scholarly journals An ensemble deep learning framework to refine large deletions in linked-reads

2021 ◽  
Author(s):  
Yunfei Hu ◽  
Sanidhya V Mangal ◽  
Lu Zhang ◽  
Xin Zhou
Keyword(s):  
Deep Learning ◽  
Genome Assembly ◽  
Binary Classification ◽  
Image Data ◽  
Read Depth ◽  
Recall Rate ◽  
Large Deletion ◽  
Reference Sequence ◽  
Diploid Genome ◽  
Large Deletions

AbstractThe detection of structural variants (SVs) remains challenging due to inconsistencies in detected breakpoints and biological complexity of some rearrangements. Linked-reads have demonstrated their superiority in diploid genome assembly and SV detection. Recently developed tools Aquila and Aquila_stLFR use a reference sequence and linked-reads to generate a high quality diploid genome assembly, using which they then detect and phase personal genetic variations. However, they both produce a substantial proportion of false positive deletion SV calls. To take full advantage of linked-reads, an effective downstream filtering and refinement framework is needed pressingly. In this work, we propose AquilaDeepFilter to filter large deletion SVs from Aquila and Aquila_stLFR. AquilaDeepFilter relies on a deep learning ensemble approach by integrating six state-of-the-art CNN backbones. The filtering of deletion SVs is formulated as a binary classification task on image data that are generated through the extraction of multiple alignment signals, including read depth, split reads and discordant read pairs. Three linked-reads libraries sequenced from the well-studied sample NA24385 and the gold standard of GiaB benchmark were used to perform thorough experiments on our proposed method. The results demonstrated that AquilaDeepFilter could increase the precision rate of Aquila while the recall rate of Aquila decreased only slightly, and the overall F1 improved by 20%. Furthermore, AquilaDeepFilter outperformed another deep learning based method for SV filtering, DeepSVFilter. Even though we designed AquilaDeepFilter for linked-reads, the framework could also be used to improve SV detection on short reads.

scholarly journals LFM: A Lightweight LCD Algorithm Based on Feature Matching between Similar Key Frames

Sensors ◽  
2021 ◽  
Vol 21 (13) ◽  
pp. 4499
Author(s):  
Zuojun Zhu ◽  
Xiangrong Xu ◽  
Xuefei Liu ◽  
Yanglin Jiang
Keyword(s):  
Deep Learning ◽  
Feature Matching ◽  
Binary Classification ◽  
Recall Rate ◽  
Current Position ◽  
Loop Closure ◽  
Localization And Mapping ◽  
Similar Images ◽  
Key Frames ◽  
Target Detection Task

Loop Closure Detection (LCD) is an important technique to improve the accuracy of Simultaneous Localization and Mapping (SLAM). In this paper, we propose an LCD algorithm based on binary classification for feature matching between similar images with deep learning, which greatly improves the accuracy of LCD algorithm. Meanwhile, a novel lightweight convolutional neural network (CNN) is proposed and applied to the target detection task of key frames. On this basis, the key frames are binary classified according to their labels. Finally, similar frames are input into the improved lightweight feature matching network based on Transformer to judge whether the current position is loop closure. The experimental results show that, compared with the traditional method, LFM-LCD has higher accuracy and recall rate in the LCD task of indoor SLAM while ensuring the number of parameters and calculation amount. The research in this paper provides a new direction for LCD of robotic SLAM, which will be further improved with the development of deep learning.

Accuracy of automated machine learning in classifying retinal pathologies from ultra-widefield pseudocolour fundus images

2021 ◽  
pp. bjophthalmol-2021-319030
Author(s):  
Fares Antaki ◽  
Razek Georges Coussa ◽  
Ghofril Kahwati ◽  
Karim Hammamji ◽  
Mikael Sebag ◽  
...  
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Binary Classification ◽  
Image Data ◽  
Fundus Images ◽  
Learning Models ◽  
Data Set ◽  
Discriminative Performance ◽  
Automated Machine Learning ◽  
Good Diagnostic Accuracy

