clinical applications of deep learning in medical image analysis.

Human-in-the-loop aims to train an accurate prediction model with minimum cost by integrating human knowledge and experience. Humans can provide training data for machine learning applications and directly accomplish some tasks that are hard for computers in the pipeline with the help of machine-based approaches. In this paper, we survey existing works on human-in-the-loop from a data perspective and classify them into three categories with a progressive relationship: (1) the work of improving model performance from data processing, (2) the work of improving model performance through interventional model training, and (3) the design of the system independent human-in-the-loop. Using the above categorization, we summarize major approaches in the field, along with their technical strengths/ weaknesses, we have simple classification and discussion in natural language processing, computer vision, and others. Besides, we provide some open challenges and opportunities. This survey intends to provide a high-level summarization for human-in-the-loop and motivates interested readers to consider approaches for designing effective human-in-the-loop solutions.

A Survey of Human-in-the-loop for Machine Learning.

Vision Transformers (ViT)s have shown great performance in self-supervised learning of global and local representations that can be transferred to downstream applications. Inspired by these results, we introduce a novel self-supervised learning framework with tailored proxy tasks for medical image analysis. Specifically, we propose: (i) a new 3D transformer-based model, dubbed Swin UNEt TRansformers (Swin UNETR), with a hierarchical encoder for self-supervised pretraining; (ii) tailored proxy tasks for learning the underlying pattern of human anatomy. We demonstrate successful pre-training of the proposed model on 5,050 publicly available computed tomography (CT) images from various body organs. The effectiveness of our approach is validated by fine-tuning the pre-trained models on the Beyond the Cranial Vault (BTCV) Segmentation Challenge with 13 abdominal organs and segmentation tasks from the Medical Segmentation Decathlon (MSD) dataset. Our model is currently the state-of-the-art on the public test leaderboards of both MSD 1 1 https://decathlon-10.grand-challenge.org/evaluation/challenge/leaderboard/ and BTCV 2 2 https://www.synapse.org/#!Synapse:syn3193805/wiki/217785/ datasets. Code: https://monai.io/research/swin-unetr.

/pdf/self-supervised-pre-training-of-swin-transformers-for-3d-1w720kea.pdf

Self-Supervised Pre-Training of Swin Transformers for 3D Medical Image Analysis

Models Genesis

Self-supervised representation learning methods aim to provide powerful deep feature learning without the requirement of large annotated datasets, thus alleviating the annotation bottleneck that is one of the main barriers to practical deployment of deep learning today. These methods have advanced rapidly in recent years, with their efficacy approaching and sometimes surpassing fully supervised pre-training alternatives across a variety of data modalities including image, video, sound, text and graphs. This article introduces this vibrant area including key concepts, the four main families of approach and associated state of the art, and how self-supervised methods are applied to diverse modalities of data. We further discuss practical considerations including workflows, representation transferability, and compute cost. Finally, we survey the major open challenges in the field that provide fertile ground for future work.

Self-Supervised Representation Learning: Introduction, Advances and Challenges.

Self-supervised learning approaches leverage unlabeled samples to acquire generic knowledge about different concepts, hence allowing for annotation-efficient downstream task learning. In this paper, we propose a novel self-supervised method that leverages multiple imaging modalities. We introduce the multimodal puzzle task, which facilitates rich representation learning from multiple image modalities. The learned representations allow for subsequent fine-tuning on different downstream tasks. To achieve that, we learn a modality-agnostic feature embedding by confusing image modalities at the data-level. Together with the Sinkhorn operator, with which we formulate the puzzle solving optimization as permutation matrix inference instead of classification, they allow for efficient solving of multimodal puzzles with varying levels of complexity. In addition, we also propose to utilize cross-modal generation techniques for multimodal data augmentation used for training self-supervised tasks. In other words, we exploit synthetic images for self-supervised pretraining, instead of downstream tasks directly, in order to circumvent quality issues associated with synthetic images, while improving data-efficiency and representations quality. Our experimental results, which assess the gains in downstream performance and data-efficiency, show that solving our multimodal puzzles yields better semantic representations, compared to treating each modality independently. Our results also highlight the benefits of exploiting synthetic images for self-supervised pretraining. We showcase our approach on four downstream tasks: Brain tumor segmentation and survival days prediction using four MRI modalities, Prostate segmentation using two MRI modalities, and Liver segmentation using unregistered CT and MRI modalities. We outperform many previous solutions, and achieve results competitive to state-of-the-art.

