scholarly journals Weakly supervised semantic segmentation of tomographic images in the diagnosis of stroke

2021 ◽  
Vol 2099 (1) ◽  
pp. 012021
Author(s):  
A V Dobshik ◽  
A A Tulupov ◽  
V B Berikov
Keyword(s):  
Computed Tomography ◽  
Network Architecture ◽  
Semantic Segmentation ◽  
Training Data ◽  
Neural Network Architecture ◽  
Brain Images ◽  
Tomographic Images ◽  
Computed Tomography Images ◽  
Segmentation Accuracy ◽  
Weakly Supervised

Abstract This paper presents an automatic algorithm for the segmentation of areas affected by an acute stroke in the non-contrast computed tomography brain images. The proposed algorithm is designed for learning in a weakly supervised scenario when some images are labeled accurately, and some images are labeled inaccurately. Wrong labels appear as a result of inaccuracy made by a radiologist in the process of manual annotation of computed tomography images. We propose methods for solving the segmentation problem in the case of inaccurately labeled training data. We use the U-Net neural network architecture with several modifications. Experiments on real computed tomography scans show that the proposed methods increase the segmentation accuracy.

Computed Tomography Brain Images Semantic Segmentation

2017 ◽  
pp. 77-104
Author(s):  
Poonam Fauzdar ◽  
Sarvesh Kumar
Keyword(s):  
Computed Tomography ◽  
Positive Predictive Value ◽  
Euclidean Distance ◽  
Global Analysis ◽  
Semantic Segmentation ◽  
Brain Images ◽  
Minimum Euclidean Distance ◽  
Computed Tomography Images ◽  
Multi Level ◽  
Reduced Time

In this paper we applianced an approach for segmenting brain tumour regions in a computed tomography images by proposing a multi-level fuzzy technique with quantization and minimum computed Euclidean distance applied to morphologically divided skull part. Since the edges identified with closed contours and further improved by adding minimum Euclidean distance, that is why the numerous results that are analyzed are very assuring and algorithm poses following advantages like less cost, global analysis of image, reduced time, more specificity and positive predictive value.

Optimal Scale of Hierarchical Image Segmentation with Scribbles Guidance for Weakly Supervised Semantic Segmentation

2021 ◽  
pp. 2154026
Author(s):  
Zaid Al-Huda ◽  
Donghai Zhai ◽  
Yan Yang ◽  
Riyadh Nazar Ali Algburi
Keyword(s):  
Image Segmentation ◽  
Graphical Model ◽  
Semantic Segmentation ◽  
Saliency Map ◽  
Training Data ◽  
Deep Convolutional Neural Networks ◽  
High Quality ◽  
Optimal Scale ◽  
Supervised Segmentation ◽  
Weakly Supervised

Deep convolutional neural networks (DCNNs) trained on the pixel-level annotated images have achieved improvements in semantic segmentation. Due to the high cost of labeling training data, their applications may have great limitation. However, weakly supervised segmentation approaches can significantly reduce human labeling efforts. In this paper, we introduce a new framework to generate high-quality initial pixel-level annotations. By using a hierarchical image segmentation algorithm to predict the boundary map, we select the optimal scale of high-quality hierarchies. In the initialization step, scribble annotations and the saliency map are combined to construct a graphic model over the optimal scale segmentation. By solving the minimal cut problem, it can spread information from scribbles to unmarked regions. In the training process, the segmentation network is trained by using the initial pixel-level annotations. To iteratively optimize the segmentation, we use a graphical model to refine segmentation masks and retrain the segmentation network to get more precise pixel-level annotations. The experimental results on Pascal VOC 2012 dataset demonstrate that the proposed framework outperforms most of weakly supervised semantic segmentation methods and achieves the state-of-the-art performance, which is [Formula: see text] mIoU.

scholarly journals DeepIsoFun: a deep domain adaptation approach to predict isoform functions

