Ubiquitination is a common post-translational modification of proteins in eukaryotic cells, and it is also a significant method of regulating protein biological function. The use of computational methods for predicting ubiquitination sites can replace costly and time-consuming experimental methods. Existing computational methods often build classifiers based on protein sequence information, physical and chemical properties of amino acids, evolutionary information, and structural parameters. However, structural information about most proteins cannot be found in existing databases directly. The features of proteins differ among species, and some species have small amounts of ubiquitinated proteins. Therefore, it is necessary to develop species-specific models that can be applied to datasets with small sample sizes. To solve these problems, we propose a species-specific model (SSUbi) based on a capsule network, which integrates proteins\' sequence and structural information. In this model, the feature extraction module is composed of two sub-modules that extract multi-dimensional features from sequence and structural information respectively. In the submodule, the convolution operation is used to extract encoding dimension features, and the channel attention mechanism is used to extract feature map dimension features. After the multi-dimensional features of the two kinds of information are integrated, the species-specific capsule network further converts the features into capsule vectors and classifies species-specific ubiquitination sites. The experimental results show that SSUbi can effectively improve the prediction performance of species with small sample sizes and outperform other models.

COVID-19 has resulted in a significant global impact on health, the economy, education, and daily life. The disease can range from mild to severe, with individuals over 65 or those with underlying medical conditions being more susceptible to severe illness. Early testing and isolation are vital due to the virus\'s variable incubation period. Chest radiographs (CXR) have gained importance as a diagnostic tool due to their efficiency and reduced radiation exposure compared to CT scans. However, the sensitivity of CXR in detecting COVID-19 may be lower. This paper introduces a deep learning framework for accurate COVID-19 classification and severity prediction using CXR images. U-Net is used for lung segmentation, achieving a precision of 0.9924. Classification is performed using a Convulation-capsule network, with high true positive rates of 86% for COVID-19, 93% for pneumonia, and 85% for normal cases. Severity assessment employs ResNet50, VGG-16, and DenseNet201, with DenseNet201 showing superior accuracy. Empirical results, validated with 95% confidence intervals, confirm the framework\'s reliability and robustness. This integration of advanced deep learning techniques with radiological imaging enhances early detection and severity assessment, improving patient management and resource allocation in clinical settings.

Conditions affecting the heel bone, such as heel spurs and sever\'s disease, pose significant challenges to patients\' daily activities. While orthopedic and traumatology doctors rely on foot X-rays for diagnosis, there is a need for more AI-based detection and classification of these conditions. Therefore, this study addresses this need by proposing MedcapsNet, a novel hybrid capsule model combining modified DenseNet201 with a capsule network, designed to accurately detect and classify heel bone diseases utilizing lateral heel x-ray foot images. We conducted a comprehensive series of experiments on the proposed hybrid architecture with several datasets, including the Heel dataset, Breast BreaKHis v1, HAM10000 skin cancer dataset, and Jun Cheng Brain MRI dataset. The first experiment evaluates the proposed model for heel diseases, while the other experiments evaluate the model on a range of medical datasets to demonstrate its performance over existing studies. On the heel dataset, MedCapsNet achieves an accuracy of 96.38%, AUC of 98.35% without data augmentation, cross-validation accuracy of 95.69%, and AUC of 98.87%. The proposed model, despite employing a fixed architecture and hyperparameters, outperformed other models across four distinct datasets, including MRI, X-ray, and microscopic images with various diseases. This is notable because different types of medical image datasets typically require different architectures and hyperparameters to achieve optimal performance.

Genes are the basic units of protein synthesis in organisms, and accurately identifying the translation initiation site (TIS) of genes is crucial for understanding the regulation, transcription, and translation processes of genes. However, the existing models cannot adequately extract the feature information in TIS sequences, and they also inadequately capture the complex hierarchical relationships among features. Therefore, a novel predictor named CapsNet-TIS is proposed in this paper. CapsNet-TIS first fully extracts the TIS sequence information using four encoding methods, including One-hot encoding, physical structure property (PSP) encoding, nucleotide chemical property (NCP) encoding, and nucleotide density (ND) encoding. Next, multi-scale convolutional neural networks are used to perform feature fusion of the encoded features to enhance the comprehensiveness of the feature representation. Finally, the fused features are classified using capsule network as the main network of the classification model to capture the complex hierarchical relationships among the features. Moreover, we improve the capsule network by introducing residual block, channel attention, and BiLSTM to enhance the model\'s feature extraction and sequence data modeling capabilities. In this paper, the performance of CapsNet-TIS is evaluated using TIS datasets from four species: human, mouse, bovine, and fruit fly, and the effectiveness of each part is demonstrated by performing ablation experiments. By comparing the experimental results with models proposed by other researchers, the results demonstrate the superior performance of CapsNet-TIS.

Prediction of binding sites for transcription factors is important to understand how the latter regulate gene expression and how this regulation can be modulated for therapeutic purposes. A consistent number of references address this issue with different approaches, Machine Learning being one of the most successful. Nevertheless, we note that many such approaches fail to propose a robust and meaningful method to embed the genetic data under analysis. We try to overcome this problem by proposing a bidirectional transformer-based encoder, empowered by bidirectional long-short term memory layers and with a capsule layer responsible for the final prediction. To evaluate the efficiency of the proposed approach, we use benchmark ChIP-seq datasets of five cell lines available in the ENCODE repository (A549, GM12878, Hep-G2, H1-hESC, and Hela). The results show that the proposed method can predict TFBS within the five different cell lines very well; moreover, cross-cell predictions provide satisfactory results as well. Experiments conducted across cell lines are reinforced by the analysis of five additional lines used only to test the model trained using the others. The results confirm that prediction across cell lines remains very high, allowing an extensive cross-transcription factor analysis to be performed from which several indications of interest for molecular biology may be drawn.

