Computers in biology and medicine最新文献

{"title":"Handwritten character classification from EEG through continuous kinematic decoding","authors":"","doi":"10.1016/j.compbiomed.2024.109132","DOIUrl":"10.1016/j.compbiomed.2024.109132","url":null,"abstract":"<div><div>The classification of handwritten letters from invasive neural signals has lately been subject of research to restore communication abilities in people with limited movement capacities. This study explores the classification of ten letters (<em>a</em>,<em>d</em>,<em>e</em>,<em>f</em>,<em>j</em>,<em>n</em>,<em>o</em>,<em>s</em>,<em>t</em>,<em>v</em>) from non-invasive neural signals of 20 participants, offering new insights into the neural correlates of handwriting. Letters were classified with two methods: the direct classification from low-frequency and broadband electroencephalogram (EEG) and a two-step approach comprising the continuous decoding of hand kinematics and the application of those in subsequent classification. The two-step approach poses a novel application of continuous movement decoding for the classification of letters from EEG. When using low-frequency EEG, results show moderate accuracies of 23.1% for ten letters and 39.0% for a subset of five letters with highest discriminability of the trajectories. The two-step approach yielded significantly higher performances of 26.2% for ten letters and 46.7% for the subset of five letters. Hand kinematics could be reconstructed with a correlation of 0.10 to 0.57 (average chance level: 0.04) between the decoded and original kinematic. The study shows the general feasibility of extracting handwritten letters from non-invasively recorded neural signals and indicates that the proposed two-step approach can improve performances. As an exploratory investigation of the neural mechanisms of handwriting in EEG, we found significant influence of the written letter on the low-frequency components of neural signals. Differences between letters occurred mostly in central and occipital channels. Further, our results suggest movement speed as the most informative kinematic for the decoding of short hand movements.</div></div>","PeriodicalId":10578,"journal":{"name":"Computers in biology and medicine","volume":null,"pages":null},"PeriodicalIF":7.0,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142322593","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deep learning enabled in vitro predicting biological tissue thickness using force measurement device","authors":"","doi":"10.1016/j.compbiomed.2024.109181","DOIUrl":"10.1016/j.compbiomed.2024.109181","url":null,"abstract":"<div><div>Accurate perception of biological tissues (BT) thickness is essential for preliminary evaluation of medical diagnosis and animal nutrition. However, traditional thickness measuring approaches of BT require complex operation, high-cost, and trigger biological stress response. Herein this study, an novel in vitro BT thickness measuring approach integrated with force test system (FST) and the discrete multiwavelet transform convolutional neural network (DMWA-CNN) prediction model based on deep learning are proposed. Simultaneously, several comprehensive experiments and model comparisons are conducted to demonstrate the superiority of the proposed approach. By establishing a DMWA-CNN demonstrates higher estimation accuracy than other traditional algorithm, achieving 100 % accuracy for artificial BT. Moreover, the experimental results indicate that proposed approach is robust to elastic modulus variation (<em>E</em>), external load variation (<em>F</em>), and small thickness differences (<em>T</em>_<em>s</em>). In addition, four kinds of the pork’ thickness are experimentally measured, and the accuracy value is not less than 98.2 %. The thickness of BT determined using the FST and DMWA-CNN algorithm demonstrate potential application in the biomechanical parameter prediction.</div></div>","PeriodicalId":10578,"journal":{"name":"Computers in biology and medicine","volume":null,"pages":null},"PeriodicalIF":7.0,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142319682","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":"Personalized food consumption detection with deep learning and Inertial Measurement Unit sensor","authors":"","doi":"10.1016/j.compbiomed.2024.109167","DOIUrl":"10.1016/j.compbiomed.2024.109167","url":null,"abstract":"<div><div>For individuals diagnosed with diabetes mellitus, it is crucial to keep a record of the carbohydrates consumed during meals, as this should be done at least three times daily, amounting to an average of six meals. Unfortunately, many individuals tend to overlook this essential task. For those who use an artificial pancreas, carbohydrate intake proves to be a critical factor, as it can activate the insulin pump in the artificial pancreas to deliver insulin to the body. To address this need, we have developed personalized deep learning model that can accurately detect carbohydrate intake with a high degree of accuracy. Our study employed a publicly available dataset gathered by an Inertial Measurement Unit (IMU), which included accelerometer and gyroscope data. The data was sampled at a rate of 15 Hz, necessitating preprocessing. For our tailored to the patient model, we utilized a recurrent network comprising Long short-term memory (LSTM) layers. Our