Research progress on prediction of RNA-protein binding sites in the past five years.

Accurately predicting RNA-protein binding sites is essential to gain a deeper comprehension of the protein-RNA interactions and their regulatory mechanisms, which are fundamental in gene expression and regulation. However, conventional biological approaches to detect these sites are often costly and time-consuming. In contrast, computational methods for predicting RNA protein binding sites are both cost-effective and expeditious. This review synthesizes already existing computational methods, summarizing commonly used databases for predicting RNA protein binding sites. In addition, applications and innovations of computational methods using traditional machine learning and deep learning for RNA protein binding site prediction during 2018-2023 are presented. These methods cover a wide range of aspects such as effective database utilization, feature selection and encoding, innovative classification algorithms, and evaluation strategies. Exploring the limitations of existing computational methods, this paper delves into the potential directions for future development. DeepRKE, RDense, and DeepDW all employ convolutional neural networks and long and short-term memory networks to construct prediction models, yet their algorithm design and feature encoding differ, resulting in diverse prediction performances.

IMU-Based Fitness Activity Recognition Using CNNs for Time Series Classification.

Mobile fitness applications provide the opportunity to show users real-time feedback on their current fitness activity. For such applications, it is essential to accurately track the user's current fitness activity using available mobile sensors, such as inertial measurement units (IMUs). Convolutional neural networks (CNNs) have been shown to produce strong results in different time series classification tasks, including the recognition of daily living activities. However, fitness activities can present unique challenges to the human activity recognition task (HAR), including greater similarity between individual activities and fewer available data for model training. In this paper, we evaluate the applicability of CNNs to the fitness activity recognition task (FAR) using IMU data and determine the impact of input data size and sensor count on performance. For this purpose, we adapted three existing CNN architectures to the FAR task and designed a fourth CNN variant, which we call the scaling fully convolutional network (Scaling-FCN). We designed a preprocessing pipeline and recorded a running exercise data set with 20 participants, in which we evaluated the respective recognition performances of the four networks, comparing them with three traditional machine learning (ML) methods commonly used in HAR. Although CNN architectures achieve at least 94% test accuracy in all scenarios, two traditional ML architectures surpass them in the default scenario, with support vector machines (SVMs) achieving 99.00 ± 0.34% test accuracy. The removal of all sensors except one foot sensor reduced the performance of traditional ML architectures but improved the performance of CNN architectures on our data set, with our Scaling-FCN reaching the highest accuracy of 99.86 ± 0.11% on the test set. Our results suggest that CNNs are generally well suited for fitness activity recognition, and noticeable performance improvements can be achieved if sensors are dropped selectively, although traditional ML architectures can still compete with or even surpass CNNs when favorable input data are utilized.

Pervasive Lying Posture Tracking.

Automated lying-posture tracking is important in preventing bed-related disorders, such as pressure injuries, sleep apnea, and lower-back pain. Prior research studied in-bed lying posture tracking using sensors of different modalities (e.g., accelerometer and pressure sensors). However, there remain significant gaps in research regarding how to design efficient in-bed lying posture tracking systems. These gaps can be articulated through several research questions, as follows. First, can we design a single-sensor, pervasive, and inexpensive system that can accurately detect lying postures? Second, what computational models are most effective in the accurate detection of lying postures? Finally, what physical configuration of the sensor system is most effective for lying posture tracking? To answer these important research questions, in this article we propose a comprehensive approach for designing a sensor system that uses a single accelerometer along with machine learning algorithms for in-bed lying posture classification. We design two categories of machine learning algorithms based on deep learning and traditional classification with handcrafted features to detect lying postures. We also investigate what wearing sites are the most effective in the accurate detection of lying postures. We extensively evaluate the performance of the proposed algorithms on nine different body locations and four human lying postures using two datasets. Our results show that a system with a single accelerometer can be used with either deep learning or traditional classifiers to accurately detect lying postures. The best models in our approach achieve an F1 score that ranges from 95.2% to 97.8% with a coefficient of variation from 0.03 to 0.05. The results also identify the thighs and chest as the most salient body sites for lying posture tracking. Our findings in this article suggest that, because accelerometers are ubiquitous and inexpensive sensors, they can be a viable source of information for pervasive monitoring of in-bed postures.

Assessing the effectiveness of artificial intelligence methods for melanoma: A retrospective review.

