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Background: International Classification of Diseases codes are widely used to describe diagnosis information, but manual coding relies heavily on human interpretation, which can be expensive, time consuming, and prone to errors. With the transition from the International Classification of Diseases, Ninth Revision, to the International Classification of Diseases, Tenth Revision (ICD-10), the coding process has become more complex, highlighting the need for automated approaches to enhance coding efficiency and accuracy. Inaccurate coding can result in substantial financial losses for hospitals, and a precise assessment of outcomes generated by a natural language processing (NLP)-driven autocoding system thus assumes a critical role in safeguarding the accuracy of the Taiwan diagnosis related groups (Tw-DRGs)., Objective: This study aims to evaluate the feasibility of applying an International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM), autocoding system that can automatically determine diagnoses and codes based on free-text discharge summaries to facilitate the assessment of Tw-DRGs, specifically principal diagnosis and major diagnostic categories (MDCs)., Methods: By using the patient discharge summaries from Kaohsiung Medical University Chung-Ho Memorial Hospital (KMUCHH) from April 2019 to December 2020 as a reference data set we developed artificial intelligence (AI)-assisted ICD-10-CM coding systems based on deep learning models. We constructed a web-based user interface for the AI-assisted coding system and deployed the system to the workflow of the certified coding specialists (CCSs) of KMUCHH. The data used for the assessment of Tw-DRGs were manually curated by a CCS with the principal diagnosis and MDC was determined from discharge summaries collected at KMUCHH from February 2023 to April 2023., Results: Both the reference data set and real hospital data were used to assess performance in determining ICD-10-CM coding, principal diagnosis, and MDC for Tw-DRGs. Among all methods, the GPT-2 (OpenAI)-based model achieved the highest F 1 -score, 0.667 (F 1 -score 0.851 for the top 50 codes), on the KMUCHH test set and a slightly lower F 1 -score, 0.621, in real hospital data. Cohen κ evaluation for the agreement of MDC between the models and the CCS revealed that the overall average κ value for GPT-2 (κ=0.714) was approximately 12.2 percentage points higher than that of the hierarchy attention network (κ=0.592). GPT-2 demonstrated superior agreement with the CCS across 6 categories of MDC, with an average κ value of approximately 0.869 (SD 0.033), underscoring the effectiveness of the developed AI-assisted coding system in supporting the work of CCSs., Conclusions: An NLP-driven AI-assisted coding system can assist CCSs in ICD-10-CM coding by offering coding references via a user interface, demonstrating the potential to reduce the manual workload and expedite Tw-DRG assessment. Consistency in performance affirmed the effectiveness of the system in supporting CCSs in ICD-10-CM coding and the judgment of Tw-DRGs., (©Hong-Jie Dai, Chen-Kai Wang, Chien-Chang Chen, Chong-Sin Liou, An-Tai Lu, Chia-Hsin Lai, Bo-Tsz Shain, Cheng-Rong Ke, William Yu Chung Wang, Tatheer Hussain Mir, Mutiara Simanjuntak, Hao-Yun Kao, Ming-Ju Tsai, Vincent S Tseng. Originally published in the Journal of Medical Internet Research (https://www.jmir.org), 20.09.2024.)

Feature Selection (FS) is essential in the Internet of Things (IoT)-based Clinical Decision Support Systems (CDSS) to improve the accuracy and efficiency of the system. With the increasing number of sensors and devices used in healthcare, the volume of data generated is vast and complex. Relevant FS from this data is crucial in reducing computational overhead, improving the system's interpretability, and enhancing the Decision-Making System (DMS) quality. FS also aids in addressing the problems of data redundancy and noise, which can negatively impact the system's performance. FS is critical to developing practical and dependable CDSS in IoT-based healthcare sectors. This research proposes a two-phase FS model. Phase-I employs an ensemble of five Filter Methods (FM), followed by a Pearson Correlation Method (PCM). Phase-II uses the Binary Optimized Genetic Grey Wolf Optimization Algorithm (BOGGWOA) as a Wrapper Method (WM). This recommended model integrates the most valuable features of each filter. Then, it uses the Pearson Correlation Coefficient (PCC) to get rid of features that aren't needed, a Support Vector Machine (SVM) to guess how accurate their classification will be, and BOGGWOA as the Wrapper Method (WM) to pick the most essential features with the best CA., (© 2024. The Author(s).)

Image stitching is a traditional but challenging computer vision task. The goal is to stitch together multiple images with overlapping areas into a single, natural-looking, high-resolution image without ghosts or seams. This article aims to increase the field of view of gastroenteroscopy and reduce the missed detection rate. To this end, an improved depth framework based on unsupervised panoramic image stitching of the gastrointestinal tract is proposed. In addition, preprocessing for aberration correction of monocular endoscope images is introduced, and a C2f module is added to the image reconstruction network to improve the network's ability to extract features. A comprehensive real image data set, GASE-Dataset, is proposed to establish an evaluation benchmark and training learning framework for unsupervised deep gastrointestinal image splicing. Experimental results show that the MSE, RMSE, PSNR, SSIM and RMSE_SW indicators are improved, while the splicing time remains within an acceptable range. Compared with traditional image stitching methods, the performance of this method is enhanced. In addition, improvements are proposed to address the problems of lack of annotated data, insufficient generalization ability and insufficient comprehensive performance in image stitching schemes based on supervised learning. These improvements provide valuable aids in gastrointestinal examination., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Yan et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Leukemia is a type of blood tumour that occurs because of abnormal enhancement in WBCs (white blood cells) in the bone marrow of the human body. Blood-forming tissue cancer influences the lymphatic and bone marrow system. The early diagnosis and detection of leukaemia, i.e., the accurate difference of malignant leukocytes with little expense at the beginning of the disease, is a primary challenge in the disease analysis field. Despite the higher occurrence of leukemia, there is a lack of flow cytometry tools, and the procedures accessible at medical diagnostics centres are time-consuming. Distinct researchers have implemented computer-aided diagnostic (CAD) and machine learning (ML) methods for laboratory image analysis, aiming to manage the restrictions of late leukemia analysis. This study proposes a new Falcon optimization algorithm with deep convolutional neural network for Leukemia detection and classification (FOADCNN-LDC) technique. The main objective of the FOADCNN-LDC technique is to classify and recognize leukemia. The FOADCNN-LDC technique utilizes a median filtering (MF) based noise removal process to eradicate the image noise. Besides, the FOADCNN-LDC technique employs the ShuffleNetv2 model for the feature extraction process. Moreover, the detection and classification of the leukemia process are performed by utilizing the convolutional denoising autoencoder (CDAE) model. The FOA is implemented to select the hyperparameter of the CDAE model. The simulation process of the FOADCNN-LDC approach is performed on a benchmark medical dataset. The investigational analysis of the FOADCNN-LDC approach highlighted a superior accuracy value of 99.62% over existing techniques., (© 2024. The Author(s).)

The world has a higher count of death rates as a result of Alcohol consumption. Identification is possible because Alcoholic EEG waves have a certain behavior that is totally different compared to the non-alcoholic individual. The available approaches take longer to provide the feedback because they analyze the data manually. For this reason, in the present paper we propose a novel approach applied to detect alcoholic EEG signals automatically by using deep learning methods. Our strategy has advantages as far as fast detection is concerned; hence people can help immediately when there is a need. The potential for a significant decrease in deaths from alcohol poisoning and improvement to public health is presented by this advancement. In order to create clusters and classify the alcoholic EEG signals, this research uses a cascaded process. To begin with, an initial clustering and feature extraction is done by LASSO regression. After that, a variety of meta-heuristics algorithms like Particle Swarm Optimization (PSO), Binary Coding Harmony Search (BCHS) as well as Binary Dragonfly Algorithm (BDA) are employed for feature minimization. When this method is used, normal and alcoholic EEG signals may be differentiated using non-linear features. PSO, BCHS, and BDA features allow for estimation of statistical parameters through t-test, Friedman statistic test, Mann-Whitney U test, and Z-Score with corresponding p-values for alcoholic EEG signals. Lastly, classification is done by the use of support vector machines (SVM) (including linear, polynomial, and Gaussian kernels), random forests, artificial neural networks (ANN), enhanced artificial neural networks (EANN), and LSTM models. Results showed that LASSO regression with BDA-based EANN proposed classifier have a classification accuracy of 99.59%, indicating that our method is highly accurate at classifying alcoholic EEG signals., (© 2024. The Author(s).)

Background: The 2022 global outbreak of mpox has significantly impacted health facilities, and necessitated additional infection prevention and control measures and alterations to clinic processes. Early identification of suspected mpox cases will assist in mitigating these impacts., Objective: We aimed to develop and evaluate an artificial intelligence (AI)-based tool to differentiate mpox lesion images from other skin lesions seen in a sexual health clinic., Methods: We used a data set with 2200 images, that included mpox and non-mpox lesions images, collected from Melbourne Sexual Health Centre and web resources. We adopted deep learning approaches which involved 6 different deep learning architectures to train our AI models. We subsequently evaluated the performance of each model using a hold-out data set and an external validation data set to determine the optimal model for differentiating between mpox and non-mpox lesions., Results: The DenseNet-121 model outperformed other models with an overall area under the receiver operating characteristic curve (AUC) of 0.928, an accuracy of 0.848, a precision of 0.942, a recall of 0.742, and an F 1 -score of 0.834. Implementation of a region of interest approach significantly improved the performance of all models, with the AUC for the DenseNet-121 model increasing to 0.982. This approach resulted in an increase in the correct classification of mpox images from 79% (55/70) to 94% (66/70). The effectiveness of this approach was further validated by a visual analysis with gradient-weighted class activation mapping, demonstrating a reduction in false detection within the background of lesion images. On the external validation data set, ResNet-18 and DenseNet-121 achieved the highest performance. ResNet-18 achieved an AUC of 0.990 and an accuracy of 0.947, and DenseNet-121 achieved an AUC of 0.982 and an accuracy of 0.926., Conclusions: Our study demonstrated it was possible to use an AI-based image recognition algorithm to accurately differentiate between mpox and common skin lesions. Our findings provide a foundation for future investigations aimed at refining the algorithm and establishing the place of such technology in a sexual health clinic., (©Nyi Nyi Soe, Zhen Yu, Phyu Mon Latt, David Lee, Ranjit Singh Samra, Zongyuan Ge, Rashidur Rahman, Jiajun Sun, Jason J Ong, Christopher K Fairley, Lei Zhang. Originally published in the Journal of Medical Internet Research (https://www.jmir.org), 13.09.2024.)

