IEEE Journal of Biomedical and Health Informatics最新文献

{"title":"Fall Detection Method based on a Human Electrostatic Field and VMD-ECANet Architecture.","authors":"Xi Chen, Jiaao Yan, Sichao Qin, Pengfei Li, Shuangqian Ning, Yuting Liu","doi":"10.1109/JBHI.2024.3481237","DOIUrl":"https://doi.org/10.1109/JBHI.2024.3481237","url":null,"abstract":"<p><p>Falls are one of the most serious health risks faced by older adults worldwide, and they can have a significant impact on their physical and mental well-being as well as their quality of life. Detecting falls promptly and accurately and providing assistance can effectively reduce the harm caused by falls to older adults. This paper proposed a noncontact fall detection method based on the human electrostatic field and a VMD-ECANet framework. An electrostatic measurement system was used to measure the electrostatic signals of four types of falling postures and five types of daily actions. The signals were randomly divided in proportion and by individuals to construct a training set and test set. A fall detection model based on the VMD-ECA network was proposed that decomposes electrostatic signals into modal component signals using the variational mode decomposition (VMD) technique. These signals were then fed into a multichannel convolutional neural network for feature extraction. Information fusion was achieved through the efficient channel attention network (ECANet) module. Finally, the extracted features were input into a classifier to obtain the output results. The constructed model achieved an accuracy of 96.44%. The proposed fall detection solution has several advantages, including being noncontact, cost-effective, and privacy friendly. It is suitable for detecting indoor falls by older individuals living alone and helps to reduce the harm caused by falls.</p>","PeriodicalId":13073,"journal":{"name":"IEEE Journal of Biomedical and Health Informatics","volume":"PP ","pages":""},"PeriodicalIF":6.7,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142464064","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"TKR-FSOD: Fetal Anatomical Structure Few-Shot Detection Utilizing Topological Knowledge Reasoning.","authors":"Xi Li, Ying Tan, Bochen Liang, Bin Pu, Jiewen Yang, Lei Zhao, Yanqing Kong, Lixian Yang, Rentie Zhang, Hao Li, Shengli Li","doi":"10.1109/JBHI.2024.3480197","DOIUrl":"https://doi.org/10.1109/JBHI.2024.3480197","url":null,"abstract":"<p><p>Fetal multi-anatomical structure detection in Ultrasound (US) images can clearly present the relationship and influence between anatomical structures, providing more comprehensive information about fetal organ structures and assisting sonographers in making more accurate diagnoses, widely used in structure evaluation. Recently, deep learning methods have shown superior performance in detecting various anatomical structures in ultrasound images but still have the potential for performance improvement in categories where it is difficult to obtain samples, such as rare diseases. Few-shot learning has attracted a lot of attention in medical image analysis due to its ability to solve the problem of data scarcity. However, existing few-shot learning research in medical image analysis focuses on classification and segmentation, and the research on object detection has been neglected. In this paper, we propose a novel fetal anatomical structure fewshot detection method in ultrasound images, TKR-FSOD, which learns topological knowledge through a Topological Knowledge Reasoning Module to help the model reason about and detect anatomical structures. Furthermore, we propose a Discriminate Ability Enhanced Feature Learning Module that extracts abundant discriminative features to enhance the model's discriminative ability. Experimental results demonstrate that our method outperforms the state-of-the-art baseline methods, exceeding the second best method with a maximum margin of 4.8% on 5-shot of split 1 under 4CC. The code is publicly available at: https://github.com/lixi92/TKR-FSOD.</p>","PeriodicalId":13073,"journal":{"name":"IEEE Journal of Biomedical and Health Informatics","volume":"PP ","pages":""},"PeriodicalIF":6.7,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142464116","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Self-Supervised Molecular Representation Learning With Topology and Geometry.","authors":"Xuan Zang, Junjie Zhang, Buzhou Tang","doi":"10.1109/JBHI.2024.3479194","DOIUrl":"https://doi.org/10.1109/JBHI.2024.3479194","url":null,"abstract":"<p><p>Molecular representation learning is of great importance for drug molecular analysis. The development in molecular representation learning has demonstrated great promise through self-supervised pre-training strategy to overcome the scarcity of labeled molecular property data. Recent studies concentrate on pre-training molecular representation encoders by integrating both 2D topological and 3D geometric structures. However, existing methods rely on molecule-level or atom-level alignment for different views, while overlooking hierarchical self-supervised learning to capture both inter-molecule and intra-molecule correlation. Additionally, most methods employ 2D or 3D encoders to individually extract molecular characteristics locally or globally for molecular property prediction. The potential for effectively fusing these two molecular representations remains to be explored. In this work, we propose a Multi-View Molecular Representation Learning method (MVMRL) for molecular property prediction. First, hierarchical pre-training pretext tasks are designed, including fine-grained atom-level tasks for 2D molecular graphs as well as coarse-grained molecule-level tasks for 3D molecular graphs to provide complementary information to each other. Subsequently, a motif-level fusion pattern of multi-view molecular representations is presented during fine-tuning to enhance the performance of molecular property prediction. We evaluate the effectiveness of the proposed MVMRL by comparing with state-of-the-art baselines on molecular property prediction tasks, and the experimental results demonstrate the superiority of MVMRL.