ARTICLE | doi:10.20944/preprints202007.0650.v1
Subject: Mathematics & Computer Science, Other Keywords: Myocarditis; Diagnosis; Convolutional Neural Network; Cardiac MRI; prediction
Online: 26 July 2020 (17:44:05 CEST)
Myocarditis is the form of an inflammation of the middle layer of the heart wall which is caused by a viral infection and can affect the heart muscle and its electrical system. It has remained as one of the most challenging diagnoses in cardiology. Myocardial is the prime cause of unexpected death in approximately 20% of adults less than 40 years of age. Cardiac MRI (CMR) has been considered as a noninvasive and golden standard diagnostic tool for suspected myocarditis and plays an indispensable role in diagnosing various cardiac diseases. However, the performance of CMR is heavily dependent on the clinical presentation and non-specific features such as chest pain, arrhythmia, and heart failure. Besides, other imaging factors like artifacts, technical errors, pulse sequence, acquisition parameters, contrast agent dose, and more importantly qualitatively visual interpretation can affect the result of the diagnosis. This paper introduces a new deep learning-based model called Convolutional Neural Network-Clustering (CNN-KCL) to diagnose the Myocarditis. The hybrid CNN-KCL method performs the early and accurate diagnosis of Myocarditis. To the best-of-our-knowledge, a Convolutional neural network has never been used before for the diagnosis of Myocarditis. In this study, we used 47 subjects to diagnose myocarditis patients from Tehran's Omid Hospital. The total number of data examined is 10425. Our results demonstrate that CNN-KCL achieves 92.3% in terms of diagnosis myocarditis prediction accuracy which is significantly better than those reported in previous studies.
ARTICLE | doi:10.20944/preprints202201.0258.v1
Subject: Mathematics & Computer Science, Artificial Intelligence & Robotics Keywords: Skin cancer; Deep learning; Hybrid feature extractor; Local binary pattern; Feature extraction
Online: 18 January 2022 (12:43:50 CET)
Skin cancer is an exquisite disease globally nowadays. Because of the poor contrast and apparent resemblance between skin and lesions, automatic identification of skin cancer is complicated. The rate of human death can be massively reduced if melanoma skin cancer can be detected quickly using dermoscopy images. In this research, an anisotropic diffusion filtering method is used on dermoscopy images to remove multiplicative speckle noise and the fast-bounding box (FBB) method is applied to segment the skin cancer region. Furthermore, the paper consists of two feature extractor parts. One of the two features extractor parts is the hybrid feature extractor (HFE) part and another is the convolutional neural network VGG19 based CNN feature extractor part. The HFE portion combines three feature extraction approaches into a single fused feature vector: Histogram-Oriented Gradient (HOG), Local Binary Pattern (LBP), and Speed Up Robust Feature (SURF). The CNN method also is used to extract additional features from test and training datasets. This two-feature vector is fused to design the classification model. This classifier performs the classification of dermoscopy images whether it is melanoma or non-melanoma skin cancer. The proposed methodology is performed on two ordinary datasets and achieved the accuracy 99.85%, sensitivity 91.65%, and specificity 95.70%, which makes it more successful than previous machine learning algorithms.
REVIEW | doi:10.20944/preprints202202.0083.v2
Subject: Mathematics & Computer Science, Artificial Intelligence & Robotics Keywords: Machine Learning; COVID-19; Internet of Things (IoT); Deep Learning; Big Data
Online: 19 April 2022 (08:21:00 CEST)
Early diagnosis, prioritization, screening, clustering and tracking of COVID-19 patients, and production of drugs and vaccines are some of the applications that have made it necessary to use a new style of technology to involve, to manage and deal with this epidemic. Strategies backed by artificial intelligence (AI) and the Internet of Things (IoT) have been undeniable to understand how the virus works and try to prevent it from spreading. Accordingly, the main aim of this survey article is to highlight the methods of ML, IoT and the integration of IoT and ML-based techniques in the applications related to COVID-19 from the diagnosis of the disease to the prediction of its outbreak. According to the main findings, IoT provided a prompt and efficient approach of following the disease spread. Most of the studies developed by ML-based techniques for handling COVID-19 based dataset provided performance criteria. The most popular performance criteria, is related to accuracy factor. It can be employed for comparing the ML-based methods with different datasets. According to the results, CNN with SVM classifier, Genetic CNN and pre-trained CNN followed by ResNet, provided highest accuracy values. On the other hand, the lowest accuracy was related to single CNN followed by XGboost and KNN methods.
ARTICLE | doi:10.20944/preprints202105.0424.v1
Subject: Mathematics & Computer Science, Algebra & Number Theory Keywords: Convolutional Neural Network (CNN); Emotion Recognition; Facial Expression; Classification; Accuracy
Online: 18 May 2021 (11:34:19 CEST)
Emotion recognition defined as identifying human emotion and is directly related to different fields such as human-computer interfaces, human emotional processing, irrational analysis, medical diagnostics, data-driven animation, human-robot communi- cation and many more. The purpose of this study is to propose a new facial emotional recognition model using convolutional neural network. Our proposed model, “ConvNet”, detects seven specific emotions from image data including anger, disgust, fear, happiness, neutrality, sadness, and surprise. This research focuses on the model’s training accuracy in a short number of epoch which the authors can develop a real-time schema that can easily fit the model and sense emotions. Furthermore, this work focuses on the mental or emotional stuff of a man or woman using the behavioral aspects. To complete the training of the CNN network model, we use the FER2013 databases, and we test the system’s success by identifying facial expressions in the real-time. ConvNet consists of four layers of convolution together with two fully connected layers. The experimental results show that the ConvNet is able to achieve 96% training accuracy which is much better than current existing models. ConvNet also achieved validation accuracy of 65% to 70% (considering different datasets used for experiments), resulting in a higher classification accuracy compared to other existing models. We also made all the materials publicly accessible for the research community at: https://github.com/Tanoy004/Emotion-recognition-through-CNN.
