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Deep Self-Attention Network (Transformer) is an encoder–decoder architectural model that excels in establishing long-distance dependencies and is first applied in natural language processing. Due to its complementary nature with the inductive bias of convolutional neural network (CNN), Transformer has been gradually applied to medical image processing, including kidney image processing. It has become a hot research topic in recent years. To further explore new ideas and directions in the field of renal image processing, this paper outlines the characteristics of the Transformer network model and summarizes the application of the Transformer-based model in renal image segmentation, classification, detection, electronic medical records, and decision-making systems, and compared with CNN-based renal image processing algorithm, analyzing the advantages and disadvantages of this technique in renal image processing. In addition, this paper gives an outlook on the development trend of Transformer in renal image processing, which provides a valuable reference for a lot of renal image analysis. [ABSTRACT FROM AUTHOR]

Background: Applying graph convolutional networks (GCN) to the classification of free-form natural language texts leveraged by graph-of-words features (TextGCN) was studied and confirmed to be an effective means of describing complex natural language texts. However, the text classification models based on the TextGCN possess weaknesses in terms of memory consumption and model dissemination and distribution. In this paper, we present a fast message passing network (FastMPN), implementing a GCN with message passing architecture that provides versatility and flexibility by allowing trainable node embedding and edge weights, helping the GCN model find the better solution. We applied the FastMPN model to the task of clinical information extraction from cancer pathology reports, extracting the following six properties: main site, subsite, laterality, histology, behavior, and grade. Results: We evaluated the clinical task performance of the FastMPN models in terms of micro- and macro-averaged F1 scores. A comparison was performed with the multi-task convolutional neural network (MT-CNN) model. Results show that the FastMPN model is equivalent to or better than the MT-CNN. Conclusions: Our implementation revealed that our FastMPN model, which is based on the PyTorch platform, can train a large corpus (667,290 training samples) with 202,373 unique words in less than 3 minutes per epoch using one NVIDIA V100 hardware accelerator. Our experiments demonstrated that using this implementation, the clinical task performance scores of information extraction related to tumors from cancer pathology reports were highly competitive. [ABSTRACT FROM AUTHOR]

Background: Mild cognitive impairment (MCI) is the transition stage between the cognitive decline expected in normal aging and more severe cognitive decline such as dementia. The early diagnosis of MCI plays an important role in human healthcare. Current methods of MCI detection include cognitive tests to screen for executive function impairments, possibly followed by neuroimaging tests. However, these methods are expensive and time-consuming. Several studies have demonstrated that MCI and dementia can be detected by machine learning technologies from different modality data. This study proposes a multi-stream convolutional neural network (MCNN) model to predict MCI from face videos. Results: The total effective data are 48 facial videos from 45 participants, including 35 videos from normal cognitive participants and 13 videos from MCI participants. The videos are divided into several segments. Then, the MCNN captures the latent facial spatial features and facial dynamic features of each segment and classifies the segment as MCI or normal. Finally, the aggregation stage produces the final detection results of the input video. We evaluate 27 MCNN model combinations including three ResNet architectures, three optimizers, and three activation functions. The experimental results showed that the ResNet-50 backbone with Swish activation function and Ranger optimizer produces the best results with an F1-score of 89% at the segment level. However, the ResNet-18 backbone with Swish and Ranger achieves the F1-score of 100% at the participant level. Conclusions: This study presents an efficient new method for predicting MCI from facial videos. Studies have shown that MCI can be detected from facial videos, and facial data can be used as a biomarker for MCI. This approach is very promising for developing accurate models for screening MCI through facial data. It demonstrates that automated, non-invasive, and inexpensive MCI screening methods are feasible and do not require highly subjective paper-and-pencil questionnaires. Evaluation of 27 model combinations also found that ResNet-50 with Swish is more stable for different optimizers. Such results provide directions for hyperparameter tuning to further improve MCI predictions. [ABSTRACT FROM AUTHOR]

The epidemic diseases such as COVID-19 are rapidly spreading all around the world. The diagnosis of epidemic at initial stage is of high importance to provide medical care to and recovery of infected people as well as protecting the uninfected population. In this paper, an automatic COVID-19 detection model using respiratory sound and medical image based on internet of health things (IoHT) is proposed. In this model, primarily to screen those people having suspected Coronavirus disease, the sound of coughing used to detect healthy people and those suffering from COVID-19, which finally obtained an accuracy of 94.999%. This approach not only expedites diagnosis and enhances accuracy but also facilitates swift screening in public places using simple equipment. Then, in the second step, in order to help radiologists to interpret medical images as best as possible, we use three pre-trained convolutional neural network models InceptionResNetV2, InceptionV3 and EfficientNetB4 and two data sets of chest radiology medical images, and CT Scan in a three-class classification. Utilizing transfer learning and pre-existing knowledge in these models leads to notable improvements in disease diagnosis and identification compared to traditional techniques. Finally, the best result obtained for CT-Scan images belonging to InceptionResNetV2 architecture with 99.414% accuracy and for radiology images related to InceptionV3 and EfficientNetB4 architectures with the accuracy is 96.943%. Therefore, the proposed model can help radiology specialists to confirm the initial assessments of the COVID-19 disease. [ABSTRACT FROM AUTHOR]

Deep learning is a highly significant technology in clinical treatment and diagnostics nowadays. Convolutional Neural Network (CNN) is a new idea in deep learning that is being used in the area of computer vision. The COVID-19 detection is the subject of our medical study. Researchers attempted to increase the detection accuracy but at the cost of high model complexity. In this paper, we desire to achieve better accuracy with little training space and time so that this model easily deployed in edge devices. In this paper, a new CNN design is proposed that has three stages: pre-processing, which removes the black padding on the side initially; convolution, which employs filter banks; and feature extraction, which makes use of deep convolutional layers with skip connections. In order to train the model, chest X-ray images are partitioned into three sets: learning(0.7), validation(0.1), and testing(0.2). The models are then evaluated using the test and training data. The LMNet, CoroNet, CVDNet, and Deep GRU-CNN models are the other four models used in the same experiment. The propose model achieved 99.47% & 98.91% accuracy on training and testing respectively. Additionally, it achieved 97.54%, 98.19%, 99.49%, and 97.86% scores for precision, recall, specificity, and f1-score respectively. The proposed model obtained nearly equivalent accuracy and other similar metrics when compared with other models but greatly reduced the model complexity. Moreover, it is found that proposed model is less prone to over fitting as compared to other models. [ABSTRACT FROM AUTHOR]