findings revealed a median F1 score of 0.99, indicating a high level of accuracy. Additionally, the confusion matrix displayed a difference of only 6 s, further validating the model’s accuracy. Therefore, we can confidently assert that our model architecture exhibits a high degree of accuracy. Our model performed well above 90% on the dataset, with most results between 98%–99%. The recurrent networks improved the problem-solving capabilities significantly, though some outliers remained. The model’s average prediction latency was 5.5 s, suggesting that later meal predictions result in extended meal progress predictions. The dataset’s limitation of mostly single-day data points raises questions about multi-day performance, which could be explored by collecting multi-day data, including night periods. Future enhancements might involve transformer networks and shorter time windows to improve model responsiveness and accuracy. Therefore, we can confidently assert that our model exhibits a high degree of accuracy.</div></div>","PeriodicalId":10578,"journal":{"name":"Computers in biology and medicine","volume":null,"pages":null},"PeriodicalIF":7.0,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142319681","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A multi-task learning model for clinically interpretable sesamoiditis grading","authors":"","doi":"10.1016/j.compbiomed.2024.109179","DOIUrl":"10.1016/j.compbiomed.2024.109179","url":null,"abstract":"<div><div>Sesamoiditis is a common equine disease with varying severity, leading to increased injury risks and performance degradation in horses. Accurate grading of sesamoiditis is crucial for effective treatment. Although deep learning-based approaches for grading sesamoiditis show promise, they remain underexplored and often lack clinical interpretability. To address this issue, we propose a novel, clinically interpretable multi-task learning model that integrates clinical knowledge with machine learning. The proposed model employs a dual-branch decoder to simultaneously perform sesamoiditis grading and vascular channel segmentation. Feature fusion is utilized to transfer knowledge between these tasks, enabling the identification of subtle radiographic variations. Additionally, our model generates a diagnostic report that, along with the vascular channel mask, serves as an explanation of the model’s grading decisions, thereby increasing the transparency of the decision-making process. We validate our model on two datasets, demonstrating its superior performance compared to state-of-the-art models in terms of accuracy and generalization. This study provides a foundational framework for the interpretable grading of similar diseases.</div></div>","PeriodicalId":10578,"journal":{"name":"Computers in biology and medicine","volume":null,"pages":null},"PeriodicalIF":7.0,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142319680","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ASCHOPLEX: A generalizable approach for the automatic segmentation of choroid plexus","authors":"","doi":"10.1016/j.compbiomed.2024.109164","DOIUrl":"10.1016/j.compbiomed.2024.109164","url":null,"abstract":"<div><h3>Background:</h3><div>The Choroid Plexus (ChP) plays a vital role in brain homeostasis, serving as part of the Blood-Cerebrospinal Fluid Barrier, contributing to brain clearance pathways and being the main source of cerebrospinal fluid. Since the involvement of ChP in neurological and psychiatric disorders is not entirely established and currently under investigation, accurate and reproducible segmentation of this brain structure on large cohorts remains challenging. This paper presents ASCHOPLEX, a deep-learning tool for the automated segmentation of human ChP from structural MRI data that integrates existing software architectures like 3D UNet, UNETR, and DynUNet to deliver accurate ChP volume estimates.</div></div><div><h3>Methods:</h3><div>Here we trained ASCHOPLEX on 128 T1-w MRI images comprising both controls and patients with Multiple Sclerosis. ASCHOPLEX’s performances were evaluated using traditional segmentation metrics; manual segmentation by experts served as ground truth. To overcome the generalizability problem that affects data-driven approaches, an additional fine-tuning procedure (ASCHOPLEX_tune) was implemented on 77 T1-w PET/MRI images of both controls and depressed patients.</div></div><div><h3>Results:</h3><div>ASCHOPLEX showed superior performance compared to commonly used methods like FreeSurfer and Gaussian Mixture Model both in terms of Dice Coefficient (ASCHOPLEX 0.80, ASCHOPLEX_tune 0.78) and estimated ChP volume error (ASCHOPLEX 9.22%, ASCHOPLEX_tune 9.23%).</div></div><div><h3>Conclusion:</h3><div>These results highlight the high accuracy, reliability, and reproducibility of ASCHOPLEX ChP segmentations.