Background: Regional Wall Motion Abnormality (RWMA) serves as an early indicator of myocardial infarction (MI), the global leader in mortality. Accurate and early detection of RWMA is vital for the successful treatment of MI. Current automated echocardiography analyses typically concentrate on peak values from left ventricular (LV) displacement curves, based on LV contour annotations or key frames during the heart's systolic or diastolic phases within a single echocardiographic cycle. This approach may overlook the rich motion field features available in multi-cycle cardiac data, which could enhance RWMA detection., Methods: In this research, we put forward an innovative approach to detect RWMA by harnessing motion information across multiple echocardiographic cycles and multi-views. Our methodology synergizes U-Net-based segmentation with optical flow algorithms for detailed cardiac structure delineation, and Temporal Convolutional Networks (ConvNet) to extract nuanced motion features. We utilize a variety of machine learning and deep learning classifiers on both A2C and A4C views echocardiograms to enhance detection accuracy. A three-phase algorithm-originating from the HMC-QU dataset-incorporates U-Net for segmentation, followed by optical flow for cardiac wall motion field features. Temporal ConvNet, inspired by the Temporal Segment Network (TSN), is then applied to interpret these motion field features, independent of traditional cardiac parameter curves or specific key phase frame inputs., Results: Employing five-fold cross-validation, our SVM classifier demonstrated high performance, with a sensitivity of 93.13%, specificity of 83.61%, precision of 88.52%, and an F1 score of 90.39%. When compared with other studies using the HMC-QU datasets, these Fig s stand out, underlining our method's effectiveness. The classifier also attained an overall accuracy of 89.25% and Area Under the Curve (AUC) of 95%, reinforcing its potential for reliable RWMA detection in echocardiographic analysis., Conclusions: This research not only demonstrates a novel technique but also contributes a more comprehensive and precise tool for early myocardial infarction diagnosis., Competing Interests: NO authors have competing interests., (Copyright: © 2024 Kasim et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Segmentation of multiple sclerosis (MS) lesions on brain MRI scans is crucial for diagnosis, disease and treatment monitoring but is a time-consuming task. Despite several automated algorithms have been proposed, there is still no consensus on the most effective method. Here, we applied a consensus-based framework to improve lesion segmentation on T1-weighted and FLAIR scans. The framework is designed to combine publicly available state-of-the-art deep learning models, by running multiple segmentation tasks before merging the outputs of each algorithm. To assess the effectiveness of the approach, we applied it to MRI datasets from two different centers, including a private and a public dataset, with 131 and 30 MS patients respectively, with manually segmented lesion masks available. No further training was performed for any of the included algorithms. Overlap and detection scores were improved, with Dice increasing by 4-8% and precision by 3-4% respectively for the private and public dataset. High agreement was obtained between estimated and true lesion load (ρ = 0.92 and ρ = 0.97) and count (ρ = 0.83 and ρ = 0.94). Overall, this framework ensures accurate and reliable results, exploiting complementary features and overcoming some of the limitations of individual algorithms., (© 2024. The Author(s).)

Inferring gene regulatory networks through deep learning and causal inference methods is a crucial task in the field of computational biology and bioinformatics. This study presents a novel approach that uses a Graph Convolutional Network (GCN) guided by causal information to infer Gene Regulatory Networks (GRN). The transfer entropy and reconstruction layer are utilized to achieve causal feature reconstruction, mitigating the information loss problem caused by multiple rounds of neighbor aggregation in GCN, resulting in a causal and integrated representation of node features. Separable features are extracted from gene expression data by the Gaussian-kernel Autoencoder to improve computational efficiency. Experimental results on the DREAM5 and the mDC dataset demonstrate that our method exhibits superior performance compared to existing algorithms, as indicated by the higher values of the AUPRC metrics. Furthermore, the incorporation of causal feature reconstruction enhances the inferred GRN, rendering them more reasonable, accurate, and reliable., (© 2024. The Author(s).)

The research aims to lift the accuracy of table tennis trajectory prediction through advanced computer vision and deep learning techniques to achieve real-time and accurate table tennis ball position and motion trajectory tracking. The study concentrates on the innovative application of a micro-miniature fourth-generation real-time target detection algorithm with a gated loop unit to table tennis ball motion analysis by combining physical models and deep learning methods. The results show that in the comparison experiments, the improved micro-miniature fourth-generation real-time target detection algorithm outperforms the traditional target detection algorithm, with the loss value decreasing to 1.54. Its average accuracy in multi-target recognition is dramatically increased to 86.74%, which is 22.36% higher than the original model, and the ping-pong ball recognition experiments show that it has an excellent accuracy in various lighting conditions, especially in low light, with an average accuracy of 89.12%. Meanwhile, the improved model achieves a processing efficiency of 85 frames/s. In addition, compared with the traditional trajectory prediction model, the constructed model performs the best in table tennis ball trajectory prediction, with errors of 4.5 mm, 25.3 mm, and 35.58 mm. The results show that the research trajectory prediction model achieves significant results in accurately tracking table tennis ball positions and trajectories. It not only has practical application value for table tennis training and competition strategies, but also provides a useful reference for the similar techniques application in other sports., Competing Interests: The authors declare that they have no competing interests., (Copyright: © 2024 He, Li. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Objectives: Despite global research on early detection of age-related macular degeneration (AMD), not enough is being done for large-scale screening. Automated analysis of retinal images captured via smartphone presents a potential solution; however, to our knowledge, such an artificial intelligence (AI) system has not been evaluated. The study aimed to assess the performance of an AI algorithm in detecting referable AMD on images captured on a portable fundus camera., Design, Setting: A retrospective image database from the Age-Related Eye Disease Study (AREDS) and target device was used., Participants: The algorithm was trained on two distinct data sets with macula-centric images: initially on 108,251 images (55% referable AMD) from AREDS and then fine-tuned on 1108 images (33% referable AMD) captured on Asian eyes using the target device. The model was designed to indicate the presence of referable AMD (intermediate and advanced AMD). Following the first training step, the test set consisted of 909 images (49% referable AMD). For the fine-tuning step, the test set consisted of 238 (34% referable AMD) images. The reference standard for the AREDS data set was fundus image grading by the central reading centre, and for the target device, it was consensus image grading by specialists., Outcome Measures: Area under receiver operating curve (AUC), sensitivity and specificity of algorithm., Results: Before fine-tuning, the deep learning (DL) algorithm exhibited a test set (from AREDS) sensitivity of 93.48% (95% CI: 90.8% to 95.6%), specificity of 82.33% (95% CI: 78.6% to 85.7%) and AUC of 0.965 (95% CI:0.95 to 0.98). After fine-tuning, the DL algorithm displayed a test set (from the target device) sensitivity of 91.25% (95% CI: 82.8% to 96.4%), specificity of 84.18% (95% CI: 77.5% to 89.5%) and AUC 0.947 (95% CI: 0.911 to 0.982)., Conclusion: The DL algorithm shows promising results in detecting referable AMD from a portable smartphone-based imaging system. This approach can potentially bring effective and affordable AMD screening to underserved areas., Competing Interests: Competing interests: FMS, DPR, TJK, BO and ASi are employees of Remidio Innovative Solutions. Remidio Innovative Solutions, Inc, USA and Medios Technologies are wholly owned subsidiaries of Remidio Innovative Solutions Pvt Ltd, India. FMS has patents and financial interests in Remidio Innovative Solutions Pvt Ltd (ESOP and Stock). ASi has patents, stock and leadership role. ASh is a consultant for Novartis, Allergan, Bayer and Intas, unrelated to this work., (© Author(s) (or their employer(s)) 2024. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Lung cancer (LC) is a life-threatening and dangerous disease all over the world. However, earlier diagnoses and treatment can save lives. Earlier diagnoses of malevolent cells in the lungs responsible for oxygenating the human body and expelling carbon dioxide due to significant procedures are critical. Even though a computed tomography (CT) scan is the best imaging approach in the healthcare sector, it is challenging for physicians to identify and interpret the tumour from CT scans. LC diagnosis in CT scan using artificial intelligence (AI) can help radiologists in earlier diagnoses, enhance performance, and decrease false negatives. Deep learning (DL) for detecting lymph node contribution on histopathological slides has become popular due to its great significance in patient diagnoses and treatment. This study introduces a computer-aided diagnosis for LC by utilizing the Waterwheel Plant Algorithm with DL (CADLC-WWPADL) approach. The primary aim of the CADLC-WWPADL approach is to classify and identify the existence of LC on CT scans. The CADLC-WWPADL method uses a lightweight MobileNet model for feature extraction. Besides, the CADLC-WWPADL method employs WWPA for the hyperparameter tuning process. Furthermore, the symmetrical autoencoder (SAE) model is utilized for classification. An investigational evaluation is performed to demonstrate the significant detection outputs of the CADLC-WWPADL technique. An extensive comparative study reported that the CADLC-WWPADL technique effectively performs with other models with a maximum accuracy of 99.05% under the benchmark CT image dataset., (© 2024. The Author(s).)

