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Saiwaeo S, Arwatchananukul S, Mungmai L, Preedalikit W, Aunsri N. Human skin type classification using image processing and deep learning approaches. Heliyon 2023; 9:e21176. [PMID: 38027689 PMCID: PMC10656243 DOI: 10.1016/j.heliyon.2023.e21176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 10/11/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
Cosmetics consumers need to be aware of their skin type before purchasing products. Identifying skin types can be challenging, especially when they vary from oily to dry in different areas, with skin specialist providing more accurate results. In recent years, artificial intelligence and machine learning have been utilized across various fields, including medicine, to assist in identifying and predicting situations. This study developed a skin type classification model using a Convolutional Neural Networks (CNN) deep learning algorithms. The dataset consisted of normal, oily, and dry skin images, with 112 images for normal skin, 120 images for oily skin, and 97 images for dry skin. Image quality was enhanced using the Contrast Limited Adaptive Histogram Equalization (CLAHE) technique, with data augmentation by rotation applied to increase dataset variety, resulting in a total of 1,316 images. CNN architectures including MobileNet-V2, EfficientNet-V2, InceptionV2, and ResNet-V1 were optimized and evaluated. Findings showed that the EfficientNet-V2 architecture performed the best, achieving an accuracy of 91.55% with average loss of 22.74%. To further improve the model, hyperparameter tuning was conducted, resulting in an accuracy of 94.57% and a loss of 13.77%. The Model performance was validated using 10-fold cross-validation and tested on unseen data, achieving an accuracy of 89.70% with a loss of 21.68%.
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Affiliation(s)
- Sirawit Saiwaeo
- School of Information Technology, Mae Fah Luang University, Chiang Rai, Thailand
| | - Sujitra Arwatchananukul
- School of Information Technology, Mae Fah Luang University, Chiang Rai, Thailand
- Integrated AgriTech Ecosystem Research Group (IATE), Mae Fah Luang University, Chiang Rai, Thailand
| | - Lapatrada Mungmai
- Division of Cosmetic Science, School of Pharmaceutical Sciences, University of Phayao, Phayao, Thailand
- Research and Innovation Center in Cosmetic Sciences and Natural products, Division of Cosmetic Sciences, School of Pharmaceutical Sciences, University of Phayao, Phayao, Thailand
| | - Weeraya Preedalikit
- Division of Cosmetic Science, School of Pharmaceutical Sciences, University of Phayao, Phayao, Thailand
- Research and Innovation Center in Cosmetic Sciences and Natural products, Division of Cosmetic Sciences, School of Pharmaceutical Sciences, University of Phayao, Phayao, Thailand
| | - Nattapol Aunsri
- School of Information Technology, Mae Fah Luang University, Chiang Rai, Thailand
- Integrated AgriTech Ecosystem Research Group (IATE), Mae Fah Luang University, Chiang Rai, Thailand
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Alrumiah SS, Alrebdi N, Ibrahim DM. Augmenting healthy brain magnetic resonance images using generative adversarial networks. PeerJ Comput Sci 2023; 9:e1318. [PMID: 37346635 PMCID: PMC10280481 DOI: 10.7717/peerj-cs.1318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 03/09/2023] [Indexed: 06/23/2023]
Abstract
Machine learning applications in the medical sector face a lack of medical data due to privacy issues. For instance, brain tumor image-based classification suffers from the lack of brain images. The lack of such images produces some classification problems, i.e., class imbalance issues which can cause a bias toward one class over the others. This study aims to solve the imbalance problem of the "no tumor" class in the publicly available brain magnetic resonance imaging (MRI) dataset. Generative adversarial network (GAN)-based augmentation techniques were used to solve the imbalance classification problem. Specifically, deep convolutional GAN (DCGAN) and single GAN (SinGAN). Moreover, the traditional-based augmentation techniques were implemented using the rotation method. Thus, several VGG16 classification experiments were conducted, including (i) the original dataset, (ii) the DCGAN-based dataset, (iii) the SinGAN-based dataset, (iv) a combination of the DCGAN and SinGAN dataset, and (v) the rotation-based dataset. However, the results show that the original dataset achieved the highest accuracy, 73%. Additionally, SinGAN outperformed DCGAN by a significant margin of 4%. In contrast, experimenting with the non-augmented original dataset resulted in the highest classification loss value, which explains the effect of the imbalance issue. These results provide a general view of the effect of different image augmentation techniques on enlarging the healthy brain dataset.
