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Editorial: Neuromodulation using spatiotemporally complex patterns. 社论:利用时空复杂模式进行神经调控
IF 2.5 4区 医学 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2024-08-05 eCollection Date: 2024-01-01 DOI: 10.3389/fninf.2024.1454834
Peter A Tass, Hemant Bokil
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引用次数: 0
Exploring white matter dynamics and morphology through interactive numerical phantoms: the White Matter Generator 通过交互式数字模型探索白质动态和形态:白质生成器
IF 3.5 4区 医学 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2024-07-31 DOI: 10.3389/fninf.2024.1354708
Sidsel Winther, Oscar Peulicke, Mariam Andersson, Hans M. Kjer, Jakob A. Bærentzen, Tim B. Dyrby
Brain white matter is a dynamic environment that continuously adapts and reorganizes in response to stimuli and pathological changes. Glial cells, especially, play a key role in tissue repair, inflammation modulation, and neural recovery. The movements of glial cells and changes in their concentrations can influence the surrounding axon morphology. We introduce the White Matter Generator (WMG) tool to enable the study of how axon morphology is influenced through such dynamical processes, and how this, in turn, influences the diffusion-weighted MRI signal. This is made possible by allowing interactive changes to the configuration of the phantom generation throughout the optimization process. The phantoms can consist of myelinated axons, unmyelinated axons, and cell clusters, separated by extra-cellular space. Due to morphological flexibility and computational advantages during the optimization, the tool uses ellipsoids as building blocks for all structures; chains of ellipsoids for axons, and individual ellipsoids for cell clusters. After optimization, the ellipsoid representation can be converted to a mesh representation which can be employed in Monte-Carlo diffusion simulations. This offers an effective method for evaluating tissue microstructure models for diffusion-weighted MRI in controlled bio-mimicking white matter environments. Hence, the WMG offers valuable insights into white matter's adaptive nature and implications for diffusion-weighted MRI microstructure models, and thereby holds the potential to advance clinical diagnosis, treatment, and rehabilitation strategies for various neurological disorders and injuries.
脑白质是一个动态的环境,会随着刺激和病理变化而不断适应和重组。尤其是神经胶质细胞,在组织修复、炎症调节和神经恢复中发挥着关键作用。神经胶质细胞的运动及其浓度变化会影响周围轴突的形态。我们引入了白质生成器(WMG)工具,以研究轴突形态如何受到此类动态过程的影响,以及这反过来又如何影响扩散加权磁共振成像信号。通过在整个优化过程中对模型生成的配置进行交互式更改,使这一研究成为可能。模型可由髓鞘轴突、无髓鞘轴突和细胞簇组成,并由细胞外空间分隔。由于形态上的灵活性和优化过程中的计算优势,该工具使用椭圆体作为所有结构的构建模块;轴突使用椭圆体链,细胞簇使用单个椭圆体。优化后,椭圆体表示法可转换为网格表示法,用于蒙特卡洛扩散模拟。这为在受控的生物模拟白质环境中评估用于扩散加权磁共振成像的组织微结构模型提供了一种有效的方法。因此,WMG 为了解白质的适应性及其对扩散加权磁共振成像微结构模型的影响提供了宝贵的见解,从而有望推动各种神经系统疾病和损伤的临床诊断、治疗和康复策略。
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引用次数: 0
LYNSU: automated 3D neuropil segmentation of fluorescent images for Drosophila brains LYNSU:果蝇大脑荧光图像的自动三维神经纤层分割
IF 3.5 4区 医学 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2024-07-29 DOI: 10.3389/fninf.2024.1429670
Kai-Yi Hsu, Chi-Tin Shih, Nan-Yow Chen, Chung-Chuan Lo