AimsAutomated machine learning (AutoML) is a novel tool in artificial intelligence (AI). This study assessed the discriminative performance of AutoML in differentiating retinal vein occlusion (RVO), retinitis pigmentosa (RP) and retinal detachment (RD) from normal fundi using ultra-widefield (UWF) pseudocolour fundus images.MethodsTwo ophthalmologists without coding experience carried out AutoML model design using a publicly available image data set (2137 labelled images). The data set was reviewed for low-quality and mislabeled images and then uploaded to the Google Cloud AutoML Vision platform for training and testing. We designed multiple binary models to differentiate RVO, RP and RD from normal fundi and compared them to bespoke models obtained from the literature. We then devised a multiclass model to detect RVO, RP and RD. Saliency maps were generated to assess the interpretability of the model.ResultsThe AutoML models demonstrated high diagnostic properties in the binary classification tasks that were generally comparable to bespoke deep-learning models (area under the precision-recall curve (AUPRC) 0.921–1, sensitivity 84.91%–89.77%, specificity 78.72%–100%). The multiclass AutoML model had an AUPRC of 0.876, a sensitivity of 77.93% and a positive predictive value of 82.59%. The per-label sensitivity and specificity, respectively, were normal fundi (91.49%, 86.75%), RVO (83.02%, 92.50%), RP (72.00%, 100%) and RD (79.55%,96.80%).ConclusionAutoML models created by ophthalmologists without coding experience can detect RVO, RP and RD in UWF images with very good diagnostic accuracy. The performance was comparable to bespoke deep-learning models derived by AI experts for RVO and RP but not for RD.

scholarly journals Covid Classification Using Audio Data

2021 ◽  
Vol 9 (10) ◽  
pp. 1633-1637
Author(s):  
Adwait Patil
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Binary Classification ◽  
Image Data ◽  
Audio Classification ◽  
Mel Frequency Cepstral Coefficients ◽  
Audio Data ◽  
Cepstral Coefficients ◽  
Audio Files

Abstract: Coronavirus outbreak has affected the entire world adversely this project has been developed in order to help common masses diagnose their chances of been covid positive just by using coughing sound and basic patient data. Audio classification is one of the most interesting applications of deep learning. Similar to image data audio data is also stored in form of bits and to understand and analyze this audio data we have used Mel frequency cepstral coefficients (MFCCs) which makes it possible to feed the audio to our neural network. In this project we have used Coughvid a crowdsource dataset consisting of 27000 audio files and metadata of same amount of patients. In this project we have used a 1D Convolutional Neural Network (CNN) to process the audio and metadata. Future scope for this project will be a model that rates how likely it is that a person is infected instead of binary classification. Keywords: Audio classification, Mel frequency cepstral coefficients, Convolutional neural network, deep learning, Coughvid

Deep Learning Approaches for Whiteboard Image Quality Enhancement

2019 ◽  
Vol 2019 (1) ◽  
pp. 360-368
Author(s):  
Mekides Assefa Abebe ◽  
Jon Yngve Hardeberg
Keyword(s):  
Deep Learning ◽  
Image Quality ◽  
Image Data ◽  
Quality Enhancement ◽  
Network Architectures ◽  
Learning Approaches ◽  
Data Set ◽  
Image Quality Enhancement ◽  
Processing Techniques ◽  
White Balancing

Different whiteboard image degradations highly reduce the legibility of pen-stroke content as well as the overall quality of the images. Consequently, different researchers addressed the problem through different image enhancement techniques. Most of the state-of-the-art approaches applied common image processing techniques such as background foreground segmentation, text extraction, contrast and color enhancements and white balancing. However, such types of conventional enhancement methods are incapable of recovering severely degraded pen-stroke contents and produce artifacts in the presence of complex pen-stroke illustrations. In order to surmount such problems, the authors have proposed a deep learning based solution. They have contributed a new whiteboard image data set and adopted two deep convolutional neural network architectures for whiteboard image quality enhancement applications. Their different evaluations of the trained models demonstrated their superior performances over the conventional methods.

scholarly journals Deep convolutional neural networks for cardiovascular vulnerable plaque detection

2019 ◽  
Vol 277 ◽  
pp. 02024 ◽  
Author(s):  
Lincan Li ◽  
Tong Jia ◽  
Tianqi Meng ◽  
Yizhe Liu
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Networks ◽  
Vulnerable Plaque ◽  
Recall Rate ◽  
Superior Performance ◽  
Learning Approaches ◽  
Deep Convolutional Neural Networks ◽  
Vulnerable Plaques ◽  
Plaque Detection

In this paper, an accurate two-stage deep learning method is proposed to detect vulnerable plaques in ultrasonic images of cardiovascular. Firstly, a Fully Convonutional Neural Network (FCN) named U-Net is used to segment the original Intravascular Optical Coherence Tomography (IVOCT) cardiovascular images. We experiment on different threshold values to find the best threshold for removing noise and background in the original images. Secondly, a modified Faster RCNN is adopted to do precise detection. The modified Faster R-CNN utilize six-scale anchors (122,162,322,642,1282,2562) instead of the conventional one scale or three scale approaches. First, we present three problems in cardiovascular vulnerable plaque diagnosis, then we demonstrate how our method solve these problems. The proposed method in this paper apply deep convolutional neural networks to the whole diagnostic procedure. Test results show the Recall rate, Precision rate, IoU (Intersection-over-Union) rate and Total score are 0.94, 0.885, 0.913 and 0.913 respectively, higher than the 1st team of CCCV2017 Cardiovascular OCT Vulnerable Plaque Detection Challenge. AP of the designed Faster RCNN is 83.4%, higher than conventional approaches which use one-scale or three-scale anchors. These results demonstrate the superior performance of our proposed method and the power of deep learning approaches in diagnose cardiovascular vulnerable plaques.