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Affiliation(s)
- Sarah S. Alrumiah
- Department of Information Technology, College of Computer, Qassim University, Buraydah, Saudi Arabia
| | - Norah Alrebdi
- Department of Information Technology, College of Computer, Qassim University, Buraydah, Saudi Arabia
| | - Dina M. Ibrahim
- Department of Information Technology, College of Computer, Qassim University, Buraydah, Saudi Arabia
- Department of Computers and Control Engineering, Faculty of Engineering, Tanta University, Tanta, Egypt
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Dhawan K, R SP, R. K. N. Identification of traffic signs for advanced driving assistance systems in smart cities using deep learning. Multimed Tools Appl 2023; 82:1-16. [PMID: 37362733 PMCID: PMC9985491 DOI: 10.1007/s11042-023-14823-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 06/22/2022] [Accepted: 02/06/2023] [Indexed: 06/28/2023]
Abstract
The ability of Advanced Driving Assistance Systems (ADAS) is to identify and understand all objects around the vehicle under varying driving conditions and environmental factors is critical. Today's vehicles are equipped with advanced driving assistance systems that make driving safer and more comfortable. A camera mounted on the car helps the system recognise and detect traffic signs and alerts the driver about various road conditions, like if construction work is ahead or if speed limits have changed. The goal is to identify the traffic sign and process the image in a minimal processing time. A custom convolutional neural network model is used to classify the traffic signs with higher accuracy than the existing models. Image augmentation techniques are used to expand the dataset artificially, and that allows one to learn how the image looks from different perspectives, such as when viewed from different angles or when it looks blurry due to poor weather conditions. The algorithms used to detect traffic signs are YOLO v3 and YOLO v4-tiny. The proposed solution for detecting a specific set of traffic signs performed well, with an accuracy rate of 95.85%.
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Affiliation(s)
- Kshitij Dhawan
- School of Computer Science and Engineering, Vellore Institute of Technology, Vellore, 632014 Tamilnadu India
| | - Srinivasa Perumal R
- School of Information Technology and Engineering, Vellore Institute of Technology, Vellore, 632014 Tamilnadu India
| | - Nadesh R. K.
- School of Information Technology and Engineering, Vellore Institute of Technology, Vellore, 632014 Tamilnadu India
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Patro KK, Allam JP, Hammad M, Tadeusiewicz R, Pławiak P. SCovNet: A skip connection-based feature union deep learning technique with statistical approach analysis for the detection of COVID-19. Biocybern Biomed Eng 2023; 43:352-368. [PMID: 36819118 PMCID: PMC9928742 DOI: 10.1016/j.bbe.2023.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/21/2022] [Accepted: 01/30/2023] [Indexed: 02/17/2023]
Abstract
Background and Objective The global population has been heavily impacted by the COVID-19 pandemic of coronavirus. Infections are spreading quickly around the world, and new spikes (Delta, Delta Plus, and Omicron) are still being made. The real-time reverse transcription-polymerase chain reaction (RT-PCR) is the method most often used to find viral RNA in a nasopharyngeal swab. However, these diagnostic approaches require human involvement and consume more time per prediction. Moreover, the existing conventional test mainly suffers from false negatives, so there is a chance for the virus to spread quickly. Therefore, a rapid and early diagnosis of COVID-19 patients is needed to overcome these problems. Methods Existing approaches based on deep learning for COVID detection are suffering from unbalanced datasets, poor performance, and gradient vanishing problems. A customized skip connection-based network with a feature union approach has been developed in this work to overcome some of the issues mentioned above. Gradient information from chest X-ray (CXR) images to subsequent layers is bypassed through skip connections. In the script's title, "SCovNet" refers to a skip-connection-based feature union network for detecting COVID-19 in a short notation. The performance of the proposed model was tested with two publicly available CXR image databases, including balanced and unbalanced datasets. Results A modified skip connection-based CNN model was suggested for a small unbalanced dataset (Kaggle) and achieved remarkable performance. In addition, the proposed model was also tested with a large GitHub database of CXR images and obtained an overall best accuracy of 98.67% with an impressive low false-negative rate of 0.0074. Conclusions The results of the experiments show that the proposed method works better than current methods at finding early signs of COVID-19. As an additional point of interest, we must mention the innovative hierarchical classification strategy provided for this work, which considered both balanced and unbalanced datasets to get the best COVID-19 identification rate.
