IEEE Journal of Biomedical and Health Informatics最新文献

{"title":"Highlighted Diffusion Model as Plug-in Priors for Polyp Segmentation.","authors":"Yuhao Du, Yuncheng Jiang, Shuangyi Tan, Si-Qi Liu, Zhen Li, Guanbin Li, Xiang Wan","doi":"10.1109/JBHI.2024.3485767","DOIUrl":"https://doi.org/10.1109/JBHI.2024.3485767","url":null,"abstract":"<p><p>Automated polyp segmentation from colonoscopy images is crucial for colorectal cancer diagnosis. The accuracy of such segmentation, however, is challenged by two main factors. First, the variability in polyps' size, shape, and color, coupled with the scarcity of well-annotated data due to the need for specialized manual annotation, hampers the efficacy of existing deep learning methods. Second, concealed polyps often blend with adjacent intestinal tissues, leading to poor contrast that challenges segmentation models. Recently, diffusion models have been explored and adapted for polyp segmentation tasks. However, the significant domain gap between RGB-colonoscopy images and grayscale segmentation masks, along with the low efficiency of the diffusion generation process, hinders the practical implementation of these models. To mitigate these challenges, we introduce the Highlighted Diffusion Model Plus (HDM+), a two-stage polyp segmentation framework. This framework incorporates the Highlighted Diffusion Model (HDM) to provide explicit semantic guidance, thereby enhancing segmentation accuracy. In the initial stage, the HDM is trained using highlighted ground-truth data, which emphasizes polyp regions while suppressing the background in the images. This approach reduces the domain gap by focusing on the image itself rather than on the segmentation mask. In the subsequent second stage, we employ the highlighted features from the trained HDM's U-Net model as plug-in priors for polyp segmentation, rather than generating highlighted images, thereby increasing efficiency. Extensive experiments conducted on six polyp segmentation benchmarks demonstrate the effectiveness of our approach.</p>","PeriodicalId":13073,"journal":{"name":"IEEE Journal of Biomedical and Health Informatics","volume":"PP ","pages":""},"PeriodicalIF":6.7,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142499413","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":"MMLmiRLocNet: miRNA Subcellular Localization Prediction based on Multi-view Multi-label Learning for Drug Design.","authors":"Tao Bai, Junxi Xie, Yumeng Liu, Bin Liu","doi":"10.1109/JBHI.2024.3483997","DOIUrl":"https://doi.org/10.1109/JBHI.2024.3483997","url":null,"abstract":"<p><p>Identifying subcellular localization of microRNAs (miRNAs) is essential for comprehensive understanding of cellular function and has significant implications for drug design. In the past, several computational methods for miRNA subcellular localization is being used for uncovering multiple facets of RNA function to facilitate the biological applications. Unfortunately, most existing classification methods rely on a single sequencebased view, making the effective fusion of data from multiple heterogeneous networks a primary challenge. Inspired by multi-view multi-label learning strategy, we propose a computational method, named MMLmiRLocNet, for predicting the subcellular localizations of miRNAs. The MMLmiRLocNet predictor extracts multi-perspective sequence representations by analyzing lexical, syntactic, and semantic aspects of biological sequences. Specifically, it integrates lexical attributes derived from k-mer physicochemical profiles, syntactic characteristics obtained via word2vec embeddings, and semantic representations generated by pre-trained feature embeddings. Finally, module for extracting multi-view consensus-level features and specific-level features was constructed to capture consensus and specific features from various perspectives. The full connection networks are utilized as the output module to predict the miRNA subcellular localization. Experimental results suggest that MMLmiRLocNet outperforms existing methods in terms of F1, subACC, and Accuracy, and achieves best performance with the help of multi-view consensus features and specific features extract network.</p>","PeriodicalId":13073,"journal":{"name":"IEEE Journal of Biomedical and Health Informatics","volume":"PP ","pages":""},"PeriodicalIF":6.7,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142499414","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":"Multi-Task Adaptive Resolution Network for Lymph Node Metastasis Diagnosis From Whole Slide Images of Colorectal Cancer","authors":"Tong Wang;Su-Jin Shin;Mingkang Wang;Qi Xu;Guiyang Jiang;Fengyu Cong;Jeonghyun Kang;Hongming Xu","doi":"10.1109/JBHI.2024.3485703","DOIUrl":"10.1109/JBHI.2024.3485703","url":null,"abstract":"Automated detection of lymph node metastasis (LNM) holds great potential to alleviate the workload of doctors and reduce misinterpretations. Despite the practical successes achieved, effectively addressing the highly complex and heterogeneous tumor microenvironment remains an open and challenging problem, especially when tumor subtypes intermingle and are difficult to delineate. In this paper, we propose a multi-task adaptive resolution network, named MAR-Net, for LNM detection and subtyping in complex mixed-type cancers. Specifically, we construct a resolution-aware module to mine heterogeneous diagnostic information, which exploits the multi-scale pyramid information and