Deep learning shows great promise for medical image analysis but often lacks explainability, hindering its adoption in healthcare. Attribution techniques that explain model reasoning can potentially increase trust in deep learning among clinical stakeholders. In the literature, much of the research on attribution in medical imaging focuses on visual inspection rather than statistical quantitative analysis. In this paper, we proposed an image-based saliency framework to enhance the explainability of deep learning models in medical image analysis. We use adaptive path-based gradient integration, gradient-free techniques, and class activation mapping along with its derivatives to attribute predictions from brain tumor MRI and COVID-19 chest X-ray datasets made by recent deep convolutional neural network models. The proposed framework integrates qualitative and statistical quantitative assessments, employing Accuracy Information Curves (AICs) and Softmax Information Curves (SICs) to measure the effectiveness of saliency methods in retaining critical image information and their correlation with model predictions. Visual inspections indicate that methods such as ScoreCAM, XRAI, GradCAM, and GradCAM++ consistently produce focused and clinically interpretable attribution maps. These methods highlighted possible biomarkers, exposed model biases, and offered insights into the links between input features and predictions, demonstrating their ability to elucidate model reasoning on these datasets. Empirical evaluations reveal that ScoreCAM and XRAI are particularly effective in retaining relevant image regions, as reflected in their higher AUC values. However, SICs highlight variability, with instances of random saliency masks outperforming established methods, emphasizing the need for combining visual and empirical metrics for a comprehensive evaluation. The results underscore the importance of selecting appropriate saliency methods for specific medical imaging tasks and suggest that combining qualitative and quantitative approaches can enhance the transparency, trustworthiness, and clinical adoption of deep learning models in healthcare. This study advances model explainability to increase trust in deep learning among healthcare stakeholders by revealing the rationale behind predictions. Future research should refine empirical metrics for stability and reliability, include more diverse imaging modalities, and focus on improving model explainability to support clinical decision-making. [ABSTRACT FROM AUTHOR]

Background: Glaucoma, the second leading cause of global blindness, demands timely detection due to its asymptomatic progression. This paper introduces an advanced computerized system, integrates Machine Learning (ML), convolutional neural networks (CNNs), and image processing for accurate glaucoma detection using medical imaging data, surpassing prior research efforts. Method: Developing a hybrid glaucoma detection framework using CNNs (ResNet50, VGG-16) and Random Forest. Models analyze pre-processed retinal images independently, and post-processing rules combine predictions for an overall glaucoma impact assessment. Result: The hybrid framework achieves a significant 95.41% accuracy, with precision and recall at 99.37% and 88.37%, respectively. The F1 score, balancing precision and recall, reaches a commendable 93.52%. These results highlight the robustness and effectiveness of the hybrid framework in accurate glaucoma diagnosis. Conclusion: In summary, our research presents an innovative hybrid framework combining CNNs and traditional ML models for glaucoma detection. Using ResNet50, VGG-16, and Random Forest in an ensemble approach yields remarkable accuracy, precision, recall, and F1 score. These results showcase the methodology's potential to enhance glaucoma diagnosis, emphasizing its promising role in early detection and preventing irreversible vision loss. The integration of ML and DNNs in medical imaging analysis suggests a valuable path for future advancements in ophthalmic healthcare. [ABSTRACT FROM AUTHOR]

Background: MicroRNAs play a critical role in regulating gene expression by binding to specific target sites within gene transcripts, making the identification of microRNA targets a prominent focus of research. Conventional experimental methods for identifying microRNA targets are both time-consuming and expensive, prompting the development of computational tools for target prediction. However, the existing computational tools exhibit limited performance in meeting the demands of practical applications, highlighting the need to improve the performance of microRNA target prediction models. Results: In this paper, we utilize the most popular natural language processing and computer vision technologies to propose a novel approach, called TEC-miTarget, for microRNA target prediction based on transformer encoder and convolutional neural networks. TEC-miTarget treats RNA sequences as a natural language and encodes them using a transformer encoder, a widely used encoder in natural language processing. It then combines the representations of a pair of microRNA and its candidate target site sequences into a contact map, which is a three-dimensional array similar to a multi-channel image. Therefore, the contact map's features are extracted using a four-layer convolutional neural network, enabling the prediction of interactions between microRNA and its candidate target sites. We applied a series of comparative experiments to demonstrate that TEC-miTarget significantly improves microRNA target prediction, compared with existing state-of-the-art models. Our approach is the first approach to perform comparisons with other approaches at both sequence and transcript levels. Furthermore, it is the first approach compared with both deep learning-based and seed-match-based methods. We first compared TEC-miTarget's performance with approaches at the sequence level, and our approach delivers substantial improvements in performance using the same datasets and evaluation metrics. Moreover, we utilized TEC-miTarget to predict microRNA targets in long mRNA sequences, which involves two steps: selecting candidate target site sequences and applying sequence-level predictions. We finally showed that TEC-miTarget outperforms other approaches at the transcript level, including the popular seed match methods widely used in previous years. Conclusions: We propose a novel approach for predicting microRNA targets at both sequence and transcript levels, and demonstrate that our approach outperforms other methods based on deep learning or seed match. We also provide our approach as an easy-to-use software, TEC-miTarget, at https://github.com/tingpeng17/TEC-miTarget. Our results provide new perspectives for microRNA target prediction. [ABSTRACT FROM AUTHOR]

Pulmonary diseases are various pathological conditions that affect respiratory tissues and organs, making the exchange of gas challenging for animals inhaling and exhaling. It varies from gentle and self-limiting such as the common cold and catarrh, to life-threatening ones, such as viral pneumonia (VP), bacterial pneumonia (BP), and tuberculosis, as well as a severe acute respiratory syndrome, such as the coronavirus 2019 (COVID-19). The cost of diagnosis and treatment of pulmonary infections is on the high side, most especially in developing countries, and since radiography images (X-ray and computed tomography (CT) scan images) have proven beneficial in detecting various pulmonary infections, many machine learning (ML) models and image processing procedures have been utilized to identify these infections. The need for timely and accurate detection can be lifesaving, especially during a pandemic. This paper, therefore, suggested a deep convolutional neural network (DCNN) founded image detection model, optimized with image augmentation technique, to detect three (3) different pulmonary diseases (COVID-19, bacterial pneumonia, and viral pneumonia). The dataset containing four (4) different classes (healthy (10,325), COVID-19 (3,749), BP (883), and VP (1,478)) was utilized as training/testing data for the suggested model. The model's performance indicates high potential in detecting the three (3) classes of pulmonary diseases. The model recorded average detection accuracy of 94%, 95.4%, 99.4%, and 98.30%, and training/detection time of about 60/50 s. This result indicates the proficiency of the suggested approach when likened to the traditional texture descriptors technique of pulmonary disease recognition utilizing X-ray and CT scan images. This study introduces an innovative deep convolutional neural network model to enhance the detection of pulmonary diseases like COVID-19 and pneumonia using radiography. This model, notable for its accuracy and efficiency, promises significant advancements in medical diagnostics, particularly beneficial in developing countries due to its potential to surpass traditional diagnostic methods. [ABSTRACT FROM AUTHOR]

