Anatomy segmentation evaluation with sparse ground truth data

2020 ◽  
Author(s):  
Jieyu Li ◽  
Jayaram K. Udupa ◽  
Yubing Tong ◽  
Lisheng Wang ◽  
Drew A. Torigian
Keyword(s):  
Ground Truth ◽  
Segmentation Evaluation ◽  
Ground Truth Data

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.

Segmentation evaluation with sparse ground truth data: Simulating true segmentations as perfect/imperfect as those generated by humans

2021 ◽  
Vol 69 ◽  
pp. 101980
Author(s):  
Jieyu Li ◽  
Jayaram K. Udupa ◽  
Yubing Tong ◽  
Lisheng Wang ◽  
Drew A. Torigian
Keyword(s):  
Ground Truth ◽  
Segmentation Evaluation ◽  
Ground Truth Data

scholarly journals Assessing Wildfire Burn Severity and Its Relationship with Environmental Factors: A Case Study in Interior Alaska Boreal Forest

2021 ◽  
Vol 13 (10) ◽  
pp. 1966
Author(s):  
Christopher W Smith ◽  
Santosh K Panda ◽  
Uma S Bhatt ◽  
Franz J Meyer ◽  
Anushree Badola ◽  
...  
Keyword(s):  
Boreal Forest ◽  
Ground Truth ◽  
Burn Severity ◽  
Classification Methods ◽  
Spectral Indices ◽  
Ground Truth Data ◽  
Burn Scar ◽  
Interior Alaska ◽  
Remote Sensing Methods ◽  
The Relationship

In recent years, there have been rapid improvements in both remote sensing methods and satellite image availability that have the potential to massively improve burn severity assessments of the Alaskan boreal forest. In this study, we utilized recent pre- and post-fire Sentinel-2 satellite imagery of the 2019 Nugget Creek and Shovel Creek burn scars located in Interior Alaska to both assess burn severity across the burn scars and test the effectiveness of several remote sensing methods for generating accurate map products: Normalized Difference Vegetation Index (NDVI), Normalized Burn Ratio (NBR), and Random Forest (RF) and Support Vector Machine (SVM) supervised classification. We used 52 Composite Burn Index (CBI) plots from the Shovel Creek burn scar and 28 from the Nugget Creek burn scar for training classifiers and product validation. For the Shovel Creek burn scar, the RF and SVM machine learning (ML) classification methods outperformed the traditional spectral indices that use linear regression to separate burn severity classes (RF and SVM accuracy, 83.33%, versus NBR accuracy, 73.08%). However, for the Nugget Creek burn scar, the NDVI product (accuracy: 96%) outperformed the other indices and ML classifiers. In this study, we demonstrated that when sufficient ground truth data is available, the ML classifiers can be very effective for reliable mapping of burn severity in the Alaskan boreal forest. Since the performance of ML classifiers are dependent on the quantity of ground truth data, when sufficient ground truth data is available, the ML classification methods would be better at assessing burn severity, whereas with limited ground truth data the traditional spectral indices would be better suited. We also looked at the relationship between burn severity, fuel type, and topography (aspect and slope) and found that the relationship is site-dependent.

scholarly journals Automatic Evaluation of Wheat Resistance to Fusarium Head Blight Using Dual Mask-RCNN Deep Learning Frameworks in Computer Vision

2020 ◽  
Vol 13 (1) ◽  
pp. 26
Author(s):  
Wen-Hao Su ◽  
Jiajing Zhang ◽  
Ce Yang ◽  
Rae Page ◽  
Tamas Szinyei ◽  
...  
Keyword(s):  
Fusarium Head Blight ◽  
Ground Truth ◽  
Wheat Breeding ◽  
Head Blight ◽  
Detection Rates ◽  
Ground Truth Data ◽  
Resistant Cultivars ◽  
Feature Pyramid ◽  
Rater Error ◽  
Wheat Lines

In many regions of the world, wheat is vulnerable to severe yield and quality losses from the fungus disease of Fusarium head blight (FHB). The development of resistant cultivars is one means of ameliorating the devastating effects of this disease, but the breeding process requires the evaluation of hundreds of lines each year for reaction to the disease. These field evaluations are laborious, expensive, time-consuming, and are prone to rater error. A phenotyping cart that can quickly capture images of the spikes of wheat lines and their level of FHB infection would greatly benefit wheat breeding programs. In this study, mask region convolutional neural network (Mask-RCNN) allowed for reliable identification of the symptom location and the disease severity of wheat spikes. Within a wheat line planted in the field, color images of individual wheat spikes and their corresponding diseased areas were labeled and segmented into sub-images. Images with annotated spikes and sub-images of individual spikes with labeled diseased areas were used as ground truth data to train Mask-RCNN models for automatic image segmentation of wheat spikes and FHB diseased areas, respectively. The feature pyramid network (FPN) based on ResNet-101 network was used as the backbone of Mask-RCNN for constructing the feature pyramid and extracting features. After generating mask images of wheat spikes from full-size images, Mask-RCNN was performed to predict diseased areas on each individual spike. This protocol enabled the rapid recognition of wheat spikes and diseased areas with the detection rates of 77.76% and 98.81%, respectively. The prediction accuracy of 77.19% was achieved by calculating the ratio of the wheat FHB severity value of prediction over ground truth. This study demonstrates the feasibility of rapidly determining levels of FHB in wheat spikes, which will greatly facilitate the breeding of resistant cultivars.

