scholarly journals Evaluation of the Classification Accuracy of the Kidney Biopsy Direct Immunofluorescence through Convolutional Neural Networks

2020 ◽  
Vol 15 (10) ◽  
pp. 1445-1454 ◽  
Author(s):  
Giulia Ligabue ◽  
Federico Pollastri ◽  
Francesco Fontana ◽  
Marco Leonelli ◽  
Luciana Furci ◽  
...  
Keyword(s):  
Neural Networks ◽  
Convolutional Neural Networks ◽  
Kidney Biopsy ◽  
Ground Truth ◽  
Light Chains ◽  
Direct Immunofluorescence ◽  
Support Tool ◽  
Glomerular Deposits ◽  
Web Platform

Background and objectivesImmunohistopathology is an essential technique in the diagnostic workflow of a kidney biopsy. Deep learning is an effective tool in the elaboration of medical imaging. We wanted to evaluate the role of a convolutional neural network as a support tool for kidney immunofluorescence reporting.Design, setting, participants, & measurementsHigh-magnification (×400) immunofluorescence images of kidney biopsies performed from the year 2001 to 2018 were collected. The report, adopted at the Division of Nephrology of the AOU Policlinico di Modena, describes the specimen in terms of “appearance,” “distribution,” “location,” and “intensity” of the glomerular deposits identified with fluorescent antibodies against IgG, IgA, IgM, C1q and C3 complement fractions, fibrinogen, and κ- and λ-light chains. The report was used as ground truth for the training of the convolutional neural networks.ResultsIn total, 12,259 immunofluorescence images of 2542 subjects undergoing kidney biopsy were collected. The test set analysis showed accuracy values between 0.79 (“irregular capillary wall” feature) and 0.94 (“fine granular” feature). The agreement test of the results obtained by the convolutional neural networks with respect to the ground truth showed similar values to three pathologists of our center. Convolutional neural networks were 117 times faster than human evaluators in analyzing 180 test images. A web platform, where it is possible to upload digitized images of immunofluorescence specimens, is available to evaluate the potential of our approach.ConclusionsThe data showed that the accuracy of convolutional neural networks is comparable with that of pathologists experienced in the field.

scholarly journals Automated cephalometric landmark detection with confidence regions using Bayesian convolutional neural networks

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Jeong-Hoon Lee ◽  
Hee-Jin Yu ◽  
Min-ji Kim ◽  
Jin-Woo Kim ◽  
Jongeun Choi
Keyword(s):  
Neural Networks ◽  
Convolutional Neural Networks ◽  
Region Of Interest ◽  
Confidence Regions ◽  
Grand Challenge ◽  
Uncertainty Prediction ◽  
Integral Role ◽  
Roi Extraction ◽  
Aided Diagnosis

Abstract Background Despite the integral role of cephalometric analysis in orthodontics, there have been limitations regarding the reliability, accuracy, etc. of cephalometric landmarks tracing. Attempts on developing automatic plotting systems have continuously been made but they are insufficient for clinical applications due to low reliability of specific landmarks. In this study, we aimed to develop a novel framework for locating cephalometric landmarks with confidence regions using Bayesian Convolutional Neural Networks (BCNN). Methods We have trained our model with the dataset from the ISBI 2015 grand challenge in dental X-ray image analysis. The overall algorithm consisted of a region of interest (ROI) extraction of landmarks and landmarks estimation considering uncertainty. Prediction data produced from the Bayesian model has been dealt with post-processing methods with respect to pixel probabilities and uncertainties. Results Our framework showed a mean landmark error (LE) of 1.53 ± 1.74 mm and achieved a successful detection rate (SDR) of 82.11, 92.28 and 95.95%, respectively, in the 2, 3, and 4 mm range. Especially, the most erroneous point in preceding studies, Gonion, reduced nearly halves of its error compared to the others. Additionally, our results demonstrated significantly higher performance in identifying anatomical abnormalities. By providing confidence regions (95%) that consider uncertainty, our framework can provide clinical convenience and contribute to making better decisions. Conclusion Our framework provides cephalometric landmarks and their confidence regions, which could be used as a computer-aided diagnosis tool and education.

scholarly journals Comparison of Classical Computer Vision vs. Convolutional Neural Networks for Weed Mapping in Aerial Images