Multimodal Self-Supervised Learning for Medical Image Analysis

Self-supervised learning approaches leverage unlabeled samples to acquire generic knowledge about different concepts, hence allowing for annotation-efficient downstream task learning. In this paper, we propose a novel self-supervised method that leverages multiple imaging modalities. We introduce the multimodal puzzle task, which facilitates representation learning from multiple image modalities. The learned modality-agnostic representations are obtained by confusing image modalities at the data-level. Together with the Sinkhorn operator, with which we formulate the puzzle solving optimization as permutation matrix inference instead of classification, they allow for efficient solving of multimodal puzzles with varying levels of complexity. In addition, we also propose to utilize generation techniques for multimodal data augmentation used for self-supervised pretraining, instead of downstream tasks directly. This aims to circumvent quality issues associated with synthetic images, while improving data-efficiency and the representations learned by self-supervised methods. Our experimental results show that solving our multimodal puzzles yields better semantic representations, compared to treating each modality independently. Our results also highlight the benefits of exploiting synthetic images for self-supervised pretraining. We showcase our approach on three segmentation tasks, and we outperform many solutions and our results are competitive to state-of-the-art.

High annotation costs are a substantial bottleneck in applying modern deep learning architectures to clinically relevant medical use cases, substantiating the need for novel algorithms to learn from unlabeled data. In this work, we propose ContIG, a self-supervised method that can learn from large datasets of unlabeled medical images and genetic data. Our approach aligns images and several genetic modalities in the feature space using a contrastive loss. We design our method to integrate multiple modalities of each individual person in the same model end-to-end, even when the available modalities vary across individuals. Our procedure outperforms state-of-the-art self-supervised methods on all evaluated downstream benchmark tasks. We also adapt gradient-based explainability algorithms to better understand the learned cross-modal associations between the images and genetic modalities. Finally, we perform genome-wide association studies on the features learned by our models, uncovering interesting relationships between images and genetic data.

ContIG: Self-supervised Multimodal Contrastive Learning for Medical Imaging with Genetics

High annotation costs are a substantial bottleneck in applying deep learning architectures to clinically relevant use cases, substantiating the need for algorithms to learn from unlabeled data. In this work, we propose employing self-supervised methods. To that end, we trained with three self-supervised algorithms on a large corpus of unlabeled dental images, which contained 38K bitewing radiographs (BWRs). We then applied the learned neural network representations on tooth-level dental caries classification, for which we utilized labels extracted from electronic health records (EHRs). Finally, a holdout test-set was established, which consisted of 343 BWRs and was annotated by three dental professionals and approved by a senior dentist. This test-set was used to evaluate the fine-tuned caries classification models. Our experimental results demonstrate the obtained gains by pretraining models using self-supervised algorithms. These include improved caries classification performance (6 p.p. increase in sensitivity) and, most importantly, improved label-efficiency. In other words, the resulting models can be fine-tuned using few labels (annotations). Our results show that using as few as 18 annotations can produce ≥45% sensitivity, which is comparable to human-level diagnostic performance. This study shows that self-supervision can provide gains in medical image analysis, particularly when obtaining labels is costly and expensive.

/pdf/self-supervised-learning-methods-for-label-efficient-dental-1836p6nl.pdf

Self-Supervised Learning Methods for Label-Efficient Dental Caries Classification

Self-supervised learning methods can be used to learn meaningful representations from unlabeled data that can be transferred to supervised downstream tasks to reduce the need for labeled data. In this paper, we propose a 3D self-supervised method that is based on the contrastive (SimCLR) method. Additionally, we show that employing Bayesian neural networks (with Monte-Carlo Dropout) during the inference phase can further enhance the results on the downstream tasks. We showcase our models on two medical imaging segmentation tasks: i) Brain Tumor Segmentation from 3D MRI, ii) Pancreas Tumor Segmentation from 3D CT. Our experimental results demonstrate the benefits of our proposed methods in both downstream data-efficiency and performance.

Self-Supervised Learning for 3D Medical Image Analysis using 3D SimCLR and Monte Carlo Dropout

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Papers

Multimodal Self-Supervised Learning for Medical Image Analysis

Multimodal Self-Supervised Learning for Medical Image Analysis

ContIG: Self-supervised Multimodal Contrastive Learning for Medical Imaging with Genetics

Self-Supervised Learning Methods for Label-Efficient Dental Caries Classification

Self-Supervised Learning for 3D Medical Image Analysis using 3D SimCLR and Monte Carlo Dropout