Application of machine learning for identification of heterotic groups in sunflower through combined approach of phenotyping, genotyping and protein profiling.

Application of machine learning in plant breeding is a recent concept, that has to be optimized for precise utilization in the breeding program of high yielding crop plants. Identification and efficient utilization of heterotic grouping pattern aided with machine learning approaches is of utmost importance in hybrid cultivar breeding as it can save time and resources required to breed a new plant hybrid/variety. In the present study, 109 genotypes of sunflower were investigated at morphological, biochemical (SDS-PAGE) and molecular levels (through micro-satellites (SSR) markers) for heterotic grouping. All the three datasets were combined, scaled, and subjected to unsupervised machine learning algorithms, i.e., Hierarchical clustering, K-means clustering and hybrid clustering algorithm (hierarchical + K-means) for assessment of efficiency and resolution power of these algorithms in practical plant breeding for heterotic grouping identification. Following the application of machine learning unsupervised clustering approach, two major groups were identified in the studied sunflower germplasm, and further classification revealed six smaller classes in each major group through hierarchical and hybrid clustering approach. Due to high resolution, obtained in hierarchical clustering, classification achieved through this algorithm was further used for selection of potential parents. One genotype from each smaller group was selected based on the maximum seed yield potential and hybridized in a line × tester mating design producing 36 F1 cross combinations. These F1s along with their parents were studied in open field conditions for validating the efficacy of identified heterotic groups in sunflowers genetic material under study. Data for 11 agronomic and qualitative traits were recorded. These 36 F1 combinations were tested for their combining ability (General/Specific), heterosis, genotypic and phenotypic correlation and path analysis. Results suggested that F1 hybrids performed better for all the traits under investigation than their respective parents. Findings of the study validated the use of machine learning approaches in practical plant breeding; however, more accurate and robust clustering algorithms need to be developed to handle the data noisiness of open field experiments.

Correction: Gastrointestinal tract disorders classification using ensemble of InceptionNet and proposed GITNet based deep feature with ant colony optimization.

[This corrects the article DOI: 10.1371/journal.pone.0292601.].

Computer vision-based plants phenotyping: A comprehensive survey.

The increasing demand for food production due to the growing population is raising the need for more food-productive environments for plants. The genetic behavior of plant traits remains different in different growing environments. However, it is tedious and impossible to look after the individual plant component traits manually. Plant breeders need computer vision-based plant monitoring systems to analyze different plants' productivity and environmental suitability. It leads to performing feasible quantitative analysis, geometric analysis, and yield rate analysis of the plants. Many of the data collection methods have been used by plant breeders according to their needs. In the presented review, most of them are discussed with their corresponding challenges and limitations. Furthermore, the traditional approaches of segmentation and classification of plant phenotyping are also discussed. The data limitation problems and their currently adapted solutions in the computer vision aspect are highlighted, which somehow solve the problem but are not genuine. The available datasets and current issues are enlightened. The presented study covers the plants phenotyping problems, suggested solutions, and current challenges from data collection to classification steps.

White blood cell image analysis for infection detection based on virtual hexagonal trellis (VHT) by using deep learning.

White blood cells (WBCs) are an indispensable constituent of the immune system. Efficient and accurate categorization of WBC is a critical task for disease diagnosis by medical experts. This categorization helps in the correct identification of medical problems. In this research work, WBC classes are categorized with the help of a transform learning model in combination with our proposed virtual hexagonal trellis (VHT) structure feature extraction method. The VHT feature extractor is a kernel-based filter model designed over a square lattice. In the first step, Graft Net CNN model is used to extract features of augmented data set images. Later, the VHT base feature extractor extracts useful features. The CNN-extracted features are passed to ant colony optimization (ACO) module for optimal features acquisition. Extracted features from the VHT base filter and ACO are serially merged to create a single feature vector. The merged features are passed to the support vector machine (SVM) variants for optimal classification. Our strategy yields 99.9% accuracy, which outperforms other existing methods.

Gastrointestinal tract disorders classification using ensemble of InceptionNet and proposed GITNet based deep feature with ant colony optimization.