2020 ◽  
Vol 27 (4) ◽  
pp. 20-33
Author(s):  
Paulo César Pereira Júnior ◽  
Alexandre Monteiro ◽  
Rafael Da Luz Ribeiro ◽  
Antonio Carlos Sobieranski ◽  
Aldo Von Wangenheim
Keyword(s):  
Neural Networks ◽  
Computer Vision ◽  
Convolutional Neural Networks ◽  
Precision Agriculture ◽  
Ground Truth ◽  
Aerial Images ◽  
Weed Mapping ◽  
Classical Models ◽  
Classical Computer ◽  
Better Than

In this paper, we present a comparison between convolutional neural networks and classicalcomputer vision approaches, for the specific precision agriculture problem of weed mapping on sugarcane fields aerial images. A systematic literature review was conducted to find which computer vision methods are being used on this specific problem. The most cited methods were implemented, as well as four models of convolutional neural networks. All implemented approaches were tested using the same dataset, and their results were quantitatively and qualitatively analyzed. The obtained results were compared to a human expert made ground truth, for validation. The results indicate that the convolutional neural networks present better precision and generalize better than the classical models

scholarly journals Automatic onset detection using convolutional neural networks

2019 ◽  
Author(s):  
Willy Cornelissen ◽  
Maurício Loureiro
Keyword(s):  
Neural Networks ◽  
Convolutional Neural Networks ◽  
Ground Truth ◽  
Onset Detection ◽  
Ground Truth Data ◽  
Music Transcription ◽  
Automatic Music Transcription ◽  
Information Research ◽  
Music Research ◽  
Music Information

A very significant task for music research is to estimate instants when meaningful events begin (onset) and when they end (offset). Onset detection is widely applied in many fields: electrocardiograms, seismographic data, stock market results and many Music Information Research(MIR) tasks, such as Automatic Music Transcription, Rhythm Detection, Speech Recognition, etc. Automatic Onset Detection(AOD) received, recently, a huge contribution coming from Artificial Intelligence (AI) methods, mainly Machine Learning and Deep Learning. In this work, the use of Convolutional Neural Networks (CNN) is explored by adapting its original architecture in order to apply the approach to automatic onset detection on audio musical signals. We used a CNN network for onset detection on a very general dataset, well acknowledged by the MIR community, and examined the accuracy of the method by comparison to ground truth data published by the dataset. The results are promising and outperform another methods of musical onset detection.

scholarly journals Object Detectors’ Convolutional Neural Networks backbones : a review and a comparative study

2021 ◽  
Vol 9 (11) ◽  
pp. 1379-1386
Keyword(s):  
Neural Networks ◽  
Computer Vision ◽  
Object Detection ◽  
Convolutional Neural Networks ◽  
Crucial Role ◽  
Extended Version ◽  
Backbone Networks ◽  
Detection Algorithms ◽  
Wide Range

Computer vision is a scientific field that deals with how computers can acquire significant level comprehension from computerized images or videos. One of the keystones of computer vision is object detection that aims to identify relevant features from video or image to detect objects. Backbone is the first stage in object detection algorithms that play a crucial role in object detection. Object detectors are usually provided with backbone networks designed for image classification. Object detection performance is highly based on features extracted by backbones, for instance, by simply replacing a backbone with its extended version, a large accuracy metric grows up. Additionally, the backbone's importance is demonstrated by its efficiency in real-time object detection. In this paper, we aim to accumulate the crucial role of the deep learning era and convolutional neural networks in particular in object detection tasks. We have analyzed and have been concentrating on a wide range of reviews on convolutional neural networks used as the backbone of object detection models. Building, therefore, a review of backbones that help researchers and scientists to use it as a guideline for their works.

scholarly journals Water Level Estimation in Sewer Pipes Using Deep Convolutional Neural Networks

Water ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 3412
Author(s):  
Joakim Bruslund Haurum ◽  
Chris H. Bahnsen ◽  
Malte Pedersen ◽  
Thomas B. Moeslund
Keyword(s):  
Neural Networks ◽  
Water Level ◽  
Convolutional Neural Networks ◽  
Contextual Information ◽  
Ground Truth ◽  
Water Levels ◽  
Deep Convolutional Neural Networks ◽  
Regression Problem ◽  
Still Images ◽  
Visual Appearance

