Reliable classification and detection of certain medical conditions, in images, with state-of-the-art semantic segmentation networks, require vast amounts of pixel-wise annotation. However, the public availability of such datasets is minimal. Therefore, semantic segmentation with image-level labels presents a promising alternative to this problem. Nevertheless, very few works have focused on evaluating this technique and its applicability to the medical sector. Due to their complexity and the small number of training examples in medical datasets, classifier-based weakly supervised networks like class activation maps (CAMs) struggle to extract useful information from them. However, most state-of-the-art approaches rely on them to achieve their improvements. Therefore, we propose a framework that can still utilize the low-quality CAM predictions of complicated datasets to improve the accuracy of our results. Our framework achieves that by first utilizing lower threshold CAMs to cover the target object with high certainty; second, by combining multiple low-threshold CAMs that even out their errors while highlighting the target object. We performed exhaustive experiments on the popular multi-modal BRATS and prostate DECATHLON segmentation challenge datasets. Using the proposed framework, we have demonstrated an improved dice score of up to 8% on BRATS and 6% on DECATHLON datasets compared to the previous state-of-the-art.
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Image compression techniques typically focus on compressing rectangular images for human consumption, however, resulting in transmitting redundant content for downstream applications. To overcome this limitation, some previous works propose to semantically structure the bitstream, which can meet specific application requirements by selective transmission and reconstruction. Nevertheless, they divide the input image into multiple rectangular regions according to semantics and ignore avoiding information interaction among them, causing waste of bitrate and distorted reconstruction of region boundaries. In this paper, we propose to decouple an image into multiple groups with irregular shapes based on a customized group mask and compress them independently. Our group mask describes the image at a finer granularity, enabling significant bitrate saving by reducing the transmission of redundant content. Moreover, to ensure the fidelity of selective reconstruction, this paper proposes the concept of group-independent transform that maintain the independence among distinct groups. And we instantiate it by the proposed Group-Independent Swin-Block (GI Swin-Block). Experimental results demonstrate that our framework structures the bitstream with negligible cost, and exhibits superior performance on both visual quality and intelligent task supporting.
Large-scale chest x-ray datasets have been curated for the detection of abnormalities using deep learning, with the potential to provide substantial benefits across many clinical applications. However, each dataset focuses only on detecting a subset of findings that can be simultaneously present in a patient, thereby limiting its clinical utility. Therefore, data harmonization is crucial to leverage these datasets in aggregate to train clinically-useful, robust models with a complete representation of all abnormalities that may occur within the thorax. To that end, we propose surgical aggregation, a collaborative learning framework for harmonizing and aggregating knowledge from distributed heterogeneous datasets with partial disease annotations. We evaluate surgical aggregation across synthetic iid datasets and real-world large-scale non-iid datasets with partial annotations. Our results indicate that surgical aggregation significantly outperforms current strategies, has better generalizability, and has the potential to revolutionize the development clinically-useful models as AI-assisted disease characterization becomes a mainstay in radiology.
We present a unified deep learning framework for the recognition of user identity and the recognition of imagined actions, based on electroencephalography (EEG) signals, for application as a brain-computer interface. Our solution exploits a novel shifted subsampling preprocessing step as a form of data augmentation, and a matrix representation to encode the inherent local spatial relationships of multi-electrode EEG signals. The resulting image-like data is then fed to a convolutional neural network to process the local spatial dependencies, and eventually analyzed through a bidirectional long-short term memory module to focus on temporal relationships. Our solution is compared against several methods in the state of the art, showing comparable or superior performance on different tasks. Specifically, we achieve accuracy levels above 90% both for action and user classification tasks. In terms of user identification, we reach 0.39% equal error rate in the case of known users and gestures, and 6.16% in the more challenging case of unknown users and gestures. Preliminary experiments are also conducted in order to direct future works towards everyday applications relying on a reduced set of EEG electrodes.
Medical image segmentation is a fundamental and critical step in many image-guided clinical approaches. Recent success of deep learning-based segmentation methods usually relies on a large amount of labeled data, which is particularly difficult and costly to obtain especially in the medical imaging domain where only experts can provide reliable and accurate annotations. Semi-supervised learning has emerged as an appealing strategy and been widely applied to medical image segmentation tasks to train deep models with limited annotations. In this paper, we present a comprehensive review of recently proposed semi-supervised learning methods for medical image segmentation and summarized both the technical novelties and empirical results. Furthermore, we analyze and discuss the limitations and several unsolved problems of existing approaches. We hope this review could inspire the research community to explore solutions for this challenge and further promote the developments in medical image segmentation field.
Following unprecedented success on the natural language tasks, Transformers have been successfully applied to several computer vision problems, achieving state-of-the-art results and prompting researchers to reconsider the supremacy of convolutional neural networks (CNNs) as {de facto} operators. Capitalizing on these advances in computer vision, the medical imaging field has also witnessed growing interest for Transformers that can capture global context compared to CNNs with local receptive fields. Inspired from this transition, in this survey, we attempt to provide a comprehensive review of the applications of Transformers in medical imaging covering various aspects, ranging from recently proposed architectural designs to unsolved issues. Specifically, we survey the use of Transformers in medical image segmentation, detection, classification, reconstruction, synthesis, registration, clinical report generation, and other tasks. In particular, for each of these applications, we develop taxonomy, identify application-specific challenges as well as provide insights to solve them, and highlight recent trends. Further, we provide a critical discussion of the field's current state as a whole, including the identification of key challenges, open problems, and outlining promising future directions. We hope this survey will ignite further interest in the community and provide researchers with an up-to-date reference regarding applications of Transformer models in medical imaging. Finally, to cope with the rapid development in this field, we intend to regularly update the relevant latest papers and their open-source implementations at \url{//github.com/fahadshamshad/awesome-transformers-in-medical-imaging}.