Computer-aided classification of diseases of the gastrointestinal tract (GIT) has become a crucial area of research. Medical science and artificial intelligence have helped medical experts find GIT diseases through endoscopic procedures. Wired endoscopy is a controlled procedure that helps the medical expert in disease diagnosis. Manual screening of the endoscopic frames is a challenging and time taking task for medical experts that also increases the missed rate of the GIT disease. An early diagnosis of GIT disease can save human beings from fatal diseases. An automatic deep feature learning-based system is proposed for GIT disease classification. The adaptive gamma correction and weighting distribution (AGCWD) preprocessing procedure is the first stage of the proposed work that is used for enhancing the intensity of the frames. The deep features are extracted from the frames by deep learning models including InceptionNetV3 and GITNet. Ant Colony Optimization (ACO) procedure is employed for feature optimization. Optimized features are fused serially. The classification operation is performed by variants of support vector machine (SVM) classifiers, including the Cubic SVM (CSVM), Coarse Gaussian SVM (CGSVM), Quadratic SVM (QSVM), and Linear SVM (LSVM) classifiers. The intended model is assessed on two challenging datasets including KVASIR and NERTHUS that consist of eight and four classes respectively. The intended model outperforms as compared with existing methods by achieving an accuracy of 99.32% over the KVASIR dataset and 99.89% accuracy using the NERTHUS dataset.

Gastrointestinal Tract Polyp Anomaly Segmentation on Colonoscopy Images Using Graft-U-Net.

Computer-aided polyp segmentation is a crucial task that supports gastroenterologists in examining and resecting anomalous tissue in the gastrointestinal tract. The disease polyps grow mainly in the colorectal area of the gastrointestinal tract and in the mucous membrane, which has protrusions of micro-abnormal tissue that increase the risk of incurable diseases such as cancer. So, the early examination of polyps can decrease the chance of the polyps growing into cancer, such as adenomas, which can change into cancer. Deep learning-based diagnostic systems play a vital role in diagnosing diseases in the early stages. A deep learning method, Graft-U-Net, is proposed to segment polyps using colonoscopy frames. Graft-U-Net is a modified version of UNet, which comprises three stages, including the preprocessing, encoder, and decoder stages. The preprocessing technique is used to improve the contrast of the colonoscopy frames. Graft-U-Net comprises encoder and decoder blocks where the encoder analyzes features, while the decoder performs the features' synthesizing processes. The Graft-U-Net model offers better segmentation results than existing deep learning models. The experiments were conducted using two open-access datasets, Kvasir-SEG and CVC-ClinicDB. The datasets were prepared from the large bowel of the gastrointestinal tract by performing a colonoscopy procedure. The anticipated model outperforms in terms of its mean Dice of 96.61% and mean Intersection over Union (mIoU) of 82.45% with the Kvasir-SEG dataset. Similarly, with the CVC-ClinicDB dataset, the method achieved a mean Dice of 89.95% and an mIoU of 81.38%.

Single Channel Image Enhancement (SCIE) of White Blood Cells Based on Virtual Hexagonal Filter (VHF) Designed over Square Trellis.

White blood cells (WBCs) are the important constituent of a blood cell. These blood cells are responsible for defending the body against infections. Abnormalities identified in WBC smears lead to the diagnosis of disease types such as leukocytosis, hepatitis, and immune system disorders. Digital image analysis for infection detection at an early stage can help fast and precise diagnosis, as compared to manual inspection. Sometimes, acquired blood cell smear images from an L2-type microscope are of very low quality. The manual handling, haziness, and dark areas of the image become problematic for an efficient and accurate diagnosis. Therefore, WBC image enhancement needs attention for an effective diagnosis of the disease. This paper proposed a novel virtual hexagonal trellis (VHT)-based image filtering method for WBC image enhancement and contrast adjustment. In this method, a filter named the virtual hexagonal filter (VHF), of size 3 × 3, and based on a hexagonal structure, is formulated by using the concept of the interpolation of real and square grid pixels. This filter is convolved with WBC ALL-IBD images for enhancement and contrast adjustment. The proposed filter improves the results both visually and statically. A comparison with existing image enhancement approaches proves the validity of the proposed work.

Generative adversarial networks and its applications in the biomedical image segmentation: a comprehensive survey.

