scholarly journals Structured crowdsourcing enables convolutional segmentation of histology images

2019 ◽  
Vol 35 (18) ◽  
pp. 3461-3467 ◽  
Author(s):  
Mohamed Amgad ◽  
Habiba Elfandy ◽  
Hagar Hussein ◽  
Lamees A Atteya ◽  
Mai A T Elsebaie ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Deep Learning ◽  
Classification Accuracy ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Digital Slide ◽  
Convolutional Networks ◽  
Fully Convolutional Networks ◽  
Annotation Data ◽  
Whole Slide Images

Abstract Motivation While deep-learning algorithms have demonstrated outstanding performance in semantic image segmentation tasks, large annotation datasets are needed to create accurate models. Annotation of histology images is challenging due to the effort and experience required to carefully delineate tissue structures, and difficulties related to sharing and markup of whole-slide images. Results We recruited 25 participants, ranging in experience from senior pathologists to medical students, to delineate tissue regions in 151 breast cancer slides using the Digital Slide Archive. Inter-participant discordance was systematically evaluated, revealing low discordance for tumor and stroma, and higher discordance for more subjectively defined or rare tissue classes. Feedback provided by senior participants enabled the generation and curation of 20 000+ annotated tissue regions. Fully convolutional networks trained using these annotations were highly accurate (mean AUC=0.945), and the scale of annotation data provided notable improvements in image classification accuracy. Availability and Implementation Dataset is freely available at: https://goo.gl/cNM4EL. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Automatic Deep Learning Semantic Segmentation of Ultrasound Thyroid Cineclips using Recurrent Fully Convolutional Networks

IEEE Access ◽  
2020 ◽  
pp. 1-1
Author(s):  
Jeremy M. Webb ◽  
Duane D. Meixner ◽  
Shaheeda A. Adusei ◽  
Eric C. Polley ◽  
Mostafa Fatemi ◽  
...  
Keyword(s):  
Deep Learning ◽  
Semantic Segmentation ◽  
Convolutional Networks ◽  
Fully Convolutional Networks

scholarly journals Ship Classification in High-Resolution SAR Images Using Deep Learning of Small Datasets

Sensors ◽  
2018 ◽  
Vol 18 (9) ◽  
pp. 2929 ◽  
Author(s):  
Yuanyuan Wang ◽  
Chao Wang ◽  
Hong Zhang
Keyword(s):  
Deep Learning ◽  
High Resolution ◽  
Classification Accuracy ◽  
Experimental Results ◽  
Fine Tuning ◽  
Classification Model ◽  
Great Success ◽  
Sar Images ◽  
Convolutional Networks ◽  
Ship Classification

With the capability to automatically learn discriminative features, deep learning has experienced great success in natural images but has rarely been explored for ship classification in high-resolution SAR images due to the training bottleneck caused by the small datasets. In this paper, convolutional neural networks (CNNs) are applied to ship classification by using SAR images with the small datasets. First, ship chips are constructed from high-resolution SAR images and split into training and validation datasets. Second, a ship classification model is constructed based on very deep convolutional networks (VGG). Then, VGG is pretrained via ImageNet, and fine tuning is utilized to train our model. Six scenes of COSMO-SkyMed images are used to evaluate our proposed model with regard to the classification accuracy. The experimental results reveal that (1) our proposed ship classification model trained by fine tuning achieves more than 95% average classification accuracy, even with 5-cross validation; (2) compared with other models, the ship classification model based on VGG16 achieves at least 2% higher accuracies for classification. These experimental results reveal the effectiveness of our proposed method.

scholarly journals Optimizing the Performance of Breast Cancer Classification by Employing the Same Domain Transfer Learning from Hybrid Deep Convolutional Neural Network Model

Electronics ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 445 ◽  
Author(s):  
Laith Alzubaidi ◽  
Omran Al-Shamma ◽  
Mohammed A. Fadhel ◽  
Laith Farhan ◽  
Jinglan Zhang ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Deep Learning ◽  
Transfer Learning ◽  
Cancer Diagnosis ◽  
Classification Accuracy ◽  
Cancer Classification ◽  
Learning Models ◽  
Proposed Model ◽  
Domain Transfer ◽  
Domain Transfer Learning

