Classification and Determination of Severity of Corneal Ulcer with Vision Transformer Based on the Analysis of Public Image Dataset of Fluorescein-Stained Corneas.

A corneal ulcer is a condition in which an injury to the corneal surface occurs as a result of infection. This can lead to severe vision loss and even blindness. For this reason, early diagnosis of this disease is of great importance. Deep learning algorithms are used in many critical health applications and are used effectively in the early diagnosis stages of diseases. Thus, a deep learning algorithm was applied in this study and corneal ulcer and severity were predicted. The study consisted of four stages over three different scenarios. In the first scenario, the types of corneal ulcers were predicted. In the second scenario, the grades of corneal ulcer types were classified. In the last scenario, the severity of corneal ulcers was classified. For each scenario, data were obtained in the first stage and separated according to the relevant labels. In the second stage, various image processing algorithms were employed, and images were analyzed. At this stage, the images were also augmented by various processes. In the third stage, ViT architecture, a new deep learning model, was used, and the images were classified. In the last stage, the performance of the classifier was determined by accuracy, precision, recall, F1-score, and AUC score. At the end of the study, the ViT deep learning model performed an effective classification, and accuracy scores of 95.77% for the first scenario, 96.43% for the second scenario, and 97.27% for the third scenario were calculated.

LieWaves: dataset for lie detection based on EEG signals and wavelets.

This study introduces an electroencephalography (EEG)-based dataset to analyze lie detection. Various analyses or detections can be performed using EEG signals. Lie detection using EEG data has recently become a significant topic. In every aspect of life, people find the need to tell lies to each other. While lies told daily may not have significant societal impacts, lie detection becomes crucial in legal, security, job interviews, or situations that could affect the community. This study aims to obtain EEG signals for lie detection, create a dataset, and analyze this dataset using signal processing techniques and deep learning methods. EEG signals were acquired from 27 individuals using a wearable EEG device called Emotiv Insight with 5 channels (AF3, T7, Pz, T8, AF4). Each person took part in two trials: one where they were honest and another where they were deceitful. During each experiment, participants evaluated beads they saw before the experiment and stole from them in front of a video clip. This study consisted of four stages. In the first stage, the LieWaves dataset was created with the EEG data obtained during these experiments. In the second stage, preprocessing was carried out. In this stage, the automatic and tunable artifact removal (ATAR) algorithm was applied to remove the artifacts from the EEG signals. Later, the overlapping sliding window (OSW) method was used for data augmentation. In the third stage, feature extraction was performed. To achieve this, EEG signals were analyzed by combining discrete wavelet transform (DWT) and fast Fourier transform (FFT) including statistical methods (SM). In the last stage, each obtained feature vector was classified separately using Convolutional Neural Network (CNN), Long Short-Term Memory (LSTM), and CNNLSTM hybrid algorithms. At the study's conclusion, the most accurate result, achieving a 99.88% accuracy score, was produced using the LSTM and DWT techniques. With this study, a new data set was introduced to the literature, and it was aimed to eliminate the deficiencies in this field with this data set. Evaluation results obtained from the data set have shown that this data set can be effective in this field.

A Novel Repetition Frequency-Based DNA Encoding Scheme to Predict Human and Mouse DNA Enhancers with Deep Learning.