Recent advancements with deep generative models have proven significant potential in the task of image synthesis, detection, segmentation, and classification. Segmenting the medical images is considered a primary challenge in the biomedical imaging field. There have been various GANs-based models proposed in the literature to resolve medical segmentation challenges. Our research outcome has identified 151 papers; after the twofold screening, 138 papers are selected for the final survey. A comprehensive survey is conducted on GANs network application to medical image segmentation, primarily focused on various GANs-based models, performance metrics, loss function, datasets, augmentation methods, paper implementation, and source codes. Secondly, this paper provides a detailed overview of GANs network application in different human diseases segmentation. We conclude our research with critical discussion, limitations of GANs, and suggestions for future directions. We hope this survey is beneficial and increases awareness of GANs network implementations for biomedical image segmentation tasks.

HSDDD: A Hybrid Scheme for the Detection of Distracted Driving through Fusion of Deep Learning and Handcrafted Features.

Traditional methods for behavior detection of distracted drivers are not capable of capturing driver behavior features related to complex temporal features. With the goal to improve transportation safety and to reduce fatal accidents on roads, this research article presents a Hybrid Scheme for the Detection of Distracted Driving called HSDDD. This scheme is based on a strategy of aggregating handcrafted and deep CNN features. HSDDD is based on three-tiered architecture. The three tiers are named as Coordination tier, Concatenation tier and Classification tier. We first obtain HOG features by using handcrafted algorithms, and then at the coordination tier, we leverage four deep CNN models including AlexNet, Inception V3, Resnet50 and VGG-16 for extracting DCNN features. DCNN extracted features are fused with HOG extracted features at the Concatenation tier. Then PCA is used as a feature selection technique. PCA takes both the extracted features and removes the redundant and irrelevant information, and it improves the classification performance. After feature fusion and feature selection, the two classifiers, KNN and SVM, at the Classification tier take the selected features and classify the ten classes of distracted driving behaviors. We evaluate our proposed scheme and observe its performance by using the accuracy metrics.

A Decision Support System for Face Sketch Synthesis Using Deep Learning and Artificial Intelligence.

The recent development in the area of IoT technologies is likely to be implemented extensively in the next decade. There is a great increase in the crime rate, and the handling officers are responsible for dealing with a broad range of cyber and Internet issues during investigation. IoT technologies are helpful in the identification of suspects, and few technologies are available that use IoT and deep learning together for face sketch synthesis. Convolutional neural networks (CNNs) and other constructs of deep learning have become major tools in recent approaches. A new-found architecture of the neural network is anticipated in this work. It is called Spiral-Net, which is a modified version of U-Net fto perform face sketch synthesis (the phase is known as the compiler network C here). Spiral-Net performs in combination with a pre-trained Vgg-19 network called the feature extractor F. It first identifies the top n matches from viewed sketches to a given photo. F is again used to formulate a feature map based on the cosine distance of a candidate sketch formed by C from the top n matches. A customized CNN configuration (called the discriminator D) then computes loss functions based on differences between the candidate sketch and the feature. Values of these loss functions alternately update C and F. The ensemble of these nets is trained and tested on selected datasets, including CUFS, CUFSF, and a part of the IIT photo-sketch dataset. Results of this modified U-Net are acquired by the legacy NLDA (1998) scheme of face recognition and its newer version, OpenBR (2013), which demonstrate an improvement of 5% compared with the current state of the art in its relevant domain.

From ECG signals to images: a transformation based approach for deep learning.

Provocative heart disease is related to ventricular arrhythmias (VA). Ventricular tachyarrhythmia is an irregular and fast heart rhythm that emerges from inappropriate electrical impulses in the ventricles of the heart. Different types of arrhythmias are associated with different patterns, which can be identified. An electrocardiogram (ECG) is the major analytical tool used to interpret and record ECG signals. ECG signals are nonlinear and difficult to interpret and analyze. We propose a new deep learning approach for the detection of VA. Initially, the ECG signals are transformed into images that have not been done before. Later, these images are normalized and utilized to train the AlexNet, VGG-16 and Inception-v3 deep learning models. Transfer learning is performed to train a model and extract the deep features from different output layers. After that, the features are fused by a concatenation approach, and the best features are selected using a heuristic entropy calculation approach. Finally, supervised learning classifiers are utilized for final feature classification. The results are evaluated on the MIT-BIH dataset and achieved an accuracy of 97.6% (using Cubic Support Vector Machine as a final stage classifier).