Sewer pipe inspections are currently conducted by professionals who remotely control a robot from above ground. This expensive and slow approach is prone to human mistakes. Therefore, there is both an economic and scientific interest in automating the inspection process by creating systems able to recognize sewer defects. However, the extent of research put into automatic water level estimation in sewers has been limited despite being a prerequisite for further analysis of the pipe as only sections above the water level can be visually inspected. In this work, we utilize a dataset of still images obtained from over 5000 inspections carried out for three different Danish water utilities companies. This dataset is used for training and testing decision tree methods and convolutional neural networks (CNNs) for automatic water level estimation. We pose the estimation problem as a classification and regression problem, and compare the results of both approaches. Furthermore, we compare the effect of using different inspection standards for labeling the ground truth water level. By treating the problem as a classification task and using the 2015 Danish sewer inspection standard, where water levels are clustered based on visual appearance, we achieve an averaged F1 score of 79.29% using a fine-tuned ResNet-50 CNN. This shows the potential of using CNNs for water level estimation. We believe including temporal and contextual information will improve the results further.

scholarly journals Building realistic structure models to train convolutional neural networks for seismic structural interpretation

Geophysics ◽  
2020 ◽  
Vol 85 (4) ◽  
pp. WA27-WA39 ◽  
Author(s):  
Xinming Wu ◽  
Zhicheng Geng ◽  
Yunzhi Shi ◽  
Nam Pham ◽  
Sergey Fomel ◽  
...  
Keyword(s):  
Neural Networks ◽  
Convolutional Neural Networks ◽  
Structural Information ◽  
Ground Truth ◽  
Structural Features ◽  
Image Features ◽  
Training Data ◽  
Structural Interpretation ◽  
Seismic Image ◽  
Seismic Images

Seismic structural interpretation involves highlighting and extracting faults and horizons that are apparent as geometric features in a seismic image. Although seismic image processing methods have been proposed to automate fault and horizon interpretation, each of which today still requires significant human effort. We improve automatic structural interpretation in seismic images by using convolutional neural networks (CNNs) that recently have shown excellent performances in detecting and extracting useful image features and objects. The main limitation of applying CNNs in seismic interpretation is the preparation of many training data sets and especially the corresponding geologic labels. Manually labeling geologic features in a seismic image is highly time-consuming and subjective, which often results in incompletely or inaccurately labeled training images. To solve this problem, we have developed a workflow to automatically build diverse structure models with realistic folding and faulting features. In this workflow, with some assumptions about typical folding and faulting patterns, we simulate structural features in a 3D model by using a set of parameters. By randomly choosing the parameters from some predefined ranges, we are able to automatically generate numerous structure models with realistic and diverse structural features. Based on these structure models with known structural information, we further automatically create numerous synthetic seismic images and the corresponding ground truth of structural labels to train CNNs for structural interpretation in field seismic images. Accurate results of structural interpretation in multiple field seismic images indicate that our workflow simulates realistic and generalized structure models from which the CNNs effectively learn to recognize real structures in field images.

scholarly journals CheXLocNet: Automatic localization of pneumothorax in chest radiographs using deep convolutional neural networks

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0242013
Author(s):  
Hongyu Wang ◽  
Hong Gu ◽  
Pan Qin ◽  
Jia Wang
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Networks ◽  
Characteristic Curve ◽  
Healthcare Delivery ◽  
Chest Radiographs ◽  
Training Dataset ◽  
Deep Convolutional Neural Networks ◽  
Support Tool