Recent studies have shown that DNA enhancers have an important role in the regulation of gene expression. They are responsible for different important biological elements and processes such as development, homeostasis, and embryogenesis. However, experimental prediction of these DNA enhancers is time-consuming and costly as it requires laboratory work. Therefore, researchers started to look for alternative ways and started to apply computation-based deep learning algorithms to this field. Yet, the inconsistency and unsuccessful prediction performance of computational-based approaches among various cell lines led to the investigation of these approaches as well. Therefore, in this study, a novel DNA encoding scheme was proposed, and solutions were sought to the problems mentioned and DNA enhancers were predicted with BiLSTM. The study consisted of four different stages for two scenarios. In the first stage, DNA enhancer data were obtained. In the second stage, DNA sequences were converted to numerical representations by both the proposed encoding scheme and various DNA encoding schemes including EIIP, integer number, and atomic number. In the third stage, the BiLSTM model was designed, and the data were classified. In the final stage, the performance of DNA encoding schemes was determined by accuracy, precision, recall, F1-score, CSI, MCC, G-mean, Kappa coefficient, and AUC scores. In the first scenario, it was determined whether the DNA enhancers belonged to humans or mice. As a result of the prediction process, the highest performance was achieved with the proposed DNA encoding scheme, and an accuracy of 92.16% and an AUC score of 0.85 were calculated, respectively. The closest accuracy score to the proposed scheme was obtained with the EIIP DNA encoding scheme and the result was observed as 89.14%. The AUC score of this scheme was measured as 0.87. Among the remaining DNA encoding schemes, the atomic number showed an accuracy score of 86.61%, while this rate decreased to 76.96% with the integer scheme. The AUC values of these schemes were 0.84 and 0.82, respectively. In the second scenario, it was determined whether there was a DNA enhancer and, if so, it was decided to which species this enhancer belonged. In this scenario, the highest accuracy score was obtained with the proposed DNA encoding scheme and the result was 84.59%. Moreover, the AUC score of the proposed scheme was determined as 0.92. EIIP and integer DNA encoding schemes showed accuracy scores of 77.80% and 73.68%, respectively, while their AUC scores were close to 0.90. The most ineffective prediction was performed with the atomic number and the accuracy score of this scheme was calculated as 68.27%. Finally, the AUC score of this scheme was 0.81. At the end of the study, it was observed that the proposed DNA encoding scheme was successful and effective in predicting DNA enhancers.

Prediction of viral-host interactions of COVID-19 by computational methods.

Experimental approaches are currently used to determine viral-host interactions, but these approaches are both time-consuming and costly. For these reasons, computational-based approaches are recommended. In this study, using computational-based approaches, viral-host interactions of SARS-CoV-2 virus and human proteins were predicted. The study consists of four different stages; in the first stage viral and host protein sequences were obtained. In the second stage, protein sequences were converted into numerical expressions by various protein mapping methods. These methods are entropy-based, AVL-tree, FIBHASH, binary encoding, CPNR, PAM250, BLOSUM62, Atchley factors, Meiler parameters, EIIP, AESNN1, Miyazawa energies, Micheletti potentials, Z-scale, and hydrophobicity. In the third stage, a deep learning model was designed and BiLSTM was used for this. In the last stage, the protein sequences were classified, and the viral-host interactions were predicted. The performances of protein mapping methods were determined by accuracy, F1-score, specificity, sensitivity, and AUC scores. According to the classification results, the best classification process was obtained by the entropy-based method. With this method, 94.74% accuracy, and 0.95 AUC score were calculated. Then, the most successful classification process was performed with the Z-scale and 91.23% accuracy, and 0.96 AUC score were obtained. Although other protein mapping methods are not as efficient as Z-scale and entropy-based methods, they have achieved successful classification. AVL-tree, FIBHASH, binary encoding, CPNR, PAM250, BLOSUM62, Atchley factors, Meiler parameters and AESNN1 methods showed over 80% accuracy, F1-score, and AUC score. Accuracy scores of EIIP, Miyazawa energies, Micheletti potentials and hydrophobicity methods remained below 80%. When the results were examined in general, it was observed that the computational approaches were successful in predicting viral-host interactions between SARS-CoV-2 virus and human proteins.

A Novel Protein Mapping Method for Predicting the Protein Interactions in COVID-19 Disease by Deep Learning.