</div></div>","PeriodicalId":10578,"journal":{"name":"Computers in biology and medicine","volume":null,"pages":null},"PeriodicalIF":7.0,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142319679","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DetSegDiff: A joint periodontal landmark detection and segmentation in intraoral ultrasound using edge-enhanced diffusion-based network","authors":"","doi":"10.1016/j.compbiomed.2024.109174","DOIUrl":"10.1016/j.compbiomed.2024.109174","url":null,"abstract":"<div><div>Individuals with malocclusion require an orthodontic diagnosis and treatment plan based on the severity of their condition. Assessing and monitoring changes in periodontal structures before, during, and after orthodontic procedures is crucial, and intraoral ultrasound (US) imaging has been shown a promising diagnostic tool in imaging periodontium. However, accurately delineating and analyzing periodontal structures in US videos is a challenging task for clinicians, as it is time-consuming and subject to interpretation errors. This paper introduces DetSegDiff, an edge-enhanced diffusion-based network developed to simultaneously detect the cementoenamel junction (CEJ) and segment alveolar bone structure in intraoral US videos. An edge feature encoder is designed to enhance edge and texture information for precise delineation of periodontal structures. Additionally, we employed the spatial squeeze-attention module (SSAM) to extract more representative features to perform both detection and segmentation tasks at global and local levels. This study used 169 videos from 17 orthodontic patients for training purposes and was subsequently tested on 41 videos from 4 additional patients. The proposed method achieved a mean distance difference of 0.17 ± 0.19 mm for the CEJ and an average Dice score of 90.1% for alveolar bone structure. As there is a lack of multi-task benchmark networks, thorough experiments were undertaken to assess and benchmark the proposed method against state-of-the-art (SOTA) detection and segmentation individual networks. The experimental results demonstrated that DetSegDiff outperformed SOTA approaches, confirming the feasibility of using automated diagnostic systems for orthodontists.</div></div>","PeriodicalId":10578,"journal":{"name":"Computers in biology and medicine","volume":null,"pages":null},"PeriodicalIF":7.0,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142315351","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":"MV-GNN: Generation of continuous geometric representations of mitral valve motion from 3D+t echocardiography","authors":"","doi":"10.1016/j.compbiomed.2024.109154","DOIUrl":"10.1016/j.compbiomed.2024.109154","url":null,"abstract":"<div><div>We present a geometric deep-learning method for reconstructing a temporally continuous mitral valve surface mesh from 3D transesophageal echocardiography sequences. Our approach features a supervised end-to-end deep learning architecture that combines a convolutional neural network-based voxel encoder and decoder with a graph neural network-based multi-resolution mesh decoder, all trained on sparse landmark annotations. Key elements of our methodology include a tube-shaped prototype mesh with labeled vertices, a specialized loss function to preserve the known inlet and outlet, and a rigid alignment system for anatomical landmarks. A custom term in the loss function prevents self-intersecting geometries within the valve mesh, promoting point correspondence and facilitating a continuous representation of valve anatomy over time. An ablation study evaluates the impact of different loss term configurations on model performance, highlighting the effectiveness of each individual loss term. Our Mitral Valve Graph Neural Network (MV-GNN) outperforms existing deep-learning methods on most distance metrics for the annulus and leaflets. The continuous valve motion representations generated by our approach (3D+t) exhibit distance measures comparable to our 3D solution, demonstrating its potential for analyzing mitral valve dynamics and enhancing personalized simulations for hemodynamic assessment and therapy planning.</div></div>","PeriodicalId":10578,"journal":{"name":"Computers in biology and medicine","volume":null,"pages":null},"PeriodicalIF":7.0,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0010482524012393/pdfft?md5=4bc6eedd0ac8002d3434fafeaf193c7d&pid=1-s2.0-S0010482524012393-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142315353","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Simulation-informed learning for time-resolved angiographic contrast agent concentration reconstruction","authors":"","doi":"10.1016/j.compbiomed.2024.109178","DOIUrl":"10.1016/j.compbiomed.2024.109178","url":null,"abstract":"<div><div>Three-dimensional Digital Subtraction Angiography (3D-DSA) is a well-established X-ray-based technique for visualizing vascular anatomy. Recently, four-dimensional DSA (4D-DSA) reconstruction algorithms have been developed to enable the visualization of volumetric contrast flow dynamics through time-series of volumes. This reconstruction problem is ill-posed mainly due to vessel overlap in the projection direction and geometric vessel foreshortening, which leads to information loss in the recorded projection images. However, knowledge about the underlying fluid dynamics can be leveraged to constrain the solution space. In our work, we implicitly include this information in a neural network-based model that is trained on a dataset of image-based blood flow simulations. The model predicts the spatially averaged contrast agent concentration for each centerline point of the vasculature over time, lowering the overall computational demand. The trained network enables the reconstruction of relative contrast agent concentrations with a mean absolute error of 0.02±0.02 and a mean absolute percentage error of 5.31±9.25 %. Moreover, the network is robust to varying degrees of vessel overlap and vessel foreshortening. Our approach demonstrates the potential of the integration of machine learning and blood flow simulations in time-resolved angiographic contrast agent concentration reconstruction.