Purpose: Convolution operator-based neural networks have shown great success in medical image segmentation over the past decade. The U-shaped network with a codec structure is one of the most widely used models. Transformer, a technology used in natural language processing, can capture long-distance dependencies and has been applied in Vision Transformer to achieve state-of-the-art performance on image classification tasks. Recently, researchers have extended transformer to medical image segmentation tasks, resulting in good models. Methods: This review comprises publications selected through a Web of Science search. We focused on papers published since 2018 that applied the transformer architecture to medical image segmentation. We conducted a systematic analysis of these studies and summarized the results. Results: To better comprehend the benefits of convolutional neural networks and transformers, the construction of the codec and transformer modules is first explained. Second, the medical image segmentation model based on transformer is summarized. The typically used assessment markers for medical image segmentation tasks are then listed. Finally, a large number of medical segmentation datasets are described. Conclusion: Even if there is a pure transformer model without any convolution operator, the sample size of medical picture segmentation still restricts the growth of the transformer, even though it can be relieved by a pretraining model. More often than not, researchers are still designing models using transformer and convolution operators. [ABSTRACT FROM AUTHOR]

Background: The active functionalities of RNA are recognized to be heavily dependent on the structure and sequence. Therefore, a model that can accurately evaluate a design by giving RNA sequence-structure pairs would be a valuable tool for many researchers. Machine learning methods have been explored to develop such tools, showing promising results. However, two key issues remain. Firstly, the performance of machine learning models is affected by the features used to characterize RNA. Currently, there is no consensus on which features are the most effective for characterizing RNA sequence-structure pairs. Secondly, most existing machine learning methods extract features describing entire RNA molecule. We argue that it is essential to define additional features that characterize nucleotides and specific sections of RNA structure to enhance the overall efficacy of the RNA design process. Results: We develop two deep learning models for evaluating RNA sequence-secondary structure pairs. The first model, NU-ResNet, uses a convolutional neural network architecture that solves the aforementioned problems by explicitly encoding RNA sequence-structure information into a 3D matrix. Building upon NU-ResNet, our second model, NUMO-ResNet, incorporates additional information derived from the characterizations of RNA, specifically the 2D folding motifs. In this work, we introduce an automated method to extract these motifs based on fundamental secondary structure descriptions. We evaluate the performance of both models on an independent testing dataset. Our proposed models outperform the models from literatures in this independent testing dataset. To assess the robustness of our models, we conduct 10-fold cross validation. To evaluate the generalization ability of NU-ResNet and NUMO-ResNet across different RNA families, we train and test our proposed models in different RNA families. Our proposed models show superior performance compared to the models from literatures when being tested across different independent RNA families. Conclusions: In this study, we propose two deep learning models, NU-ResNet and NUMO-ResNet, to evaluate RNA sequence-secondary structure pairs. These two models expand the field of data-driven approaches for learning RNA. Furthermore, these two models provide the new method to encode RNA sequence-secondary structure pairs. [ABSTRACT FROM AUTHOR]

Parkinson's disease (PD) is classified as a neurological, progressive illness brought on by cell death in the posterior midbrain. Early PD detection will assist doctors in reducing the disease's consequences. A collection of skilled models that may be applied to regression as well as classification is known as artificial intelligence (AI). PD can be detected using a variety of dataset formats, including text, speech, and picture datasets. For the purpose of classifying Parkinson's disease, this study suggests merging deep with machine learning recognition approaches. The three primary components of the suggested approach are designed to enhance the accuracy of Parkinson's disease early diagnosis. These sections cover the topics of categorising, combining, and separating. Convolutional Neural Networks (CNN) as well as attention procedures are used to create feature extractors. The related motion signals are fed to a combination of convolutional neural network and long-short-memory model for feature extraction. Besides, for the classification of patients from non-suffers of Parkinson's disease, Random Forest, Logistic Regression, Support Vector Machine, Extreme Boot Classifier, and voting classifier were used. Our result shows that for the PD handwriting and related motion datasets, using the proposed CNN with an attention and voting classifier yields 99.95% accuracy, 99.99% precision, 99.98% sensitivity, and 99.95% F1-score. Based on these results, it is warranted to conclude that the proposed methodology of feature extraction from photos of handwriting and relating motor symptoms, fusing of those features, and following it with a voting classifier yields excellent results for PD classification. [ABSTRACT FROM AUTHOR]

Background: Locating small molecule binding sites in target proteins, in the resolution of either pocket or residue, is critical in many drug-discovery scenarios. Since it is not always easy to find such binding sites using conventional methods, different deep learning methods to predict binding sites out of protein structures have been developed in recent years. The existing deep learning based methods have several limitations, including (1) the inefficiency of the CNN-only architecture, (2) loss of information due to excessive post-processing, and (3) the under-utilization of available data sources. Methods: We present a new model architecture and training method that resolves the aforementioned problems. First, by layering geometric self-attention units on top of residue-level 3D CNN outputs, our model overcomes the problems of CNN-only architectures. Second, by configuring the fundamental units of computation as residues and pockets instead of voxels, our method reduced the information loss from post-processing. Lastly, by employing inter-resolution transfer learning and homology-based augmentation, our method maximizes the utilization of available data sources to a significant extent. Results: The proposed method significantly outperformed all state-of-the-art baselines regarding both resolutions—pocket and residue. An ablation study demonstrated the indispensability of our proposed architecture, as well as transfer learning and homology-based augmentation, for achieving optimal performance. We further scrutinized our model's performance through a case study involving human serum albumin, which demonstrated our model's superior capability in identifying multiple binding sites of the protein, outperforming the existing methods. Conclusions: We believe that our contribution to the literature is twofold. Firstly, we introduce a novel computational method for binding site prediction with practical applications, substantiated by its strong performance across diverse benchmarks and case studies. Secondly, the innovative aspects in our method— specifically, the design of the model architecture, inter-resolution transfer learning, and homology-based augmentation—would serve as useful components for future work. [ABSTRACT FROM AUTHOR]

Background: Recently, the process of evolution information and the deep learning network has promoted the improvement of protein contact prediction methods. Nevertheless, still remain some bottleneck: (1) One of the bottlenecks is the prediction of orphans and other fewer evolution information proteins. (2) The other bottleneck is the method of predicting single-sequence-based proteins mainly focuses on selecting protein sequence features and tuning the neural network architecture, However, while the deeper neural networks improve prediction accuracy, there is still the problem of increasing the computational burden. Compared with other neural networks in the field of protein prediction, the graph neural network has the following advantages: due to the advantage of revealing the topology structure via graph neural network and being able to take advantage of the hierarchical structure and local connectivity of graph neural networks has certain advantages in capturing the features of different levels of abstraction in protein molecules. When using protein sequence and structure information for joint training, the dependencies between the two kinds of information can be better captured. And it can process protein molecular structures of different lengths and shapes, while traditional neural networks need to convert proteins into fixed-size vectors or matrices for processing. Results: Here, we propose a single-sequence-based protein contact map predictor PCP-GC-LM, with dual-level graph neural networks and convolution networks. Our method performs better with other single-sequence-based predictors in different independent tests. In addition, to verify the validity of our method against complex protein structures, we will also compare it with other methods in two homodimers protein test sets (DeepHomo test dataset and CASP-CAPRI target dataset). Furthermore, we also perform ablation experiments to demonstrate the necessity of a dual graph network. In all, our framework presents new modules to accurately predict inter-chain contact maps in protein and it's also useful to analyze interactions in other types of protein complexes. [ABSTRACT FROM AUTHOR]