2018 ◽  
Vol 35 (15) ◽  
pp. 2535-2544 ◽  
Author(s):  
Dipan Shaw ◽  
Hao Chen ◽  
Tao Jiang
Keyword(s):  
Network Architecture ◽  
Domain Adaptation ◽  
Multiple Instance Learning ◽  
Training Data ◽  
Supplementary Information ◽  
Operating Characteristics ◽  
Neural Network Architecture ◽  
Receiver Operating Characteristics Curve ◽  
Gene Functions ◽  
Better Than

AbstractMotivationIsoforms are mRNAs produced from the same gene locus by alternative splicing and may have different functions. Although gene functions have been studied extensively, little is known about the specific functions of isoforms. Recently, some computational approaches based on multiple instance learning have been proposed to predict isoform functions from annotated gene functions and expression data, but their performance is far from being desirable primarily due to the lack of labeled training data. To improve the performance on this problem, we propose a novel deep learning method, DeepIsoFun, that combines multiple instance learning with domain adaptation. The latter technique helps to transfer the knowledge of gene functions to the prediction of isoform functions and provides additional labeled training data. Our model is trained on a deep neural network architecture so that it can adapt to different expression distributions associated with different gene ontology terms.ResultsWe evaluated the performance of DeepIsoFun on three expression datasets of human and mouse collected from SRA studies at different times. On each dataset, DeepIsoFun performed significantly better than the existing methods. In terms of area under the receiver operating characteristics curve, our method acquired at least 26% improvement and in terms of area under the precision-recall curve, it acquired at least 10% improvement over the state-of-the-art methods. In addition, we also study the divergence of the functions predicted by our method for isoforms from the same gene and the overall correlation between expression similarity and the similarity of predicted functions.Availability and implementationhttps://github.com/dls03/DeepIsoFun/Supplementary informationSupplementary data are available at Bioinformatics online.

scholarly journals Deep learning of stochastic contagion dynamics on complex networks

2020 ◽  
Author(s):  
Charles Murphy ◽  
Edward Laurence ◽  
Antoine Allard
Keyword(s):  
Deep Learning ◽  
Network Architecture ◽  
Time Series Data ◽  
Training Data ◽  
Series Data ◽  
Neural Network Architecture ◽  
Complementary Approach ◽  
Quantitative Accuracy ◽  
Simplifying Assumptions ◽  
Effective Models

Abstract Forecasting the evolution of contagion dynamics is still an open problem to which mechanistic models only offer a partial answer. To remain mathematically and/or computationally tractable, these models must rely on simplifying assumptions, thereby limiting the quantitative accuracy of their predictions and the complexity of the dynamics they can model. Here, we propose a complementary approach based on deep learning where the effective local mechanisms governing a dynamic are learned automatically from time series data. Our graph neural network architecture makes very few assumptions about the dynamics, and we demonstrate its accuracy using stochastic contagion dynamics of increasing complexity on static and temporal networks. By allowing simulations on arbitrary network structures, our approach makes it possible to explore the properties of the learned dynamics beyond the training data. Our results demonstrate how deep learning offers a new and complementary perspective to build effective models of contagion dynamics on networks.

scholarly journals Diagnosis of COVID-19 Infection Using Three-Dimensional Semantic Segmentation and Classification of Computed Tomography Images

2021 ◽  
Vol 68 (2) ◽  
pp. 2451-2467
Author(s):  
Javaria Amin ◽  
Muhammad Sharif ◽  
Muhammad Almas Anjum ◽  
Yunyoung Nam ◽  
Seifedine Kadry ◽  
...  
Keyword(s):  
Computed Tomography ◽  
Three Dimensional ◽  
Semantic Segmentation ◽  
Computed Tomography Images

scholarly journals U-Net Plus: Deep Semantic Segmentation for Esophagus and Esophageal Cancer in Computed Tomography Images