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Affiliation(s)
- Kiran Kumar Patro
- Department of ECE, Aditya Institute of Technology and Management, Tekkali AP-532201, India
| | - Jaya Prakash Allam
- Department of EC, National Institute of Technology Rourkela, Rourkela, Odisha 769008, India
| | - Mohamed Hammad
- Information Technology Dept., Faculty of Computers and Information, Menoufia University, Menoufia, Egypt
| | - Ryszard Tadeusiewicz
- Department of Biocybernetics and Biomedical Engineering, AGH University of Science and Technology, Krakow, Poland
| | - Paweł Pławiak
- Department of Computer Science, Faculty of Computer Science and Telecommunications, Cracow University of Technology, Warszawska 24, 31-155 Krakow, Poland
- Institute of Theoretical and Applied Informatics, Polish Academy of Sciences, Bałtycka 5, 44-100 Gliwice, Poland
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Tang Z, Duan J, Sun Y, Zeng Y, Zhang Y, Yao X. A combined deformable model and medical transformer algorithm for medical image segmentation. Med Biol Eng Comput 2023; 61:129-137. [PMID: 36323981 PMCID: PMC9816223 DOI: 10.1007/s11517-022-02702-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 10/19/2022] [Indexed: 01/07/2023]
Abstract
Deep learning-based segmentation models usually require substantial data, and the model usually suffers from poor generalization due to the lack of training data and inefficient network structure. We proposed to combine the deformable model and medical transformer neural network on the image segmentation task to alleviate the aforementioned problems. The proposed method first employs a statistical shape model to generate simulated contours of the target object, and then the thin plate spline is applied to create a realistic texture. Finally, a medical transformer network was constructed to segment three types of medical images, including prostate MR image, heart US image, and tongue color images. The segmentation accuracy of the three tasks achieved 89.97%, 91.90%, and 94.25%, respectively. The experimental results show that the proposed method improves medical image segmentation performance.
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Affiliation(s)
- Zhixian Tang
- grid.507037.60000 0004 1764 1277College of Medical Imaging, Shanghai University of Medicine & Health Sciences, Shanghai, 201318 China ,grid.507037.60000 0004 1764 1277Radiology Department, Shanghai University of Medicine & Health Sciences Affiliated Jiading Hospital, Shanghai, 201800 China
| | - Jintao Duan
- grid.507037.60000 0004 1764 1277College of Medical Instrumentation, Shanghai University of Medicine & Health Sciences, Shanghai, 201318 China
| | - Yanming Sun
- grid.507037.60000 0004 1764 1277College of Medical Instrumentation, Shanghai University of Medicine & Health Sciences, Shanghai, 201318 China
| | - Yanan Zeng
- grid.507037.60000 0004 1764 1277College of Medical Instrumentation, Shanghai University of Medicine & Health Sciences, Shanghai, 201318 China
| | - Yile Zhang
- grid.507037.60000 0004 1764 1277College of Medical Instrumentation, Shanghai University of Medicine & Health Sciences, Shanghai, 201318 China
| | - Xufeng Yao
- grid.507037.60000 0004 1764 1277College of Medical Imaging, Shanghai University of Medicine & Health Sciences, Shanghai, 201318 China
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Uryu H, Migita O, Ozawa M, Kamijo C, Aoto S, Okamura K, Hasegawa F, Okuyama T, Kosuga M, Hata K. Automated urinary sediment detection for Fabry disease using deep-learning algorithms. Mol Genet Metab Rep 2022; 33:100921. [PMID: 36186840 DOI: 10.1016/j.ymgmr.2022.100921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 11/24/2022] Open
Abstract
Fabry disease is a congenital lysosomal storage disease, and most of these cases develop organ damage in middle age. There are some promising therapeutic options for this disorder, which can stabilize the progression of the disease. However, a long delay in diagnosis prevents early intervention, resulting in treatment failure. Because Fabry disease is a rare disease, it is not well recognized and disease specific screening tests are rarely performed. Hence, a novel approach to for detecting patients with a widely practiced clinical test is crucial for the early detection of the disease. Recently, decision support systems based on artificial intelligence (AI) have been developed in many clinical fields. However, the construction of these models requires datasets from a large number of samples; this aspect is one of the main obstacles in AI-based approaches for rare diseases. In this study, with a novel image amplification method to construct the dataset for AI-model training, we built the deep neural-network model to detect Fabry cases from their urine samples. Sensitivity, specificity, and the AUC of the models on validation dataset were 0.902 (95% CI, 0.900–0.903), 0.977 (0.950–0.980), and 0.968 (0.964–0.972), respectively. This model could also extract disease-specific findings that are interpretable with human recognition. These results indicate that we can apply novel AI models for rare diseases based on this image amplification method we developed. We expect this approach could contribute to the diagnosis of Fabry disease. Synopsis This is the first reported AI-based decision support system to detect undiagnosed Fabry cases, and our new image amplification method will contribute to the AI models for other rare disorders.