Background: This study aims to evaluate the performance of a deep learning system for the evaluation of tooth development stages on images obtained from panoramic radiographs from child patients., Methods: The study collected a total of 1500 images obtained from panoramic radiographs from child patients between the ages of 5 and 14 years. YOLOv5, a convolutional neural network (CNN)-based object detection model, was used to automatically detect the calcification states of teeth. Images obtained from panoramic radiographs from child patients were trained and tested in the YOLOv5 algorithm. True-positive (TP), false-positive (FP), and false-negative (FN) ratios were calculated. A confusion matrix was used to evaluate the performance of the model., Results: Among the 146 test group images with 1022 labels, there were 828 TPs, 308 FPs, and 1 FN. The sensitivity, precision, and F1-score values of the detection model of the tooth stage development model were 0.99, 0.72, and 0.84, respectively., Conclusions: In conclusion, utilizing a deep learning-based approach for the detection of dental development on pediatric panoramic radiographs may facilitate a precise evaluation of the chronological correlation between tooth development stages and age. This can help clinicians make treatment decisions and aid dentists in finding more accurate treatment options., (© 2024. The Author(s).)

Target-aware drug discovery has greatly accelerated the drug discovery process to design small-molecule ligands with high binding affinity to disease-related protein targets. Conditioned on targeted proteins, previous works utilize various kinds of deep generative models and have shown great potential in generating molecules with strong protein-ligand binding interactions. However, beyond binding affinity, effective drug molecules must manifest other essential properties such as high drug-likeness, which are not explicitly addressed by current target-aware generative methods. In this article, aiming to bridge the gap of multi-objective target-aware molecule generation in the field of deep learning-based drug discovery, we propose ParetoDrug, a Pareto Monte Carlo Tree Search (MCTS) generation algorithm. ParetoDrug searches molecules on the Pareto Front in chemical space using MCTS to enable synchronous optimization of multiple properties. Specifically, ParetoDrug utilizes pretrained atom-by-atom autoregressive generative models for the exploration guidance to desired molecules during MCTS searching. Besides, when selecting the next atom symbol, a scheme named ParetoPUCT is proposed to balance exploration and exploitation. Benchmark experiments and case studies demonstrate that ParetoDrug is highly effective in traversing the large and complex chemical space to discover novel compounds with satisfactory binding affinities and drug-like properties for various multi-objective target-aware drug discovery tasks., (© 2024. The Author(s).)

Background: Skin cancer is one of the highly occurring diseases in human life. Early detection and treatment are the prime and necessary points to reduce the malignancy of infections. Deep learning techniques are supplementary tools to assist clinical experts in detecting and localizing skin lesions. Vision transformers (ViT) based on image segmentation classification using multiple classes provide fairly accurate detection and are gaining more popularity due to legitimate multiclass prediction capabilities., Materials and Methods: In this research, we propose a new ViT Gradient-Weighted Class Activation Mapping (GradCAM) based architecture named ViT-GradCAM for detecting and classifying skin lesions by spreading ratio on the lesion's surface area. The proposed system is trained and validated using a HAM 10000 dataset by studying seven skin lesions. The database comprises 10 015 dermatoscopic images of varied sizes. The data preprocessing and data augmentation techniques are applied to overcome the class imbalance issues and improve the model's performance., Result: The proposed algorithm is based on ViT models that classify the dermatoscopic images into seven classes with an accuracy of 97.28%, precision of 98.51, recall of 95.2%, and an F1 score of 94.6, respectively. The proposed ViT-GradCAM obtains better and more accurate detection and classification than other state-of-the-art deep learning-based skin lesion detection models. The architecture of ViT-GradCAM is extensively visualized to highlight the actual pixels in essential regions associated with skin-specific pathologies., Conclusion: This research proposes an alternate solution to overcome the challenges of detecting and classifying skin lesions using ViTs and GradCAM, which play a significant role in detecting and classifying skin lesions accurately rather than relying solely on deep learning models., (© 2024 The Author(s). Skin Research and Technology published by John Wiley & Sons Ltd.)

Objective: To assess the effect of a new lung enhancement filter combined with deep learning image reconstruction (DLIR) algorithm on image quality and ground-glass nodule (GGN) sharpness compared to hybrid iterative reconstruction or DLIR alone., Materials and Methods: Five artificial spherical GGNs with various densities (-250, -350, -450, -550, and -630 Hounsfield units) and 10 mm in diameter were placed in a thorax anthropomorphic phantom. Four scans at four different radiation dose levels were performed using a 256-slice CT (Revolution Apex CT, GE Healthcare). Each scan was reconstructed using three different reconstruction algorithms: adaptive statistical iterative reconstruction-V at a level of 50% (AR50), Truefidelity (TF), which is a DLIR method, and TF with a lung enhancement filter (TF + Lu). Thus, 12 sets of reconstructed images were obtained and analyzed. Image noise, signal-to-noise ratio, and contrast-to-noise ratio were compared among the three reconstruction algorithms. Nodule sharpness was compared among the three reconstruction algorithms using the full-width at half-maximum value. Furthermore, subjective image quality analysis was performed., Results: AR50 demonstrated the highest level of noise, which was decreased by using TF + Lu and TF alone ( P = 0.001). TF + Lu significantly improved nodule sharpness at all radiation doses compared to TF alone ( P = 0.001). The nodule sharpness of TF + Lu was similar to that of AR50. Using TF alone resulted in the lowest nodule sharpness., Conclusion: Adding a lung enhancement filter to DLIR (TF + Lu) significantly improved the nodule sharpness compared to DLIR alone (TF). TF + Lu can be an effective reconstruction technique to enhance image quality and GGN evaluation in ultralow-dose chest CT scans., Competing Interests: The authors have no potential conflicts of interest to disclose., (Copyright © 2024 The Korean Society of Radiology.)

Mass spectrometry is crucial in proteomics analysis, particularly using Data Independent Acquisition (DIA) for reliable and reproducible mass spectrometry data acquisition, enabling broad mass-to-charge ratio coverage and high throughput. DIA-NN, a prominent deep learning software in DIA proteome analysis, generates peptide results but may include low-confidence peptides. Conventionally, biologists have to manually screen peptide fragment ion chromatogram peaks (XIC) for identifying high-confidence peptides, a time-consuming and subjective process prone to variability. In this study, we introduce SeFilter-DIA, a deep learning algorithm, aiming at automating the identification of high-confidence peptides. Leveraging compressed excitation neural network and residual network models, SeFilter-DIA extracts XIC features and effectively discerns between high and low-confidence peptides. Evaluation of the benchmark datasets demonstrates SeFilter-DIA achieving 99.6% AUC on the test set and 97% for other performance indicators. Furthermore, SeFilter-DIA is applicable for screening peptides with phosphorylation modifications. These results demonstrate the potential of SeFilter-DIA to replace manual screening, providing an efficient and objective approach for high-confidence peptide identification while mitigating associated limitations., (© 2024. International Association of Scientists in the Interdisciplinary Areas.)

An artificial intelligence (AI) model was designed to assist pathologists in diagnosing and quantifying structural changes in tongue lesions induced by chemical carcinogens. Using a tongue cancer model induced by 4-nitroquinoline-N-oxide and treated with β-elemene, a total of 183 digital pathology slides were processed. The Segment Anything Model (SAM) was employed for initial segmentation, followed by conventional algorithms for more detailed segmentation. The epithelial contour area was computed using OpenCV's findcontour method, and the skeletonize method was used to calculate the distance map and skeletonized representation. The AI model demonstrated high accuracy in measuring tongue epithelial thickness and the number of papilla-like protrusions. Results indicated that the model group had significantly higher epithelial thickness and fewer papillae compared with the blank group. Furthermore, the treatment group exhibited reduced epithelial thickness and fewer papilla-like protrusions compared with the model group, though these differences were less pronounced. Overall, the SAM framework algorithm proved effective in quantifying tongue epithelial thickness and the number of papilla-like protrusions, thereby assisting healthcare professionals in understanding pathological changes and assessing treatment outcomes., (© 2024 Wiley‐VCH GmbH. Published by John Wiley & Sons Ltd.)

The breakthrough of AlphaFold2 and the publication of AlphaFold DB represent a significant advance in the field of predicting static protein structures. However, AlphaFold2 models tend to represent a single static structure, and multiple-conformation prediction remains a challenge. In this work, we proposed a method named MultiSFold, which uses a distance-based multi-objective evolutionary algorithm to predict multiple conformations. To begin, multiple energy landscapes are constructed using different competing constraints generated by deep learning. Subsequently, an iterative modal exploration and exploitation strategy is designed to sample conformations, incorporating multi-objective optimization, geometric optimization and structural similarity clustering. Finally, the final population is generated using a loop-specific sampling strategy to adjust the spatial orientations. MultiSFold was evaluated against state-of-the-art methods using a benchmark set containing 80 protein targets, each characterized by two representative conformational states. Based on the proposed metric, MultiSFold achieves a remarkable success ratio of 56.25% in predicting multiple conformations, while AlphaFold2 only achieves 10.00%, which may indicate that conformational sampling combined with knowledge gained through deep learning has the potential to generate conformations spanning the range between different conformational states. In addition, MultiSFold was tested on 244 human proteins with low structural accuracy in AlphaFold DB to test whether it could further improve the accuracy of static structures. The experimental results demonstrate the performance of MultiSFold, with a TM-score better than that of AlphaFold2 by 2.97% and RoseTTAFold by 7.72%. The online server is at http://zhanglab-bioinf.com/MultiSFold ., (© 2024. International Association of Scientists in the Interdisciplinary Areas.)