Efforts to enhance the accuracy of protein sequence classification are of utmost importance in driving forward biological analyses and facilitating significant medical advancements. This study presents a cutting-edge model called ProtICNN-BiLSTM, which combines attention-based Improved Convolutional Neural Networks (ICNN) and Bidirectional Long Short-Term Memory (BiLSTM) units seamlessly. Our main goal is to improve the accuracy of protein sequence classification by carefully optimizing performance through Bayesian Optimisation. ProtICNN-BiLSTM combines the power of CNN and BiLSTM architectures to effectively capture local and global protein sequence dependencies. In the proposed model, the ICNN component uses convolutional operations to identify local patterns. Captures long-range associations by analyzing sequence data forward and backwards. In advanced biological studies, Bayesian Optimisation optimizes model hyperparameters for efficiency and robustness. The model was extensively confirmed with PDB-14,189 and other protein data. We found that ProtICNN-BiLSTM outperforms traditional categorization models. Bayesian Optimization's fine-tuning and seamless integration of local and global sequence information make it effective. The precision of ProtICNN-BiLSTM improves comparative protein sequence categorization. The study improves computational bioinformatics for complex biological analysis. Good results from the ProtICNN-BiLSTM model improve protein sequence categorization. This powerful tool could improve medical and biological research. The breakthrough protein sequence classification model is ProtICNN-BiLSTM. Bayesian optimization, ICNN, and BiLSTM analyze biological data accurately. [ABSTRACT FROM AUTHOR]

Leukemia is a type of blood cell cancer that is in the bone marrow's blood-forming cells. Two types of Leukemia are acute and chronic; acute enhances fast and chronic growth gradually which are further classified into lymphocytic and myeloid leukemias. This work evaluates a unique deep convolutional neural network (CNN) classifier that improves identification precision by carefully examining concatenated peptide patterns. The study uses leukemia protein expression for experiments supporting two different techniques including independence and applied cross-validation. In addition to CNN, multilayer perceptron (MLP), gated recurrent unit (GRU), and recurrent neural network (RNN) are applied. The experimental results show that the CNN model surpasses competitors with its outstanding predictability in independent and cross-validation testing applied on different features extracted from protein expressions such as amino acid composition (AAC) with a group of AAC (GAAC), tripeptide composition (TPC) with a group of TPC (GTPC), and dipeptide composition (DPC) for calculating its accuracies with their receiver operating characteristic (ROC) curve. In independence testing, a feature expression of AAC and a group of GAAC are applied using MLP and CNN modules, and ROC curves are achieved with overall 100% accuracy for the detection of protein patterns. In cross-validation testing, a feature expression on a group of AAC and GAAC patterns achieved 98.33% accuracy which is the highest for the CNN module. Furthermore, ROC curves show a 0.965% extraordinary result for the GRU module. The findings show that the CNN model is excellent at figuring out leukemia illnesses from protein expressions with higher accuracy. [ABSTRACT FROM AUTHOR]

Metagenomic data plays a crucial role in analyzing the relationship between microbes and diseases. However, the limited number of samples, high dimensionality, and sparsity of metagenomic data pose significant challenges for the application of deep learning in data classification and prediction. Previous studies have shown that utilizing the phylogenetic tree structure to transform metagenomic abundance data into a 2D matrix input for convolutional neural networks (CNNs) improves classification performance. Inspired by the success of a Permutable MLP-like architecture in visual recognition, we propose Metagenomic Permutator (MetaP), which applied the Permutable MLP-like network structure to capture the phylogenetic information of microbes within the 2D matrix formed by phylogenetic tree. Our experiments demonstrate that our model achieved competitive performance compared to other deep neural networks and traditional machine learning, and has good prospects for multi-classification and large sample sizes. Furthermore, we utilize the SHAP (SHapley Additive exPlanations) method to interpret our model predictions, identifying the microbial features that are associated with diseases. [ABSTRACT FROM AUTHOR]

Objectives: To develop and validate a novel interpretable artificial intelligence (AI) model that integrates radiomic features, deep learning features, and imaging features at multiple semantic levels to predict the prognosis of intracerebral hemorrhage (ICH) patients at 6 months post-onset. Materials and methods: Retrospectively enrolled 222 patients with ICH for Non-contrast Computed Tomography (NCCT) images and clinical data, who were divided into a training cohort (n = 186, medical center 1) and an external testing cohort (n = 36, medical center 2). Following image preprocessing, the entire hematoma region was segmented by two radiologists as the volume of interest (VOI). Pyradiomics algorithm library was utilized to extract 1762 radiomics features, while a deep convolutional neural network (EfficientnetV2-L) was employed to extract 1000 deep learning features. Additionally, radiologists evaluated imaging features. Based on the three different modalities of features mentioned above, the Random Forest (RF) model was trained, resulting in three models (Radiomics Model, Radiomics-Clinical Model, and DL-Radiomics-Clinical Model). The performance and clinical utility of the models were assessed using the Area Under the Receiver Operating Characteristic Curve (AUC), calibration curve, and Decision Curve Analysis (DCA), with AUC compared using the DeLong test. Furthermore, this study employs three methods, Shapley Additive Explanations (SHAP), Grad-CAM, and Guided Grad-CAM, to conduct a multidimensional interpretability analysis of model decisions. Results: The Radiomics-Clinical Model and DL-Radiomics-Clinical Model exhibited relatively good predictive performance, with an AUC of 0.86 [95% Confidence Intervals (CI): 0.71, 0.95; P < 0.01] and 0.89 (95% CI: 0.74, 0.97; P < 0.01), respectively, in the external testing cohort. Conclusion: The multimodal explainable AI model proposed in this study can accurately predict the prognosis of ICH. Interpretability methods such as SHAP, Grad-CAM, and Guided Grad-Cam partially address the interpretability limitations of AI models. Integrating multimodal imaging features can effectively improve the performance of the model. Clinical relevance statement: Predicting the prognosis of patients with ICH is a key objective in emergency care. Accurate and efficient prognostic tools can effectively prevent, manage, and monitor adverse events in ICH patients, maximizing treatment outcomes. Key points: •A multimodal AI model combining imaging features, deep learning features, and radiomics features at three different semantic levels outperforms traditional radiomics models; •This study proposes an interpretable deep learning radiomics model that enables the model to maintain a certain level of interpretability while meeting high-performance requirements; [ABSTRACT FROM AUTHOR]