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Key Words
- AI, artificial intelligence
- AUC, area under the curve
- AdHE, adaptive histogram equalization
- Artificial intelligence
- CNN, convolutional neural network
- CntStr, contrast stretching
- Deep learning
- ERT, enzyme replacement therapy
- Fabry disease
- Image augmentation
- InceptResNet, InceptionResNetV2
- Mulberry cells
- OrdHE, ordinary histogram equalization
- ROC, receiver operating characteristic
- Xcep, Xception
- alpha-Gal A, α- galactosidase A
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Fan J, Feng Y, Mo J, Wang S, Liang Q. Texture-less surface reconstruction using shape-based image augmentation. Comput Biol Med 2022; 150:106114. [PMID: 36179513 DOI: 10.1016/j.compbiomed.2022.106114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 09/09/2022] [Accepted: 09/17/2022] [Indexed: 11/24/2022]
Abstract
The development of intelligent Robot-Assisted Minimally Invasive Surgery demands geometric reconstruction from endoscopic images. However, images of human tissue surfaces are commonly texture-less. Obtaining the dense depth map of a texture-less scene is very difficult because traditional feature-based 3D reconstruction methods cannot detect enough features to build dense correspondences for depth computation. Given this problem, this study proposes a novel reconstruction method based on our shape-based image augmentation method. The main contribution of this method is the provision of a novel means to resolve the texture-less problem mainly on the input data level. In our method, we first calculate two shape gradient maps using Shape-From-Shading (SFS) method and we build Fast Point Feature Histogram (FPFH) 3D descriptor map according to the shape. Second, a series of augmented images can be computed by combining shape gradient maps, FPFH map, and the original image with different weights. Finally, we detect features on the new augmented images. Based on feature calculated sparse depth information and SFS calculated dense shape information, we further integrate a rectified dense depth map. Experiments show that our method can reconstruct texture-less surfaces with good accuracy.
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Affiliation(s)
- Jiacheng Fan
- School of Mechanical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, CN, 200240, China.
| | - Yuan Feng
- School of Mechanical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, CN, 200240, China
| | - Jinqiu Mo
- School of Mechanical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, CN, 200240, China
| | - Shigang Wang
- School of Mechanical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, CN, 200240, China
| | - Qinghua Liang
- School of Mechanical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, CN, 200240, China.
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Huang ML, Wu YS. A dataset of fortunella margarita images for object detection of deep learning based methods. Data Brief 2021; 38:107293. [PMID: 34466635 PMCID: PMC8385152 DOI: 10.1016/j.dib.2021.107293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/07/2021] [Accepted: 08/12/2021] [Indexed: 11/29/2022] Open
Abstract
Crops require appropriate planting techniques at different growth stages. Judgments on crop maturity affect the yield of crops. The planting and management of crops rely heavily on experienced farmers, which can reduce planting costs and increase yields. With the advancement of smart agriculture [1], images of crops can be used to accurately determine the growth stage of crops and estimate crop yields [2]. This can be combined with drones or smartphones to predict the growth stage and yield of Fortunella margarita for farmers in the future. This article presents an F. margarita image dataset. We classified F. margarita into three growth stages: mature, immature, and growing. In this dataset, an image may contain plants in several growth stages. The images were divided into seven categories according to growth stage. The dataset contains a total of 1031 original images. The total number of images was increased to 6611 through data augmentation. In addition, the dataset includes 6611 annotations with 7 categories of manually marked positions of F. margarita. Field images were captured in Jiaoxi, Yilan County, Taiwan, using smartphones. The dataset can serve as a resource for researchers who use different algorithms of machine learning or deep learning for object detection, image segmentation, and multiclass classification.