</p>","PeriodicalId":13073,"journal":{"name":"IEEE Journal of Biomedical and Health Informatics","volume":"PP ","pages":""},"PeriodicalIF":6.7,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142464115","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hierarchical graph transformer with contrastive learning for gene regulatory network inference.","authors":"Wentao Cui, Qingqing Long, Wenhao Liu, Chen Fang, Xuezhi Wang, Pengfei Wang, Yuanchun Zhou","doi":"10.1109/JBHI.2024.3476490","DOIUrl":"https://doi.org/10.1109/JBHI.2024.3476490","url":null,"abstract":"<p><p>Gene regulatory networks (GRNs) are crucial for understanding gene regulation and cellular processes. Inferring GRNs helps uncover regulatory pathways, shedding light on the regulation and development of cellular processes. With the rise of high-throughput sequencing and advancements in computational technology, computational models have emerged as cost-effective alternatives to traditional experimental studies. Moreover, the surge in ChIPseq data for TF-DNA binding has catalyzed the development of graph neural network (GNN)-based methods, greatly advancing GRN inference capabilities. However, most existing GNN-based methods suffer from the inability to capture long-distance structural semantic correlations due to transitive interactions. In this paper, we introduce a novel GNN-based model named Hierarchical Graph Transformer with Contrastive Learning for GRN (HGTCGRN) inference. HGTCGRN excels at capturing structural semantics using a hierarchical graph Transformer, which introduces a series of gene family nodes representing gene functions as virtual nodes to interact with nodes in the GRNS. These semanticaware virtual-node embeddings are aggregated to produce node representations with varying emphasis. Additionally, we leverage gene ontology information to construct gene interaction networks for contrastive learning optimization of GRNs. Experimental results demonstrate that HGTCGRN achieves superior performance in GRN inference.</p>","PeriodicalId":13073,"journal":{"name":"IEEE Journal of Biomedical and Health Informatics","volume":"PP ","pages":""},"PeriodicalIF":6.7,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142464107","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Alzheimer's Disease Detection in EEG Sleep Signals.","authors":"Lorena Gallego-Vinaras, Juan Miguel Mira-Tomas, Anna Michela Gaeta, Gerard Pinol-Ripoll, Ferran Barbe, Pablo M Olmos, Arrate Munoz-Barrutia","doi":"10.1109/JBHI.2024.3478380","DOIUrl":"https://doi.org/10.1109/JBHI.2024.3478380","url":null,"abstract":"<p><p>Alzheimer's disease (AD) and sleep disorders exhibit a close association, where disruptions in sleep patterns often precede the onset of Mild Cognitive Impairment (MCI) and early-stage AD. This study delves into the potential of utilizing sleep-related electroencephalography (EEG) signals acquired through polysomnography (PSG) for the early detection of AD. Our primary focus is on exploring semi-supervised Deep Learning techniques for the classification of EEG signals due to the clinical scenario characterized by the limited data availability. The methodology entails testing and comparing the performance of semi-supervised models, benchmarked against an unsupervised and a supervised model. The study highlights the significance of spatial and temporal analysis capabilities, conducting independent analyses of each sleep stage. Results demonstrate the effectiveness of one semi-supervised model in leveraging limited labeled data, achieving stable metrics across all sleep stages, and reaching 90% accuracy in its supervised form. Comparative analyses reveal this superior performance over the unsupervised model, while the supervised model ranges between 92-94% . These findings underscore the potential of semi-supervised models in early AD detection, particularly in overcoming the challenges associated with the scarcity of labeled data. Ablation tests affirm the critical role of spatio-temporal feature extraction in semi-supervised predictive performance, and t-SNE visualizations validate the model's proficiency in distinguishing AD patterns. Overall, this research contributes to the advancement of AD detection through innovative Deep Learning approaches, highlighting the crucial role of semi-supervised learning in addressing data limitations.