Breast cancer is a significant factor in female mortality. An early cancer diagnosis leads to a reduction in the breast cancer death rate. With the help of a computer-aided diagnosis system, the efficiency increased, and the cost was reduced for the cancer diagnosis. Traditional breast cancer classification techniques are based on handcrafted features techniques, and their performance relies upon the chosen features. They also are very sensitive to different sizes and complex shapes. However, histopathological breast cancer images are very complex in shape. Currently, deep learning models have become an alternative solution for diagnosis, and have overcome the drawbacks of classical classification techniques. Although deep learning has performed well in various tasks of computer vision and pattern recognition, it still has some challenges. One of the main challenges is the lack of training data. To address this challenge and optimize the performance, we have utilized a transfer learning technique which is where the deep learning models train on a task, and then fine-tune the models for another task. We have employed transfer learning in two ways: Training our proposed model first on the same domain dataset, then on the target dataset, and training our model on a different domain dataset, then on the target dataset. We have empirically proven that the same domain transfer learning optimized the performance. Our hybrid model of parallel convolutional layers and residual links is utilized to classify hematoxylin–eosin-stained breast biopsy images into four classes: invasive carcinoma, in-situ carcinoma, benign tumor and normal tissue. To reduce the effect of overfitting, we have augmented the images with different image processing techniques. The proposed model achieved state-of-the-art performance, and it outperformed the latest methods by achieving a patch-wise classification accuracy of 90.5%, and an image-wise classification accuracy of 97.4% on the validation set. Moreover, we have achieved an image-wise classification accuracy of 96.1% on the test set of the microscopy ICIAR-2018 dataset.

scholarly journals Detecting Objects from Space: An Evaluation of Deep-Learning Modern Approaches

Electronics ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 583 ◽  
Author(s):  
Khang Nguyen ◽  
Nhut T. Huynh ◽  
Phat C. Nguyen ◽  
Khanh-Duy Nguyen ◽  
Nguyen D. Vo ◽  
...  
Keyword(s):  
Deep Learning ◽  
Object Detection ◽  
Unmanned Aircraft ◽  
Aerial Images ◽  
Great Success ◽  
Single Shot ◽  
Convolutional Networks ◽  
Image Pyramids ◽  
Fully Convolutional Networks ◽  
Wide Range

Unmanned aircraft systems or drones enable us to record or capture many scenes from the bird’s-eye view and they have been fast deployed to a wide range of practical domains, i.e., agriculture, aerial photography, fast delivery and surveillance. Object detection task is one of the core steps in understanding videos collected from the drones. However, this task is very challenging due to the unconstrained viewpoints and low resolution of captured videos. While deep-learning modern object detectors have recently achieved great success in general benchmarks, i.e., PASCAL-VOC and MS-COCO, the robustness of these detectors on aerial images captured by drones is not well studied. In this paper, we present an evaluation of state-of-the-art deep-learning detectors including Faster R-CNN (Faster Regional CNN), RFCN (Region-based Fully Convolutional Networks), SNIPER (Scale Normalization for Image Pyramids with Efficient Resampling), Single-Shot Detector (SSD), YOLO (You Only Look Once), RetinaNet, and CenterNet for the object detection in videos captured by drones. We conduct experiments on VisDrone2019 dataset which contains 96 videos with 39,988 annotated frames and provide insights into efficient object detectors for aerial images.

scholarly journals A Stacked Fully Convolutional Networks with Feature Alignment Framework for Multi-Label Land-cover Segmentation

2019 ◽  
Vol 11 (9) ◽  
pp. 1051 ◽  
Author(s):  
Guangming Wu ◽  
Yimin Guo ◽  
Xiaoya Song ◽  
Zhiling Guo ◽  
Haoran Zhang ◽  
...  
Keyword(s):  
Deep Learning ◽  
Land Cover ◽  
Superior Performance ◽  
Learning Methods ◽  
Convolutional Networks ◽  
Fully Convolutional Networks ◽  
Optimal Feature ◽  
Imaging Conditions ◽  
Very High ◽  
Feature Alignment

