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Register a new userSpatio-Temporal Dual-Stream Neural Network for Sequential Whole-Body PET Segmentation
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Sequential whole-body 18F-Fluorodeoxyglucose (FDG) positron emission tomography (PET) scans are regarded as the imaging modality of choice for the assessment of treatment response in the lymphomas because they detect treatment response when there may not be changes on anatomical imaging. Any computerized analysis of lymphomas in whole-body PET requires automatic segmentation of the studies so that sites of disease can be quantitatively monitored over time. State-of-the-art PET image segmentation methods are based on convolutional neural networks (CNNs) given their ability to leverage annotated datasets to derive high-level features about the disease process. Such methods, however, focus on PET images from a single time-point and discard information from other scans or are targeted towards specific organs and cannot cater for the multiple structures in whole-body PET images. In this study, we propose a spatio-temporal dual-stream neural network (ST-DSNN) to segment sequential whole-body PET scans. Our ST-DSNN learns and accumulates image features from the PET images done over time. The accumulated image features are used to enhance the organs / structures that are consistent over time to allow easier identification of sites of active lymphoma. Our results show that our method outperforms the state-of-the-art PET image segmentation methods.
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Colonoscopy is the gold standard for examination and detection of colorectal polyps. Localization and delineation of polyps can play a vital role in treatment (e.g., surgical planning) and prognostic decision making. Polyp segmentation can provide detailed boundary information for clinical analysis. Convolutional neural networks have improved the performance in colonoscopy. However, polyps usually possess various challenges, such as intra-and inter-class variation and noise. While manual labeling for polyp assessment requires time from experts and is prone to human error (e.g., missed lesions), an automated, accurate, and fast segmentation can improve the quality of delineated lesion boundaries and reduce missed rate. The Endotect challenge provides an opportunity to benchmark computer vision methods by training on the publicly available Hyperkvasir and testing on a separate unseen dataset. In this paper, we propose a novel architecture called ``DDANet based on a dual decoder attention network. Our experiments demonstrate that the model trained on the Kvasir-SEG dataset and tested on an unseen dataset achieves a dice coefficient of 0.7874, mIoU of 0.7010, recall of 0.7987, and a precision of 0.8577, demonstrating the generalization ability of our model.
Building robust deep learning-based models requires diverse training data, ideally from several sources. However, these datasets cannot be combined easily because of patient privacy concerns or regulatory hurdles, especially if medical data is involved. Federated learning (FL) is a way to train machine learning models without the need for centralized datasets. Each FL client trains on their local data while only sharing model parameters with a global server that aggregates the parameters from all clients. At the same time, each clients data can exhibit differences and inconsistencies due to the local variation in the patient population, imaging equipment, and acquisition protocols. Hence, the federated learned models should be able to adapt to the local particularities of a clients data. In this work, we combine FL with an AutoML technique based on local neural architecture search by training a supernet. Furthermore, we propose an adaptation scheme to allow for personalized model architectures at each FL clients site. The proposed method is evaluated on four different datasets from 3D prostate MRI and shown to improve the local models performance after adaptation through selecting an optimal path through the AutoML supernet.
We propose HookNet, a semantic segmentation model for histopathology whole-slide images, which combines context and details via multiple branches of encoder-decoder convolutional neural networks. Concentricpatches at multiple resolutions with different fields of view are used to feed different branches of HookNet, and intermediate representations are combined via a hooking mechanism. We describe a framework to design and train HookNet for achieving high-resolution semantic segmentation and introduce constraints to guarantee pixel-wise alignment in feature maps during hooking. We show the advantages of using HookNet in two histopathology image segmentation tasks where tissue type prediction accuracy strongly depends on contextual information, namely (1) multi-class tissue segmentation in breast cancer and, (2) segmentation of tertiary lymphoid structures and germinal centers in lung cancer. Weshow the superiority of HookNet when compared with single-resolution U-Net models working at different resolutions as well as with a recently published multi-resolution model for histopathology image segmentation
The Medico: Multimedia Task 2020 focuses on developing an efficient and accurate computer-aided diagnosis system for automatic segmentation [3]. We participate in task 1, Polyps segmentation task, which is to develop algorithms for segmenting polyps on a comprehensive dataset. In this task, we propose methods combining Residual module, Inception module, Adaptive Convolutional neural network with U-Net model, and PraNet for semantic segmentation of various types of polyps in endoscopic images. We select 5 runs with different architecture and parameters in our methods. Our methods show potential results in accuracy and efficiency through multiple experiments, and our team is in the Top 3 best results with a Jaccard index of 0.765.
Semantic image segmentation is the process of labeling each pixel of an image with its corresponding class. An encoder-decoder based approach, like U-Net and its variants, is a popular strategy for solving medical image segmentation tasks. To improve the performance of U-Net on various segmentation tasks, we propose a novel architecture called DoubleU-Net, which is a combination of two U-Net architectures stacked on top of each other. The first U-Net uses a pre-trained VGG-19 as the encoder, which has already learned features from ImageNet and can be transferred to another task easily. To capture more semantic information efficiently, we added another U-Net at the bottom. We also adopt Atrous Spatial Pyramid Pooling (ASPP) to capture contextual information within the network. We have evaluated DoubleU-Net using four medical segmentation datasets, covering various imaging modalities such as colonoscopy, dermoscopy, and microscopy. Experiments on the MICCAI 2015 segmentation challenge, the CVC-ClinicDB, the 2018 Data Science Bowl challenge, and the Lesion boundary segmentation datasets demonstrate that the DoubleU-Net outperforms U-Net and the baseline models. Moreover, DoubleU-Net produces more accurate segmentation masks, especially in the case of the CVC-ClinicDB and MICCAI 2015 segmentation challenge datasets, which have challenging images such as smaller and flat polyps. These results show the improvement over the existing U-Net model. The encouraging results, produced on various medical image segmentation datasets, show that DoubleU-Net can be used as a strong baseline for both medical image segmentation and cross-dataset evaluation testing to measure the generalizability of Deep Learning (DL) models.
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