Metal artifact reduction (MAR) is important for clinical diagnosis with CT images. The existing state-of-the-art deep learning methods usually suppress metal artifacts in sinogram or image domains or both. However, their performance is limited by the inherent characteristics of the two domains, i.e., the errors introduced by local manipulations in the sinogram domain would propagate throughout the whole image during backprojection and lead to serious secondary artifacts, while it is difficult to distinguish artifacts from actual image features in the image domain. To alleviate these limitations, this study analyzes the desirable properties of wavelet transform in-depth and proposes to perform MAR in the wavelet domain. First, wavelet transform yields components that possess spatial correspondence with the image, thereby preventing the spread of local errors to avoid secondary artifacts. Second, using wavelet transform could facilitate identification of artifacts from image since metal artifacts are mainly high-frequency signals. Taking these advantages of the wavelet transform, this paper decomposes an image into multiple wavelet components and introduces multi-perspective regularizations into the proposed MAR model. To improve the transparency and validity of the model, all the modules in the proposed MAR model are designed to reflect their mathematical meanings. In addition, an adaptive wavelet module is also utilized to enhance the flexibility of the model. To optimize the model, an iterative algorithm is developed. The evaluation on both synthetic and real clinical datasets consistently confirms the superior performance of the proposed method over the competing methods.

Elucidating unknown structures of proteins, such as metastable states, is critical in designing therapeutic agents. Protein structure exploration has been performed using advanced computational methods, especially molecular dynamics and Markov chain Monte Carlo simulations, which require untenably long calculation times and prior structural knowledge. Here, we developed an innovative method for protein structure determination called never give up protein exploration (NPEX) with deep reinforcement learning. The NPEX method leverages the soft actor-critic algorithm and the intrinsic reward system, effectively adding a bias potential without the need for prior knowledge. To demonstrate the method's effectiveness, we applied it to four models: a double well, a triple well, the alanine dipeptide, and the tryptophan cage. Compared with Markov chain Monte Carlo simulations, NPEX had markedly greater sampling efficiency. The significantly enhanced computational efficiency and lack of prior domain knowledge requirements of the NPEX method will revolutionize protein structure exploration., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Introduction: Small molecules often bind to multiple targets, a behavior termed polypharmacology. Anticipating polypharmacology is essential for drug discovery since unknown off-targets can modulate safety and efficacy - profoundly affecting drug discovery success. Unfortunately, experimental methods to assess selectivity present significant limitations and drugs still fail in the clinic due to unanticipated off-targets. Computational methods are a cost-effective, complementary approach to predict polypharmacology., Areas Covered: This review aims to provide a comprehensive overview of the state of polypharmacology prediction and discuss its strengths and limitations, covering both classical cheminformatics methods and bioinformatic approaches. The authors review available data sources, paying close attention to their different coverage. The authors then discuss major algorithms grouped by the types of data that they exploit using selected examples., Expert Opinion: Polypharmacology prediction has made impressive progress over the last decades and contributed to identify many off-targets. However, data incompleteness currently limits most approaches to comprehensively predict selectivity. Moreover, our limited agreement on model assessment challenges the identification of the best algorithms - which at present show modest performance in prospective real-world applications. Despite these limitations, the exponential increase of multidisciplinary Big Data and AI hold much potential to better polypharmacology prediction and de-risk drug discovery.

World Health Organization (WHO) has identified depression as a significant contributor to global disability, creating a complex thread in both public and private health. Electroencephalogram (EEG) can accurately reveal the working condition of the human brain, and it is considered an effective tool for analyzing depression. However, manual depression detection using EEG signals is time-consuming and tedious. To address this, fully automatic depression identification models have been designed using EEG signals to assist clinicians. In this study, we propose a novel automated deep learning-based depression detection system using EEG signals. The required EEG signals are gathered from publicly available databases, and three sets of features are extracted from the original EEG signal. Firstly, spectrogram images are generated from the original EEG signal, and 3-dimensional Convolutional Neural Networks (3D-CNN) are employed to extract deep features. Secondly, 1D-CNN is utilized to extract deep features from the collected EEG signal. Thirdly, spectral features are extracted from the collected EEG signal. Following feature extraction, optimal weights are fused with the three sets of features. The selection of optimal features is carried out using the developed Chaotic Owl Invasive Weed Search Optimization (COIWSO) algorithm. Subsequently, the fused features undergo analysis using the Self-Attention-based Gated Densenet (SA-GDensenet) for depression detection. The parameters within the detection network are optimized with the assistance of the same COIWSO. Finally, implementation results are analyzed in comparison to existing detection models. The experimentation findings of the developed model show 96% of accuracy. Throughout the empirical result, the findings of the developed model show better performance than traditional approaches.

Over the past decade, deep-learning (DL) algorithms have become a promising tool to aid clinicians in identifying fetal head standard planes (FHSPs) during ultrasound (US) examination. However, the adoption of these algorithms in clinical settings is still hindered by the lack of large annotated datasets. To overcome this barrier, we introduce FetalBrainAwareNet, an innovative framework designed to synthesize anatomically accurate images of FHSPs. FetalBrainAwareNet introduces a cutting-edge approach that utilizes class activation maps as a prior in its conditional adversarial training process. This approach fosters the presence of the specific anatomical landmarks in the synthesized images. Additionally, we investigate specialized regularization terms within the adversarial training loss function to control the morphology of the fetal skull and foster the differentiation between the standard planes, ensuring that the synthetic images faithfully represent real US scans in both structure and overall appearance. The versatility of our FetalBrainAwareNet framework is highlighted by its ability to generate high-quality images of three predominant FHSPs using a singular, integrated framework. Quantitative (Fréchet inception distance of 88.52) and qualitative (t-SNE) results suggest that our framework generates US images with greater variability compared to state-of-the-art methods. By using the synthetic images generated with our framework, we increase the accuracy of FHSP classifiers by 3.2% compared to training the same classifiers solely with real acquisitions. These achievements suggest that using our synthetic images to increase the training set could provide benefits to enhance the performance of DL algorithms for FHSPs classification that could be integrated in real clinical scenarios., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Deep cascaded networks have been extensively studied and applied to accelerate Magnetic Resonance Imaging (MRI) and have shown promising results. Most existing works employ a large cascading number for the sake of superior performances. However, due to the lack of proper guidance, the reconstruction performance can easily reach a plateau and even face degradation if simply increasing the cascading number. In this paper, we aim to boost the reconstruction performance from a novel perspective by proposing a parallel architecture called DIRECTION that fully exploits the guiding value of the reconstruction residual of each subnetwork. Specifically, we introduce a novel Reconstruction Residual-Based Feature Modulation Mechanism (RRFMM) which utilizes the reconstruction residual of the previous subnetwork to guide the next subnetwork at the feature level. To achieve this, a Residual Attention Modulation Block (RAMB) is proposed to generate attention maps using multi-scale residual features to modulate the image features of the corresponding scales. Equipped with this strategy, each subnetwork within the cascaded network possesses its unique optimization objective and emphasis rather than blindly updating its parameters. To further boost the performance, we introduce the Cross-Stage Feature Reuse Connection (CSFRC) and the Reconstruction Dense Connection (RDC), which can reduce information loss and enhance representative ability. We conduct sufficient experiments and evaluate our method on the fastMRI knee dataset using multiple subsampling masks. Comprehensive experimental results show that our method can markedly boost the performance of cascaded networks and significantly outperforms other compared state-of-the-art methods quantitatively and qualitatively., (Copyright © 2024. Published by Elsevier Inc.)