BACKGROUND: Artificial intelligence methods for the classification of melanoma have been studied extensively. However, few studies compare these methods under the same standards. OBJECTIVE: To seek the best artificial intelligence method for diagnosis of melanoma. METHODS: The contrast test used 2200 dermoscopic images. Image segmentations, feature extractions, and classifications were performed in sequence for evaluation of traditional machine learning algorithms. The recent popular convolutional neural network frameworks were used for transfer learning training classification. RESULTS: The region growing algorithm has the best segmentation performance, with an intersection over union of 70.06% and a false-positive rate of 17.67%. Classification performance was better with logistic regression, with a sensitivity of 76.36% and a specificity of 87.04%. The Inception V3 model (Google, Mountain View, CA) worked best in deep learning algorithms: the accuracy was 93.74%, the sensitivity was 94.36%, and the specificity was 85.64%. LIMITATIONS: There was no division in the severity of melanoma samples used in this experiment. The data set was relatively small for deep learning. CONCLUSION: The performance of traditional machine learning is satisfactory for the small data set of melanoma dermoscopic images, and the potential for deep learning in the future big data era is enormous.

Recognizing the Differentiation Degree of Human Induced Pluripotent Stem Cell-Derived Retinal Pigment Epithelium Cells Using Machine Learning and Deep Learning-Based Approaches.

Induced pluripotent stem cells (iPSCs) can be differentiated into mesenchymal stem cells (iPSC-MSCs), retinal ganglion cells (iPSC-RGCs), and retinal pigmental epithelium cells (iPSC-RPEs) to meet the demand of regeneration medicine. Since the production of iPSCs and iPSC-derived cell lineages generally requires massive and time-consuming laboratory work, artificial intelligence (AI)-assisted approach that can facilitate the cell classification and recognize the cell differentiation degree is of critical demand. In this study, we propose the multi-slice tensor model, a modified convolutional neural network (CNN) designed to classify iPSC-derived cells and evaluate the differentiation efficiency of iPSC-RPEs. We removed the fully connected layers and projected the features using principle component analysis (PCA), and subsequently classified iPSC-RPEs according to various differentiation degree. With the assistance of the support vector machine (SVM), this model further showed capabilities to classify iPSCs, iPSC-MSCs, iPSC-RPEs, and iPSC-RGCs with an accuracy of 97.8%. In addition, the proposed model accurately recognized the differentiation of iPSC-RPEs and showed the potential to identify the candidate cells with ideal features and simultaneously exclude cells with immature/abnormal phenotypes. This rapid screening/classification system may facilitate the translation of iPSC-based technologies into clinical uses, such as cell transplantation therapy.

Analyzing the public sentiment on COVID-19 vaccination in social media: Bangladesh context.

Since December 2019, the world has been fighting against the COVID-19 pandemic. This epidemic has revealed a bitter truth that though humans have advanced to unprecedented heights in the last few decades in terms of technology, they are lagging far behind in the fields of medical science and health care. Several institutes and research organizations have stepped up to introduce different vaccines to combat the pandemic. Bangladesh government has also taken steps to provide widespread vaccinations from January 2021. The Bangladeshi netizens are frequently sharing their thoughts, emotions, and experiences about the COVID-19 vaccines and the vaccination process on different social media sites like Facebook, Twitter, etc. This study has analyzed the views and opinions that they have expressed on different social media platforms about the vaccines and the ongoing vaccination program. For performing this study, the reactions of the Bangladeshi netizens on social media have been collected. The Latent Dirichlet Allocation (LDA) model has been used to extract the most common topics expressed by the netizens regarding the vaccines and vaccination process in Bangladesh. Finally, this study has applied different deep learning as well as traditional machine learning algorithms to identify the sentiments and polarity of the opinions of the netizens. The performance of these models has been assessed using a variety of metrics such as accuracy, precision, sensitivity, specificity, and F1-score to identify the best one. Sentiment analysis lessons from these opinions can help the government to prepare itself for the future pandemic.

UPFPSR: a ubiquitylation predictor for plant through combining sequence information and random forest.