Purpose: In this study, we present DeepVirusClassifier, a tool capable of accurately classifying Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) viral sequences among other subtypes of the coronaviridae family. This classification is achieved through a deep neural network model that relies on convolutional neural networks (CNNs). Since viruses within the same family share similar genetic and structural characteristics, the classification process becomes more challenging, necessitating more robust models. With the rapid evolution of viral genomes and the increasing need for timely classification, we aimed to provide a robust and efficient tool that could increase the accuracy of viral identification and classification processes. Contribute to advancing research in viral genomics and assist in surveilling emerging viral strains. Methods: Based on a one-dimensional deep CNN, the proposed tool is capable of training and testing on the Coronaviridae family, including SARS-CoV-2. Our model's performance was assessed using various metrics, including F1-score and AUROC. Additionally, artificial mutation tests were conducted to evaluate the model's generalization ability across sequence variations. We also used the BLAST algorithm and conducted comprehensive processing time analyses for comparison. Results: DeepVirusClassifier demonstrated exceptional performance across several evaluation metrics in the training and testing phases. Indicating its robust learning capacity. Notably, during testing on more than 10,000 viral sequences, the model exhibited a more than 99% sensitivity for sequences with fewer than 2000 mutations. The tool achieves superior accuracy and significantly reduced processing times compared to the Basic Local Alignment Search Tool algorithm. Furthermore, the results appear more reliable than the work discussed in the text, indicating that the tool has great potential to revolutionize viral genomic research. Conclusion: DeepVirusClassifier is a powerful tool for accurately classifying viral sequences, specifically focusing on SARS-CoV-2 and other subtypes within the Coronaviridae family. The superiority of our model becomes evident through rigorous evaluation and comparison with existing methods. Introducing artificial mutations into the sequences demonstrates the tool's ability to identify variations and significantly contributes to viral classification and genomic research. As viral surveillance becomes increasingly critical, our model holds promise in aiding rapid and accurate identification of emerging viral strains. [ABSTRACT FROM AUTHOR]

Background: Pneumoconiosis has a significant impact on the quality of patient survival due to its difficult staging diagnosis and poor prognosis. This study aimed to develop a computer-aided diagnostic system for the screening and staging of pneumoconiosis based on a multi-stage joint deep learning approach using X-ray chest radiographs of pneumoconiosis patients. Methods: In this study, a total of 498 medical chest radiographs were obtained from the Department of Radiology of West China Fourth Hospital. The dataset was randomly divided into a training set and a test set at a ratio of 4:1. Following histogram equalization for image enhancement, the images were segmented using the U-Net model, and staging was predicted using a convolutional neural network classification model. We first used Efficient-Net for multi-classification staging diagnosis, but the results showed that stage I/II of pneumoconiosis was difficult to diagnose. Therefore, based on clinical practice we continued to improve the model by using the Res-Net 34 Multi-stage joint method. Results: Of the 498 cases collected, the classification model using the Efficient-Net achieved an accuracy of 83% with a Quadratic Weighted Kappa (QWK) score of 0.889. The classification model using the multi-stage joint approach of Res-Net 34 achieved an accuracy of 89% with an area under the curve (AUC) of 0.98 and a high QWK score of 0.94. Conclusions: In this study, the diagnostic accuracy of pneumoconiosis staging was significantly improved by an innovative combined multi-stage approach, which provided a reference for clinical application and pneumoconiosis screening. [ABSTRACT FROM AUTHOR]

Background: Schizophrenia (SZ), a psychiatric disorder for which there is no precise diagnosis, has had a serious impact on the quality of human life and social activities for many years. Therefore, an advanced approach for accurate treatment is required. New method: In this study, we provide a classification approach for SZ patients based on a spatial–temporal residual graph convolutional neural network (STRGCN). The model primarily collects spatial frequency features and temporal frequency features by spatial graph convolution and single-channel temporal convolution, respectively, and blends them both for the classification learning, in contrast to traditional approaches that only evaluate temporal frequency information in EEG and disregard spatial frequency features across brain regions. Results: We conducted extensive experiments on the publicly available dataset Zenodo and our own collected dataset. The classification accuracy of the two datasets on our proposed method reached 96.32% and 85.44%, respectively. In the experiment, the dataset using delta has the best classification performance in the sub-bands. Comparison with existing methods: Other methods mainly rely on deep learning models dominated by convolutional neural networks and long and short time memory networks, lacking exploration of the functional connections between channels. In contrast, the present method can treat the EEG signal as a graph and integrate and analyze the temporal frequency and spatial frequency features in the EEG signal. Conclusion: We provide an approach to not only performs better than other classic machine learning and deep learning algorithms on the dataset we used in diagnosing schizophrenia, but also understand the effects of schizophrenia on brain network features. [ABSTRACT FROM AUTHOR]

Objective: To construct the deep learning convolution neural network (CNN) model and machine learning support vector machine (SVM) model of bone remodeling of chronic maxillary sinusitis (CMS) based on CT image data to improve the accuracy of image diagnosis. Methods: Maxillary sinus CT data of 1000 samples in 500 patients from January 2018 to December 2021 in our hospital was collected. The first part is the establishment and testing of chronic maxillary sinusitis detection model by 461 images. The second part is the establishment and testing of the detection model of chronic maxillary sinusitis with bone remodeling by 802 images. The sensitivity, specificity and accuracy and area under the curve (AUC) value of the test set were recorded, respectively. Results: Preliminary application results of CT based AI in the diagnosis of chronic maxillary sinusitis and bone remodeling. The sensitivity, specificity and accuracy of the test set of 93 samples of CMS, were 0.9796, 0.8636 and 0.9247, respectively. Simultaneously, the value of AUC was 0.94. And the sensitivity, specificity and accuracy of the test set of 161 samples of CMS with bone remodeling were 0.7353, 0.9685 and 0.9193, respectively. Simultaneously, the value of AUC was 0.89. Conclusion: It is feasible to use artificial intelligence research methods such as deep learning and machine learning to automatically identify CMS and bone remodeling in MSCT images of paranasal sinuses, which is helpful to standardize imaging diagnosis and meet the needs of clinical application. [ABSTRACT FROM AUTHOR]

Background: Compared with the time-consuming and labor-intensive for biological validation in vitro or in vivo, the computational models can provide high-quality and purposeful candidates in an instant. Existing computational models face limitations in effectively utilizing sparse local structural information for accurate predictions in circRNA-disease associations. This study addresses this challenge with a proposed method, CDA-DGRL (Prediction of CircRNA-Disease Association based on Double-line Graph Representation Learning), which employs a deep learning framework leveraging graph networks and a dual-line representation model integrating graph node features. Method: CDA-DGRL comprises several key steps: initially, the integration of diverse biological information to compute integrated similarities among circRNAs and diseases, leading to the construction of a heterogeneous network specific to circRNA-disease associations. Subsequently, circRNA and disease node features are derived using sparse autoencoders. Thirdly, a graph convolutional neural network is employed to capture the local graph network structure by inputting the circRNA-disease heterogeneous network alongside node features. Fourthly, the utilization of node2vec facilitates depth-first sampling of the circRNA-disease heterogeneous network to grasp the global graph network structure, addressing issues associated with sparse raw data. Finally, the fusion of local and global graph network structures is inputted into an extra trees classifier to identify potential circRNA-disease associations. Results: The results, obtained through a rigorous five-fold cross-validation on the circR2Disease dataset, demonstrate the superiority of CDA-DGRL with an AUC value of 0.9866 and an AUPR value of 0.9897 compared to existing state-of-the-art models. Notably, the hyper-random tree classifier employed in this model outperforms other machine learning classifiers. Conclusion: Thus, CDA-DGRL stands as a promising methodology for reliably identifying circRNA-disease associations, offering potential avenues to alleviate the necessity for extensive traditional biological experiments. The source code and data for this study are available at https://github.com/zywait/CDA-DGRL. [ABSTRACT FROM AUTHOR]