Background: Risk prediction plays a crucial role in planning for prevention, monitoring, and treatment. Electronic Health Records (EHRs) offer an expansive repository of temporal medical data encompassing both risk factors and outcome indicators essential for effective risk prediction. However, challenges emerge due to the lack of readily available gold-standard outcomes and the complex effects of various risk factors. Compounding these challenges are the false positives in diagnosis codes, and formidable task of pinpointing the onset timing in annotations., Objective: We develop a Semi-supervised Double Deep Learning Temporal Risk Prediction (SeDDLeR) algorithm based on extensive unlabeled longitudinal Electronic Health Records (EHR) data augmented by a limited set of gold standard labels on the binary status information indicating whether the clinical event of interest occurred during the follow-up period., Methods: The SeDDLeR algorithm calculates an individualized risk of developing future clinical events over time using each patient's baseline EHR features via the following steps: (1) construction of an initial EHR-derived surrogate as a proxy for the onset status; (2) deep learning calibration of the surrogate along gold-standard onset status; and (3) semi-supervised deep learning for risk prediction combining calibrated surrogates and gold-standard onset status. To account for missing onset time and heterogeneous follow-up, we introduce temporal kernel weighting. We devise a Gated Recurrent Units (GRUs) module to capture temporal characteristics. We subsequently assess our proposed SeDDLeR method in simulation studies and apply the method to the Massachusetts General Brigham (MGB) Biobank to predict type 2 diabetes (T2D) risk., Results: SeDDLeR outperforms benchmark risk prediction methods, including Semi-parametric Transformation Model (STM) and DeepHit, with consistently best accuracy across experiments. SeDDLeR achieved the best C-statistics ( 0.815, SE 0.023; vs STM +.084, SE 0.030, P-value .004; vs DeepHit +.055, SE 0.027, P-value .024) and best average time-specific AUC (0.778, SE 0.022; vs STM + 0.059, SE 0.039, P-value .067; vs DeepHit + 0.168, SE 0.032, P-value <0.001) in the MGB T2D study., Conclusion: SeDDLeR can train robust risk prediction models in both real-world EHR and synthetic datasets with minimal requirements of labeling event times. It holds the potential to be incorporated for future clinical trial recruitment or clinical decision-making., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Purpose: To determine the role of deep learning-based arterial subtraction images in viability assessment on extracellular agents-enhanced MRI using LR-TR algorithm., Methods: Patients diagnosed with HCC who underwent locoregional therapy were retrospectively collected. We constructed a deep learning-based subtraction model and automatically generated arterial subtraction images. Two radiologists evaluated LR-TR category on ordinary images and then evaluated again on ordinary images plus arterial subtraction images after a 2-month washout period. The reference standard for viability was tumor stain on the digital subtraction hepatic angiography within 1 month after MRI., Results: 286 observations of 105 patients were ultimately enrolled. 157 observations were viable and 129 observations were nonviable according to the reference standard. The sensitivity and accuracy of LR-TR algorithm for detecting viable HCC significantly increased with the application of arterial subtraction images (87.9% vs. 67.5%, p < 0.001; 86.4% vs. 75.9%, p < 0.001). And the specificity slightly decreased without significant difference when the arterial subtraction images were added (84.5% vs. 86.0%, p = 0.687). The AUC of LR-TR algorithm significantly increased with the addition of arterial subtraction images (0.862 vs. 0.768, p < 0.001). The arterial subtraction images also improved inter-reader agreement (0.857 vs. 0.727)., Conclusion: Extended application of deep learning-based arterial subtraction images on extracellular agents-enhanced MRI can increase the sensitivity of LR-TR algorithm for detecting viable HCC without significant change in specificity., (© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Background/objectives: Artificial intelligence can assist with ocular image analysis for screening and diagnosis, but it is not yet capable of autonomous full-spectrum screening. Hypothetically, false-positive results may have unrealized screening potential arising from signals persisting despite training and/or ambiguous signals such as from biomarker overlap or high comorbidity. The study aimed to explore the potential to detect clinically useful incidental ocular biomarkers by screening fundus photographs of hypertensive adults using diabetic deep learning algorithms., Subjects/methods: Patients referred for treatment-resistant hypertension were imaged at a hospital unit in Perth, Australia, between 2016 and 2022. The same 45° colour fundus photograph selected for each of the 433 participants imaged was processed by three deep learning algorithms. Two expert retinal specialists graded all false-positive results for diabetic retinopathy in non-diabetic participants., Results: Of the 29 non-diabetic participants misclassified as positive for diabetic retinopathy, 28 (97%) had clinically useful retinal biomarkers. The models designed to screen for fewer diseases captured more incidental disease. All three algorithms showed a positive correlation between severity of hypertensive retinopathy and misclassified diabetic retinopathy., Conclusions: The results suggest that diabetic deep learning models may be responsive to hypertensive and other clinically useful retinal biomarkers within an at-risk, hypertensive cohort. Observing that models trained for fewer diseases captured more incidental pathology increases confidence in signalling hypotheses aligned with using self-supervised learning to develop autonomous comprehensive screening. Meanwhile, non-referable and false-positive outputs of other deep learning screening models could be explored for immediate clinical use in other populations., (© 2024. The Author(s).)

Owing to the success of transformer models, recent works study their applicability in 3D medical segmentation tasks. Within the transformer models, the self-attention mechanism is one of the main building blocks that strives to capture long-range dependencies, compared to the local convolutional-based design. However, the self-attention operation has quadratic complexity which proves to be a computational bottleneck, especially in volumetric medical imaging, where the inputs are 3D with numerous slices. In this paper, we propose a 3D medical image segmentation approach, named UNETR++, that offers both high-quality segmentation masks as well as efficiency in terms of parameters, compute cost, and inference speed. The core of our design is the introduction of a novel efficient paired attention (EPA) block that efficiently learns spatial and channel-wise discriminative features using a pair of inter-dependent branches based on spatial and channel attention. Our spatial attention formulation is efficient and has linear complexity with respect to the input. To enable communication between spatial and channel-focused branches, we share the weights of query and key mapping functions that provide a complimentary benefit (paired attention), while also reducing the complexity. Our extensive evaluations on five benchmarks, Synapse, BTCV, ACDC, BraTS, and Decathlon-Lung, reveal the effectiveness of our contributions in terms of both efficiency and accuracy. On Synapse, our UNETR++ sets a new state-of-the-art with a Dice Score of 87.2%, while significantly reducing parameters and FLOPs by over 71%, compared to the best method in the literature. Our code and models are available at: https://tinyurl.com/2p87x5xn.

In the world, grapes are considered as the most significant fruit, and it comprises various nutrients, like Vitamin C and it is utilized to produce wines and raisins. The major six general grape leaf diseases and pests are brown spots, leaf blight, downy mildew, anthracnose, and black rot. However, the existing manual detection methods are time-consuming and require more efforts. In this paper, an effectual grape leaf disease finding and percentage of pesticide detection approach is devised usingan optimized deep learning scheme. Here, the input image is pre-processed and then, black spot segmentation is done using proposed Taylor Remora Optimization Procedure (TROA). The TROA is the combination of Taylor concept and Remora Optimization Algorithm (ROA). After that, the multi-classification of grape leaf disease is performed to classify the disease as Black rot, Black measles, Isariopsis leaf spot and healthy. Accordingly, the training process of the Deep Neuro-Fuzzy Optimizer (DNFN) is done using Sine Cosine Butterfly Optimization (SCBO). Then, pesticide classification is done using Deep Maxout Network (DMN) and the training of the DMN is done using the Monarch Anti Corona Optimization (MACO) algorithm. Finally, the pesticide percentage level detection is performed using Deep Belief Network (DBN), which is trained by the TROA. The devised scheme obtained highest accuracy of 0.9327, sensitivity of 0.9383, and 0.9429. Thus, this method can assist as an effectual decision provision system for assisting the farmers to find the percentage of pesticide affected in grape leaf diseases., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Magnetic resonance imaging produces detailed anatomical and physiological images of the human body that can be used in the clinical diagnosis and treatment of diseases. However, MRI suffers its comparatively longer acquisition time than other imaging methods and is thus vulnerable to motion artifacts, which ultimately lead to likely failed or even wrong diagnosis. In order to perform faster reconstruction, deep learning-based methods along with traditional strategies such as parallel imaging and compressed sensing come into play in recent years in this field. Meanwhile, in order to better analyze the diseases, it is also often necessary to acquire images in the same region of interest under different modalities, which yield images with different contrast levels. However, most of these aforementioned methods tend to use single-modal images for reconstruction, neglecting the correlation and redundancy information embedded in MR images acquired with different modalities. While there are works on multi-modal reconstruction, the information is yet to be efficiently explored. In this paper, we propose an end-to-end neural network called MLMFNet, which helps the reconstruction of the target modality by using information from the auxiliary modality across feature channels and layers. Specifically, this is highlighted by three components: (I) An encoder based on UNet with a single-stream strategy that fuses auxiliary and target modalities; (II) a decoder that tends to multi-level features from all layers of the encoder, and (III) a channel attention module. Quantitative and qualitative analyses are performed on a public brain dataset and knee brain dataset, which show that the proposed method achieves satisfying results in MRI reconstruction within the multi-modal context, and also demonstrate its effectiveness and potential to be used in clinical practice., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier Inc.)

Purpose: To introduce a novel deep model-based architecture (DMBA), SPICER, that uses pairs of noisy and undersampled k-space measurements of the same object to jointly train a model for MRI reconstruction and automatic coil sensitivity estimation., Methods: SPICER consists of two modules to simultaneously reconstructs accurate MR images and estimates high-quality coil sensitivity maps (CSMs). The first module, CSM estimation module, uses a convolutional neural network (CNN) to estimate CSMs from the raw measurements. The second module, DMBA-based MRI reconstruction module, forms reconstructed images from the input measurements and the estimated CSMs using both the physical measurement model and learned CNN prior. With the benefit of our self-supervised learning strategy, SPICER can be efficiently trained without any fully sampled reference data., Results: We validate SPICER on both open-access datasets and experimentally collected data, showing that it can achieve state-of-the-art performance in highly accelerated data acquisition settings (up to 10 × $$ 10\times $$ ). Our results also highlight the importance of different modules of SPICER-including the DMBA, the CSM estimation, and the SPICER training loss-on the final performance of the method. Moreover, SPICER can estimate better CSMs than pre-estimation methods especially when the ACS data is limited., Conclusion: Despite being trained on noisy undersampled data, SPICER can reconstruct high-quality images and CSMs in highly undersampled settings, which outperforms other self-supervised learning methods and matches the performance of the well-known E2E-VarNet trained on fully sampled ground-truth data., (© 2024 International Society for Magnetic Resonance in Medicine.)

