Isfahan and Covid-19: Deep spatiotemporal representation.

The coronavirus COVID-19 is affecting 213 countries and territories around the world. Iran was one of the first affected countries by this virus. Isfahan, as the third most populated province of Iran, experienced a noticeable epidemic. The prediction of epidemic size, peak value, and peak time can help policymakers in correct decisions. In this study, deep learning is selected as a powerful tool for forecasting this epidemic in Isfahan. A combination of effective Social Determinant of Health (SDH) and the occurrences of COVID-19 data are used as spatiotemporal input by using time-series information from different locations. Different models are utilized, and the best performance is found to be for a tailored type of long short-term memory (LSTM). This new method incorporates the mutual effect of all classes (confirmed/ death / recovered) in the prediction process. The future trajectory of the outbreak in Isfahan is forecasted with the proposed model. The paper demonstrates the positive effect of adding SDHs in pandemic prediction. Furthermore, the effectiveness of different SDHs is discussed, and the most effective terms are introduced. The method expresses high ability in both short- and long- term forecasting of the outbreak. The model proves that in predicting one class (like the number of confirmed cases), the effect of other accompanying numbers (like death and recovered cases) cannot be ignored. In conclusion, the superiorities of this model (particularity the long term predication ability) turn it into a reliable tool for helping the health decision-makers.

Discrimination of multiple sclerosis using scanning laser ophthalmoscopy images with autoencoder-based feature extraction.

OBJECTIVE: Optical coherence tomography (OCT) investigations have revealed that the thickness of inner retinal layers becomes decreased in multiple sclerosis (MS) patients, compared to healthy control (HC) individuals. To date, a number of studies have applied machine learning to OCT thickness measurements, aiming to enable accurate and automated diagnosis of the disease. However, there have much less emphasis on other less common retinal imaging modalities, like infrared scanning laser ophthalmoscopy (IR-SLO), for classifying MS. IR-SLO uses laser light to capture high-resolution fundus images, often performed in conjunction with OCT to lock B-scans at a fixed position. METHODS: We incorporated two independent datasets of IR-SLO images from the Isfahan and Johns Hopkins centers, consisting of 164 MS and 150 HC images. A subject-wise data splitting approach was employed to ensure that there was no leakage between training and test datasets. Several state-of-the-art convolutional neural networks (CNNs), including VGG-16, VGG-19, ResNet-50, and InceptionV3, and a CNN with a custom architecture were employed. In the next step, we designed a convolutional autoencoder (CAE) to extract semantic features subsequently given as inputs to four conventional ML classifiers, including support vector machine (SVM), k-nearest neighbor (K-NN), random forest (RF), and multi-layer perceptron (MLP). RESULTS: The custom CNN (85 % accuracy, 85 % sensitivity, 87 % specificity, 93 % area under the receiver operating characteristics [AUROC], and 94 % area under the precision-recall curve [AUPRC]) outperformed state-of-the-art models (84 % accuracy, 83 % sensitivity, 87 % specificity, 92 % AUROC, and 94 % AUPRC); however, utilizing a combination of the CAE and MLP yields even superior results (88 % accuracy, 86 % sensitivity, 91 % specificity, 94 % AUROC, and 95 % AUPRC). CONCLUSIONS: We utilized IR-SLO images to differentiate between MS and HC eyes, with promising results achieved using a combination of CAE and MLP. Future multi-center studies involving more heterogenous data are necessary to assess the feasibility of integrating IR-SLO images into routine clinical practice.

SLO-Net: Enhancing Multiple Sclerosis Diagnosis Beyond Optical Coherence Tomography Using Infrared Reflectance Scanning Laser Ophthalmoscopy Images.

Purpose: Several machine learning studies have used optical coherence tomography (OCT) for multiple sclerosis (MS) classification with promising outcomes. Infrared reflectance scanning laser ophthalmoscopy (IR-SLO) captures high-resolution fundus images, commonly combined with OCT for fixed B-scan positions. However, no machine learning research has utilized IR-SLO images for automated MS diagnosis. Methods: This study utilized a dataset comprised of IR-SLO images and OCT data from Isfahan, Iran, encompassing 32 MS and 70 healthy individuals. A number of convolutional neural networks (CNNs)-namely, VGG-16, VGG-19, ResNet-50, ResNet-101, and a custom architecture-were trained with both IR-SLO images and OCT thickness maps as two separate input datasets. The highest performing models for each modality were then integrated to create a bimodal model that receives the combination of OCT thickness maps and IR-SLO images. Subject-wise data splitting was employed to prevent data leakage among training, validation, and testing sets. Results: Overall, images of the 102 patients from the internal dataset were divided into test, validation, and training subsets. Subsequently, we employed a bootstrapping approach on the training data through iterative sampling with replacement. The performance of the proposed bimodal model was evaluated on the internal test dataset, demonstrating an accuracy of 92.40% ± 4.1% (95% confidence interval [CI], 83.61-98.08), sensitivity of 95.43% ± 5.75% (95% CI, 83.71-100.0), specificity of 92.82% ± 3.72% (95% CI, 81.15-96.77), area under the receiver operating characteristic (AUROC) curve of 96.99% ± 2.99% (95% CI, 86.11-99.78), and area under the precision-recall curve (AUPRC) of 97.27% ± 2.94% (95% CI, 86.83-99.83). Furthermore, to assess the model generalization ability, we examined its performance on an external test dataset following the same bootstrap methodology, achieving promising results, with accuracy of 85.43% ± 0.08% (95% CI, 71.43-100.0), sensitivity of 97.33% ± 0.06% (95% CI, 83.33-100.0), specificity of 84.6% ± 0.10% (95% CI, 71.43-100.0), AUROC curve of 99.67% ± 0.02% (95% CI, 95.63-100.0), and AUPRC of 99.65% ± 0.02% (95% CI, 94.90-100.0). Conclusions: Incorporating both modalities improves the performance of automated diagnosis of MS, showcasing the potential of utilizing IR-SLO as a complementary tool alongside OCT. Translational Relevance: Should the results of our proposed bimodal model be validated in future work with larger and more diverse datasets, diagnosis of MS based on both OCT and IR-SLO can be reliably integrated into routine clinical practice.

