scholarly journals Pavement Image Datasets: A New Benchmark Dataset to Classify and Densify Pavement Distresses

2020 ◽  
Vol 2674 (2) ◽  
pp. 328-339 ◽  
Author(s):  
Hamed Majidifard ◽  
Peng Jin ◽  
Yaw Adu-Gyamfi ◽  
William G. Buttlar
Keyword(s):  
Deep Learning ◽  
Ground Truth ◽  
Application Programming Interface ◽  
Assessment System ◽  
Top Down ◽  
Research Activity ◽  
Data Set ◽  
Ground Truth Data ◽  
Pavement Distresses ◽  
Learning Frameworks

Automated pavement distresses detection using road images remains a challenging topic in the computer vision research community. Recent developments in deep learning have led to considerable research activity directed towards improving the efficacy of automated pavement distress identification and rating. Deep learning models require a large ground truth data set, which is often not readily available in the case of pavements. In this study, a labeled dataset approach is introduced as a first step towards a more robust, easy-to-deploy pavement condition assessment system. The technique is termed herein as the pavement image dataset (PID) method. The dataset consists of images captured from two camera views of an identical pavement segment, that is, a wide view and a top-down view. The wide-view images were used to classify the distresses and to train the deep learning frameworks, while the top-down-view images allowed calculation of distress density, which will be used in future studies aimed at automated pavement rating. For the wide view group dataset, 7,237 images were manually annotated and distresses classified into nine categories. Images were extracted using the Google application programming interface (API), selecting street-view images using a python-based code developed for this project. The new dataset was evaluated using two mainstream deep learning frameworks: You Only Look Once (YOLO v2) and Faster Region Convolution Neural Network (Faster R-CNN). Accuracy scores using the F1 index were found to be 0.84 for YOLOv2 and 0.65 for the Faster R-CNN model runs; both quite acceptable considering the convenience of utilizing Google Maps images.

scholarly journals Flying Free: A Research Overview of Deep Learning in Drone Navigation Autonomy

Drones ◽  
2021 ◽  
Vol 5 (2) ◽  
pp. 52
Author(s):  
Thomas Lee ◽  
Susan Mckeever ◽  
Jane Courtney
Keyword(s):  
Deep Learning ◽  
Research Work ◽  
Learning Approaches ◽  
Clear Definition ◽  
Top Down ◽  
Research Activity ◽  
Comprehensive Overview ◽  
The Past ◽  
Computer Vision Applications ◽  
Definition Of

With the rise of Deep Learning approaches in computer vision applications, significant strides have been made towards vehicular autonomy. Research activity in autonomous drone navigation has increased rapidly in the past five years, and drones are moving fast towards the ultimate goal of near-complete autonomy. However, while much work in the area focuses on specific tasks in drone navigation, the contribution to the overall goal of autonomy is often not assessed, and a comprehensive overview is needed. In this work, a taxonomy of drone navigation autonomy is established by mapping the definitions of vehicular autonomy levels, as defined by the Society of Automotive Engineers, to specific drone tasks in order to create a clear definition of autonomy when applied to drones. A top–down examination of research work in the area is conducted, focusing on drone navigation tasks, in order to understand the extent of research activity in each area. Autonomy levels are cross-checked against the drone navigation tasks addressed in each work to provide a framework for understanding the trajectory of current research. This work serves as a guide to research in drone autonomy with a particular focus on Deep Learning-based solutions, indicating key works and areas of opportunity for development of this area in the future.

scholarly journals Deep Learning Based Cardiac MRI Segmentation: Do We Need Experts?

Algorithms ◽  
2021 ◽  
Vol 14 (7) ◽  
pp. 212
Author(s):  
Youssef Skandarani ◽  
Pierre-Marc Jodoin ◽  
Alain Lalande
Keyword(s):  
Deep Learning ◽  
Cardiac Mri ◽  
Expert Knowledge ◽  
Medical Image Analysis ◽  
Ground Truth ◽  
Cine Mri ◽  
Data Sets ◽  
Mri Segmentation ◽  
Segmentation Evaluation ◽  
Ground Truth Data

Deep learning methods are the de facto solutions to a multitude of medical image analysis tasks. Cardiac MRI segmentation is one such application, which, like many others, requires a large number of annotated data so that a trained network can generalize well. Unfortunately, the process of having a large number of manually curated images by medical experts is both slow and utterly expensive. In this paper, we set out to explore whether expert knowledge is a strict requirement for the creation of annotated data sets on which machine learning can successfully be trained. To do so, we gauged the performance of three segmentation models, namely U-Net, Attention U-Net, and ENet, trained with different loss functions on expert and non-expert ground truth for cardiac cine–MRI segmentation. Evaluation was done with classic segmentation metrics (Dice index and Hausdorff distance) as well as clinical measurements, such as the ventricular ejection fractions and the myocardial mass. The results reveal that generalization performances of a segmentation neural network trained on non-expert ground truth data is, to all practical purposes, as good as that trained on expert ground truth data, particularly when the non-expert receives a decent level of training, highlighting an opportunity for the efficient and cost-effective creation of annotations for cardiac data sets.