scholarly journals Classification of Cattle Behaviours Using Neck-Mounted Accelerometer-Equipped Collars and Convolutional Neural Networks

Sensors ◽  
2021 ◽  
Vol 21 (12) ◽  
pp. 4050
Author(s):  
Dejan Pavlovic ◽  
Christopher Davison ◽  
Andrew Hamilton ◽  
Oskar Marko ◽  
Robert Atkinson ◽  
...  
Keyword(s):  
Neural Network ◽  
Model Performance ◽  
Ground Truth ◽  
Practical Implementation ◽  
Ground Truth Data ◽  
Battery Lifetime ◽  
Implementation Challenges ◽  
Memory Footprint ◽  
Commercial Farms ◽  
Using Data

Monitoring cattle behaviour is core to the early detection of health and welfare issues and to optimise the fertility of large herds. Accelerometer-based sensor systems that provide activity profiles are now used extensively on commercial farms and have evolved to identify behaviours such as the time spent ruminating and eating at an individual animal level. Acquiring this information at scale is central to informing on-farm management decisions. The paper presents the development of a Convolutional Neural Network (CNN) that classifies cattle behavioural states (`rumination’, `eating’ and `other’) using data generated from neck-mounted accelerometer collars. During three farm trials in the United Kingdom (Easter Howgate Farm, Edinburgh, UK), 18 steers were monitored to provide raw acceleration measurements, with ground truth data provided by muzzle-mounted pressure sensor halters. A range of neural network architectures are explored and rigorous hyper-parameter searches are performed to optimise the network. The computational complexity and memory footprint of CNN models are not readily compatible with deployment on low-power processors which are both memory and energy constrained. Thus, progressive reductions of the CNN were executed with minimal loss of performance in order to address the practical implementation challenges, defining the trade-off between model performance versus computation complexity and memory footprint to permit deployment on micro-controller architectures. The proposed methodology achieves a compression of 14.30 compared to the unpruned architecture but is nevertheless able to accurately classify cattle behaviours with an overall F1 score of 0.82 for both FP32 and FP16 precision while achieving a reasonable battery lifetime in excess of 5.7 years.

A machine learning approach to estimate the strain energy absorption in expanded polystyrene foams

2021 ◽  
pp. 0021955X2110210
Author(s):  
Alejandro E Rodríguez-Sánchez ◽  
Héctor Plascencia-Mora
Keyword(s):  
Neural Network ◽  
Energy Absorption ◽  
Mechanical Energy ◽  
Compressive Loading ◽  
Ground Truth ◽  
Expanded Polystyrene ◽  
Polystyrene Foam ◽  
Stress Strain ◽  
Ground Truth Data ◽  
Expanded Polystyrene Foam

Traditional modeling of mechanical energy absorption due to compressive loadings in expanded polystyrene foams involves mathematical descriptions that are derived from stress/strain continuum mechanics models. Nevertheless, most of those models are either constrained using the strain as the only variable to work at large deformation regimes and usually neglect important parameters for energy absorption properties such as the material density or the rate of the applying load. This work presents a neural-network-based approach that produces models that are capable to map the compressive stress response and energy absorption parameters of an expanded polystyrene foam by considering its deformation, compressive loading rates, and different densities. The models are trained with ground-truth data obtained in compressive tests. Two methods to select neural network architectures are also presented, one of which is based on a Design of Experiments strategy. The results show that it is possible to obtain a single artificial neural networks model that can abstract stress and energy absorption solution spaces for the conditions studied in the material. Additionally, such a model is compared with a phenomenological model, and the results show than the neural network model outperforms it in terms of prediction capabilities, since errors around 2% of experimental data were obtained. In this sense, it is demonstrated that by following the presented approach is possible to obtain a model capable to reproduce compressive polystyrene foam stress/strain data, and consequently, to simulate its energy absorption parameters.

scholarly journals Multi-Temporal Arable Land Monitoring in Arid Region of Northwest China Using a New Extraction Index