Background: Over 60% of epilepsy patients globally are children, whose early diagnosis and treatment are critical for their development and can substantially reduce the disease's burden on both families and society. Numerous algorithms for automated epilepsy detection from EEGs have been proposed. Yet, the occurrence of epileptic seizures during an EEG exam cannot always be guaranteed in clinical practice. Models that exclusively use seizure EEGs for detection risk artificially enhanced performance metrics. Therefore, there is a pressing need for a universally applicable model that can perform automatic epilepsy detection in a variety of complex real-world scenarios. Method: To address this problem, we have devised a novel technique employing a temporal convolutional neural network with self-attention (TCN-SA). Our model comprises two primary components: a TCN for extracting time-variant features from EEG signals, followed by a self-attention (SA) layer that assigns importance to these features. By focusing on key features, our model achieves heightened classification accuracy for epilepsy detection. Results: The efficacy of our model was validated on a pediatric epilepsy dataset we collected and on the Bonn dataset, attaining accuracies of 95.50% on our dataset, and 97.37% (A v. E), and 93.50% (B vs E), respectively. When compared with other deep learning architectures (temporal convolutional neural network, self-attention network, and standardized convolutional neural network) using the same datasets, our TCN-SA model demonstrated superior performance in the automated detection of epilepsy. Conclusion: The proven effectiveness of the TCN-SA approach substantiates its potential as a valuable tool for the automated detection of epilepsy, offering significant benefits in diverse and complex real-world clinical settings. [ABSTRACT FROM AUTHOR]

Brain tumor diagnosis using MRI scans poses significant challenges due to the complex nature of tumor appearances and variations. Traditional methods often require extensive manual intervention and are prone to human error, leading to misdiagnosis and delayed treatment. Current approaches primarily include manual examination by radiologists and conventional machine learning techniques. These methods rely heavily on feature extraction and classification algorithms, which may not capture the intricate patterns present in brain MRI images. Conventional techniques often suffer from limited accuracy and generalizability, mainly due to the high variability in tumor appearance and the subjective nature of manual interpretation. Additionally, traditional machine learning models may struggle with the high-dimensional data inherent in MRI images. To address these limitations, our research introduces a deep learning-based model utilizing convolutional neural networks (CNNs).Our model employs a sequential CNN architecture with multiple convolutional, max-pooling, and dropout layers, followed by dense layers for classification. The proposed model demonstrates a significant improvement in diagnostic accuracy, achieving an overall accuracy of 98% on the test dataset. The proposed model demonstrates a significant improvement in diagnostic accuracy, achieving an overall accuracy of 98% on the test dataset. The precision, recall, and F1-scores ranging from 97 to 98% with a roc-auc ranging from 99 to 100% for each tumor category further substantiate the model's effectiveness. Additionally, the utilization of Grad-CAM visualizations provides insights into the model's decision-making process, enhancing interpretability. This research addresses the pressing need for enhanced diagnostic accuracy in identifying brain tumors through MRI imaging, tackling challenges such as variability in tumor appearance and the need for rapid, reliable diagnostic tools. [ABSTRACT FROM AUTHOR]

Background: Recent Convolutional Neural Networks (CNNs) perform low-error reconstruction in fast Magnetic Resonance Imaging (MRI). Most of them convolve the image with kernels and successfully explore the local information. Nonetheless, the non-local image information, which is embedded among image patches relatively far from each other, may be lost due to the limitation of the receptive field of the convolution kernel. We aim to incorporate a graph to represent non-local information and improve the reconstructed images by using the Graph Convolutional Enhanced Self-Similarity (GCESS) network. Methods: First, the image is reconstructed into the graph to extract the non-local self-similarity in the image. Second, GCESS uses spatial convolution and graph convolution to process the information in the image, so that local and non-local information can be effectively utilized. The network strengthens the non-local similarity between similar image patches while reconstructing images, making the reconstruction of structure more reliable. Results: Experimental results on in vivo knee and brain data demonstrate that the proposed method achieves better artifact suppression and detail preservation than state-of-the-art methods, both visually and quantitatively. Under 1D Cartesian sampling with 4 × acceleration (AF = 4), the PSNR of knee data reached 34.19 dB, 1.05 dB higher than that of the compared methods; the SSIM achieved 0.8994, 2% higher than the compared methods. Similar results were obtained for the reconstructed images under other sampling templates as demonstrated in our experiment. Conclusions: The proposed method successfully constructs a hybrid graph convolution and spatial convolution network to reconstruct images. This method, through its training process, amplifies the non-local self-similarities, significantly benefiting the structural integrity of the reconstructed images. Experiments demonstrate that the proposed method outperforms the state-of-the-art reconstruction method in suppressing artifacts, as well as in preserving image details. [ABSTRACT FROM AUTHOR]

Background: Most of the important biological mechanisms and functions of transmembrane proteins (TMPs) are realized through their interactions with non-transmembrane proteins(nonTMPs). The interactions between TMPs and nonTMPs in cells play vital roles in intracellular signaling, energy metabolism, investigating membrane-crossing mechanisms, correlations between disease and drugs. Results: Despite the importance of TMP-nonTMP interactions, the study of them remains in the wet experimental stage, lacking specific and comprehensive studies in the field of bioinformatics. To fill this gap, we performed a comprehensive statistical analysis of known TMP-nonTMP interactions and constructed a deep learning-based predictor to identify potential interactions. The statistical analysis describes known TMP-nonTMP interactions from various perspectives, such as distributions of species and protein families, enrichment of GO and KEGG pathways, as well as hub proteins and subnetwork modules in the PPI network. The predictor implemented by an end-to-end deep learning model can identify potential interactions from protein primary sequence information. The experimental results over the independent validation demonstrated considerable prediction performance with an MCC of 0.541. Conclusions: To our knowledge, we were the first to focus on TMP-nonTMP interactions. We comprehensively analyzed them using bioinformatics methods and predicted them via deep learning-based solely on their sequence. This research completes a key link in the protein network, benefits the understanding of protein functions, and helps in pathogenesis studies of diseases and associated drug development. [ABSTRACT FROM AUTHOR]