</div></div>","PeriodicalId":10578,"journal":{"name":"Computers in biology and medicine","volume":null,"pages":null},"PeriodicalIF":7.0,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0010482524012630/pdfft?md5=d402d6a132f3f9ced1d8f862d270edb5&pid=1-s2.0-S0010482524012630-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142315348","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Boosting medical diagnostics with a novel gradient-based sample selection method","authors":"","doi":"10.1016/j.compbiomed.2024.109165","DOIUrl":"10.1016/j.compbiomed.2024.109165","url":null,"abstract":"<div><div>In the rapidly expanding landscape of medical data, the need for innovative approaches to maximize classification performance has become increasingly critical. As data volumes grow, ensuring that diagnostic systems work with accurate and relevant data is paramount for effective and generalizable classification. This study introduces a novel gradient-based sample selection method, the first of its kind in the literature, specifically designed to enhance classification accuracy by removing redundant and non-informative data. Unlike traditional methods that focus solely on feature selection, this approach integrates an advanced sample selection technique to optimize the input data, leading to more accurate and efficient diagnostics. The method is validated on multiple disease datasets, including the Wisconsin Diagnostic Breast Cancer (WDBC) dataset and the Cleveland Coronary Artery Disease (CAD) dataset, demonstrating its broad applicability and effectiveness. To address dataset imbalance, the Adaptive Synthetic Sampling (ADASYN) method is employed, followed by Particle Swarm Optimization (PSO) for feature selection. The refined datasets are then classified using a Support Vector Machine (SVM), showing that even traditional classifiers can achieve substantial improvements when enhanced with advanced sample selection. The results underscore the critical importance of precise sample selection in boosting classification performance, setting a new standard for computer-aided diagnostics and paving the way for future innovations in handling large and complex medical datasets.</div></div>","PeriodicalId":10578,"journal":{"name":"Computers in biology and medicine","volume":null,"pages":null},"PeriodicalIF":7.0,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142315350","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":"Efficient bladder cancer diagnosis using an improved RIME algorithm with Orthogonal Learning","authors":"","doi":"10.1016/j.compbiomed.2024.109175","DOIUrl":"10.1016/j.compbiomed.2024.109175","url":null,"abstract":"<div><div>Bladder cancer (BC) diagnosis presents a critical challenge in biomedical research, necessitating accurate tumor classification from diverse datasets for effective treatment planning. This paper introduces a novel wrapper feature selection (FS) method that leverages a hybrid optimization algorithm combining Orthogonal Learning (OL) with a rime optimization algorithm (RIME), termed mRIME. The mRIME algorithm is designed to avoid local optima, streamline the search process, and select the most relevant features without compromising classifier performance. It also introduces mRIME-SVM, a novel hybrid model integrating modified mRIME for FS with Support Vector Machine (SVM) for classification. The mRIME algorithm is employed as an FS method and is also utilized to fine-tune the hyperparameters of it the It SVM, enhancing the overall classification accuracy. Specifically, mRIME navigates complex search spaces to optimize FS without compromising classifier performance. Evaluated on eight diverse BC datasets, mRIME-SVM outperforms popular metaheuristic algorithms, ensuring precise and reliable diagnostic outcomes. Moreover, the proposed mRIME was employed for tackling global optimization problems. It has been thoroughly assessed using the IEEE Congress on Evolutionary Computation 2022 (CEC’2022) test suite. Comparative analyzes with Gray wolf optimization (GWO), Whale optimization algorithm (WOA), Harris hawks optimization (HHO), Golden Jackal Optimization (GJO), Hunger Game optimization algorithm (HGS), Sinh Cosh Optimizer (SCHO), and the original RIME highlight mRIME’s competitiveness and efficacy across diverse optimization tasks. Leveraging mRIME’s success, mRIME-SVM achieves high classification accuracy on nine BC datasets, surpassing existing models. Results underscore mRIME’s competitiveness and applicability across diverse optimization tasks, extending its utility to enhance BC classification. This study contributes to advancing BC diagnostics with a robust computational framework, promising broader applications in bioinformatics and AI-driven medical research.</div></div>","PeriodicalId":10578,"journal":{"name":"Computers in biology and medicine","volume":null,"pages":null},"PeriodicalIF":7.0,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142315349","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}