Image content identification systems have many applications in industry and academia. In particular, a hash-based content identification system uses a robust image hashing function that computes a short binary identifier summarizing the perceptual content in a picture and is invariant against a set of expected manipulations while being capable of differentiating between different pictures. A common approach to designing these algorithms is crafting a processing pipeline by hand. Unfortunately, once the context changes, the researcher may need to define a new function to adapt. A deep hashing approach exploits the feature learning capabilities in deep networks to generate a feature vector that summarizes the perceptual content in the image, achieving outstanding performance for the image retrieval task, which requires measuring semantic and perceptual similarity between items. However, its application to robust content identification systems is an open area of opportunity. Also, image hashing functions are valuable tools for image authentication. However, to our knowledge, its application to content-preserving manipulation detection for image forensics tasks is still an open research area. In this work, we propose a deep hashing method exploiting the metric learning capabilities in contrastive self-supervised learning with a new modular loss function for robust image hashing. Moreover, we propose a novel approach for content-preserving manipulation detection for image forensics through a sensitivity component in our loss function. We validate our method through extensive experimentation in different data sets and configurations, validating the generalization properties in our work., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier Ltd.)

Objective: Echocardiographic videos are commonly used for automatic semantic segmentation of endocardium, which is crucial in evaluating cardiac function and assisting doctors to make accurate diagnoses of heart disease. However, this task faces two distinct challenges: one is the edge blurring, which is caused by the presence of speckle noise or excessive de-noising operation, and the other is the lack of an effective feature fusion approach for multilevel features for obtaining accurate endocardium., Methods: In this study, a deep learning model, based on multilevel edge perception and calibration fusion is proposed to improve the segmentation performance. First, a multilevel edge perception module is proposed to comprehensively extract edge features through both a detail branch and a semantic branch to alleviate the adverse impact of noise. Second, a calibration fusion module is proposed that calibrates and integrates various features, including semantic and detailed information, to maximize segmentation performance. Furthermore, the features obtained from the calibration fusion module are stored by using a memory architecture to achieve semi-supervised segmentation through both labeled and unlabeled data., Results: Our method is evaluated on two public echocardiography video data sets, achieving average Dice coefficients of 93.05% and 93.93%, respectively. Additionally, we validated our method on a local hospital clinical data set, achieving a Pearson correlation of 0.765 for predicting left ventricular ejection fraction., Conclusion: The proposed model effectively solves the challenges encountered in echocardiography by using semi-supervised networks, thereby improving the segmentation accuracy of the ventricles. This indicates that the proposed model can assist cardiologists in obtaining accurate and effective research and diagnostic results., Competing Interests: Conflict of interest The authors declare no competing interests., (Copyright © 2024 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.)

Diabetic retinopathy (DR) poses a significant challenge in diabetes management, with its progression often asymptomatic until advanced stages. This underscores the urgent need for cost-effective and reliable screening methods. Consequently, the integration of artificial intelligence (AI) tools presents a promising avenue to address this need effectively. We provide an overview of the current state of the art results and techniques in DR screening using AI, while also identifying gaps in research for future exploration. By synthesizing existing database and pinpointing areas requiring further investigation, this paper seeks to guide the direction of future research in the field of automatic diabetic retinopathy screening. There has been a continuous rise in the number of articles detailing deep learning (DL) methods designed for the automatic screening of diabetic retinopathy especially by the year 2021. Researchers utilized various databases, with a primary focus on the IDRiD dataset. This dataset consists of color fundus images captured at an ophthalmological clinic situated in India. It comprises 516 images that depict various stages of DR and diabetic macular edema. Each of the chosen papers concentrates on various DR signs. Nevertheless, a significant portion primarily focused on detecting exudates, which remains insufficient to assess the overall presence of this disease. Various AI methods have been employed to identify DR signs. Among the chosen papers, 4.7 % utilized detection methods, 46.5 % employed classification techniques, 41.9 % relied on segmentation, and 7 % opted for a combination of classification and segmentation. Metrics calculated from 80 % of the articles employing preprocessing techniques demonstrated the significant benefits of this approach in enhancing results quality. In addition, multiple DL techniques, starting by classification, detection then segmentation. Researchers used mostly YOLO for detection, ViT for classification, and U-Net for segmentation. Another perspective on the evolving landscape of AI models for diabetic retinopathy screening lies in the increasing adoption of Convolutional Neural Networks for classification tasks and U-Net architectures for segmentation purposes; however, there is a growing realization within the research community that these techniques, while powerful individually, can be even more effective when integrated. This integration holds promise for not only diagnosing DR, but also accurately classifying its different stages, thereby enabling more tailored treatment strategies. Despite this potential, the development of AI models for DR screening is fraught with challenges. Chief among these is the difficulty in obtaining the high-quality, labeled data necessary for training models to perform effectively. This scarcity of data poses significant barriers to achieving robust performance and can hinder progress in developing accurate screening systems. Moreover, managing the complexity of these models, particularly deep neural networks, presents its own set of challenges. Additionally, interpreting the outputs of these models and ensuring their reliability in real-world clinical settings remain ongoing concerns. Furthermore, the iterative process of training and adapting these models to specific datasets can be time-consuming and resource-intensive. These challenges underscore the multifaceted nature of developing effective AI models for DR screening. Addressing these obstacles requires concerted efforts from researchers, clinicians, and technologists to develop new approaches and overcome existing limitations. By doing so, a full potential of AI may transform DR screening and improve patient outcomes., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Objectives: Severity of degenerative scoliosis (DS) is assessed by measuring the Cobb angle on anteroposterior radiographs. However, MRI images are often available to study the degenerative spine. This retrospective study aims to develop and evaluate the reliability of a novel automatic method that measures coronal Cobb angles on lumbar MRI in DS patients., Materials and Methods: Vertebrae and intervertebral discs were automatically segmented using a 3D AI algorithm, trained on 447 lumbar MRI series. The segmentations were used to calculate all possible angles between the vertebral endplates, with the largest being the Cobb angle. The results were validated with 50 high-resolution sagittal lumbar MRI scans of DS patients, in which three experienced readers measured the Cobb angle. Reliability was determined using the intraclass correlation coefficient (ICC)., Results: The ICCs between the readers ranged from 0.90 (95% CI 0.83-0.94) to 0.93 (95% CI 0.88-0.96). The ICC between the maximum angle found by the algorithm and the average manually measured Cobb angles was 0.83 (95% CI 0.71-0.90). In 9 out of the 50 cases (18%), all readers agreed on both vertebral levels for Cobb angle measurement. When using the algorithm to extract the angles at the vertebral levels chosen by the readers, the ICCs ranged from 0.92 (95% CI 0.87-0.96) to 0.97 (95% CI 0.94-0.98)., Conclusion: The Cobb angle can be accurately measured on MRI using the newly developed algorithm in patients with DS. The readers failed to consistently choose the same vertebral level for Cobb angle measurement, whereas the automatic approach ensures the maximum angle is consistently measured., Clinical Relevance Statement: Our AI-based algorithm offers reliable Cobb angle measurement on routine MRI for degenerative scoliosis patients, potentially reducing the reliance on conventional radiographs, ensuring consistent assessments, and therefore improving patient care., Key Points: • While often available, MRI images are rarely utilized to determine the severity of degenerative scoliosis. • The presented MRI Cobb angle algorithm is more reliable than humans in patients with degenerative scoliosis. • Radiographic imaging for Cobb angle measurements is mitigated when lumbar MRI images are available., (© 2024. The Author(s).)

Researchers face the challenge of defining subject selection criteria when training algorithms for human activity recognition tasks. The ongoing uncertainty revolves around which characteristics should be considered to ensure algorithmic robustness across diverse populations. This study aims to address this challenge by conducting an analysis of heterogeneity in the training data to assess the impact of physical characteristics and soft-biometric attributes on activity recognition performance. The performance of various state-of-the-art deep neural network architectures (tCNN, hybrid-LSTM, Transformer model) processing time-series data using the IntelliRehab (IRDS) dataset was evaluated. By intentionally introducing bias into the training data based on human characteristics, the objective is to identify the characteristics that influence algorithms in motion analysis. Experimental findings reveal that the CNN-LSTM model achieved the highest accuracy, reaching 88%. Moreover, models trained on heterogeneous distributions of disability attributes exhibited notably higher accuracy, reaching 51%, compared to those not considering such factors, which scored an average of 33%. These evaluations underscore the significant influence of subjects' characteristics on activity recognition performance, providing valuable insights into the algorithm's robustness across diverse populations. This study represents a significant step forward in promoting fairness and trustworthiness in artificial intelligence by quantifying representation bias in multi-channel time-series activity recognition data within the healthcare domain., Competing Interests: Declaration of competing interest All authors have participated in (a) conception and design, or analysis and interpretation of the data; (b) drafting the article or revising it critically for important intellectual content; and (c) approval of the final version. This manuscript has not been submitted to, nor is under review at, another journal or other publishing venue. The authors have no affiliation with any organization with a direct or indirect financial interest in the subject matter discussed in the manuscript, (Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

With the adoption of smart systems, artificial neural networks (ANNs) have become ubiquitous. Conventional ANN implementations have high energy consumption, limiting their use in embedded and mobile applications. Spiking neural networks (SNNs) mimic the dynamics of biological neural networks by distributing information over time through binary spikes. Neuromorphic hardware has emerged to leverage the characteristics of SNNs, such as asynchronous processing and high activation sparsity. Therefore, SNNs have recently gained interest in the machine learning community as a brain-inspired alternative to ANNs for low-power applications. However, the discrete representation of the information makes the training of SNNs by backpropagation-based techniques challenging. In this survey, we review training strategies for deep SNNs targeting deep learning applications such as image processing. We start with methods based on the conversion from an ANN to an SNN and compare these with backpropagation-based techniques. We propose a new taxonomy of spiking backpropagation algorithms into three categories, namely, spatial, spatiotemporal, and single-spike approaches. In addition, we analyze different strategies to improve accuracy, latency, and sparsity, such as regularization methods, training hybridization, and tuning of the parameters specific to the SNN neuron model. We highlight the impact of input encoding, network architecture, and training strategy on the accuracy-latency tradeoff. Finally, in light of the remaining challenges for accurate and efficient SNN solutions, we emphasize the importance of joint hardware-software codevelopment.