As one of the most significant protein post-translational modifications (PTMs) in eukaryotes, ubiquitylation plays an essential role in regulating diverse cellular functions, such as apoptosis, cell division, DNA repair and replication, intracellular transport and immune reactions. Traditional experimental methods have the defect of being time-consuming, costly and labor-intensive. Therefore, it is highly desired to develop automated computational methods that can recognize potential ubiquitylation sites rapidly and accurately. In this study, we propose a novel predictor, named UPFPSR, for predicting lysine ubiquitylation sites in plant. UPFPSR is developed using multiple physicochemical properties of amino acids and sequence-based statistical information. In order to find a suitable classification algorithm, four traditional algorithms and two deep learning networks are compared, and the random forest with superior performance is selected ultimately. An extensive benchmarking shows that UPFPSR outperforms the most advanced ubiquitylation prediction tool on each measurement indicator, with the accuracy of 77.3%, precision of 75%, recall of 81.7%, F1-score of 0.7824, and AUC of 0.84 on the independent test dataset. The results indicate that UPFPSR can provide new guidance for further experimental study on ubiquitylation. The data sets and source code used in this study are freely available at https://github.com/ysw-sunshine/UPFPSR.

A review: The detection of cancer cells in histopathology based on machine vision.

Machine vision is being employed in defect detection, size measurement, pattern recognition, image fusion, target tracking and 3D reconstruction. Traditional cancer detection methods are dominated by manual detection, which wastes time and manpower, and heavily relies on the pathologists' skill and work experience. Therefore, these manual detection approaches are not convenient for the inheritance of domain knowledge, and are not suitable for the rapid development of medical care in the future. The emergence of machine vision can iteratively update and learn the domain knowledge of cancer cell pathology detection to achieve automated, high-precision, and consistent detection. Consequently, this paper reviews the use of machine vision to detect cancer cells in histopathology images, as well as the benefits and drawbacks of various detection approaches. First, we review the application of image preprocessing and image segmentation in histopathology for the detection of cancer cells, and compare the benefits and drawbacks of different algorithms. Secondly, for the characteristics of histopathological cancer cell images, the research progress of shape, color and texture features and other methods is mainly reviewed. Furthermore, for the classification methods of histopathological cancer cell images, the benefits and drawbacks of traditional machine vision approaches and deep learning methods are compared and analyzed. Finally, the above research is discussed and forecasted, with the expected future development tendency serving as a guide for future research.

Prediction of Type 2 Diabetes Risk and Its Effect Evaluation Based on the XGBoost Model.

In view of the harm of diabetes to the population, we have introduced an ensemble learning algorithm-EXtreme Gradient Boosting (XGBoost) to predict the risk of type 2 diabetes and compared it with Support Vector Machines (SVM), the Random Forest (RF) and K-Nearest Neighbor (K-NN) algorithm in order to improve the prediction effect of existing models. The combination of convenient sampling and snowball sampling in Xicheng District, Beijing was used to conduct a questionnaire survey on the personal data, eating habits, exercise status and family medical history of 380 middle-aged and elderly people. Then, we trained the models and obtained the disease risk index for each sample with 10-fold cross-validation. Experiments were made to compare the commonly used machine learning algorithms mentioned above and we found that XGBoost had the best prediction effect, with an average accuracy of 0.8909 and the area under the receiver's working characteristic curve (AUC) was 0.9182. Therefore, due to the superiority of its architecture, XGBoost has more outstanding prediction accuracy and generalization ability than existing algorithms in predicting the risk of type 2 diabetes, which is conducive to the intelligent prevention and control of diabetes in the future.

A review on brain tumor diagnosis from MRI images: Practical implications, key achievements, and lessons learned.

The successful early diagnosis of brain tumors plays a major role in improving the treatment outcomes and thus improving patient survival. Manually evaluating the numerous magnetic resonance imaging (MRI) images produced routinely in the clinic is a difficult process. Thus, there is a crucial need for computer-aided methods with better accuracy for early tumor diagnosis. Computer-aided brain tumor diagnosis from MRI images consists of tumor detection, segmentation, and classification processes. Over the past few years, many studies have focused on traditional or classical machine learning techniques for brain tumor diagnosis. Recently, interest has developed in using deep learning techniques for diagnosing brain tumors with better accuracy and robustness. This study presents a comprehensive review of traditional machine learning techniques and evolving deep learning techniques for brain tumor diagnosis. This review paper identifies the key achievements reflected in the performance measurement metrics of the applied algorithms in the three diagnosis processes. In addition, this study discusses the key findings and draws attention to the lessons learned as a roadmap for future research.