scholarly journals Fast Multi-Focus Fusion Based on Deep Learning for Early-Stage Embryo Image Enhancement

Sensors ◽  
2021 ◽  
Vol 21 (3) ◽  
pp. 863
Author(s):  
Vidas Raudonis ◽  
Agne Paulauskaite-Taraseviciene ◽  
Kristina Sutiene
Keyword(s):  
Deep Learning ◽  
Image Fusion ◽  
Early Stage ◽  
Image Data ◽  
Cell Detection ◽  
Processing Times ◽  
Fused Image ◽  
Stage Embryo ◽  
Early Stage Embryo

Background: Cell detection and counting is of essential importance in evaluating the quality of early-stage embryo. Full automation of this process remains a challenging task due to different cell size, shape, the presence of incomplete cell boundaries, partially or fully overlapping cells. Moreover, the algorithm to be developed should process a large number of image data of different quality in a reasonable amount of time. Methods: Multi-focus image fusion approach based on deep learning U-Net architecture is proposed in the paper, which allows reducing the amount of data up to 7 times without losing spectral information required for embryo enhancement in the microscopic image. Results: The experiment includes the visual and quantitative analysis by estimating the image similarity metrics and processing times, which is compared to the results achieved by two wellknown techniques—Inverse Laplacian Pyramid Transform and Enhanced Correlation Coefficient Maximization. Conclusion: Comparatively, the image fusion time is substantially improved for different image resolutions, whilst ensuring the high quality of the fused image.

scholarly journals U-Infuse: Democratization of Customizable Deep Learning for Object Detection

Sensors ◽  
2021 ◽  
Vol 21 (8) ◽  
pp. 2611
Author(s):  
Andrew Shepley ◽  
Greg Falzon ◽  
Christopher Lawson ◽  
Paul Meek ◽  
Paul Kwan
Keyword(s):  
Deep Learning ◽  
Intellectual Property ◽  
Object Detection ◽  
Image Data ◽  
Learning Technologies ◽  
Training Data ◽  
Learning Models ◽  
Ecological Data ◽  
Single Class ◽  
Large Numbers

Image data is one of the primary sources of ecological data used in biodiversity conservation and management worldwide. However, classifying and interpreting large numbers of images is time and resource expensive, particularly in the context of camera trapping. Deep learning models have been used to achieve this task but are often not suited to specific applications due to their inability to generalise to new environments and inconsistent performance. Models need to be developed for specific species cohorts and environments, but the technical skills required to achieve this are a key barrier to the accessibility of this technology to ecologists. Thus, there is a strong need to democratize access to deep learning technologies by providing an easy-to-use software application allowing non-technical users to train custom object detectors. U-Infuse addresses this issue by providing ecologists with the ability to train customised models using publicly available images and/or their own images without specific technical expertise. Auto-annotation and annotation editing functionalities minimize the constraints of manually annotating and pre-processing large numbers of images. U-Infuse is a free and open-source software solution that supports both multiclass and single class training and object detection, allowing ecologists to access deep learning technologies usually only available to computer scientists, on their own device, customised for their application, without sharing intellectual property or sensitive data. It provides ecological practitioners with the ability to (i) easily achieve object detection within a user-friendly GUI, generating a species distribution report, and other useful statistics, (ii) custom train deep learning models using publicly available and custom training data, (iii) achieve supervised auto-annotation of images for further training, with the benefit of editing annotations to ensure quality datasets. Broad adoption of U-Infuse by ecological practitioners will improve ecological image analysis and processing by allowing significantly more image data to be processed with minimal expenditure of time and resources, particularly for camera trap images. Ease of training and use of transfer learning means domain-specific models can be trained rapidly, and frequently updated without the need for computer science expertise, or data sharing, protecting intellectual property and privacy.

scholarly journals Advancing Stress Detection Methodology with Deep Learning Techniques Targeting UX Evaluation in AAL Scenarios: Applying Embeddings for Categorical Variables