Chemical Proportionality within Molecular Networks

2021 ◽  
Author(s):  
Daniel Petras ◽  
Andrés Mauricio Caraballo-Rodríguez ◽  
Alan K. Jarmusch ◽  
Carlos Molina-Santiago ◽  
Julia M. Gauglitz ◽  
...  
Keyword(s):  
Natural Products ◽  
Ground Truth ◽  
Mass Spectrometry Data ◽  
Molecular Networks ◽  
Data Series ◽  
Sequential Data ◽  
Chemical Transformations ◽  
Data Set ◽  
Molecular Networking ◽  
Ground Truth Data

Molecular networking of non-targeted tandem mass spectrometry data connects structurally related molecules based on similar fragmentation spectra. Here we report the Chemical Proportionality contextualization of molecular networks. ChemProp scores the changes of abundance between two connected nodes over sequential data series which can be displayed as a direction within the network to prioritize potential biological and chemical transformations or proportional changes of related compounds. We tested the ChemProp workflow on a ground truth data set of defined mixture and highlighted the utility of the tool to prioritize specific molecules within biological samples, including bacterial transformations of bile acids, human drug metabolism and bacterial natural products biosynthesis. The ChemProp workflow is freely available through the Global Natural Products Social Molecular Networking environment.<br><b> </b>

Abstract 20: Deep Learning-Based Automated Intracranial Hemorrhage Detection and Notification

Stroke ◽  
2020 ◽  
Vol 51 (Suppl_1) ◽  
Author(s):  
Benjamin Zahneisen ◽  
Matus Straka ◽  
Shalini Bammer ◽  
Greg Albers ◽  
Roland Bammer
Keyword(s):  
Deep Learning ◽  
Sensitivity And Specificity ◽  
Intracranial Hemorrhage ◽  
Health Care Professionals ◽  
Gold Standard ◽  
Ground Truth ◽  
Mobile App ◽  
Training Dataset ◽  
Convolutional Network ◽  
Ground Truth Data

Introduction: Ruling out hemorrhage (stroke or traumatic) prior to administration of thrombolytics is critical for Code Strokes. A triage software that identifies hemorrhages on head CTs and alerts radiologists would help to streamline patient care and increase diagnostic confidence and patient safety. ML approach: We trained a deep convolutional network with a hybrid 3D/2D architecture on unenhanced head CTs of 805 patients. Our training dataset comprised 348 positive hemorrhage cases (IPH=245, SAH=67, Sub/Epi-dural=70, IVH=83) (128 female) and 457 normal controls (217 female). Lesion outlines were drawn by experts and stored as binary masks that were used as ground truth data during the training phase (random 80/20 train/test split). Diagnostic sensitivity and specificity were defined on a per patient study level, i.e. a single, binary decision for presence/absence of a hemorrhage on a patient’s CT scan. Final validation was performed in 380 patients (167 positive). Tool: The hemorrhage detection module was prototyped in Python/Keras. It runs on a local LINUX server (4 CPUs, no GPUs) and is embedded in a larger image processing platform dedicated to stroke. Results: Processing time for a standard whole brain CT study (3-5mm slices) was around 2min. Upon completion, an instant notification (by email and/or mobile app) was sent to users to alert them about the suspected presence of a hemorrhage. Relative to neuroradiologist gold standard reads the algorithm’s sensitivity and specificity is 90.4% and 92.5% (95% CI: 85%-94% for both). Detection of acute intracranial hemorrhage can be automatized by deploying deep learning. It yielded very high sensitivity/specificity when compared to gold standard reads by a neuroradiologist. Volumes as small as 0.5mL could be detected reliably in the test dataset. The software can be deployed in busy practices to prioritize worklists and alert health care professionals to speed up therapeutic decision processes and interventions.

scholarly journals Deep learning algorithms out-perform veterinary pathologists in detecting the mitotically most active tumor region

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Marc Aubreville ◽  
Christof A. Bertram ◽  
Christian Marzahl ◽  
Corinne Gurtner ◽  
Martina Dettwiler ◽  
...  
Keyword(s):  
Deep Learning ◽  
Ground Truth ◽  
Mitotic Count ◽  
Mitotic Figure ◽  
Two Stage ◽  
Data Set ◽  
Area Selection ◽  
Tumor Region ◽  
Cutaneous Mast Cell ◽  
Mitotic Figures