Applying deep-learning methods, especially fully convolutional networks (FCNs), has become a popular option for land-cover classification or segmentation in remote sensing. Compared with traditional solutions, these approaches have shown promising generalization capabilities and precision levels in various datasets of different scales, resolutions, and imaging conditions. To achieve superior performance, a lot of research has focused on constructing more complex or deeper networks. However, using an ensemble of different fully convolutional models to achieve better generalization and to prevent overfitting has long been ignored. In this research, we design four stacked fully convolutional networks (SFCNs), and a feature alignment framework for multi-label land-cover segmentation. The proposed feature alignment framework introduces an alignment loss of features extracted from basic models to balance their similarity and variety. Experiments on a very high resolution(VHR) image dataset with six categories of land-covers indicates that the proposed SFCNs can gain better performance when compared to existing deep learning methods. In the 2nd variant of SFCN, the optimal feature alignment gains increments of 4.2% (0.772 vs. 0.741), 6.8% (0.629 vs. 0.589), and 5.5% (0.727 vs. 0.689) for its f1-score, jaccard index, and kappa coefficient, respectively.

scholarly journals DEEPrior: a deep learning tool for the prioritization of gene fusions

2020 ◽  
Vol 36 (10) ◽  
pp. 3248-3250
Author(s):  
Marta Lovino ◽  
Maria Serena Ciaburri ◽  
Gianvito Urgese ◽  
Santa Di Cataldo ◽  
Elisa Ficarra
Keyword(s):  
Deep Learning ◽  
Amino Acid ◽  
Gene Fusion ◽  
Supplementary Information ◽  
Gene Fusions ◽  
Supplementary Data ◽  
Learning Tool ◽  
Cancer Driver ◽  
Open Issue ◽  
Passenger Mutation

Abstract Summary In the last decade, increasing attention has been paid to the study of gene fusions. However, the problem of determining whether a gene fusion is a cancer driver or just a passenger mutation is still an open issue. Here we present DEEPrior, an inherently flexible deep learning tool with two modes (Inference and Retraining). Inference mode predicts the probability of a gene fusion being involved in an oncogenic process, by directly exploiting the amino acid sequence of the fused protein. Retraining mode allows to obtain a custom prediction model including new data provided by the user. Availability and implementation Both DEEPrior and the protein fusions dataset are freely available from GitHub at (https://github.com/bioinformatics-polito/DEEPrior). The tool was designed to operate in Python 3.7, with minimal additional libraries. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals A Novel Object-Based Deep Learning Framework for Semantic Segmentation of Very High-Resolution Remote Sensing Data: Comparison with Convolutional and Fully Convolutional Networks

2019 ◽  
Vol 11 (6) ◽  
pp. 684 ◽  
Author(s):  
Maria Papadomanolaki ◽  
Maria Vakalopoulou ◽  
Konstantinos Karantzalos
Keyword(s):  
Deep Learning ◽  
State Of The Art ◽  
Semantic Segmentation ◽  
Novel Object ◽  
Convolutional Networks ◽  
Learning Framework ◽  
Fully Convolutional Networks ◽  
Object Based ◽  
Deep Networks ◽  
Very High

Deep learning architectures have received much attention in recent years demonstrating state-of-the-art performance in several segmentation, classification and other computer vision tasks. Most of these deep networks are based on either convolutional or fully convolutional architectures. In this paper, we propose a novel object-based deep-learning framework for semantic segmentation in very high-resolution satellite data. In particular, we exploit object-based priors integrated into a fully convolutional neural network by incorporating an anisotropic diffusion data preprocessing step and an additional loss term during the training process. Under this constrained framework, the goal is to enforce pixels that belong to the same object to be classified at the same semantic category. We compared thoroughly the novel object-based framework with the currently dominating convolutional and fully convolutional deep networks. In particular, numerous experiments were conducted on the publicly available ISPRS WGII/4 benchmark datasets, namely Vaihingen and Potsdam, for validation and inter-comparison based on a variety of metrics. Quantitatively, experimental results indicate that, overall, the proposed object-based framework slightly outperformed the current state-of-the-art fully convolutional networks by more than 1% in terms of overall accuracy, while intersection over union results are improved for all semantic categories. Qualitatively, man-made classes with more strict geometry such as buildings were the ones that benefit most from our method, especially along object boundaries, highlighting the great potential of the developed approach.