Electronics ◽  
2021 ◽  
Vol 10 (13) ◽  
pp. 1550
Author(s):  
Alexandros Liapis ◽  
Evanthia Faliagka ◽  
Christos P. Antonopoulos ◽  
Georgios Keramidas ◽  
Nikolaos Voros
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
User Experience ◽  
Electrodermal Activity ◽  
Binary Classification ◽  
Research Question ◽  
Classification Problem ◽  
Categorical Variables ◽  
Stress Detection ◽  
Software Failures

Physiological measurements have been widely used by researchers and practitioners in order to address the stress detection challenge. So far, various datasets for stress detection have been recorded and are available to the research community for testing and benchmarking. The majority of the stress-related available datasets have been recorded while users were exposed to intense stressors, such as songs, movie clips, major hardware/software failures, image datasets, and gaming scenarios. However, it remains an open research question if such datasets can be used for creating models that will effectively detect stress in different contexts. This paper investigates the performance of the publicly available physiological dataset named WESAD (wearable stress and affect detection) in the context of user experience (UX) evaluation. More specifically, electrodermal activity (EDA) and skin temperature (ST) signals from WESAD were used in order to train three traditional machine learning classifiers and a simple feed forward deep learning artificial neural network combining continues variables and entity embeddings. Regarding the binary classification problem (stress vs. no stress), high accuracy (up to 97.4%), for both training approaches (deep-learning, machine learning), was achieved. Regarding the stress detection effectiveness of the created models in another context, such as user experience (UX) evaluation, the results were quite impressive. More specifically, the deep-learning model achieved a rather high agreement when a user-annotated dataset was used for validation.

scholarly journals Deep-Learning-Based Pupil Center Detection and Tracking Technology for Visible-Light Wearable Gaze Tracking Devices

2021 ◽  
Vol 11 (2) ◽  
pp. 851
Author(s):  
Wei-Liang Ou ◽  
Tzu-Ling Kuo ◽  
Chin-Chieh Chang ◽  
Chih-Peng Fan
Keyword(s):  
Deep Learning ◽  
Visible Light ◽  
Tracking System ◽  
Recall Rate ◽  
Detection Accuracy ◽  
Learning Technology ◽  
Tracking Errors ◽  
Gaze Tracking ◽  
Detection Technology ◽  
Pupil Tracking

In this study, for the application of visible-light wearable eye trackers, a pupil tracking methodology based on deep-learning technology is developed. By applying deep-learning object detection technology based on the You Only Look Once (YOLO) model, the proposed pupil tracking method can effectively estimate and predict the center of the pupil in the visible-light mode. By using the developed YOLOv3-tiny-based model to test the pupil tracking performance, the detection accuracy is as high as 80%, and the recall rate is close to 83%. In addition, the average visible-light pupil tracking errors of the proposed YOLO-based deep-learning design are smaller than 2 pixels for the training mode and 5 pixels for the cross-person test, which are much smaller than those of the previous ellipse fitting design without using deep-learning technology under the same visible-light conditions. After the combination of calibration process, the average gaze tracking errors by the proposed YOLOv3-tiny-based pupil tracking models are smaller than 2.9 and 3.5 degrees at the training and testing modes, respectively, and the proposed visible-light wearable gaze tracking system performs up to 20 frames per second (FPS) on the GPU-based software embedded platform.

scholarly journals InstantDL: an easy-to-use deep learning pipeline for image segmentation and classification

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Dominik Jens Elias Waibel ◽  
Sayedali Shetab Boushehri ◽  
Carsten Marr
Keyword(s):  
Image Processing ◽  
Deep Learning ◽  
Specific Problem ◽  
State Of The Art ◽  
Image Data ◽  
Semantic Segmentation ◽  
Parameter Tuning ◽  
Cellular Processes ◽  
Minimal Effort ◽  
Instance Segmentation

Abstract Background Deep learning contributes to uncovering molecular and cellular processes with highly performant algorithms. Convolutional neural networks have become the state-of-the-art tool to provide accurate and fast image data processing. However, published algorithms mostly solve only one specific problem and they typically require a considerable coding effort and machine learning background for their application. Results We have thus developed InstantDL, a deep learning pipeline for four common image processing tasks: semantic segmentation, instance segmentation, pixel-wise regression and classification. InstantDL enables researchers with a basic computational background to apply debugged and benchmarked state-of-the-art deep learning algorithms to their own data with minimal effort. To make the pipeline robust, we have automated and standardized workflows and extensively tested it in different scenarios. Moreover, it allows assessing the uncertainty of predictions. We have benchmarked InstantDL on seven publicly available datasets achieving competitive performance without any parameter tuning. For customization of the pipeline to specific tasks, all code is easily accessible and well documented. Conclusions With InstantDL, we hope to empower biomedical researchers to conduct reproducible image processing with a convenient and easy-to-use pipeline.

Sign in / Sign up

Export Citation Format

Share Document