Cancer of the brain is deadly and requires careful surgical segmentation. The brain tumors were segmented using U-Net using a Convolutional Neural Network (CNN). When looking for overlaps of necrotic, edematous, growing, and healthy tissue, it might be hard to get relevant information from the images. The 2D U-Net network was improved and trained with the BraTS datasets to find these four areas. U-Net can set up many encoder and decoder routes that can be used to get information from images that can be used in different ways. To reduce computational time, we use image segmentation to exclude insignificant background details. Experiments on the BraTS datasets show that our proposed model for segmenting brain tumors from MRI (MRI) works well. In this study, we demonstrate that the BraTS datasets for 2017, 2018, 2019, and 2020 do not significantly differ from the BraTS 2019 dataset's attained dice scores of 0.8717 (necrotic), 0.9506 (edema), and 0.9427 (enhancing).
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Owing to the success of transformer models, recent works study their applicability in 3D medical segmentation tasks. Within the transformer models, the self-attention mechanism is one of the main building blocks that strives to capture long-range dependencies, compared to the local convolutional-based design. However, the self-attention operation has quadratic complexity which proves to be a computational bottleneck, especially in volumetric medical imaging, where the inputs are 3D with numerous slices. In this paper, we propose a 3D medical image segmentation approach, named UNETR++, that offers both high-quality segmentation masks as well as efficiency in terms of parameters and compute cost. The core of our design is the introduction of a novel efficient paired attention (EPA) block that efficiently learns spatial and channel-wise discriminative features using a pair of inter-dependent branches based on spatial and channel attention. Our spatial attention formulation is efficient having linear complexity with respect to the input sequence length. To enable communication between spatial and channel-focused branches, we share the weights of query and key mapping functions that provide a complimentary benefit (paired attention), while also reducing the overall network parameters. Our extensive evaluations on three benchmarks, Synapse, BTCV and ACDC, reveal the effectiveness of the proposed contributions in terms of both efficiency and accuracy. On Synapse dataset, our UNETR++ sets a new state-of-the-art with a Dice Similarity Score of 87.2%, while being significantly efficient with a reduction of over 71% in terms of both parameters and FLOPs, compared to the best existing method in the literature. Code: //github.com/Amshaker/unetr_plus_plus.
How to effectively leverage the plentiful existing datasets to train a robust and high-performance model is of great significance for many practical applications. However, a model trained on a naive merge of different datasets tends to obtain poor performance due to annotation conflicts and domain divergence.In this paper, we attempt to train a unified model that is expected to perform well across domains on several popularity segmentation datasets.We conduct a detailed analysis of the impact on model generalization from three aspects of data augmentation, training strategies, and model capacity.Based on the analysis, we propose a robust solution that is able to improve model generalization across domains.Our solution ranks 2nd on RVC 2022 semantic segmentation task, with a dataset only 1/3 size of the 1st model used.
Source-free domain adaptation (SFDA) aims to transfer knowledge learned from a source domain to an unlabeled target domain, where the source data is unavailable during adaptation. Existing approaches for SFDA focus on self-training usually including well-established entropy minimization techniques. One of the main challenges in SFDA is to reduce accumulation of errors caused by domain misalignment. A recent strategy successfully managed to reduce error accumulation by pseudo-labeling the target samples based on class-wise prototypes (centroids) generated by their clustering in the representation space. However, this strategy also creates cases for which the cross-entropy of a pseudo-label and the minimum entropy have a conflict in their objectives. We call this conflict the centroid-hypothesis conflict. We propose to reconcile this conflict by aligning the entropy minimization objective with that of the pseudo labels' cross entropy. We demonstrate the effectiveness of aligning the two loss objectives on three domain adaptation datasets. In addition, we provide state-of-the-art results using up-to-date architectures also showing the consistency of our method across these architectures.
Social networking sites, blogs, and online articles are instant sources of news for internet users globally. However, in the absence of strict regulations mandating the genuineness of every text on social media, it is probable that some of these texts are fake news or rumours. Their deceptive nature and ability to propagate instantly can have an adverse effect on society. This necessitates the need for more effective detection of fake news and rumours on the web. In this work, we annotate four fake news detection and rumour detection datasets with their emotion class labels using transfer learning. We show the correlation between the legitimacy of a text with its intrinsic emotion for fake news and rumour detection, and prove that even within the same emotion class, fake and real news are often represented differently, which can be used for improved feature extraction. Based on this, we propose a multi-task framework for fake news and rumour detection, predicting both the emotion and legitimacy of the text. We train a variety of deep learning models in single-task and multi-task settings for a more comprehensive comparison. We further analyze the performance of our multi-task approach for fake news detection in cross-domain settings to verify its efficacy for better generalization across datasets, and to verify that emotions act as a domain-independent feature. Experimental results verify that our multi-task models consistently outperform their single-task counterparts in terms of accuracy, precision, recall, and F1 score, both for in-domain and cross-domain settings. We also qualitatively analyze the difference in performance in single-task and multi-task learning models.
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.
In this paper, we adopt 3D Convolutional Neural Networks to segment volumetric medical images. Although deep neural networks have been proven to be very effective on many 2D vision tasks, it is still challenging to apply them to 3D tasks due to the limited amount of annotated 3D data and limited computational resources. We propose a novel 3D-based coarse-to-fine framework to effectively and efficiently tackle these challenges. The proposed 3D-based framework outperforms the 2D counterpart to a large margin since it can leverage the rich spatial infor- mation along all three axes. We conduct experiments on two datasets which include healthy and pathological pancreases respectively, and achieve the current state-of-the-art in terms of Dice-S{\o}rensen Coefficient (DSC). On the NIH pancreas segmentation dataset, we outperform the previous best by an average of over 2%, and the worst case is improved by 7% to reach almost 70%, which indicates the reliability of our framework in clinical applications.
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.
We propose a novel attention gate (AG) model for medical imaging that automatically learns to focus on target structures of varying shapes and sizes. Models trained with AGs implicitly learn to suppress irrelevant regions in an input image while highlighting salient features useful for a specific task. This enables us to eliminate the necessity of using explicit external tissue/organ localisation modules of cascaded convolutional neural networks (CNNs). AGs can be easily integrated into standard CNN architectures such as the U-Net model with minimal computational overhead while increasing the model sensitivity and prediction accuracy. The proposed Attention U-Net architecture is evaluated on two large CT abdominal datasets for multi-class image segmentation. Experimental results show that AGs consistently improve the prediction performance of U-Net across different datasets and training sizes while preserving computational efficiency. The code for the proposed architecture is publicly available.
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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