Detection and Classification of Gastrointestinal Diseases using Machine Learning.

BACKGROUND: Traditional endoscopy is an invasive and painful method of examining the gastrointestinal tract (GIT) not supported by physicians and patients. To handle this issue, video endoscopy (VE) or wireless capsule endoscopy (WCE) is recommended and utilized for GIT examination. Furthermore, manual assessment of captured images is not possible for an expert physician because it's a time taking task to analyze thousands of images thoroughly. Hence, there comes the need for a Computer-Aided-Diagnosis (CAD) method to help doctors analyze images. Many researchers have proposed techniques for automated recognition and classification of abnormality in captured images. METHODS: In this article, existing methods for automated classification, segmentation and detection of several GI diseases are discussed. Paper gives a comprehensive detail about these state-of-theart methods. Furthermore, literature is divided into several subsections based on preprocessing techniques, segmentation techniques, handcrafted features based techniques and deep learning based techniques. Finally, issues, challenges and limitations are also undertaken. RESULTS: A comparative analysis of different approaches for the detection and classification of GI infections. CONCLUSION: This comprehensive review article combines information related to a number of GI diseases diagnosis methods at one place. This article will facilitate the researchers to develop new algorithms and approaches for early detection of GI diseases detection with more promising results as compared to the existing ones of literature.

Brain Tumor Detection by Using Stacked Autoencoders in Deep Learning.

Brain tumor detection depicts a tough job because of its shape, size and appearance variations. In this manuscript, a deep learning model is deployed to predict input slices as a tumor (unhealthy)/non-tumor (healthy). This manuscript employs a high pass filter image to prominent the inhomogeneities field effect of the MR slices and fused with the input slices. Moreover, the median filter is applied to the fused slices. The resultant slices quality is improved with smoothen and highlighted edges of the input slices. After that, based on these slices' intensity, a 4-connected seed growing algorithm is applied, where optimal threshold clusters the similar pixels from the input slices. The segmented slices are then supplied to the fine-tuned two layers proposed stacked sparse autoencoder (SSAE) model. The hyperparameters of the model are selected after extensive experiments. At the first layer, 200 hidden units and at the second layer 400 hidden units are utilized. The testing is performed on the softmax layer for the prediction of the images having tumors and no tumors. The suggested model is trained and checked on BRATS datasets i.e., 2012(challenge and synthetic), 2013, and 2013 Leaderboard, 2014, and 2015 datasets. The presented model is evaluated with a number of performance metrics which demonstrates the improved performance.

Oral Rivaroxaban in Symptomatic Deep Vein Thrombosis.

OBJECTIVE: To evaluate the efficacy of oral rivaroxaban compared to warfarin in patients with deep vein thrombosis (DVT). STUDY DESIGN: Open label randomized controlled study. PLACE AND DURATION OF STUDY: Department of General Medicine, Pakistan Institute of Medical Sciences (PIMS), Islamabad from January 2016 to January 2018. METHODOLOGY: Patients of both genders between 18 and 60 years of age with Doppler ultrasound-confirmed DVT were included in the study. Pregnant patients and those with advanced liver, renal disease, those with a previous history of DVT, malignancy, with a platelets count of less than 50000/ul were excluded from the study. Rivaroxaban was given in a dose of 15 mg twice daily for 21 days followed by 20 mg once daily. Patients in the warfarin group were given heparin for 3 to 5 days followed by warfarin for 3 to 6 months. The primary efficacy outcome was patency of the vessel at 3 and 6 months of treatment. The principal safety outcomes were major and minor bleeding during the study period. RESULTS: A total of 151 patients with acute symptomatic deep vein thrombosis were enrolled in the study. Half of the patients were given warfarin and the other half rivaroxaban for 6 months. At three months, there were no significant differences observed in vessel patency in the rivaroxaban group (22.4%) as compared to warfarin group (26.7%) but after 6 months of therapy, vessel patency was significantly more in the rivaroxaban group. Adverse events did not show any significant differences Conclusion: Rivaroxaban had an efficacy superior to warfarin in terms of vessel patency after six months of therapy but adverse events were similar in both the groups.