adaptively combines multi-resolution structured features for comprehensive representation. Additionally, we adopt a multi-task learning approach that simultaneously addresses LNM detection and subtyping, reducing model instability during optimization and improving performance across both tasks. More importantly, to rectify the potential misclassification of tumor subtypes, we elaborately design a hierarchical subtying refinement (HSR) algorithm that leverages a generic segmentation model informed by pathologists' prior knowledge. Evaluations have been conducted on three private and one public cancer datasets (554 WSIs, 4.8 million patches). Our experimental results demonstrate that the proposed method consistently achieves superior performance compared to the state-of-the-art methods, achieving 0.5% to 3.2% higher AUC in LNM detection and 3.8% to 4.4% higher AUC in LNM subtyping.","PeriodicalId":13073,"journal":{"name":"IEEE Journal of Biomedical and Health Informatics","volume":"29 1","pages":"420-432"},"PeriodicalIF":6.7,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142499416","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":"Power of Multi-Modality Variables in Predicting Parkinson's Disease Progression.","authors":"Yishan Jiang, Hyung-Jeong Yang, Jahae Kim, Zhenzhou Tang, Xiukai Ruan","doi":"10.1109/JBHI.2024.3482180","DOIUrl":"https://doi.org/10.1109/JBHI.2024.3482180","url":null,"abstract":"<p><p>Parkinson's disease (PD) is one of the most common neurodegenerative disorders. The increasing demand for high-accuracy forecasts of disease progression has led to a surge in research employing multi-modality variables for prediction. In this review, we selected articles published from 2016 through June 2024, adhering strictly to our exclusion-inclusion criteria. These articles employed a minimum of two types of variables, including clinical, genetic, biomarker, and neuroimaging modalities. We conducted a comprehensive review and discussion on the application of multi-modality approaches in predicting PD progression. The predictive mechanisms, advantages, and shortcomings of relevant key modalities in predicting PD progression are discussed in the paper. The findings suggest that integrating multiple modalities resulted in more accurate predictions compared to those of fewer modalities in similar conditions. Furthermore, we identified some limitations in the existing field. Future studies that harness advancements in multi-modality variables and machine learning algorithms can mitigate these limitations and enhance predictive accuracy in PD progression.</p>","PeriodicalId":13073,"journal":{"name":"IEEE Journal of Biomedical and Health Informatics","volume":"PP ","pages":""},"PeriodicalIF":6.7,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142499418","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":"ContraSurv: Enhancing Prognostic Assessment of Medical Images via Data-Efficient Weakly Supervised Contrastive Learning.","authors":"Hailin Li, Di Dong, Mengjie Fang, Bingxi He, Shengyuan Liu, Chaoen Hu, Zaiyi Liu, Hexiang Wang, Linglong Tang, Jie Tian","doi":"10.1109/JBHI.2024.3484991","DOIUrl":"10.1109/JBHI.2024.3484991","url":null,"abstract":"<p><p>Prognostic assessment remains a critical challenge in medical research, often limited by the lack of well-labeled data. In this work, we introduce ContraSurv, a weakly-supervised learning framework based on contrastive learning, designed to enhance prognostic predictions in 3D medical images. ContraSurv utilizes both the self-supervised information inherent in unlabeled data and the weakly-supervised cues present in censored data, refining its capacity to extract prognostic representations. For this purpose, we establish a Vision Transformer architecture optimized for our medical image datasets and introduce novel methodologies for both self-supervised and supervised contrastive learning for prognostic assessment. Additionally, we propose a specialized supervised contrastive loss function and introduce SurvMix, a novel data augmentation technique for survival analysis. Evaluations were conducted across three cancer types and two imaging modalities on three real-world datasets. The results confirmed the enhanced performance of ContraSurv over competing methods, particularly in data with a high censoring rate.</p>","PeriodicalId":13073,"journal":{"name":"IEEE Journal of Biomedical and Health Informatics","volume":"PP ","pages":""},"PeriodicalIF":6.7,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142499412","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":"Continuous Prediction of Wrist Joint Kinematics Using Surface Electromyography From the Perspective of Muscle Anatomy and Muscle Synergy Feature Extraction","authors":"Zijun Wei;Meiju Li;Zhi-Qiang Zhang;Sheng Quan Xie","doi":"10.1109/JBHI.2024.3484994","DOIUrl":"10.1109/JBHI.2024.3484994","url":null,"abstract":"Post-stroke upper limb dysfunction severely impacts patients' daily life quality. Utilizing sEMG signals to predict patients' motion intentions enables more effective rehabilitation by precisely adjusting the assistance level of rehabilitation robots. Employing the muscle synergy (MS) features can establish more accurate and robust mappings between sEMG and motion intentions. However, traditional matrix factorization algorithms based on blind source separation still exhibit certain limitations in extracting MS features. This paper proposes four