</p>","PeriodicalId":13073,"journal":{"name":"IEEE Journal of Biomedical and Health Informatics","volume":"PP ","pages":""},"PeriodicalIF":6.7,"publicationDate":"2024-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142406368","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"LKAN: LLM-Based Knowledge-Aware Attention Network for Clinical Staging of Liver Cancer.","authors":"Ya Li, Xuecong Zheng, Jiaping Li, Qingyun Dai, Chang-Dong Wang, Min Chen","doi":"10.1109/JBHI.2024.3478809","DOIUrl":"https://doi.org/10.1109/JBHI.2024.3478809","url":null,"abstract":"<p><p>Clinical staging of liver cancer (CSoLC), an important indicator for evaluating the degree of deterioration of primary liver cancer cells (PLCCs), is key in the diagnosis, treatment, and rehabilitation of liver cancer. In China, the current CSoLC adopts the China liver cancer (CNLC) staging, which is usually evaluated by clinicians based on the patient's radiology reports. Therefore, inferring clinical information from unstructured radiology reports can provide auxiliary decision support for clinicians. The key to solving the challenging task is to guide the model to pay attention to the staging-related words or sentences, and the following issues may occur: 1) Imbalanced categories: The symptoms of liver cancer in the early- or mid-stage are not obvious, resulting in more data in the end-stage. 2) Domain sensitivity of liver cancer data: The liver cancer dataset contains a large amount of domain knowledge, and the conventional methods can exacerbate out-of-vocabulary, which greatly affects the accuracy of classification. 3) Free-text and lengthy report: The radiology report of liver cancer sparsely describes various lesions with domain-specific terms, which poses difficulties in mining key information related to staging. To tackle these challenges, this article proposes a large language model (LLM)-based Knowledge-aware Attention Network (LKAN) for CSoLC. First, for maintaining semantic consistency, LLM and a rule-based algorithm are integrated to generate more diverse and reasonable data. Second, unlabeled radiology corpus of liver cancer are pre-trained to introduce domain knowledge for subsequent representation learning. Third, attention is improved by incorporating both global and local features, which can provide professional guidance for the classifier to focus on the important information. Compared with the baseline models, the classification accuracy of LKAN has achieved the best results with 90.3% Accuracy, 90.0% Macro_F1 score, and 90.0% Macro_Recall. The code is available at https://github.com/xczhh/Supplemental-Material.</p>","PeriodicalId":13073,"journal":{"name":"IEEE Journal of Biomedical and Health Informatics","volume":"PP ","pages":""},"PeriodicalIF":6.7,"publicationDate":"2024-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142406369","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"TrustEMG-Net: Using Representation-Masking Transformer with U-Net for Surface Electromyography Enhancement.","authors":"Kuan-Chen Wang, Kai-Chun Liu, Ping-Cheng Yeh, Sheng-Yu Peng, Yu Tsao","doi":"10.1109/JBHI.2024.3475817","DOIUrl":"https://doi.org/10.1109/JBHI.2024.3475817","url":null,"abstract":"<p><p>Surface electromyography (sEMG) is a widely employed bio-signal that captures human muscle activity via electrodes placed on the skin. Several studies have proposed methods to remove sEMG contaminants, as non-invasive measurements render sEMG susceptible to various contaminants. However, these approaches often rely on heuristic-based optimization and are sensitive to the contaminant type. A more potent, robust, and generalized sEMG denoising approach should be developed for various healthcare and human-computer interaction applications. This paper proposes a novel neural network (NN)-based sEMG denoising method called TrustEMG-Net. It leverages the potent nonlinear mapping capability and data-driven nature of NNs. TrustEMG-Net adopts a denoising autoencoder structure by combining U-Net with a Transformer encoder using a representation-masking approach. The proposed approach is evaluated using the Ninapro sEMG database with five common contamination types and signal-to-noise ratio (SNR) conditions. Compared with existing sEMG denoising methods, TrustEMG-Net achieves exceptional performance across the five evaluation metrics, exhibiting a minimum improvement of 20%. Its superiority is consistent under various conditions, including SNRs ranging from -14 to 2 dB and five contaminant types. An ablation study further proves that the design of TrustEMG-Net contributes to its optimality, providing high-quality sEMG and serving as an effective, robust, and generalized denoising solution for sEMG applications.</p>","PeriodicalId":13073,"journal":{"name":"IEEE Journal of Biomedical and Health Informatics","volume":"PP ","pages":""},"PeriodicalIF":6.7,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142400195","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nonparametric Dynamic Granger Causality based on Multi-Space Spectrum Fusion for Time-varying Directed Brain Network Construction.","authors":"Chanlin Yi, Jiamin Zhang, Zihan Weng, Wanjun Chen, Dezhong Yao, Fali Li, Zehong Cao, Peiyang Li, Peng Xu","doi":"10.1109/JBHI.2024.3477944","DOIUrl":"https://doi.org/10.1109/JBHI.2024.3477944","url":null,"abstract":"<p><p>Nonparametric estimation of time-varying directed networks can unveil the intricate transient organization of directed brain communication while circumventing constraints imposed by prescribed model-driven methods. A robust time-frequency representation - the foundation of its causality inference - is critical for enhancing its reliability. This study proposed a novel method, i.e., nonparametric