Brain tumor detection using statistical and machine learning method.

BACKGROUND AND OBJECTIVE: Brain tumor occurs because of anomalous development of cells. It is one of the major reasons of death in adults around the globe. Millions of deaths can be prevented through early detection of brain tumor. Earlier brain tumor detection using Magnetic Resonance Imaging (MRI) may increase patient's survival rate. In MRI, tumor is shown more clearly that helps in the process of further treatment. This work aims to detect tumor at an early phase. METHODS: In this manuscript, Weiner filter with different wavelet bands is used to de-noise and enhance the input slices. Subsets of tumor pixels are found with Potential Field (PF) clustering. Furthermore, global threshold and different mathematical morphology operations are used to isolate the tumor region in Fluid Attenuated Inversion Recovery (Flair) and T2 MRI. For accurate classification, Local Binary Pattern (LBP) and Gabor Wavelet Transform (GWT) features are fused. RESULTS: The proposed approach is evaluated in terms of peak signal to noise ratio (PSNR), mean squared error (MSE) and structured similarity index (SSIM) yielding results as 76.38, 0.037 and 0.98 on T2 and 76.2, 0.039 and 0.98 on Flair respectively. The segmentation results have been evaluated based on pixels, individual features and fused features. At pixels level, the comparison of proposed approach is done with ground truth slices and also validated in terms of foreground (FG) pixels, background (BG) pixels, error region (ER) and pixel quality (Q). The approach achieved 0.93 FG and 0.98 BG precision and 0.010 ER on a local dataset. On multimodal brain tumor segmentation challenge dataset BRATS 2013, 0.93 FG and 0.99 BG precision and 0.005 ER are acquired. Similarly on BRATS 2015, 0.97 FG and 0.98 BG precision and 0.015 ER are obtained. In terms of quality, the average Q value and deviation are 0.88 and 0.017. At the fused feature based level, specificity, sensitivity, accuracy, area under the curve (AUC) and dice similarity coefficient (DSC) are 1.00, 0.92, 0.93, 0.96 and 0.96 on BRATS 2013, 0.90, 1.00, 0.97, 0.98 and 0.98 on BRATS 2015 and 0.90, 0.91, 0.90, 0.77 and 0.95 on local dataset respectively. CONCLUSION: The presented approach outperformed as compared to existing approaches.

Diabetic retinopathy detection and classification using hybrid feature set.

Complicated stages of diabetes are the major cause of Diabetic Retinopathy (DR) and no symptoms appear at the initial stage of DR. At the early stage diagnosis of DR, screening and treatment may reduce vision harm. In this work, an automated technique is applied for detection and classification of DR. A local contrast enhancement method is used on grayscale images to enhance the region of interest. An adaptive threshold method with mathematical morphology is used for the accurate lesions region segmentation. After that, the geometrical and statistical features are fused for better classification. The proposed method is validated on DIARETDB1, E-ophtha, Messidor, and local data sets with different metrics such as area under the curve (AUC) and accuracy (ACC).

Fundus image classification methods for the detection of glaucoma: A review.

Glaucoma is a neurodegenerative illness and is considered as a standout amongst the most widely recognized reasons for visual impairment. Nerve's degeneration is an irretrievable procedure, so the diagnosis of the illness at an early stage is an absolute requirement to stay away from lasting loss of vision. Glaucoma effected mainly because of increased intraocular pressure, if it is not distinguished and looked early, it can result in visual impairment. There are not generally evident side effects of glaucoma; thus, patients attempt to get treatment just when the seriousness of malady is advanced altogether. Determination of glaucoma often comprises of review of the basic crumbling of the nerve in conjunction with the examination of visual function capacity. This article shows the persistent illustration of glaucoma, its side effects, and the potential people inclined to this malady. The essence of this article is on different classification methods being utilized and proposed by various scientists for the identification of glaucoma. This article audits a few division and segmentation methodologies that are exceptionally useful for recognizable proof, identification, and diagnosis of glaucoma. The research related to the findings and the treatment is likewise evaluated in this article.