Abstract Manual count of mitotic figures, which is determined in the tumor region with the highest mitotic activity, is a key parameter of most tumor grading schemes. It can be, however, strongly dependent on the area selection due to uneven mitotic figure distribution in the tumor section. We aimed to assess the question, how significantly the area selection could impact the mitotic count, which has a known high inter-rater disagreement. On a data set of 32 whole slide images of H&E-stained canine cutaneous mast cell tumor, fully annotated for mitotic figures, we asked eight veterinary pathologists (five board-certified, three in training) to select a field of interest for the mitotic count. To assess the potential difference on the mitotic count, we compared the mitotic count of the selected regions to the overall distribution on the slide. Additionally, we evaluated three deep learning-based methods for the assessment of highest mitotic density: In one approach, the model would directly try to predict the mitotic count for the presented image patches as a regression task. The second method aims at deriving a segmentation mask for mitotic figures, which is then used to obtain a mitotic density. Finally, we evaluated a two-stage object-detection pipeline based on state-of-the-art architectures to identify individual mitotic figures. We found that the predictions by all models were, on average, better than those of the experts. The two-stage object detector performed best and outperformed most of the human pathologists on the majority of tumor cases. The correlation between the predicted and the ground truth mitotic count was also best for this approach (0.963–0.979). Further, we found considerable differences in position selection between pathologists, which could partially explain the high variance that has been reported for the manual mitotic count. To achieve better inter-rater agreement, we propose to use a computer-based area selection for support of the pathologist in the manual mitotic count.

Ground-truth uncertainty-aware metrics for machine learning applications on seismic image interpretation: Application to faults and horizon extraction

2020 ◽  
Vol 39 (10) ◽  
pp. 734-741
Author(s):  
Sébastien Guillon ◽  
Frédéric Joncour ◽  
Pierre-Emmanuel Barrallon ◽  
Laurent Castanié
Keyword(s):  
Deep Learning ◽  
Image Interpretation ◽  
Ground Truth ◽  
Learning Model ◽  
Seismic Interpretation ◽  
Data Set ◽  
Seismic Image ◽  
Machine Learning Applications ◽  
Deep Learning Model

We propose new metrics to measure the performance of a deep learning model applied to seismic interpretation tasks such as fault and horizon extraction. Faults and horizons are thin geologic boundaries (1 pixel thick on the image) for which a small prediction error could lead to inappropriately large variations in common metrics (precision, recall, and intersection over union). Through two examples, we show how classical metrics could fail to indicate the true quality of fault or horizon extraction. Measuring the accuracy of reconstruction of thin objects or boundaries requires introducing a tolerance distance between ground truth and prediction images to manage the uncertainties inherent in their delineation. We therefore adapt our metrics by introducing a tolerance function and illustrate their ability to manage uncertainties in seismic interpretation. We compare classical and new metrics through different examples and demonstrate the robustness of our metrics. Finally, we show on a 3D West African data set how our metrics are used to tune an optimal deep learning model.

Deep learning-driven velocity model building workflow

2019 ◽  
Vol 38 (11) ◽  
pp. 872a1-872a9 ◽  
Author(s):  
Mauricio Araya-Polo ◽  
Stuart Farris ◽  
Manuel Florez
Keyword(s):  
Deep Learning ◽  
Seismic Data ◽  
Model Building ◽  
Ground Truth ◽  
Velocity Model ◽  
Training Data ◽  
Quality Data ◽  
Generative Adversarial Network ◽  
Data Set ◽  
Velocity Models

Exploration seismic data are heavily manipulated before human interpreters are able to extract meaningful information regarding subsurface structures. This manipulation adds modeling and human biases and is limited by methodological shortcomings. Alternatively, using seismic data directly is becoming possible thanks to deep learning (DL) techniques. A DL-based workflow is introduced that uses analog velocity models and realistic raw seismic waveforms as input and produces subsurface velocity models as output. When insufficient data are used for training, DL algorithms tend to overfit or fail. Gathering large amounts of labeled and standardized seismic data sets is not straightforward. This shortage of quality data is addressed by building a generative adversarial network (GAN) to augment the original training data set, which is then used by DL-driven seismic tomography as input. The DL tomographic operator predicts velocity models with high statistical and structural accuracy after being trained with GAN-generated velocity models. Beyond the field of exploration geophysics, the use of machine learning in earth science is challenged by the lack of labeled data or properly interpreted ground truth, since we seldom know what truly exists beneath the earth's surface. The unsupervised approach (using GANs to generate labeled data)illustrates a way to mitigate this problem and opens geology, geophysics, and planetary sciences to more DL applications.

scholarly journals DeepFRET: Rapid and automated single molecule FRET data classification using deep learning