The brain atlas, which provides information about the distribution of genes, proteins, neurons, or anatomical regions, plays a crucial role in contemporary neuroscience research. To analyze the spatial distribution of those substances based on images from different brain samples, we often need to warp and register individual brain images to a standard brain template. However, the process of warping and registration may lead to spatial errors, thereby severely reducing the accuracy of the analysis. To address this issue, we develop an automated method for segmenting neuropils in the Drosophila brain for fluorescence images from the FlyCircuit database. This technique allows future brain atlas studies to be conducted accurately at the individual level without warping and aligning to a standard brain template. Our method, LYNSU (Locating by YOLO and Segmenting by U-Net), consists of two stages. In the first stage, we use the YOLOv7 model to quickly locate neuropils and rapidly extract small-scale 3D images as input for the second stage model. This stage achieves a 99.4% accuracy rate in neuropil localization. In the second stage, we employ the 3D U-Net model to segment neuropils. LYNSU can achieve high accuracy in segmentation using a small training set consisting of images from merely 16 brains. We demonstrate LYNSU on six distinct neuropils or structures, achieving a high segmentation accuracy comparable to professional manual annotations with a 3D Intersection-over-Union (IoU) reaching up to 0.869. Our method takes only about 7 s to segment a neuropil while achieving a similar level of performance as the human annotators. To demonstrate a use case of LYNSU, we applied it to all female Drosophila brains from the FlyCircuit database to investigate the asymmetry of the mushroom bodies (MBs), the learning center of fruit flies. We used LYNSU to segment bilateral MBs and compare the volumes between left and right for each individual. Notably, of 8,703 valid brain samples, 10.14% showed bilateral volume differences that exceeded 10%. The study demonstrated the potential of the proposed method in high-throughput anatomical analysis and connectomics construction of the Drosophila brain.
脑图谱可提供基因、蛋白质、神经元或解剖区域的分布信息,在当代神经科学研究中起着至关重要的作用。为了根据不同大脑样本的图像分析这些物质的空间分布,我们通常需要将单个大脑图像扭曲并配准到标准大脑模板上。然而,扭曲和配准过程可能会导致空间误差,从而严重降低分析的准确性。为了解决这个问题,我们开发了一种自动方法,用于根据 FlyCircuit 数据库中的荧光图像分割果蝇大脑中的神经线。这项技术使未来的脑图谱研究能够在个体水平上精确进行,而无需根据标准脑模板进行扭曲和对齐。我们的方法 LYNSU(通过 YOLO 定位和 U-Net 分割)包括两个阶段。在第一阶段,我们使用 YOLOv7 模型快速定位神经瞳孔,并快速提取小比例三维图像作为第二阶段模型的输入。这一阶段的神经瞳孔定位准确率达到 99.4%。在第二阶段,我们采用三维 U-Net 模型来分割神经瞳孔。LYNSU 只需使用由 16 个大脑图像组成的小型训练集,就能达到很高的分割准确率。我们在六种不同的神经瞳孔或结构上演示了 LYNSU,其分割准确率可与专业人工注释相媲美,三维交集-联合(IoU)高达 0.869。我们的方法只需 7 秒钟就能分割一个神经瞳孔,同时达到与人工标注相似的性能水平。为了演示 LYNSU 的使用案例,我们将其应用于 FlyCircuit 数据库中的所有雌果蝇大脑,以研究果蝇学习中心蘑菇体 (MB) 的不对称性。我们使用 LYNSU 对双侧蘑菇体进行分割,并比较每个个体的左右体积。值得注意的是,在 8703 个有效大脑样本中,10.14% 的样本显示双侧体积差异超过 10%。这项研究证明了所提出的方法在果蝇大脑高通量解剖分析和连接组学构建方面的潜力。
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引用次数: 0
M3: using mask-attention and multi-scale for multi-modal brain MRI classification M3:利用遮挡注意力和多尺度进行多模态脑磁共振成像分类
IF 3.5 4区 医学 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2024-07-29 DOI: 10.3389/fninf.2024.1403732
Guanqing Kong, Chuanfu Wu, Zongqiu Zhang, Chuansheng Yin, Dawei Qin