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Affiliation(s)
- Mei-Ling Huang
- Department of Industrial Engineering & Management, National Chin-Yi University of Technology, Taichung, Taiwan
| | - Yi-Shun Wu
- Department of Industrial Engineering & Management, National Chin-Yi University of Technology, Taichung, Taiwan
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Abstract
Deep learning proved its efficiency in many fields of computer science such as computer vision, image classifications, object detection, image segmentation, and more. Deep learning models primarily depend on the availability of huge datasets. Without the existence of many images in datasets, different deep learning models will not be able to learn and produce accurate models. Unfortunately, several fields don't have access to large amounts of evidence, such as medical image processing. For example. The world is suffering from the lack of COVID-19 virus datasets, and there is no benchmark dataset from the beginning of 2020. This pandemic was the main motivation of this survey to deliver and discuss the current image data augmentation techniques which can be used to increase the number of images. In this paper, a survey of data augmentation for digital images in deep learning will be presented. The study begins and with the introduction section, which reflects the importance of data augmentation in general. The classical image data augmentation taxonomy and photometric transformation will be presented in the second section. The third section will illustrate the deep learning image data augmentation. Finally, the fourth section will survey the state of the art of using image data augmentation techniques in the different deep learning research and application.
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Chen Q, Huang J, Salehi HS, Zhu H, Lian L, Lai X, Wei K. Hierarchical CNN-based occlusal surface morphology analysis for classifying posterior tooth type using augmented images from 3D dental surface models. Comput Methods Programs Biomed 2021; 208:106295. [PMID: 34329895 DOI: 10.1016/j.cmpb.2021.106295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 07/15/2021] [Indexed: 06/13/2023]
Abstract
OBJECTIVE 3D Digitization of dental model is growing in popularity for dental application. Classification of tooth type from single 3D point cloud model without assist of relative position among teeth is still a challenging task. METHODS In this paper, 8-class posterior tooth type classification (first premolar, second premolar, first molar, second molar in maxilla and mandible respectively) was investigated by convolutional neural network (CNN)-based occlusal surface morphology analysis. 3D occlusal surface was transformed to depth image for basic CNN-based classification. Considering the logical hierarchy of tooth categories, a hierarchical classification structure was proposed to decompose 8-class classification task into two-stage cascaded classification subtasks. Image augmentations including traditional geometrical transformation and deep convolutional generative adversarial networks (DCGANs) were applied for each subnetworks and cascaded network. RESULTS Results indicate that combing traditional and DCGAN-based augmented images to train CNN models can improve classification performance. In the paper, we achieve overall accuracy 91.35%, macro precision 91.49%, macro-recall 91.29%, and macro-F1 0.9139 for the 8-class posterior tooth type classification, which outperform other deep learning models. Meanwhile, Grad-cam results demonstrate that CNN model trained by our augmented images will focus on smaller important region for better generality. And anatomic landmarks of cusp, fossa, and groove work as important regions for cascaded classification model. CONCLUSION The reported work has proved that using basic CNN to construct two-stage hierarchical structure can achieve the best classification performance of posterior tooth type in 3D model without assistance of relative position information. The proposed method has advantages of easy training, great ability to learn discriminative features from small image region.