2020 ◽  
Author(s):  
Johannes Thomsen ◽  
Magnus B. Sletfjerding ◽  
Stefano Stella ◽  
Bijoya Paul ◽  
Simon Bo Jensen ◽  
...  
Keyword(s):  
Deep Learning ◽  
Structural Biology ◽  
Single Molecule ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Ground Truth ◽  
Real Data ◽  
Ground Truth Data ◽  
Single Molecule Fret ◽  
Human Operators

AbstractSingle molecule Förster Resonance energy transfer (smFRET) is a mature and adaptable method for studying the structure of biomolecules and integrating their dynamics into structural biology. The development of high throughput methodologies and the growth of commercial instrumentation have outpaced the development of rapid, standardized, and fully automated methodologies to objectively analyze the wealth of produced data. Here we present DeepFRET, an automated standalone solution based on deep learning, where the only crucial human intervention in transiting from raw microscope images to histogram of biomolecule behavior, is a user-adjustable quality threshold. Integrating all standard features of smFRET analysis, DeepFRET will consequently output common kinetic information metrics for biomolecules. We validated the utility of DeepFRET by performing quantitative analysis on simulated, ground truth, data and real smFRET data. The accuracy of classification by DeepFRET outperformed human operators and current commonly used hard threshold and reached >95% precision accuracy only requiring a fraction of the time (<1% as compared to human operators) on ground truth data. Its flawless and rapid operation on real data demonstrates its wide applicability. This level of classification was achieved without any preprocessing or parameter setting by human operators, demonstrating DeepFRET’s capacity to objectively quantify biomolecular dynamics. The provided a standalone executable based on open source code capitalises on the widespread adaptation of machine learning and may contribute to the effort of benchmarking smFRET for structural biology insights.

scholarly journals Terrestrial Laser Scanning and Ground Truth Data for Characterizing Downed Dead Wood

2020 ◽  
Author(s):  
Tuomas Yrttimaa ◽  
Ninni Saarinen ◽  
Ville Luoma ◽  
Topi Tanhuanpää ◽  
Ville Kankare ◽  
...  
Keyword(s):  
Boreal Forests ◽  
Laser Scanning ◽  
Dead Wood ◽  
Terrestrial Laser Scanning ◽  
Ground Truth ◽  
Point Clouds ◽  
Data Set ◽  
Ground Truth Data ◽  
Standing Trees ◽  
Downed Dead Wood

The feasibility of terrestrial laser scanning (TLS) in characterizing standing trees has been frequently investigated, while less effort has been put in quantifying downed dead wood using TLS. To advance dead wood characterization using TLS, we collected TLS point clouds and downed dead wood information from 20 sample plots (32 m x 32 m in size) located in southern Finland. This data set can be used in developing new algorithms for downed dead wood detection and characterization as well as for understanding spatial patterns of downed dead wood in boreal forests.

scholarly journals Assignment Flow for Order-Constrained OCT Segmentation

2021 ◽  
Author(s):  
Dmitrij Sitenko ◽  
Bastian Boll ◽  
Christoph Schnörr
Keyword(s):  
Geometric Approach ◽  
Ground Truth ◽  
Retinal Cell ◽  
Dice Similarity Coefficient ◽  
Retinal Layer ◽  
Healthy Human ◽  
Data Set ◽  
Ground Truth Data ◽  
Global Shape ◽  
Layer Segmentation

AbstractAt the present time optical coherence tomography (OCT) is among the most commonly used non-invasive imaging methods for the acquisition of large volumetric scans of human retinal tissues and vasculature. The substantial increase of accessible highly resolved 3D samples at the optic nerve head and the macula is directly linked to medical advancements in early detection of eye diseases. To resolve decisive information from extracted OCT volumes and to make it applicable for further diagnostic analysis, the exact measurement of retinal layer thicknesses serves as an essential task be done for each patient separately. However, manual examination of OCT scans is a demanding and time consuming task, which is typically made difficult by the presence of tissue-dependent speckle noise. Therefore, the elaboration of automated segmentation models has become an important task in the field of medical image processing. We propose a novel, purely data driven geometric approach to order-constrained 3D OCT retinal cell layer segmentation which takes as input data in any metric space and can be implemented using only simple, highly parallelizable operations. As opposed to many established retinal layer segmentation methods, we use only locally extracted features as input and do not employ any global shape prior. The physiological order of retinal cell layers and membranes is achieved through the introduction of a smoothed energy term. This is combined with additional regularization of local smoothness to yield highly accurate 3D segmentations. The approach thereby systematically avoid bias pertaining to global shape and is hence suited for the detection of anatomical changes of retinal tissue structure. To demonstrate its robustness, we compare two different choices of features on a data set of manually annotated 3D OCT volumes of healthy human retina. The quality of computed segmentations is compared to the state of the art in automatic retinal layer segmention as well as to manually annotated ground truth data in terms of mean absolute error and Dice similarity coefficient. Visualizations of segmented volumes are also provided.

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