scholarly journals Breast Tumor Cellularity Assessment using Deep Neural Networks

2019 ◽  
Author(s):  
Alexander Rakhlin ◽  
Aleksei Tiulpin ◽  
Alexey A. Shvets ◽  
Alexandr A. Kalinin ◽  
Vladimir I. Iglovikov ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Deep Learning ◽  
Automatic Assessment ◽  
Appropriate Treatment ◽  
Image Patches ◽  
Expert Pathologist ◽  
Hematoxylin And Eosin ◽  
Treated Breast ◽  
Intra Class Correlation Coefficient ◽  
Whole Slide Images

AbstractBreast cancer is one of the main causes of death world-wide. Histopathological cellularity assessment of residual tumors in post-surgical tissues is used to analyze a tumor’s response to a therapy. Correct cellularity assessment increases the chances of getting an appropriate treatment and facilitates the patient’s survival. In current clinical practice, tumor cellularity is manually estimated by pathologists; this process is tedious and prone to errors or low agreement rates between assessors. In this work, we evaluated three strong novel Deep Learning-based approaches for automatic assessment of tumor cellularity from post-treated breast surgical specimens stained with hematoxylin and eosin. We validated the proposed methods on the BreastPathQ SPIE challenge dataset that consisted of 2395 image patches selected from whole slide images acquired from 64 patients. Compared to expert pathologist scoring, our best performing method yielded the Cohen’s kappa coefficient of 0.69 (vs. 0.42 previously known in literature) and the intra-class correlation coefficient of 0.89 (vs. 0.83). Our results suggest that Deep Learning-based methods have a significant potential to alleviate the burden on pathologists, enhance the diagnostic workflow, and, thereby, facilitate better clinical outcomes in breast cancer treatment.

scholarly journals Genetic mutation and biological pathway prediction based on whole slide images in breast carcinoma using deep learning

2021 ◽  
Vol 5 (1) ◽  
Author(s):  
Hui Qu ◽  
Mu Zhou ◽  
Zhennan Yan ◽  
He Wang ◽  
Vinod K. Rustgi ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Deep Learning ◽  
Breast Carcinoma ◽  
Targeted Therapies ◽  
Metastatic Breast ◽  
Image Features ◽  
Genetic Mutations ◽  
Biological Pathway ◽  
Visual Interactions ◽  
Whole Slide Images

AbstractBreast carcinoma is the most common cancer among women worldwide that consists of a heterogeneous group of subtype diseases. The whole-slide images (WSIs) can capture the cell-level heterogeneity, and are routinely used for cancer diagnosis by pathologists. However, key driver genetic mutations related to targeted therapies are identified by genomic analysis like high-throughput molecular profiling. In this study, we develop a deep-learning model to predict the genetic mutations and biological pathway activities directly from WSIs. Our study offers unique insights into WSI visual interactions between mutation and its related pathway, enabling a head-to-head comparison to reinforce our major findings. Using the histopathology images from the Genomic Data Commons Database, our model can predict the point mutations of six important genes (AUC 0.68–0.85) and copy number alteration of another six genes (AUC 0.69–0.79). Additionally, the trained models can predict the activities of three out of ten canonical pathways (AUC 0.65–0.79). Next, we visualized the weight maps of tumor tiles in WSI to understand the decision-making process of deep-learning models via a self-attention mechanism. We further validated our models on liver and lung cancers that are related to metastatic breast cancer. Our results provide insights into the association between pathological image features, molecular outcomes, and targeted therapies for breast cancer patients.

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