IntroductionBrain diseases, particularly the classification of gliomas and brain metastases and the prediction of HT in strokes, pose significant challenges in healthcare. Existing methods, relying predominantly on clinical data or imaging-based techniques such as radiomics, often fall short in achieving satisfactory classification accuracy. These methods fail to adequately capture the nuanced features crucial for accurate diagnosis, often hindered by noise and the inability to integrate information across various scales.MethodsWe propose a novel approach that mask attention mechanisms with multi-scale feature fusion for Multimodal brain disease classification tasks, termed M3, which aims to extract features highly relevant to the disease. The extracted features are then dimensionally reduced using Principal Component Analysis (PCA), followed by classification with a Support Vector Machine (SVM) to obtain the predictive results.ResultsOur methodology underwent rigorous testing on multi-parametric MRI datasets for both brain tumors and strokes. The results demonstrate a significant improvement in addressing critical clinical challenges, including the classification of gliomas, brain metastases, and the prediction of hemorrhagic stroke transformations. Ablation studies further validate the effectiveness of our attention mechanism and feature fusion modules.DiscussionThese findings underscore the potential of our approach to meet and exceed current clinical diagnostic demands, offering promising prospects for enhancing healthcare outcomes in the diagnosis and treatment of brain diseases.
导言脑部疾病,尤其是胶质瘤和脑转移瘤的分类以及脑卒中高血压的预测,给医疗保健带来了巨大挑战。现有的方法主要依赖临床数据或基于成像的技术(如放射组学),往往无法达到令人满意的分类准确性。这些方法未能充分捕捉到对准确诊断至关重要的细微特征,往往受到噪声和无法整合不同尺度信息的阻碍。方法我们提出了一种新方法,将注意力机制与多尺度特征融合,用于多模态脑疾病分类任务,称为 M3,旨在提取与疾病高度相关的特征。然后使用主成分分析法(PCA)对提取的特征进行降维处理,再使用支持向量机(SVM)进行分类,从而获得预测结果。结果我们的方法在脑肿瘤和脑卒中的多参数磁共振成像数据集上进行了严格测试。结果表明,在应对关键临床挑战方面,包括胶质瘤、脑转移瘤的分类以及出血性中风转变的预测方面,我们的方法都有了显著的改进。消融研究进一步验证了我们的注意机制和特征融合模块的有效性。 讨论这些发现强调了我们的方法在满足和超越当前临床诊断需求方面的潜力,为提高脑部疾病诊断和治疗的医疗效果提供了广阔的前景。
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引用次数: 0
Frontiers | A canonical polyadic tensor basis for fast Bayesian estimation of multi-subject brain activation patterns 前沿|用于快速贝叶斯估计多受试者大脑激活模式的典型多面体张量基础
IF 3.5 4区 医学 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2024-07-29 DOI: 10.3389/fninf.2024.1399391
Michelle F. Miranda
Task-evoked functional magnetic resonance imaging studies, such as the Human Connectome Project (HCP), are a powerful tool for exploring how brain activity is influenced by cognitive tasks like memory retention, decision-making, and language processing. A fast Bayesian function-on-scalar model is proposed for estimating population-level activation maps linked to the working memory task. The model is based on the canonical polyadic (CP) tensor decomposition of coefficient maps obtained for each subject. This decomposition effectively yields a tensor basis capable of extracting both common features and subject-specific features from the coefficient maps. These subject-specific features, in turn, are modeled as a function of covariates of interest using a Bayesian model that accounts for the correlation of the CP-extracted features. The dimensionality reduction achieved with the tensor basis allows for a fast MCMC estimation of population-level activation maps. This model is applied to one hundred unrelated subjects from the HCP dataset, yielding significant insights into brain signatures associated with working memory.