The new type of corona virus (SARS-COV-2) emerging in Wuhan, China has spread rapidly to the world and has become a pandemic. In addition to having a significant impact on daily life, it also shows its effect in different areas, including public health and economy. Currently, there is no vaccine or antiviral drug available to prevent the COVID-19 disease. Therefore, determination of protein interactions of new types of corona virus is vital in clinical studies, drug therapy, identification of preclinical compounds and protein functions. Protein-protein interactions are important to examine protein functions and pathways involved in various biological processes and to determine the cause and progression of diseases. Various high-throughput experimental methods have been used to identify protein-protein interactions in organisms, yet, there is still a huge gap in specifying all possible protein interactions in an organism. In addition, since the experimental methods used include cloning, labeling, affinity purification mass spectrometry, the processes take a long time. Determining these interactions with artificial intelligence-based methods rather than experimental approaches may help to identify protein functions faster. Thus, protein-protein interaction prediction using deep-learning algorithms has been employed in conjunction with experimental method to explore new protein interactions. However, to predict protein interactions with artificial intelligence techniques, protein sequences need to be mapped. There are various types and numbers of protein-mapping methods in the literature. In this study, we wanted to contribute to the literature by proposing a novel protein-mapping method based on the AVL tree. The proposed method was inspired by the fast search performance on the dictionary structure of AVL tree and was used to verify the protein interactions between SARS-COV-2 virus and human. First, protein sequences were mapped by both the proposed method and various protein-mapping methods. Then, the mapped protein sequences were normalized and classified by bidirectional recurrent neural networks. The performance of the proposed method was evaluated with accuracy, f1-score, precision, recall, and AUC scores. Our results indicated that our mapping method predicts the protein interactions between SARS-COV-2 virus proteins and human proteins at an accuracy of 97.76%, precision of 97.60%, recall of 98.33%, f1-score of 79.42%, and with AUC 89% in average.

Convolutional capsnet: A novel artificial neural network approach to detect COVID-19 disease from X-ray images using capsule networks.

Coronavirus is an epidemic that spreads very quickly. For this reason, it has very devastating effects in many areas worldwide. It is vital to detect COVID-19 diseases as quickly as possible to restrain the spread of the disease. The similarity of COVID-19 disease with other lung infections makes the diagnosis difficult. In addition, the high spreading rate of COVID-19 increased the need for a fast system for the diagnosis of cases. For this purpose, interest in various computer-aided (such as CNN, DNN, etc.) deep learning models has been increased. In these models, mostly radiology images are applied to determine the positive cases. Recent studies show that, radiological images contain important information in the detection of coronavirus. In this study, a novel artificial neural network, Convolutional CapsNet for the detection of COVID-19 disease is proposed by using chest X-ray images with capsule networks. The proposed approach is designed to provide fast and accurate diagnostics for COVID-19 diseases with binary classification (COVID-19, and No-Findings), and multi-class classification (COVID-19, and No-Findings, and Pneumonia). The proposed method achieved an accuracy of 97.24%, and 84.22% for binary class, and multi-class, respectively. It is thought that the proposed method may help physicians to diagnose COVID-19 disease and increase the diagnostic performance. In addition, we believe that the proposed method may be an alternative method to diagnose COVID-19 by providing fast screening.

Comparison of deep learning approaches to predict COVID-19 infection.

The SARS-CoV2 virus, which causes COVID-19 (coronavirus disease) has become a pandemic and has expanded all over the world. Because of increasing number of cases day by day, it takes time to interpret the laboratory findings thus the limitations in terms of both treatment and findings are emerged. Due to such limitations, the need for clinical decisions making system with predictive algorithms has arisen. Predictive algorithms could potentially ease the strain on healthcare systems by identifying the diseases. In this study, we perform clinical predictive models that estimate, using deep learning and laboratory data, which patients are likely to receive a COVID-19 disease. To evaluate the predictive performance of our models, precision, F1-score, recall, AUC, and accuracy scores calculated. Models were tested with 18 laboratory findings from 600 patients and validated with 10 fold cross-validation and train-test split approaches. The experimental results indicate that our predictive models identify patients that have COVID-19 disease at an accuracy of 86.66%, F1-score of 91.89%, precision of 86.75%, recall of 99.42%, and AUC of 62.50%. It is observed that predictive models trained on laboratory findings could be used to predict COVID-19 infection, and can be helpful for medical experts to prioritize the resources correctly. Our models (available at (https://github.com/burakalakuss/COVID-19-Clinical)) can be employed to assists medical experts in validating their initial laboratory findings, and can also be used for clinical prediction studies.