IEEE Access ◽  
2019 ◽  
Vol 7 ◽  
pp. 82867-82877 ◽  
Author(s):  
Shuchao Chen ◽  
Han Yang ◽  
Jiawen Fu ◽  
Weijian Mei ◽  
Shuai Ren ◽  
...  
Keyword(s):  
Computed Tomography ◽  
Esophageal Cancer ◽  
Semantic Segmentation ◽  
Computed Tomography Images

scholarly journals U-Net-Id, an Instance Segmentation Model for Building Extraction from Satellite Images—Case Study in the Joanópolis City, Brazil

2020 ◽  
Vol 12 (10) ◽  
pp. 1544 ◽  
Author(s):  
Fabien H. Wagner ◽  
Ricardo Dalagnol ◽  
Yuliya Tarabalka ◽  
Tassiana Y. F. Segantine ◽  
Rogério Thomé ◽  
...  
Keyword(s):  
Network Architecture ◽  
Satellite Images ◽  
Semantic Segmentation ◽  
Developed Countries ◽  
Building Extraction ◽  
Neural Network Architecture ◽  
Rgb Images ◽  
The City ◽  
Instance Segmentation

Currently, there exists a growing demand for individual building mapping in regions of rapid urban growth in less-developed countries. Most existing methods can segment buildings but cannot discriminate adjacent buildings. Here, we present a new convolutional neural network architecture (CNN) called U-net-id that performs building instance segmentation. The proposed network is trained with WorldView-3 satellite RGB images (0.3 m) and three different labeled masks. The first is the building mask; the second is the border mask, which is the border of the building segment with 4 pixels added outside and 3 pixels inside; and the third is the inner segment mask, which is the segment of the building diminished by 2 pixels. The architecture consists of three parallel paths, one for each mask, all starting with a U-net model. To accurately capture the overlap between the masks, all activation layers of the U-nets are copied and concatenated on each path and sent to two additional convolutional layers before the output activation layers. The method was tested with a dataset of 7563 manually delineated individual buildings of the city of Joanópolis-SP, Brazil. On this dataset, the semantic segmentation showed an overall accuracy of 97.67% and an F1-Score of 0.937 and the building individual instance segmentation showed good performance with a mean intersection over union (IoU) of 0.582 (median IoU = 0.694).

scholarly journals Efficient Semantic Segmentation Using Multi-Path Decoder

2020 ◽  
Vol 10 (18) ◽  
pp. 6386
Author(s):  
Xing Bai ◽  
Jun Zhou
Keyword(s):  
Neural Network ◽  
Real Time ◽  
Network Architecture ◽  
Resource Constraints ◽  
Cost Effective ◽  
Semantic Segmentation ◽  
Classification Model ◽  
Neural Network Architecture ◽  
Great Progress ◽  
Different Types

Benefiting from the booming of deep learning, the state-of-the-art models achieved great progress. But they are huge in terms of parameters and floating point operations, which makes it hard to apply them to real-time applications. In this paper, we propose a novel deep neural network architecture, named MPDNet, for fast and efficient semantic segmentation under resource constraints. First, we use a light-weight classification model pretrained on ImageNet as the encoder. Second, we use a cost-effective upsampling datapath to restore prediction resolution and convert features for classification into features for segmentation. Finally, we propose to use a multi-path decoder to extract different types of features, which are not ideal to process inside only one convolutional neural network. The experimental results of our model outperform other models aiming at real-time semantic segmentation on Cityscapes. Based on our proposed MPDNet, we achieve 76.7% mean IoU on Cityscapes test set with only 118.84GFLOPs and achieves 37.6 Hz on 768 × 1536 images on a standard GPU.

scholarly journals ORTHOSEG: A DEEP MULTIMODAL CONVOLUTONAL NEURAL NETWORK ARCHITECTURE FOR SEMANTIC SEGMENTATION OF ORTHOIMAGERY