Background: Motif finding in Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) data is essential to reveal the intricacies of transcription factor binding sites (TFBSs) and their pivotal roles in gene regulation. Deep learning technologies including convolutional neural networks (CNNs) and graph neural networks (GNNs), have achieved success in finding ATAC-seq motifs. However, CNN-based methods are limited by the fixed width of the convolutional kernel, which makes it difficult to find multiple transcription factor binding sites with different lengths. GNN-based methods has the limitation of using the edge weight information directly, makes it difficult to aggregate the neighboring nodes' information more efficiently when representing node embedding. Results: To address this challenge, we developed a novel graph attention network framework named MMGAT, which employs an attention mechanism to adjust the attention coefficients among different nodes. And then MMGAT finds multiple ATAC-seq motifs based on the attention coefficients of sequence nodes and k-mer nodes as well as the coexisting probability of k-mers. Our approach achieved better performance on the human ATAC-seq datasets compared to existing tools, as evidenced the highest scores on the precision, recall, F1_score, ACC, AUC, and PRC metrics, as well as finding 389 higher quality motifs. To validate the performance of MMGAT in predicting TFBSs and finding motifs on more datasets, we enlarged the number of the human ATAC-seq datasets to 180 and newly integrated 80 mouse ATAC-seq datasets for multi-species experimental validation. Specifically on the mouse ATAC-seq dataset, MMGAT also achieved the highest scores on six metrics and found 356 higher-quality motifs. To facilitate researchers in utilizing MMGAT, we have also developed a user-friendly web server named MMGAT-S that hosts the MMGAT method and ATAC-seq motif finding results. Conclusions: The advanced methodology MMGAT provides a robust tool for finding ATAC-seq motifs, and the comprehensive server MMGAT-S makes a significant contribution to genomics research. The open-source code of MMGAT can be found at https://github.com/xiaotianr/MMGAT, and MMGAT-S is freely available at https://www.mmgraphws.com/MMGAT-S/. [ABSTRACT FROM AUTHOR]

Background: Tele-rehabilitation is the provision of physiotherapy services to individuals in their own homes. Activity recognition plays a crucial role in the realm of automatic tele-rehabilitation. By assessing patient movements, identifying exercises, and providing feedback, these platforms can offer insightful information to clinicians, thereby facilitating an improved plan of care. This study introduces a novel deep learning approach aimed at identifying lower limb rehabilitation exercises. This is achieved through the integration of depth data and pressure heatmaps. We hypothesized that combining pressure heatmaps and depth data could improve the model's overall performance. Methods: In this study, depth videos and body pressure data from an accessible online dataset were used. This dataset comprises data from 30 healthy individuals performing 7 lower limb rehabilitation exercises. To accomplish the classification task, three deep learning models were developed, all based on an established 3D-CNN architecture. The models were designed to classify the depth videos, sequences of pressure data frames, and combination of depth videos and pressure frames. The models' performance was assessed through leave-one-subject-out and leave-multiple-subjects-out cross-validation methods. Performance metrics, including accuracy, precision, recall, and F1 score, were reported for each model. Results: Our findings indicated that the model trained on the fusion of depth and pressure data showed the highest and most stable performance when compared with models using individual modality inputs. This model could effectively identify the exercises with an accuracy of 95.71%, precision of 95.83%, recall of 95.71%, and an F1 score of 95.74%. Conclusion: Our results highlight the impact of data fusion for accurately classifying lower limb rehabilitation exercises. We showed that our model could capture different aspects of exercise movements using the visual and weight distribution data from the depth camera and pressure mat, respectively. This integration of data provides a better representation of exercise patterns, leading to higher classification performance. Notably, our results indicate the potential application of this model in automatic tele-rehabilitation platforms. [ABSTRACT FROM AUTHOR]

Background: Decubitus ulcers are prevalent among the aging population due to a gradual decline in their overall health, such as nutrition, mental health, and mobility, resulting in injury to the skin and tissue. The most common technique to prevent these ulcers is through frequent repositioning to redistribute body pressures. Therefore, the main goal of this study is to facilitate the timely repositioning of patients through the use of a pressure mat to identify in-bed postures in various sleep environments. Pressure data were collected from 10 healthy participants lying down on a pressure mat in 19 various in-bed postures, correlating to the supine, prone, right-side, and left-side classes. In addition, pressure data were collected from participants sitting at the edge of the bed as well as an empty bed. Each participant was asked to lie in these 19 postures in three distinct testing environments: a hospital bed, a home bed, and a home bed with a foam mattress topper. To categorize each posture into its respective class, the pre-trained 2D ResNet-18 CNN and the pre-trained Inflated 3D CNN algorithms were trained and validated using image and video pressure mapped data, respectively. Results: The ResNet-18 and Inflated 3D CNN algorithms were validated using leave-one-subject-out (LOSO) and leave-one-environment-out (LOEO) cross-validation techniques. LOSO provided an average accuracy of 92.07% ± 5.72% and 82.22% ± 8.50%, for the ResNet-18 and Inflated 3D CNN algorithms, respectively. Contrastingly, LOEO provided a reduced average accuracy of 85.37% ± 14.38% and 77.79% ± 9.76%, for the ResNet-18 and Inflated 3D CNN algorithms, respectively. Conclusion: These pilot results indicate that the proposed algorithms can accurately distinguish between in-bed postures, on unseen participant data as well as unseen mattress environment data. The proposed algorithms can establish the basis of a decubitus ulcer prevention platform that can be applied to various sleeping environments. To the best of our knowledge, the impact of mattress stiffness has not been considered in previous studies regarding in-bed posture monitoring. [ABSTRACT FROM AUTHOR]

RNA-protein interaction (RPI) is crucial to the life processes of diverse organisms. Various researchers have identified RPI through long-term and high-cost biological experiments. Although numerous machine learning and deep learning-based methods for predicting RPI currently exist, their robustness and generalizability have significant room for improvement. This study proposes LPI-MFF, an RPI prediction model based on multi-source information fusion, to address these issues. The LPI-MFF employed protein–protein interactions features, sequence features, secondary structure features, and physical and chemical properties as the information sources with the corresponding coding scheme, followed by the random forest algorithm for feature screening. Finally, all information was combined and a classification method based on convolutional neural networks is used. The experimental results of fivefold cross-validation demonstrated that the accuracy of LPI-MFF on RPI1807 and NPInter was 97.60% and 97.67%, respectively. In addition, the accuracy rate on the independent test set RPI1168 was 84.9%, and the accuracy rate on the Mus musculus dataset was 90.91%. Accordingly, LPI-MFF demonstrated greater robustness and generalization than other prevalent RPI prediction methods. [ABSTRACT FROM AUTHOR]