2021 ◽  
Vol 13 (9) ◽  
pp. 5274
Author(s):  
Xinyang Yu ◽  
Younggu Her ◽  
Xicun Zhu ◽  
Changhe Lu ◽  
Xuefei Li
Keyword(s):  
Arable Land ◽  
Ground Truth ◽  
Northwest China ◽  
Hexi Corridor ◽  
Ground Truth Data ◽  
Land Protection ◽  
Promising Tool ◽  
Study Results ◽  
Multi Temporal ◽  
The Mean

Development of a high-accuracy method to extract arable land using effective data sources is crucial to detect and monitor arable land dynamics, servicing land protection and sustainable development. In this study, a new arable land extraction index (ALEI) based on spectral analysis was proposed, examined by ground truth data, and then applied to the Hexi Corridor in northwest China. The arable land and its change patterns during 1990–2020 were extracted and identified using 40 Landsat TM/OLI images acquired in 1990, 2000, 2010, and 2020. The results demonstrated that the proposed method can distinguish arable land areas accurately, with the User’s (Producer’s) accuracy and overall accuracy (kappa coefficient) exceeding 0.90 (0.88) and 0.89 (0.87), respectively. The mean relative error calculated using field survey data obtained in 2012 and 2020 was 0.169 and 0.191, respectively, indicating the feasibility of the ALEI method in arable land extracting. The study found that arable land area in the Hexi Corridor was 13217.58 km2 in 2020, significantly increased by 25.33% compared to that in 1990. At 10-year intervals, the arable land experienced different change patterns. The study results indicate that ALEI index is a promising tool used to effectively extract arable land in the arid area.

scholarly journals Detection of heat pumps from smart meter and open data

2020 ◽  
Vol 3 (S1) ◽  
Author(s):  
Andreas Weigert ◽  
Konstantin Hopf ◽  
Nicolai Weinig ◽  
Thorsten Staake
Keyword(s):  
Heat Pump ◽  
Open Data ◽  
Ground Truth ◽  
Heat Pumps ◽  
Geographical Information ◽  
Weather Data ◽  
Smart Meters ◽  
Ground Truth Data ◽  
Thermal Reservoir ◽  
Grid Operators

Abstract Heat pumps embody solutions that heat or cool buildings effectively and sustainably, with zero emissions at the place of installation. As they pose significant load on the power grid, knowledge on their existence is crucial for grid operators, e.g., to forecast load and to plan grid operation. Further details, like the thermal reservoir (ground or air source) or the age of a heat pump installation renders energy-related services possible that utility companies can offer in the future (e.g., detecting wrongly calibrated installations, household energy efficiency checks). This study investigates the prediction of heat pump installations, their thermal reservoir and age. For this, we obtained a dataset with 397 households in Switzerland, all equipped with smart meters, collected ground truth data on installed heat pumps and enriched this data with weather data and geographical information. Our investigation replicates the state of the art in the area of heat pump detection and goes beyond it, as we obtain three major findings: First, machine learning can detect the existence of heat pumps with an AUC performance metric of 0.82, their heat reservoir with an AUC of 0.86, and their age with an AUC of 0.73. Second, heat pump existence can be better detected using data during the heating period than during summer. Third the number of training samples to detect the existence of heat pumps must not be necessarily large in terms of the number of training instances and observation period.

scholarly journals WattScale

2021 ◽  
Vol 2 (1) ◽  
pp. 1-25
Author(s):  
Srinivasan Iyengar ◽  
Stephen Lee ◽  
David Irwin ◽  
Prashant Shenoy ◽  
Benjamin Weil
Keyword(s):  
Cooling System ◽  
Large Population ◽  
Ground Truth ◽  
Detection Algorithm ◽  
Building Envelope ◽  
Ground Truth Data ◽  
Heating And Cooling ◽  
Data Driven Approach ◽  
Execution Mode ◽  
The Individual

Buildings consume over 40% of the total energy in modern societies, and improving their energy efficiency can significantly reduce our energy footprint. In this article, we present WattScale, a data-driven approach to identify the least energy-efficient buildings from a large population of buildings in a city or a region. Unlike previous methods such as least-squares that use point estimates, WattScale uses Bayesian inference to capture the stochasticity in the daily energy usage by estimating the distribution of parameters that affect a building. Further, it compares them with similar homes in a given population. WattScale also incorporates a fault detection algorithm to identify the underlying causes of energy inefficiency. We validate our approach using ground truth data from different geographical locations, which showcases its applicability in various settings. WattScale has two execution modes—(i) individual and (ii) region-based, which we highlight using two case studies. For the individual execution mode, we present results from a city containing >10,000 buildings and show that more than half of the buildings are inefficient in one way or another indicating a significant potential from energy improvement measures. Additionally, we provide probable cause of inefficiency and find that 41%, 23.73%, and 0.51% homes have poor building envelope, heating, and cooling system faults, respectively. For the region-based execution mode, we show that WattScale can be extended to millions of homes in the U.S. due to the recent availability of representative energy datasets.

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