2018 ◽  
Vol XLII-5 ◽  
pp. 621-628 ◽  
Author(s):  
P. Bodani ◽  
K. Shreshtha ◽  
S. Sharma
Keyword(s):  
Neural Network ◽  
Network Architecture ◽  
Multiple Scales ◽  
Semantic Segmentation ◽  
Effective Field ◽  
Surface Model ◽  
Training Procedure ◽  
Feature Maps ◽  
Neural Network Architecture ◽  
Wide Range

<p><strong>Abstract.</strong> This paper addresses the task of semantic segmentation of orthoimagery using multimodal data e.g. optical RGB, infrared and digital surface model. We propose a deep convolutional neural network architecture termed OrthoSeg for semantic segmentation using multimodal, orthorectified and coregistered data. We also propose a training procedure for supervised training of OrthoSeg. The training procedure complements the inherent architectural characteristics of OrthoSeg for preventing complex co-adaptations of learned features, which may arise due to probable high dimensionality and spatial correlation in multimodal and/or multispectral coregistered data. OrthoSeg consists of parallel encoding networks for independent encoding of multimodal feature maps and a decoder designed for efficiently fusing independently encoded multimodal feature maps. A softmax layer at the end of the network uses the features generated by the decoder for pixel-wise classification. The decoder fuses feature maps from the parallel encoders locally as well as contextually at multiple scales to generate per-pixel feature maps for final pixel-wise classification resulting in segmented output. We experimentally show the merits of OrthoSeg by demonstrating state-of-the-art accuracy on the ISPRS Potsdam 2D Semantic Segmentation dataset. Adaptability is one of the key motivations behind OrthoSeg so that it serves as a useful architectural option for a wide range of problems involving the task of semantic segmentation of coregistered multimodal and/or multispectral imagery. Hence, OrthoSeg is designed to enable independent scaling of parallel encoder networks and decoder network to better match application requirements, such as the number of input channels, the effective field-of-view, and model capacity.</p>

scholarly journals CEREBRUM-7T: Fast and Fully-volumetric Brain Segmentation of 7 Tesla MR Volumes

2020 ◽  
Author(s):  
Michele Svanera ◽  
Sergio Benini ◽  
Dennis Bontempi ◽  
Lars Muckli
Keyword(s):  
Brain Mri ◽  
Turing Test ◽  
Fine Tuning ◽  
7 Tesla ◽  
Brain Images ◽  
Subjective Analysis ◽  
Segmentation Accuracy ◽  
Resolution Imaging ◽  
Mr Brain Images ◽  
Weakly Supervised

ABSTRACTUltra high-field MRI enables sub-millimetre resolution imaging of the human brain, allowing for the resolution of functional circuits at the meso-scale of cortical layers. An essential step in many functional and structural neuroimaging studies is segmentation, the operation of partitioning the MR brain images to delineate anatomical structures. Despite recent efforts in brain imaging analysis, the literature lacks of accurate and fast methods for segmenting 7 Tesla (7T) brain MRI. We here present CEREBRUM-7T, an optimised end-to-end Convolutional Neural Network (CNN) architecture, that allows for the segmentation of a whole 7T T1w MRI brain volume at once, thus overcoming the drawbacks of partitioning the volume into 2D or 3D tiles. Training is performed in a weakly supervised fashion, exploiting labelling with errors obtained with automatic state-of-the-art methods. The trained model is able to produce accurate multi-structure segmentation masks on six different classes in only a few seconds. In the experimental part, a combination of objective numerical evaluations and subjective analysis carried out by experienced neuroimaging users, confirms that the proposed solution outperforms the training labels it was trained on in segmentation accuracy, and is suitable for neuroimaging studies, such as layer fMRI studies. Taking advantage of a fine-tuning operation on a reduced set of volumes, we also show how it is possible to efficiently and effectively apply CEREBRUM-7T to data from different sites. Furthermore, to allow replicability and encourage extensions, we release the code, 7T data (142 volumes), and other materials, including the training labels and the Turing test.

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