Background: Epilepsy is a common neurological disorder that affects approximately 60 million people worldwide. Characterized by unpredictable neural electrical activity abnormalities, it results in seizures with varying intensity levels. Electroencephalography (EEG), as a crucial technology for monitoring and predicting epileptic seizures, plays an essential role in improving the quality of life for people with epilepsy. Method: This study introduces an innovative deep learning model, a lightweight triscale yielding convolutional neural network" (LTY-CNN), that is specifically designed for EEG signal analysis. The model integrates a parallel convolutional structure with a multihead attention mechanism to capture complex EEG signal features across multiple scales and enhance the efficiency achieved when processing time series data. The lightweight design of the LTY-CNN enables it to maintain high performance in environments with limited computational resources while preserving the interpretability and maintainability of the model. Results: In tests conducted on the SWEC-ETHZ and CHB-MIT datasets, the LTY-CNN demonstrated outstanding performance. On the SWEC-ETHZ dataset, the LTY-CNN achieved an accuracy of 99.9%, an area under the receiver operating characteristic curve (AUROC) of 0.99, a sensitivity of 99.9%, and a specificity of 98.8%. Furthermore, on the CHB-MIT dataset, it recorded an accuracy of 99%, an AUROC of 0.932, a sensitivity of 99.1%, and a specificity of 93.2%. These results signify the remarkable ability of the LTY-CNN to distinguish between epileptic seizures and nonseizure events. Compared to other existing epilepsy detection classifiers, the LTY-CNN attained higher accuracy and sensitivity. Conclusion: The high accuracy and sensitivity of the LTY-CNN model demonstrate its significant potential for epilepsy management, particularly in terms of predicting and mitigating epileptic seizures. Its value in personalized treatments and widespread clinical applications reflects the broad prospects of deep learning in the health care sector. This also highlights the crucial role of technological innovation in enhancing the quality of life experienced by patients. [ABSTRACT FROM AUTHOR]

Background: Lysine crotonylation (Kcr) is a crucial protein post-translational modification found in histone and non-histone proteins. It plays a pivotal role in regulating diverse biological processes in both animals and plants, including gene transcription and replication, cell metabolism and differentiation, as well as photosynthesis. Despite the significance of Kcr, detection of Kcr sites through biological experiments is often time-consuming, expensive, and only a fraction of crotonylated peptides can be identified. This reality highlights the need for efficient and rapid prediction of Kcr sites through computational methods. Currently, several machine learning models exist for predicting Kcr sites in humans, yet models tailored for plants are rare. Furthermore, no downloadable Kcr site predictors or datasets have been developed specifically for plants. To address this gap, it is imperative to integrate existing Kcr sites detected in plant experiments and establish a dedicated computational model for plants. Results: Most plant Kcr sites are located on non-histones. In this study, we collected non-histone Kcr sites from five plants, including wheat, tabacum, rice, peanut, and papaya. We then conducted a comprehensive analysis of the amino acid distribution surrounding these sites. To develop a predictive model for plant non-histone Kcr sites, we combined a convolutional neural network (CNN), a bidirectional long short-term memory network (BiLSTM), and attention mechanism to build a deep learning model called PlantNh-Kcr. On both five-fold cross-validation and independent tests, PlantNh-Kcr outperformed multiple conventional machine learning models and other deep learning models. Furthermore, we conducted an analysis of species-specific effect on the PlantNh-Kcr model and found that a general model trained using data from multiple species outperforms species-specific models. Conclusion: PlantNh-Kcr represents a valuable tool for predicting plant non-histone Kcr sites. We expect that this model will aid in addressing key challenges and tasks in the study of plant crotonylation sites. [ABSTRACT FROM AUTHOR]

Deep learning recently achieved advancement in the segmentation of medical images. In this regard, U-Net is the most predominant deep neural network, and its architecture is the most prevalent in the medical imaging society. Experiments conducted on difficult datasets directed us to the conclusion that the traditional U-Net framework appears to be deficient in certain respects, despite its overall excellence in segmenting multimodal medical images. Therefore, we propose several modifications to the existing cutting-edge U-Net model. The technical approach involves applying a Multi-Dimensional U-Convolutional Neural Network to achieve accurate segmentation of multimodal biomedical images, enhancing precision and comprehensiveness in identifying and analyzing structures across diverse imaging modalities. As a result of the enhancements, we propose a novel framework called Multi-Dimensional U-Convolutional Neural Network (MDU-CNN) as a potential successor to the U-Net framework. On a large set of multimodal medical images, we compared our proposed framework, MDU-CNN, to the classical U-Net. There have been small changes in the case of perfect images, and a huge improvement is obtained in the case of difficult images. We tested our model on five distinct datasets, each of which presented unique challenges, and found that it has obtained a better performance of 1.32%, 5.19%, 4.50%, 10.23% and 0.87%, respectively. [ABSTRACT FROM AUTHOR]

Purpose: Recent technological advancements in data acquisition tools allowed neuroscientists to acquire different modality data to diagnosis Alzheimer's disease (AD). However, how to fuse these enormous amount different modality data to improve recognizing rate and find significance brain regions is still challenging. Methods: The algorithm used multimodal medical images [structural magnetic resonance imaging (sMRI) and positron emission tomography (PET)] as experimental data. Deep feature representations of sMRI and PET images are extracted by 3D convolution neural network (3DCNN). An improved Transformer is then used to progressively learn global correlation information among features. Finally, the information from different modalities is fused for identification. A model-based visualization method is used to explain the decisions of the model and identify brain regions related to AD. Results: The model attained a noteworthy classification accuracy of 98.1% for Alzheimer's disease (AD) using the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset. Upon examining the visualization results, distinct brain regions associated with AD diagnosis were observed across different image modalities. Notably, the left parahippocampal region emerged consistently as a prominent and significant brain area. Conclusions: A large number of comparative experiments have been carried out for the model, and the experimental results verify the reliability of the model. In addition, the model adopts a visualization analysis method based on the characteristics of the model, which improves the interpretability of the model. Some disease-related brain regions were found in the visualization results, which provides reliable information for AD clinical research. [ABSTRACT FROM AUTHOR]

Background: Convolutional neural network-based image processing research is actively being conducted for pathology image analysis. As a convolutional neural network model requires a large amount of image data for training, active learning (AL) has been developed to produce efficient learning with a small amount of training data. However, existing studies have not specifically considered the characteristics of pathological data collected from the workplace. For various reasons, noisy patches can be selected instead of clean patches during AL, thereby reducing its efficiency. This study proposes an effective AL method for cancer pathology that works robustly on noisy datasets. Methods: Our proposed method to develop a robust AL approach for noisy histopathology datasets consists of the following three steps: 1) training a loss prediction module, 2) collecting predicted loss values, and 3) sampling data for labeling. This proposed method calculates the amount of information in unlabeled data as predicted loss values and removes noisy data based on predicted loss values to reduce the rate at which noisy data are selected from the unlabeled dataset. We identified a suitable threshold for optimizing the efficiency of AL through sensitivity analysis. Results: We compared the results obtained with the identified threshold with those of existing representative AL methods. In the final iteration, the proposed method achieved a performance of 91.7% on the noisy dataset and 92.4% on the clean dataset, resulting in a performance reduction of less than 1%. Concomitantly, the noise selection ratio averaged only 2.93% on each iteration. Conclusions: The proposed AL method showed robust performance on datasets containing noisy data by avoiding data selection in predictive loss intervals where noisy data are likely to be distributed. The proposed method contributes to medical image analysis by screening data and producing a robust and effective classification model tailored for cancer pathology image processing in the workplace. [ABSTRACT FROM AUTHOR]