Stroke, a sudden cerebrovascular ailment resulting from brain tissue damage, has prompted the use of motor imagery (MI)-based Brain-Computer Interface (BCI) systems in stroke rehabilitation. However, analyzing EEG signals from stroke patients is challenging because of their low signal-to-noise ratio and high variability. Therefore, we propose a novel approach that combines the modified S-transform (MST) and a dense graph convolutional network (DenseGCN) algorithm to enhance the MI-BCI performance across time, frequency, and space domains. MST is a time-frequency analysis method that efficiently concentrates energy in EEG signals, while DenseGCN is a deep learning model that uses EEG feature maps from each layer as inputs for subsequent layers, facilitating feature reuse and hyper-parameters optimization. Our approach outperforms conventional networks, achieving a peak classification accuracy of 90.22% and an average information transfer rate (ITR) of 68.52 bits per minute. Moreover, we conduct an in-depth analysis of the event-related desynchronization/event-related synchronization (ERD/ERS) phenomenon in the deep-level EEG features of stroke patients. Our experimental results confirm the feasibility and efficacy of the proposed approach for MI-BCI rehabilitation systems.

Robust segmenting with noisy labels is an important problem in medical imaging due to the difficulty of acquiring high-quality annotations. Despite the enormous success of recent developments, these developments still require multiple networks to construct their frameworks and focus on limited application scenarios, which leads to inflexibility in practical applications. They also do not explicitly consider the coarse boundary label problem, which results in sub-optimal results. To overcome these challenges, we propose a novel Simultaneous Edge Alignment and Memory-Assisted Learning (SEAMAL) framework for noisy-label robust segmentation. It achieves single-network robust learning, which is applicable for both 2D and 3D segmentation, in both Set-HQ-knowable and Set-HQ-agnostic scenarios. Specifically, to achieve single-model noise robustness, we design a Memory-assisted Selection and Correction module (MSC) that utilizes predictive history consistency from the Prediction Memory Bank to distinguish between reliable and non-reliable labels pixel-wisely, and that updates the reliable ones at the superpixel level. To overcome the coarse boundary label problem, which is common in practice, and to better utilize shape-relevant information at the boundary, we propose an Edge Detection Branch (EDB) that explicitly learns the boundary via an edge detection layer with only slight additional computational cost, and we improve the sharpness and precision of the boundary with a thinning loss. Extensive experiments verify that SEAMAL outperforms previous works significantly.

Background and Objective: Breast cancer is a multifaceted condition characterized by diverse features and a substantial mortality rate, underscoring the imperative for timely detection and intervention. The utilization of multi-omics data has gained significant traction in recent years to identify biomarkers and classify subtypes in breast cancer. This kind of research idea from part to whole will also be an inevitable trend in future life science research. Deep learning can integrate and analyze multi-omics data to predict cancer subtypes, which can further drive targeted therapies. However, there are few articles leveraging the nature of deep learning for feature selection. Therefore, this paper proposes a Neural Network and Binary grey Wolf Optimization based BReast CAncer bioMarker (NNBGWO-BRCAMarker) discovery framework using multi-omics data to obtain a series of biomarkers for precise classification of breast cancer subtypes., Methods: NNBGWO-BRCAMarker consists of two phases: in the first phase, relevant genes are selected using the weights obtained from a trained feedforward neural network; in the second phase, the binary grey wolf optimization algorithm is leveraged to further screen the selected genes, resulting in a set of potential breast cancer biomarkers., Results: The SVM classifier with RBF kernel achieved a classification accuracy of 0.9242 ± 0.03 when trained using the 80 biomarkers identified by NNBGWO-BRCAMarker, as evidenced by the experimental results. We conducted a comprehensive gene set analysis, prognostic analysis, and druggability analysis, unveiling 25 druggable genes, 16 enriched pathways strongly linked to specific subtypes of breast cancer, and 8 genes linked to prognostic outcomes., Conclusions: The proposed framework successfully identified 80 biomarkers from the multi-omics data, enabling accurate classification of breast cancer subtypes. This discovery may offer novel insights for clinicians to pursue in further studies., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Mobile health apps are widely used for breast cancer detection using artificial intelligence algorithms, providing radiologists with second opinions and reducing false diagnoses. This study aims to develop an open-source mobile app named "BraNet" for 2D breast imaging segmentation and classification using deep learning algorithms. During the phase off-line, an SNGAN model was previously trained for synthetic image generation, and subsequently, these images were used to pre-trained SAM and ResNet18 segmentation and classification models. During phase online, the BraNet app was developed using the react native framework, offering a modular deep-learning pipeline for mammography (DM) and ultrasound (US) breast imaging classification. This application operates on a client-server architecture and was implemented in Python for iOS and Android devices. Then, two diagnostic radiologists were given a reading test of 290 total original RoI images to assign the perceived breast tissue type. The reader's agreement was assessed using the kappa coefficient. The BraNet App Mobil exhibited the highest accuracy in benign and malignant US images (94.7%/93.6%) classification compared to DM during training I (80.9%/76.9%) and training II (73.7/72.3%). The information contrasts with radiological experts' accuracy, with DM classification being 29%, concerning US 70% for both readers, because they achieved a higher accuracy in US ROI classification than DM images. The kappa value indicates a fair agreement (0.3) for DM images and moderate agreement (0.4) for US images in both readers. It means that not only the amount of data is essential in training deep learning algorithms. Also, it is vital to consider the variety of abnormalities, especially in the mammography data, where several BI-RADS categories are present (microcalcifications, nodules, mass, asymmetry, and dense breasts) and can affect the API accuracy model., (© 2024. The Author(s).)

Background: For time-consuming diffusion-weighted imaging (DWI) of the breast, deep learning-based imaging acceleration appears particularly promising., Purpose: To investigate a combined k-space-to-image reconstruction approach for scan time reduction and improved spatial resolution in breast DWI., Study Type: Retrospective., Population: 133 women (age 49.7 ± 12.1 years) underwent multiparametric breast MRI., Field Strength/sequence: 3.0T/T2 turbo spin echo, T1 3D gradient echo, DWI (800 and 1600 sec/mm 2 )., Assessment: DWI data were retrospectively processed using deep learning-based k-space-to-image reconstruction (DL-DWI) and an additional super-resolution algorithm (SRDL-DWI). In addition to signal-to-noise ratio and apparent diffusion coefficient (ADC) comparisons among standard, DL- and SRDL-DWI, a range of quantitative similarity (e.g., structural similarity index [SSIM]) and error metrics (e.g., normalized root mean square error [NRMSE], symmetric mean absolute percent error [SMAPE], log accuracy error [LOGAC]) was calculated to analyze structural variations. Subjective image evaluation was performed independently by three radiologists on a seven-point rating scale., Statistical Tests: Friedman's rank-based analysis of variance with Bonferroni-corrected pairwise post-hoc tests. P < 0.05 was considered significant., Results: Both DL- and SRDL-DWI allowed for a 39% reduction in simulated scan time over standard DWI (5 vs. 3 minutes). The highest image quality ratings were assigned to SRDL-DWI with good interreader agreement (ICC 0.834; 95% confidence interval 0.818-0.848). Irrespective of b-value, both standard and DL-DWI produced superior SNR compared to SRDL-DWI. ADC values were slightly higher in SRDL-DWI (+0.5%) and DL-DWI (+3.4%) than in standard DWI. Structural similarity was excellent between DL-/SRDL-DWI and standard DWI for either b value (SSIM ≥ 0.86). Calculation of error metrics (NRMSE ≤ 0.05, SMAPE ≤ 0.02, and LOGAC ≤ 0.04) supported the assumption of low voxel-wise error., Data Conclusion: Deep learning-based k-space-to-image reconstruction reduces simulated scan time of breast DWI by 39% without influencing structural similarity. Additionally, super-resolution interpolation allows for substantial improvement of subjective image quality., Evidence Level: 4 TECHNICAL EFFICACY: Stage 1., (© 2023 The Authors. Journal of Magnetic Resonance Imaging published by Wiley Periodicals LLC on behalf of International Society for Magnetic Resonance in Medicine.)