Kiwifruit soft rot is highly contagious and causes serious economic loss. Therefore, early detection and elimination of soft rot are important for postharvest treatment and storage of kiwifruit. This study aims to accurately detect kiwifruit soft rot based on hyperspectral images by using a deep learning approach for image classification. A dual-branch selective attention capsule network (DBSACaps) was proposed to improve the classification accuracy. The network uses two branches to separately extract the spectral and spatial features so as to reduce their mutual interference, followed by fusion of the two features through the attention mechanism. Capsule network was used instead of convolutional neural networks to extract the features and complete the classification. Compared with existing methods, the proposed method exhibited the best classification performance on the kiwifruit soft rot dataset, with an overall accuracy of 97.08% and a 97.83% accuracy for soft rot. Our results confirm that potential soft rot of kiwifruit can be detected using hyperspectral images, which may contribute to the construction of smart agriculture.

Diabetic retinopathy is considered one of the most common diseases that can lead to blindness in the working age, and the chance of developing it increases as long as a person suffers from diabetes. Protecting the sight of the patient or decelerating the evolution of this disease depends on its early detection as well as identifying the exact levels of this pathology, which is done manually by ophthalmologists. This manual process is very consuming in terms of the time and experience of an expert ophthalmologist, which makes developing an automated method to aid in the diagnosis of diabetic retinopathy an essential and urgent need. In this paper, we aim to propose a new hybrid deep learning method based on a fine-tuning vision transformer and a modified capsule network for automatic diabetic retinopathy severity level prediction. The proposed approach consists of a new range of computer vision operations, including the power law transformation technique and the contrast-limiting adaptive histogram equalization technique in the preprocessing step. While the classification step builds up on a fine-tuning vision transformer, a modified capsule network, and a classification model combined with a classification model, The effectiveness of our approach was evaluated using four datasets, including the APTOS, Messidor-2, DDR, and EyePACS datasets, for the task of severity levels of diabetic retinopathy. We have attained excellent test accuracy scores on the four datasets, respectively: 88.18%, 87.78%, 80.36%, and 78.64%. Comparing our results with the state-of-the-art, we reached a better performance.

Cropping-and-segmenting pattern parsers often combine diverse inner correlations into a single metric/scheme, resulting in over-generalizations and redundant representations. It is proposed to streamline pattern parsing by using presenting a redundant association elimination network (RAEN) with capsule attention twisters (CATs) and capsule-attention routing agreement (CARA). CATs trim delicate relationships between parts and wholes that are weak and interchangeable. Senior entities can only be updated by primary entities that meet the requirements of inter-part diversity and intra-object cohesiveness. In order to enhance results, CARA is designed to protect against the unnecessary voting signals of traditional routing protocols. Experiments involving facial and human segmentation show that RAEN is better than current remarkable methods, particularly for defining detailed semantic boundaries.

Skin cancer is a prevalent type of malignancy on a global scale, and the early and accurate diagnosis of this condition is of utmost importance for the survival of patients. The clinical assessment of cutaneous lesions is a crucial aspect of medical practice, although it encounters several obstacles, such as prolonged waiting time and misinterpretation. The intricate nature of skin lesions, coupled with variations in appearance and texture, presents substantial barriers to accurate classification. As such, skilled clinicians often struggle to differentiate benign moles from early malignant tumors in skin images. Although deep learning-based approaches such as convolution neural networks have made significant improvements, their stability and generalization continue to experience difficulties, and their performance in accurately delineating lesion borders, capturing refined spatial connections among features, and using contextual information for classification is suboptimal. To address these limitations, we propose a novel approach for skin lesion classification that combines snake models of active contour (AC) segmentation, ResNet50 for feature extraction, and a capsule network with a fusion of lightweight attention mechanisms to attain the different feature channels and spatial regions within feature maps, enhance the feature discrimination, and improve accuracy. We employed the stochastic gradient descent (SGD) optimization algorithm to optimize the model\'s parameters. The proposed model is implemented on publicly available datasets, namely, HAM10000 and ISIC 2020. The experimental results showed that the proposed model achieved an accuracy of 98% and AUC-ROC of 97.3%, showcasing substantial potential in terms of effective model generalization compared to existing state-of-the-art (SOTA) approaches. These results highlight the potential for our approach to reshape automated dermatological diagnosis and provide a helpful tool for medical practitioners.

DNA N6-methyladenine (6mA) modifications play a pivotal role in the regulation of growth, development, and diseases in organisms. As a significant epigenetic marker, 6mA modifications extensively participate in the intricate regulatory networks of the genome. Hence, gaining a profound understanding of how 6mA is intricately involved in these biological processes is imperative for deciphering the gene regulatory networks within organisms. In this study, we propose PSAC-6mA (Position-self-attention Capsule-6mA), a sequence-location-based self-attention capsule network. The positional layer in the model enables positional relationship extraction and independent parameter setting for each base position, avoiding parameter sharing inherent in convolutional approaches. Simultaneously, the self-attention capsule network enhances dimensionality, capturing correlation information between capsules and achieving exceptional results in feature extraction across multiple spatial dimensions within the model. Experimental results demonstrate the superior performance of PSAC-6mA in recognizing 6mA motifs across various species.