A new convolutional neural network based on combination of circlets and wavelets for macular OCT classification.

Artificial intelligence (AI) algorithms, encompassing machine learning and deep learning, can assist ophthalmologists in early detection of various ocular abnormalities through the analysis of retinal optical coherence tomography (OCT) images. Despite considerable progress in these algorithms, several limitations persist in medical imaging fields, where a lack of data is a common issue. Accordingly, specific image processing techniques, such as time-frequency transforms, can be employed in conjunction with AI algorithms to enhance diagnostic accuracy. This research investigates the influence of non-data-adaptive time-frequency transforms, specifically X-lets, on the classification of OCT B-scans. For this purpose, each B-scan was transformed using every considered X-let individually, and all the sub-bands were utilized as the input for a designed 2D Convolutional Neural Network (CNN) to extract optimal features, which were subsequently fed to the classifiers. Evaluating per-class accuracy shows that the use of the 2D Discrete Wavelet Transform (2D-DWT) yields superior outcomes for normal cases, whereas the circlet transform outperforms other X-lets for abnormal cases characterized by circles in their retinal structure (due to the accumulation of fluid). As a result, we propose a novel transform named CircWave by concatenating all sub-bands from the 2D-DWT and the circlet transform. The objective is to enhance the per-class accuracy of both normal and abnormal cases simultaneously. Our findings show that classification results based on the CircWave transform outperform those derived from original images or any individual transform. Furthermore, Grad-CAM class activation visualization for B-scans reconstructed from CircWave sub-bands highlights a greater emphasis on circular formations in abnormal cases and straight lines in normal cases, in contrast to the focus on irrelevant regions in original B-scans. To assess the generalizability of our method, we applied it to another dataset obtained from a different imaging system. We achieved promising accuracies of 94.5% and 90% for the first and second datasets, respectively, which are comparable with results from previous studies. The proposed CNN based on CircWave sub-bands (i.e. CircWaveNet) not only produces superior outcomes but also offers more interpretable results with a heightened focus on features crucial for ophthalmologists.

COVID-19 in Iran: Forecasting Pandemic Using Deep Learning.

COVID-19 has led to a pandemic, affecting almost all countries in a few months. In this work, we applied selected deep learning models including multilayer perceptron, random forest, and different versions of long short-term memory (LSTM), using three data sources to train the models, including COVID-19 occurrences, basic information like coded country names, and detailed information like population, and area of different countries. The main goal is to forecast the outbreak in nine countries (Iran, Germany, Italy, Japan, Korea, Switzerland, Spain, China, and the USA). The performances of the models are measured using four metrics, including mean average percentage error (MAPE), root mean square error (RMSE), normalized RMSE (NRMSE), and R 2. The best performance was found for a modified version of LSTM, called M-LSTM (winner model), to forecast the future trajectory of the pandemic in the mentioned countries. For this purpose, we collected the data from January 22 till July 30, 2020, for training, and from 1 August 2020 to 31 August 2020, for the testing phase. Through experimental results, the winner model achieved reasonably accurate predictions (MAPE, RMSE, NRMSE, and R 2 are 0.509, 458.12, 0.001624, and 0.99997, respectively). Furthermore, we stopped the training of the model on some dates related to main country actions to investigate the effect of country actions on predictions by the model.

Protein kinase inhibitors' classification using K-Nearest neighbor algorithm.

Protein kinases are enzymes acting as a source of phosphate through ATP to regulate protein biological activities by phosphorylating groups of specific amino acids. For that reason, inhibiting protein kinases with an active small molecule plays a significant role in cancer treatment. To achieve this aim, computational drug design, especially QSAR model, is one of the best economical approaches to reduce time and save in costs. In this respect, active inhibitors are attempted to be distinguished from inactive ones using hybrid QSAR model. Therefore, genetic algorithm and K-Nearest Neighbor method were suggested as a dimensional reduction and classification model, respectively. Finally, to evaluate the proposed model's performance, support vector machine and Naïve Bayesian algorithm were examined. The outputs of the proposed model demonstrated significant superiority to other QSAR models.