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Affiliation(s)
- Qingguang Chen
- School of Automation, Hangzhou Dianzi University, 310018, Hangzhou, China.
| | - Junchao Huang
- School of Automation, Hangzhou Dianzi University, 310018, Hangzhou, China
| | - Hassan S Salehi
- Department of Electrical and Computer Engineering, California State University, Chico, 95929, United States
| | - Haihua Zhu
- Hospital of Stomatology of Zhejiang University, Hangzhou, 310018, China
| | - Luya Lian
- Hospital of Stomatology of Zhejiang University, Hangzhou, 310018, China
| | - Xiaomin Lai
- School of Automation, Hangzhou Dianzi University, 310018, Hangzhou, China
| | - Kaihua Wei
- School of Automation, Hangzhou Dianzi University, 310018, Hangzhou, China
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McCombe KD, Craig SG, Viratham Pulsawatdi A, Quezada-Marín JI, Hagan M, Rajendran S, Humphries MP, Bingham V, Salto-Tellez M, Gault R, James JA. HistoClean: Open-source software for histological image pre-processing and augmentation to improve development of robust convolutional neural networks. Comput Struct Biotechnol J 2021; 19:4840-4853. [PMID: 34522291 PMCID: PMC8426467 DOI: 10.1016/j.csbj.2021.08.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/20/2021] [Accepted: 08/20/2021] [Indexed: 12/23/2022] Open
Abstract
The growth of digital pathology over the past decade has opened new research pathways and insights in cancer prediction and prognosis. In particular, there has been a surge in deep learning and computer vision techniques to analyse digital images. Common practice in this area is to use image pre-processing and augmentation to prevent bias and overfitting, creating a more robust deep learning model. This generally requires consultation of documentation for multiple coding libraries, as well as trial and error to ensure that the techniques used on the images are appropriate. Herein we introduce HistoClean; a user-friendly, graphical user interface that brings together multiple image processing modules into one easy to use toolkit. HistoClean is an application that aims to help bridge the knowledge gap between pathologists, biomedical scientists and computer scientists by providing transparent image augmentation and pre-processing techniques which can be applied without prior coding knowledge. In this study, we utilise HistoClean to pre-process images for a simple convolutional neural network used to detect stromal maturity, improving the accuracy of the model at a tile, region of interest, and patient level. This study demonstrates how HistoClean can be used to improve a standard deep learning workflow via classical image augmentation and pre-processing techniques, even with a relatively simple convolutional neural network architecture. HistoClean is free and open-source and can be downloaded from the Github repository here: https://github.com/HistoCleanQUB/HistoClean.
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Affiliation(s)
- Kris D. McCombe
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast, Northern Ireland
| | - Stephanie G. Craig
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast, Northern Ireland
| | | | - Javier I. Quezada-Marín
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast, Northern Ireland
| | - Matthew Hagan
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast, Northern Ireland
| | - Simon Rajendran
- Belfast Health and Social Care Trust, Belfast, Northern Ireland
| | - Matthew P. Humphries
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast, Northern Ireland
| | - Victoria Bingham
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast, Northern Ireland
| | - Manuel Salto-Tellez
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast, Northern Ireland
- Belfast Health and Social Care Trust, Belfast, Northern Ireland
- The Institute of Cancer Research, London United Kingdom
| | - Richard Gault
- The School of Electronics, Electrical Engineering and Computer Science, Queen’s University Belfast, Belfast, Northern Ireland
| | - Jacqueline A. James
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast, Northern Ireland
- Belfast Health and Social Care Trust, Belfast, Northern Ireland
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Fotouhi J, Taylor G, Unberath M, Johnson A, Lee SC, Osgood G, Armand M, Navab N. Exploring partial intrinsic and extrinsic symmetry in 3D medical imaging. Med Image Anal 2021; 72:102127. [PMID: 34147832 DOI: 10.1016/j.media.2021.102127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 05/25/2021] [Accepted: 05/27/2021] [Indexed: 11/20/2022]
Abstract
We present a novel methodology to detect imperfect bilateral symmetry in CT of human anatomy. In this paper, the structurally symmetric nature of the pelvic bone is explored and is used to provide interventional image augmentation for treatment of unilateral fractures in patients with traumatic injuries. The mathematical basis of our solution is based on the incorporation of attributes and characteristics that satisfy the properties of intrinsic and extrinsic symmetry and are robust to outliers. In the first step, feature points that satisfy intrinsic symmetry are automatically detected in the Möbius space defined on the CT data. These features are then pruned via a two-stage RANSAC to attain correspondences that satisfy also the extrinsic symmetry. Then, a disparity function based on Tukey's biweight robust estimator is introduced and minimized to identify a symmetry plane parametrization that yields maximum contralateral similarity. Finally, a novel regularization term is introduced to enhance similarity between bone density histograms across the partial symmetry plane, relying on the important biological observation that, even if injured, the dislocated bone segments remain within the body. Our extensive evaluations on various cases of common fracture types demonstrate the validity of the novel concepts and the accuracy of the proposed method.