deep learning models to extract MS features from four distinct perspectives: spatiotemporal convolutional kernels, compression and reconstruction of sEMG, graph topological structure, and the anatomy of target muscles. Among these models, the one based on 3DCNN predicts motion intentions from the muscle anatomy perspective for the first time. It reconstructs 1D sEMG samples collected at each time point into 2D sEMG frames based on the anatomical distribution of target muscles and sEMG electrode placement. These 2D frames are then stacked as video segments and input into 3DCNN for MS feature extraction. Experimental results on both our wrist motion dataset and public Ninapro DB2 dataset demonstrate that the proposed 3DCNN model outperforms other models in terms of prediction accuracy, robustness, training efficiency, and MS feature extraction for continuous prediction of wrist flexion/extension angles. Specifically, the average nRMSE and R\u0000²\u0000 values of 3DCNN on these two datasets are (0.14/0.93) and (0.04/0.95), respectively. Furthermore, compared to existing studies, the 3DCNN outperforms musculoskeletal models based on direct collocation optimization, physics-informed GANs, and CNN-LSTM-based deep Kalman filter models when evaluated on our dataset.","PeriodicalId":13073,"journal":{"name":"IEEE Journal of Biomedical and Health Informatics","volume":"29 1","pages":"43-55"},"PeriodicalIF":6.7,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142499411","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":"Score Prior Guided Iterative Solver for Speckles Removal in Optical Coherent Tomography Images","authors":"Sanqian Li;Risa Higashita;Huazhu Fu;Bing Yang;Jiang Liu","doi":"10.1109/JBHI.2024.3480928","DOIUrl":"10.1109/JBHI.2024.3480928","url":null,"abstract":"Optical coherence tomography (OCT) is a widely used non-invasive imaging modality for ophthalmic diagnosis. However, the inherent speckle noise becomes the leading cause of OCT image quality, and efficient speckle removal algorithms can improve image readability and benefit automated clinical analysis. As an ill-posed inverse problem, it is of utmost importance for speckle removal to learn suitable priors. In this work, we develop a score prior guided iterative solver (SPIS) with logarithmic space to remove speckles in OCT images. Specifically, we model the posterior distribution of raw OCT images as a data consistency term and transform the speckle removal from a nonlinear into a linear inverse problem in the logarithmic domain. Subsequently, the learned prior distribution through the score function from the diffusion model is utilized as a constraint for the data consistency term into the linear inverse optimization, resulting in an iterative speckle removal procedure that alternates between the score prior predictor and the subsequent non-expansive data consistency corrector. Experimental results on the private and public OCT datasets demonstrate that the proposed SPIS has an excellent performance in speckle removal and out-of-distribution (OOD) generalization. Further downstream automatic analysis on the OCT images verifies that the proposed SPIS can benefit clinical applications.","PeriodicalId":13073,"journal":{"name":"IEEE Journal of Biomedical and Health Informatics","volume":"29 1","pages":"248-258"},"PeriodicalIF":6.7,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142499419","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":"Benchmarking Large Language Models in Evidence-Based Medicine.","authors":"Jin Li, Yiyan Deng, Qi Sun, Junjie Zhu, Yu Tian, Jingsong Li, Tingting Zhu","doi":"10.1109/JBHI.2024.3483816","DOIUrl":"https://doi.org/10.1109/JBHI.2024.3483816","url":null,"abstract":"<p><p>Evidence-based medicine (EBM) represents a paradigm of providing patient care grounded in the most current and rigorously evaluated research. Recent advances in large language models (LLMs) offer a potential solution to transform EBM by automating labor-intensive tasks and thereby improving the efficiency of clinical decision-making. This study explores integrating LLMs into the key stages in EBM, evaluating their ability across evidence retrieval (PICO extraction, biomedical question answering), synthesis (summarizing randomized controlled trials), and dissemination (medical text simplification). We conducted a comparative analysis of seven LLMs, including both proprietary and open-source models, as well as those fine-tuned on medical corpora. Specifically, we benchmarked the performance of various LLMs on each EBM task under zero-shot settings as baselines, and employed prompting techniques, including in-context learning, chain-of-thought reasoning, and knowledge-guided prompting to enhance their capabilities. Our extensive experiments revealed the strengths of LLMs, such as remarkable understanding capabilities even in zero-shot settings, strong summarization skills, and effective knowledge transfer via prompting. Promoting strategies such as knowledge-guided prompting proved highly effective (e.g., improving the performance of GPT-4 by 13.10% over zero-shot in PICO extraction). However, the experiments also showed limitations, with LLM performance falling well below state-of-the-art baselines like PubMedBERT in handling named entity recognition tasks. Moreover, human evaluation revealed persisting challenges with factual inconsistencies and domain inaccuracies, underscoring the need for rigorous quality control before clinical application. This study provides insights into enhancing EBM using LLMs while highlighting critical areas for further research. The code is publicly available on Github.