A key requirement for the success of supervised deep learning is a large labeled dataset - a condition that is difficult to meet in medical image analysis. Self-supervised learning (SSL) can help in this regard by providing a strategy to pre-train a neural network with unlabeled data, followed by fine-tuning for a downstream task with limited annotations. Contrastive learning, a particular variant of SSL, is a powerful technique for learning image-level representations. In this work, we propose strategies for extending the contrastive learning framework for segmentation of volumetric medical images in the semi-supervised setting with limited annotations, by leveraging domain-specific and problem-specific cues. Specifically, we propose (1) novel contrasting strategies that leverage structural similarity across volumetric medical images (domain-specific cue) and (2) a local version of the contrastive loss to learn distinctive representations of local regions that are useful for per-pixel segmentation (problem-specific cue). We carry out an extensive evaluation on three Magnetic Resonance Imaging (MRI) datasets. In the limited annotation setting, the proposed method yields substantial improvements compared to other self-supervision and semi-supervised learning techniques. When combined with a simple data augmentation technique, the proposed method reaches within 8% of benchmark performance using only two labeled MRI volumes for training, corresponding to only 4% (for ACDC) of the training data used to train the benchmark.
The U-Net was presented in 2015. With its straight-forward and successful architecture it quickly evolved to a commonly used benchmark in medical image segmentation. The adaptation of the U-Net to novel problems, however, comprises several degrees of freedom regarding the exact architecture, preprocessing, training and inference. These choices are not independent of each other and substantially impact the overall performance. The present paper introduces the nnU-Net ('no-new-Net'), which refers to a robust and self-adapting framework on the basis of 2D and 3D vanilla U-Nets. We argue the strong case for taking away superfluous bells and whistles of many proposed network designs and instead focus on the remaining aspects that make out the performance and generalizability of a method. We evaluate the nnU-Net in the context of the Medical Segmentation Decathlon challenge, which measures segmentation performance in ten disciplines comprising distinct entities, image modalities, image geometries and dataset sizes, with no manual adjustments between datasets allowed. At the time of manuscript submission, nnU-Net achieves the highest mean dice scores across all classes and seven phase 1 tasks (except class 1 in BrainTumour) in the online leaderboard of the challenge.
Deep neural network architectures have traditionally been designed and explored with human expertise in a long-lasting trial-and-error process. This process requires huge amount of time, expertise, and resources. To address this tedious problem, we propose a novel algorithm to optimally find hyperparameters of a deep network architecture automatically. We specifically focus on designing neural architectures for medical image segmentation task. Our proposed method is based on a policy gradient reinforcement learning for which the reward function is assigned a segmentation evaluation utility (i.e., dice index). We show the efficacy of the proposed method with its low computational cost in comparison with the state-of-the-art medical image segmentation networks. We also present a new architecture design, a densely connected encoder-decoder CNN, as a strong baseline architecture to apply the proposed hyperparameter search algorithm. We apply the proposed algorithm to each layer of the baseline architectures. As an application, we train the proposed system on cine cardiac MR images from Automated Cardiac Diagnosis Challenge (ACDC) MICCAI 2017. Starting from a baseline segmentation architecture, the resulting network architecture obtains the state-of-the-art results in accuracy without performing any trial-and-error based architecture design approaches or close supervision of the hyperparameters changes.
Medical image segmentation requires consensus ground truth segmentations to be derived from multiple expert annotations. A novel approach is proposed that obtains consensus segmentations from experts using graph cuts (GC) and semi supervised learning (SSL). Popular approaches use iterative Expectation Maximization (EM) to estimate the final annotation and quantify annotator's performance. Such techniques pose the risk of getting trapped in local minima. We propose a self consistency (SC) score to quantify annotator consistency using low level image features. SSL is used to predict missing annotations by considering global features and local image consistency. The SC score also serves as the penalty cost in a second order Markov random field (MRF) cost function optimized using graph cuts to derive the final consensus label. Graph cut obtains a global maximum without an iterative procedure. Experimental results on synthetic images, real data of Crohn's disease patients and retinal images show our final segmentation to be accurate and more consistent than competing methods.
Recent advances in 3D fully convolutional networks (FCN) have made it feasible to produce dense voxel-wise predictions of volumetric images. In this work, we show that a multi-class 3D FCN trained on manually labeled CT scans of several anatomical structures (ranging from the large organs to thin vessels) can achieve competitive segmentation results, while avoiding the need for handcrafting features or training class-specific models. To this end, we propose a two-stage, coarse-to-fine approach that will first use a 3D FCN to roughly define a candidate region, which will then be used as input to a second 3D FCN. This reduces the number of voxels the second FCN has to classify to ~10% and allows it to focus on more detailed segmentation of the organs and vessels. We utilize training and validation sets consisting of 331 clinical CT images and test our models on a completely unseen data collection acquired at a different hospital that includes 150 CT scans, targeting three anatomical organs (liver, spleen, and pancreas). In challenging organs such as the pancreas, our cascaded approach improves the mean Dice score from 68.5 to 82.2%, achieving the highest reported average score on this dataset. We compare with a 2D FCN method on a separate dataset of 240 CT scans with 18 classes and achieve a significantly higher performance in small organs and vessels. Furthermore, we explore fine-tuning our models to different datasets. Our experiments illustrate the promise and robustness of current 3D FCN based semantic segmentation of medical images, achieving state-of-the-art results. Our code and trained models are available for download: //github.com/holgerroth/3Dunet_abdomen_cascade.
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