Background Pneumothorax can lead to a life-threatening emergency. The experienced radiologists can offer precise diagnosis according to the chest radiographs. The localization of the pneumothorax lesions will help to quickly diagnose, which will be benefit for the patients in the underdevelopment areas lack of the experienced radiologists. In recent years, with the development of large neural network architectures and medical imaging datasets, deep learning methods have become a methodology of choice for analyzing medical images. The objective of this study was to the construct convolutional neural networks to localize the pneumothorax lesions in chest radiographs. Methods and findings We developed a convolutional neural network, called CheXLocNet, for the segmentation of pneumothorax lesions. The SIIM-ACR Pneumothorax Segmentation dataset was used to train and validate CheXLocNets. The training dataset contained 2079 radiographs with the annotated lesion areas. We trained six CheXLocNets with various hyperparameters. Another 300 annotated radiographs were used to select parameters of these CheXLocNets as the validation set. We determined the optimal parameters by the AP50 (average precision at the intersection over union (IoU) equal to 0.50), a segmentation evaluation metric used by several well-known competitions. Then CheXLocNets were evaluated by a test set (1082 normal radiographs and 290 disease radiographs), based on the classification metrics: area under the receiver operating characteristic curve (AUC), sensitivity, specificity, and positive predictive value (PPV); segmentation metrics: IoU and Dice score. For the classification, CheXLocNet with best sensitivity produced an AUC of 0.87, sensitivity of 0.78 (95% CI 0.73-0.83), and specificity of 0.78 (95% CI 0.76-0.81). CheXLocNet with best specificity produced an AUC of 0.79, sensitivity of 0.46 (95% CI 0.40-0.52), and specificity of 0.92 (95% CI 0.90-0.94). For the segmentation, CheXLocNet with best sensitivity produced an IoU of 0.69 and Dice score of 0.72. CheXLocNet with best specificity produced an IoU of 0.77 and Dice score of 0.79. We combined them to form an ensemble CheXLocNet. The ensemble CheXLocNet produced an IoU of 0.81 and Dice score of 0.82. Our CheXLocNet succeeded in automatically detecting pneumothorax lesions, without any human guidance. Conclusions In this study, we proposed a deep learning network, called, CheXLocNet, for the automatic segmentation of chest radiographs to detect pneumothorax. Our CheXLocNets generated accurate classification results and high-quality segmentation masks for the pneumothorax at the same time. This technology has the potential to improve healthcare delivery and increase access to chest radiograph expertise for the detection of diseases. Furthermore, the segmentation results can offer comprehensive geometric information of lesions, which can benefit monitoring the sequential development of lesions with high accuracy. Thus, CheXLocNets can be further extended to be a reliable clinical decision support tool. Although we used transfer learning in training CheXLocNet, the parameters of CheXLocNet was still large for the radiograph dataset. Further work is necessary to prune CheXLocNet suitable for the radiograph dataset.

scholarly journals High-Throughput Phenotyping of Soybean Maturity Using Time Series UAV Imagery and Convolutional Neural Networks

2020 ◽  
Author(s):  
Rodrigo Trevisan ◽  
Osvaldo Pérez ◽  
Nathan Schmitz ◽  
Brian Diers ◽  
Nicolas Martin
Keyword(s):  
Neural Networks ◽  
Convolutional Neural Networks ◽  
High Throughput ◽  
Mean Squared Error ◽  
Ground Truth ◽  
Breeding Programs ◽  
Growing Seasons ◽  
Maturity Date ◽  
High Throughput Phenotyping ◽  
Commercial Breeding

Soybean maturity is a trait of critical importance for the development of new soybean cultivars, nevertheless, its characterization based on visual ratings has many challenges. Unmanned aerial vehicles (UAVs) imagery-based high-throughput phenotyping methodologies have been proposed as an alternative to the traditional visual ratings of pod senescence. However, the lack of scalable and accurate methods to extract the desired information from the images remains a significant bottleneck in breeding programs. The objective of this study was to develop an image-based high-throughput phenotyping system for evaluating soybean maturity in breeding programs. Images were acquired twice a week, starting when the earlier lines began maturation until the latest ones were mature. Two complementary convolutional neural networks (CNN) were developed to predict the maturity date. The first using a single date and the second using the five best image dates identified by the first model. The proposed CNN architecture was validated using more than 15,000 ground truth observations from five trials, including data from three growing seasons and two countries. The trained model showed good generalization capability with a root mean squared error lower than two days in four out of five trials. Four methods of estimating prediction uncertainty showed potential at identifying different sources of errors in the maturity date predictions. The architecture used solves limitations of previous research and can be used at scale in commercial breeding programs.

scholarly journals The role of convolutional neural networks in scanning probe microscopy: a review

2021 ◽  
Vol 12 ◽  
pp. 878-901
Author(s):  
Ido Azuri ◽  
Irit Rosenhek-Goldian ◽  
Neta Regev-Rudzki ◽  
Georg Fantner ◽  
Sidney R Cohen
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Networks ◽  
Scanning Probe Microscopy ◽  
Scanning Probe ◽  
Data Set ◽  
Probe Microscopy ◽  
Instrumental Control

Progress in computing capabilities has enhanced science in many ways. In recent years, various branches of machine learning have been the key facilitators in forging new paths, ranging from categorizing big data to instrumental control, from materials design through image analysis. Deep learning has the ability to identify abstract characteristics embedded within a data set, subsequently using that association to categorize, identify, and isolate subsets of the data. Scanning probe microscopy measures multimodal surface properties, combining morphology with electronic, mechanical, and other characteristics. In this review, we focus on a subset of deep learning algorithms, that is, convolutional neural networks, and how it is transforming the acquisition and analysis of scanning probe data.

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