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Catak FO, Ahmed J, Sahinbas K, Khand ZH. Data augmentation based malware detection using convolutional neural networks. PeerJ Comput Sci 2021; 7:e346. [PMID: 33816996 PMCID: PMC7924722 DOI: 10.7717/peerj-cs.346] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
Due to advancements in malware competencies, cyber-attacks have been broadly observed in the digital world. Cyber-attacks can hit an organization hard by causing several damages such as data breach, financial loss, and reputation loss. Some of the most prominent examples of ransomware attacks in history are WannaCry and Petya, which impacted companies' finances throughout the globe. Both WannaCry and Petya caused operational processes inoperable by targeting critical infrastructure. It is quite impossible for anti-virus applications using traditional signature-based methods to detect this type of malware because they have different characteristics on each contaminated computer. The most important feature of this type of malware is that they change their contents using their mutation engines to create another hash representation of the executable file as they propagate from one computer to another. To overcome this method that attackers use to camouflage malware, we have created three-channel image files of malicious software. Attackers make different variants of the same software because they modify the contents of the malware. In the solution to this problem, we created variants of the images by applying data augmentation methods. This article aims to provide an image augmentation enhanced deep convolutional neural network (CNN) models for detecting malware families in a metamorphic malware environment. The main contributions of the article consist of three components, including image generation from malware samples, image augmentation, and the last one is classifying the malware families by using a CNN model. In the first component, the collected malware samples are converted into binary file to 3-channel images using the windowing technique. The second component of the system create the augmented version of the images, and the last part builds a classification model. This study uses five different deep CNN model for malware family detection. The results obtained by the classifier demonstrate accuracy up to 98%, which is quite satisfactory.
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Affiliation(s)
| | - Javed Ahmed
- Center of Excellence for Robotics, Artificial Intelligence and Blockchain (CRAIB), Department of Computer Science, Sukkur IBA University, Sukkur, Pakistan
| | - Kevser Sahinbas
- Department of Management Information System, Istanbul Medipol University, Istanbul, Turkey
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Saleh AM, Hamoud T. Analysis and best parameters selection for person recognition based on gait model using CNN algorithm and image augmentation. J Big Data 2021; 8:1. [PMID: 33425651 PMCID: PMC7778727 DOI: 10.1186/s40537-020-00387-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/26/2020] [Indexed: 05/20/2023]
Abstract
Person Recognition based on Gait Model (PRGM) and motion features is are indeed a challenging and novel task due to their usages and to the critical issues of human pose variation, human body occlusion, camera view variation, etc. In this project, a deep convolution neural network (CNN) was modified and adapted for person recognition with Image Augmentation (IA) technique depending on gait features. Adaptation aims to get best values for CNN parameters to get best CNN model. In Addition to the CNN parameters Adaptation, the design of CNN model itself was adapted to get best model structure; Adaptation in the design was affected the type, the number of layers in CNN and normalization between them. After choosing best parameters and best design, Image augmentation was used to increase the size of train dataset with many copies of the image to boost the number of different images that will be used to train Deep learning algorithms. The tests were achieved using known dataset (Market dataset). The dataset contains sequential pictures of people in different gait status. The image in CNN model as matrix is extracted to many images or matrices by the convolution, so dataset size may be bigger by hundred times to make the problem a big data issue. In this project, results show that adaptation has improved the accuracy of person recognition using gait model comparing to model without adaptation. In addition, dataset contains images of person carrying things. IA technique improved the model to be robust to some variations such as image dimensions (quality and resolution), rotations and carried things by persons. Results for 200 persons recognition, validation accuracy was about 82% without IA and 96.23 with IA. For 800 persons recognition, validation accuracy was 93.62% without IA.
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Affiliation(s)
- Abeer Mohsin Saleh
- Damascus University, Damascus, Syria
- Syrian Private University, Damascus, Syria
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