ARTICLE | doi:10.20944/preprints202108.0413.v3
Subject: Medicine & Pharmacology, Dentistry Keywords: Dental Age Measurement; Dental Radiography; Orthopantomogram; Convolutional Neural Network; K-Nearest Neighbour; Health Data Analytics; Biomedical Machine Learning
Online: 12 April 2022 (10:12:48 CEST)
Age estimation in dental radiographs Orthopantomography (OPG) is a medical imaging technique that physicians and pathologists utilise for disease identification and legal matters. For example, for estimating post-mortem interval, detecting child abuse, drug trafficking, and identifying an unknown body. Recent development in automated image processing models improved the age estimation's limited precision to an approximate range of +/- one year. While this estimation is often accepted as accurate measurement, age estimation should be as precise as possible in most serious matters, such as homicide. Current age estimation techniques are highly dependent on manual and time-consuming image processing. Age estimation is often a time-sensitive matter in which the image processing time is vital. Recent development in Machine learning-based data processing methods has decreased the imaging time processing; however, the accuracy of these techniques remains to be further improved. We proposed an ensemble method of image classifiers and transfer learning techniques to enhance the accuracy of age estimation using OPGs from one year to a couple of months (1-3-6). This hybrid model is based on convolutional neural networks (CNN) and K nearest neighbours (KNN). The hybrid (HCNN-KNN) model was used to investigate 1,922 panoramic dental radiographs of patients aged 15 to 23. These OPGs were obtained from the various teaching institutes and private dental clinics in Malaysia. To minimise the chance of overfitting in our model, we used the principal component analysis (PCA) algorithm and eliminated the features with high correlation. To further enhance the performance of our hybrid model, we performed systematic image pre-processing. We applied a series of classifications to train our model. We have successfully demonstrated that combining these innovative approaches has improved the classification and segmentation and thus the age-estimation outcome of the model. Our findings suggest that our innovative model, for the first time, to the best of our knowledge, successfully estimated the age in classified studies of one year old, six months, three months and one-month-old cases with accuracies of 99.98, 99.96, 99.87, and 98.78 respectively.
ARTICLE | doi:10.20944/preprints202108.0368.v1
Subject: Life Sciences, Genetics Keywords: pancreatic cancer; cancer subtype identification; somatic point mutations; genotype and phenotype characterization; therapeutic targets; personalized medicine
Online: 17 August 2021 (22:24:57 CEST)
It has now known that at least 10% of samples with pancreatic cancers (PC) contain a causative mutation in the known susceptibility genes, suggesting the importance of identifying cancer-associated genes that carry the causative mutations in high-risk individuals for early detection of PC. In this study, we develop a statistical pipeline using a new concept, called gene-motif, that utilizes both mutated genes and mutational processes to identify 4,211 3-nucleotide PC-associated gene-motifs within 203 significantly mutated genes in PC. Using these gene-motifs as distinguishable features for pancreatic cancer subtyping results in identifying five PC subtypes with distinguishable phenotypes and genotypes. Our comprehensive biological characterization reveals that these PC subtypes are associated with different molecular mechanisms including unique cancer related signaling pathways, in which for most of the subtypes targeted treatment options are currently available. Some of the pathways we identified in all five PC subtypes, including cell cycle and the Axon guidance pathway are frequently seen and mutated in cancer. We also identified Protein kinase C, EGFR (epidermal growth factor receptor) signaling pathway and P53 signaling pathways as potential targets for treatment of the PC subtypes. Altogether, our results uncover the importance of considering both the mutation type and mutated genes in the identification of cancer subtypes and biomarkers.
ARTICLE | doi:10.20944/preprints202111.0266.v1
Subject: Engineering, Biomedical & Chemical Engineering Keywords: Pan-Cancer; somatic point mutations; cancer subtyping; biomarker discovery; driver genes; per-sonalized medicine; health data analytics
Online: 15 November 2021 (13:51:33 CET)
The advent of high throughput sequencing has enabled researchers to systematically evaluate the genetic variations in cancer, resulting in identifying many cancer-associated genes. Although cancers in the same tissue are widely categorized in the same group, they demonstrate many differences concerning their mutational profiles. Hence there is no “silver bullet” for the treatment of a cancer type. This reveals the importance of developing a pipeline to identify cancer-associated genes accurately and re-classify patients with similar mutational profiles. Classification of cancer patients with similar mutational profiles may help discover subtypes of cancer patients who might benefit from specific treatment types. In this study, we propose a new machine learning pipeline to identify protein-coding genes mutated in a significant portion of samples to identify cancer subtypes. We applied our pipeline to 12270 samples collected from the International Cancer Genome Consortium (ICGC), covering 19 cancer types. Here we identified 17 different cancer subtypes. Comprehensive phenotypic and genotypic analysis indicates distinguishable properties, including unique cancer-related signaling pathways, in which, for most of them, targeted treatment options are currently available. This new subtyping approach offers a novel opportunity for cancer drug development based on the mutational profile of patients. We also comprehensive study the causes of mutations among samples in each subtype by mining the mutational signatures, which provides important insight into their active molecular mechanisms. Some of the pathways we identified in most subtypes, including the cell cycle and the Axon guidance pathways, are frequently observed in cancer disease. Interestingly, we also identified several mutated genes and different rates of mutation in multiple cancer subtypes. In addition, our study on “gene-motif” suggests the importance of considering both the context of the mutations and mutational processes in identifying cancer-associated genes. The source codes for our proposed clustering pipeline and analysis are publicly available at: https://github.com/bcb-sut/Pan-Cancer.