</p>","PeriodicalId":13073,"journal":{"name":"IEEE Journal of Biomedical and Health Informatics","volume":"PP ","pages":""},"PeriodicalIF":6.7,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142499410","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":"MRGCDDI: Multi-Relation Graph Contrastive Learning without Data Augmentation for Drug-Drug Interaction Events Prediction.","authors":"Yu Li, Lin-Xuan Hou, Zhu-Hong You, Yang Yuan, Cheng-Gang Mi, Yu-An Huang, Hai-Cheng Yi","doi":"10.1109/JBHI.2024.3483812","DOIUrl":"https://doi.org/10.1109/JBHI.2024.3483812","url":null,"abstract":"<p><p>Predicting drug-drug interactions (DDIs) is a significant concern in the field of deep learning. It can effectively reduce potential adverse consequences and improve therapeutic safety. Graph neural network (GNN)-based models have made satisfactory progress in DDI event prediction. However, most existing models overlook crucial drug structure and interaction information, which is necessary for accurate DDI event prediction. To tackle this issue, we introduce a new method called MRGCDDI. This approach employs contrastive learning, but unlike conventional methods, it does not require data augmentation, thereby avoiding additional noise. MRGCDDI maintains the semantics of the graphical data during encoder perturbation through a simple yet effective contrastive learning approach, without the need for manual trial and error, tedious searching, or expensive domain knowledge to select enhancements. The approach presented in this study effectively integrates drug features extracted from drug molecular graphs and information from multi-relational drug-drug interaction (DDI) networks. Extensive experimental results demonstrate that MRGCDDI outperforms state-of-the-art methods on both datasets. Specifically, on Deng's dataset, MRGCDDI achieves an average increase of 4.33% in accuracy, 11.57% in Macro-F1, 10.97% in Macro-Recall, and 10.64% in Macro-Precision. Similarly, on Ryu's dataset, the model shows improvements with an average increase of 2.42% in accuracy, 3.86% in Macro-F1, 3.49% in Macro-Recall, and 2.75% in Macro-Precision. All the data and codes of this work are available at https://github.com/Nokeli/MRGCDDI.</p>","PeriodicalId":13073,"journal":{"name":"IEEE Journal of Biomedical and Health Informatics","volume":"PP ","pages":""},"PeriodicalIF":6.7,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142499415","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":"Physical Activity Integration in Blood Glucose Level Prediction: Different Levels of Data Fusion.","authors":"Hoda Nemat, Heydar Khadem, Jackie Elliott, Mohammed Benaissa","doi":"10.1109/JBHI.2024.3483999","DOIUrl":"https://doi.org/10.1109/JBHI.2024.3483999","url":null,"abstract":"<p><p>Blood glucose level (BGL) prediction contributes to more effective management of type 1 diabetes. Physical activity (PA) is a crucial factor in diabetes management. It affects BGL, and it is imperative to effectively deploy PA in BGL prediction to support diabetes management systems by incorporating this crucial factor. Due to the erratic nature of PA's impact on BGL inter- and intra-patients and insufficient knowledge, deploying PA in BGL prediction is challenging. Hence, optimal approaches for PA fusion with BGL are demanded to improve the performance of BGL prediction. To address this gap, we propose novel methodologies for extracting and integrating information from PA data into BGL prediction. This paper proposes several novel PA-informed prediction models by developing different approaches for extracting information from PA data and fusing this information with BGL data in signal, feature, and decision levels to find the optimal approach for deploying PA in BGL prediction models. For signal-level fusion, different automatically-recorded PA data are fused with BGL data. Also, three feature engineering approaches are developed for feature-level fusion: subjective assessments of PA, objective assessments of PA, and statistics of PA. Furthermore, in decision-level fusion, ensemble learning is used to combine predictions from models trained with different inputs. Then, a comparative investigation is performed between the developed PA-informed approaches and the no-fusion approach, as well as between themselves. The analyses are performed on the publicly available Ohio dataset with rigorous evaluation. The results show that deploying PA can statistically significantly improve BGL prediction performance. The results show that deploying PA can statistically significantly improve BGL prediction performance. Also, among the developed approaches to leveraging PA in BGL prediction, fusing heart rate data at the signal-level and PA intensity categories at the feature-level with BGL data are the most effective ways. Our developed methodologies contribute to determining optimal approaches, including the kind of PA information and fusion method, to improve the performance of BGL prediction effectively.</p>","PeriodicalId":13073,"journal":{"name":"IEEE Journal of Biomedical and Health Informatics","volume":"PP ","pages":""},"PeriodicalIF":6.7,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142499417","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}