Background and Objective: Deep learning usually achieves good performance in the supervised way, which requires a large amount of labeled data. However, manual labeling of electrocardiograms (ECGs) is laborious that requires much medical knowledge. Semi-supervised learning (SSL) provides an effective way of leveraging unlabeled data to improve model performance, providing insight for solving this problem. The objective of this study is to improve the performance of cardiovascular disease (CVD) detection by fully utilizing unlabeled ECG., Methods: A novel SSL algorithm fusing consistency regularization and pseudo-labeling techniques (CPSS) is proposed. CPSS consists of supervised learning and unsupervised learning. For supervised learning, the labeled ECGs are mapped into prediction vectors by the classifier. The cross-entropy loss function is used to optimize the classifier. For unsupervised learning, the unlabeled ECGs are weakly and strongly augmented, and a consistency loss is used to minimize the difference between the classifier's predictions for the two augmentations. Pseudo-labeling techniques include positive pseudo-labeling (PL) and ranking-based negative pseudo-labeling (RNL). PL introduces pseudo-labels for data with high prediction confidence. RNL assigns negative pseudo-labels to the lower-ranked categories in the prediction vectors to leverage data with low prediction confidence. In this study, VGGNet and ResNet are used as classifiers, which are jointly optimized by labeled and unlabeled ECGs., Results: CPSS has been validated on several databases. With the same number of labeled ECGs (10%), it improves the accuracies over pure supervised learning by 13.59%, 4.60%, and 5.38% in the CPSC2018, PTB-XL, and Chapman databases, respectively. CPSS achieves comparable results to the fully supervised method with only 10% of labeled ECGs, which reduces the labeling workload by 90%. In addition, to verify the practicality of CPSS, a cardiovascular disease monitoring system is designed by heterogeneously deploying the trained classifiers on an SoC (system-on-a-chip), which can detect CVD in real time., Conclusion: The results of this study indicate that the proposed CPSS can significantly improve the performance of CVD detection using unlabeled ECG, which reduces the burden of ECG labeling in deep learning. In addition, the designed monitoring system makes the proposed CPSS promising for real-world applications., Competing Interests: Declaration of competing interest We declare that we have no financial and personal relationships with other people or organizations that can inappropriately influence our work, there is no professional or other personal interest of any nature or kind in any product, service and/or company that could be construed as influencing the position presented in, or the review of, the manuscript entitled., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Named entity recognition is a critical task in the electronic medical record management system for rehabilitation robots. Handwritten documents often contain spelling errors and illegible handwriting, and healthcare professionals frequently use different terminologies. These issues adversely affect the robot's judgment and precise operations. Additionally, the same entity can have different meanings in various contexts, leading to category inconsistencies, which further increase the system's complexity. To address these challenges, a novel medical entity recognition algorithm for Chinese electronic medical records is developed to enhance the processing and understanding capabilities of rehabilitation robots for patient data. This algorithm is based on a fusion classification strategy. Specifically, a preprocessing strategy is proposed according to clinical medical knowledge, which includes redefining entities, removing outliers, and eliminating invalid characters. Subsequently, a medical entity recognition model is developed to identify Chinese electronic medical records, thereby enhancing the data analysis capabilities of rehabilitation robots. To extract semantic information, the ALBERT network is utilized, and BILSTM and MHA networks are combined to capture the dependency relationships between words, overcoming the problem of different meanings for the same entity in different contexts. The CRF network is employed to determine the boundaries of different entities. The research results indicate that the proposed model significantly enhances the recognition accuracy of electronic medical texts by rehabilitation robots, particularly in accurately identifying entities and handling terminology diversity and contextual differences. This model effectively addresses the key challenges faced by rehabilitation robots in processing Chinese electronic medical texts, and holds important theoretical and practical value.

The Cox regression model or accelerated failure time regression models are often used for describing the relationship between survival outcomes and potential explanatory variables. These models assume the studied covariates are connected to the survival time or its distribution or their transformations through a function of a linear regression form. In this article, we propose nonparametric, nonlinear algorithms (deepAFT methods) based on deep artificial neural networks to model survival outcome data in the broad distribution family of accelerated failure time models. The proposed methods predict survival outcomes directly and tackle the problem of censoring via an imputation algorithm as well as re-weighting and transformation techniques based on the inverse probabilities of censoring. Through extensive simulation studies, we confirm that the proposed deepAFT methods achieve accurate predictions. They outperform the existing regression models in prediction accuracy, while being flexible and robust in modeling covariate effects of various nonlinear forms. Their prediction performance is comparable to other established deep learning methods such as deepSurv and random survival forest methods. Even though the direct output is the expected survival time, the proposed AFT methods also provide predictions for distributional functions such as the cumulative hazard and survival functions without additional learning efforts. For situations where the popular Cox regression model may not be appropriate, the deepAFT methods provide useful and effective alternatives, as shown in simulations, and demonstrated in applications to a lymphoma clinical trial study., (© 2024 The Author(s). Statistics in Medicine published by John Wiley & Sons Ltd.)

Real-time seed detection on resource-constrained embedded devices is essential for the agriculture industry and crop yield. However, traditional seed variety detection methods either suffer from low accuracy or cannot directly run on embedded devices with desirable real-time performance. In this paper, we focus on the detection of rapeseed varieties and design a dual-dimensional (spatial and channel) pruning method to lighten the YOLOv7 (a popular object detection model based on deep learning). We design experiments to prove the effectiveness of the spatial dimension pruning strategy. And after evaluating three different channel pruning methods, we select the custom ratio layer-by-layer pruning, which offers the best performance for the model. The results show that using custom ratio layer-by-layer pruning can achieve the best model performance. Compared to the YOLOv7 model, this approach results in mAP increasing from 96.68% to 96.89%, the number of parameters reducing from 36.5 M to 9.19 M, and the inference time per image on the Raspberry Pi 4B reducing from 4.48 s to 1.18 s. Overall, our model is suitable for deployment on embedded devices and can perform real-time detection tasks accurately and efficiently in various application scenarios.

Objective . Brain-computer interfaces (BCIs) have the potential to preserve or restore speech in patients with neurological disorders that weaken the muscles involved in speech production. However, successful training of low-latency speech synthesis and recognition models requires alignment of neural activity with intended phonetic or acoustic output with high temporal precision. This is particularly challenging in patients who cannot produce audible speech, as ground truth with which to pinpoint neural activity synchronized with speech is not available. Approach . In this study, we present a new iterative algorithm for neural voice activity detection (nVAD) called iterative alignment discovery dynamic time warping (IAD-DTW) that integrates DTW into the loss function of a deep neural network (DNN). The algorithm is designed to discover the alignment between a patient's electrocorticographic (ECoG) neural responses and their attempts to speak during collection of data for training BCI decoders for speech synthesis and recognition. Main results . To demonstrate the effectiveness of the algorithm, we tested its accuracy in predicting the onset and duration of acoustic signals produced by able-bodied patients with intact speech undergoing short-term diagnostic ECoG recordings for epilepsy surgery. We simulated a lack of ground truth by randomly perturbing the temporal correspondence between neural activity and an initial single estimate for all speech onsets and durations. We examined the model's ability to overcome these perturbations to estimate ground truth. IAD-DTW showed no notable degradation (<1% absolute decrease in accuracy) in performance in these simulations, even in the case of maximal misalignments between speech and silence. Significance . IAD-DTW is computationally inexpensive and can be easily integrated into existing DNN-based nVAD approaches, as it pertains only to the final loss computation. This approach makes it possible to train speech BCI algorithms using ECoG data from patients who are unable to produce audible speech, including those with Locked-In Syndrome., (Creative Commons Attribution license.)

With the advancement of computer-aided diagnosis, the automatic segmentation of COVID-19 infection areas holds great promise for assisting in the timely diagnosis and recovery of patients in clinical practice. Currently, methods relying on U-Net face challenges in effectively utilizing fine-grained semantic information from input images and bridging the semantic gap between the encoder and decoder. To address these issues, we propose an FMD-UNet dual-decoder U-Net network for COVID-19 infection segmentation, which integrates a Fine-grained Feature Squeezing (FGFS) decoder and a Multi-scale Dilated Semantic Aggregation (MDSA) decoder. The FGFS decoder produces fine feature maps through the compression of fine-grained features and a weighted attention mechanism, guiding the model to capture detailed semantic information. The MDSA decoder consists of three hierarchical MDSA modules designed for different stages of input information. These modules progressively fuse different scales of dilated convolutions to process the shallow and deep semantic information from the encoder, and use the extracted feature information to bridge the semantic gaps at various stages, this design captures extensive contextual information while decoding and predicting segmentation, thereby suppressing the increase in model parameters. To better validate the robustness and generalizability of the FMD-UNet, we conducted comprehensive performance evaluations and ablation experiments on three public datasets, and achieved leading Dice Similarity Coefficient (DSC) scores of 84.76, 78.56 and 61.99% in COVID-19 infection segmentation, respectively. Compared to previous methods, the FMD-UNet has fewer parameters and shorter inference time, which also demonstrates its competitiveness., (© 2024 IOP Publishing Ltd. All rights, including for text and data mining, AI training, and similar technologies, are reserved.)

Annotating active sites in enzymes is crucial for advancing multiple fields including drug discovery, disease research, enzyme engineering, and synthetic biology. Despite the development of numerous automated annotation algorithms, a significant trade-off between speed and accuracy limits their large-scale practical applications. We introduce EasIFA, an enzyme active site annotation algorithm that fuses latent enzyme representations from the Protein Language Model and 3D structural encoder, and then aligns protein-level information with the knowledge of enzymatic reactions using a multi-modal cross-attention framework. EasIFA outperforms BLASTp with a 10-fold speed increase and improved recall, precision, f1 score, and MCC by 7.57%, 13.08%, 9.68%, and 0.1012, respectively. It also surpasses empirical-rule-based algorithm and other state-of-the-art deep learning annotation method based on PSSM features, achieving a speed increase ranging from 650 to 1400 times while enhancing annotation quality. This makes EasIFA a suitable replacement for conventional tools in both industrial and academic settings. EasIFA can also effectively transfer knowledge gained from coarsely annotated enzyme databases to smaller, high-precision datasets, highlighting its ability to model sparse and high-quality databases. Additionally, EasIFA shows potential as a catalytic site monitoring tool for designing enzymes with desired functions beyond their natural distribution., (© 2024. The Author(s).)