dynamic Granger causality based on Multi-space Spectrum Fusion (ndGCMSF), which integrates complementary spectrum information from different spaces to generate reliable spectral representations to estimate dynamic causalities across brain regions. Systematic simulations and validations demonstrate that ndGCMSF exhibits superior noise resistance and a powerful ability to capture subtle dynamic changes in directed brain networks. Particularly, ndGCMSF revealed that during instruction response movements, the laterality in the hemisphere ipsilateral to the hemiplegic limb emerges upon instruction onset and diminishes upon task accomplishment. These intrinsic variations further provide reliable features for distinguishing two types of hemiplegia (left vs. right) and assessing motor functions. The ndGCMSF offers powerful functional patterns to derive effective brain networks in dynamically changing operational settings and contributes to extensive areas involving dynamical and directed communications.</p>","PeriodicalId":13073,"journal":{"name":"IEEE Journal of Biomedical and Health Informatics","volume":"PP ","pages":""},"PeriodicalIF":6.7,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142400183","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SCKansformer: Fine-Grained Classification of Bone Marrow Cells via Kansformer Backbone and Hierarchical Attention Mechanisms.","authors":"Yifei Chen, Zhu Zhu, Shenghao Zhu, Linwei Qiu, Binfeng Zou, Fan Jia, Yunpeng Zhu, Chenyan Zhang, Zhaojie Fang, Feiwei Qin, Jin Fan, Changmiao Wang, Gang Yu, Yu Gao","doi":"10.1109/JBHI.2024.3471928","DOIUrl":"10.1109/JBHI.2024.3471928","url":null,"abstract":"<p><p>The incidence and mortality rates of malignant tumors, such as acute leukemia, have risen significantly. Clinically, hospitals rely on cytological examination of peripheral blood and bone marrow smears to diagnose malignant tumors, with accurate blood cell counting being crucial. Existing automated methods face challenges such as low feature expression capability, poor interpretability, and redundant feature extraction when processing highdimensional microimage data. We propose a novel finegrained classification model, SCKansformer, for bone marrow blood cells, which addresses these challenges and enhances classification accuracy and efficiency. The model integrates the Kansformer Encoder, SCConv Encoder, and Global-Local Attention Encoder. The Kansformer Encoder replaces the traditional MLP layer with the KAN, improving nonlinear feature representation and interpretability. The SCConv Encoder, with its Spatial and Channel Reconstruction Units, enhances feature representation and reduces redundancy. The Global-Local Attention Encoder combines Multi-head Self-Attention with a Local Part module to capture both global and local features. We validated our model using the Bone Marrow Blood Cell FineGrained Classification Dataset (BMCD-FGCD), comprising over 10,000 samples and nearly 40 classifications, developed with a partner hospital. Comparative experiments on our private dataset, as well as the publicly available PBC and ALL-IDB datasets, demonstrate that SCKansformer outperforms both typical and advanced microcell classification methods across all datasets.</p>","PeriodicalId":13073,"journal":{"name":"IEEE Journal of Biomedical and Health Informatics","volume":"PP ","pages":""},"PeriodicalIF":6.7,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142400194","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MiRS-HF: A Novel Deep Learning Predictor for Cancer Classification and miRNA Expression Patterns.","authors":"Jie Ni, Donghui Yan, Shan Lu, Zhuoying Xie, Yun Liu, Xin Zhang","doi":"10.1109/JBHI.2024.3476672","DOIUrl":"https://doi.org/10.1109/JBHI.2024.3476672","url":null,"abstract":"<p><p>Cancer classification and biomarker identification are crucial for guiding personalized treatment. To make effective use of miRNA associations and expression data, we have developed a deep learning model for cancer classification and biomarker identification. To make effective use of miRNA associations and expression data, we have developed a deep learning model for cancer classification and biomarker identification. We propose an approach for cancer classification called MiRNA Selection and Hybrid Fusion (MiRS-HF), which consists of early fusion and intermediate fusion. The early fusion involves applying a Layer Attention Graph Convolutional Network (LAGCN) to a miRNA-disease heterogeneous network, resulting in a miRNA-disease association degree score matrix. The intermediate fusion employs a Graph Convolutional Network (GCN) in the classification tasks, weighting the expression data based on the miRNA-disease association degree score. Furthermore, MiRS-HF can identify the important miRNA biomarkers and their expression patterns. The proposed method demonstrates superior performance in the classification tasks of six cancers compared to other methods. Simultaneously, we incorporated the feature weighting strategy into the comparison algorithm, leading to a significant improvement in the algorithm's results, highlighting the extreme importance of this strategy.</p>","PeriodicalId":13073,"journal":{"name":"IEEE Journal of Biomedical and Health Informatics","volume":"PP ","pages":""},"PeriodicalIF":6.7,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142390172","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}