任务诱发功能磁共振成像研究,如人类连接组计划(HCP),是探索大脑活动如何受记忆保持、决策和语言处理等认知任务影响的有力工具。本文提出了一种快速贝叶斯尺度函数模型,用于估算与工作记忆任务相关的群体水平激活图谱。该模型基于对每个受试者的系数图进行典型多面体(CP)张量分解。这种分解有效地产生了一个张量基础,能够从系数图中提取共性特征和特定受试者特征。这些特定受试者特征反过来又通过贝叶斯模型作为相关协变量的函数进行建模,该模型考虑了 CP 提取特征的相关性。利用张量基础实现的降维可以对群体级激活图进行快速的 MCMC 估算。该模型被应用于 HCP 数据集中的 100 名无关受试者,从而对与工作记忆相关的大脑特征有了重要的了解。
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引用次数: 0
Dynamic topological data analysis: a novel fractal dimension-based testing framework with application to brain signals 动态拓扑数据分析:基于分形维度的新型测试框架在大脑信号中的应用
IF 3.5 4区 医学 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2024-07-12 DOI: 10.3389/fninf.2024.1387400
Anass B. El-Yaagoubi, Moo K. Chung, Hernando Ombao
Topological data analysis (TDA) is increasingly recognized as a promising tool in the field of neuroscience, unveiling the underlying topological patterns within brain signals. However, most TDA related methods treat brain signals as if they were static, i.e., they ignore potential non-stationarities and irregularities in the statistical properties of the signals. In this study, we develop a novel fractal dimension-based testing approach that takes into account the dynamic topological properties of brain signals. By representing EEG brain signals as a sequence of Vietoris-Rips filtrations, our approach accommodates the inherent non-stationarities and irregularities of the signals. The application of our novel fractal dimension-based testing approach in analyzing dynamic topological patterns in EEG signals during an epileptic seizure episode exposes noteworthy alterations in total persistence across 0, 1, and 2-dimensional homology. These findings imply a more intricate influence of seizures on brain signals, extending beyond mere amplitude changes.
拓扑数据分析(TDA)被越来越多的人认为是神经科学领域的一种有前途的工具,它可以揭示大脑信号中潜在的拓扑模式。然而,大多数拓扑数据分析相关方法都将大脑信号视为静态信号,即忽略了信号统计特性中潜在的非静态性和不规则性。在本研究中,我们开发了一种基于分形维度的新型测试方法,该方法考虑到了大脑信号的动态拓扑特性。通过将脑电图信号表示为一串 Vietoris-Rips 滤波,我们的方法能够适应信号固有的非稳态性和不规则性。在分析癫痫发作期间脑电信号的动态拓扑模式时,应用我们新颖的基于分形维度的测试方法,发现在 0 维、1 维和 2 维同源性中总的持续性发生了值得注意的变化。这些发现意味着癫痫发作对大脑信号的影响更为复杂,超出了单纯的振幅变化。
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引用次数: 0
Explainable deep-learning framework: decoding brain states and prediction of individual performance in false-belief task at early childhood stage 可解释的深度学习框架:解码大脑状态和预测幼儿期虚假信念任务中的个体表现
IF 3.5 4区 医学 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2024-06-28 DOI: 10.3389/fninf.2024.1392661
Km Bhavna, Azman Akhter, Romi Banerjee, Dipanjan Roy
Decoding of cognitive states aims to identify individuals' brain states and brain fingerprints to predict behavior. Deep learning provides an important platform for analyzing brain signals at different developmental stages to understand brain dynamics. Due to their internal architecture and feature extraction techniques, existing machine-learning and deep-learning approaches are suffering from low classification performance and explainability issues that must be improved. In the current study, we hypothesized that even at the early childhood stage (as early as 3-years), connectivity between brain regions could decode brain states and predict behavioral performance in false-belief tasks. To this end, we proposed an explainable deep learning framework to decode brain states (Theory of Mind and Pain states) and predict individual performance on ToM-related false-belief tasks in a developmental dataset. We proposed an explainable spatiotemporal connectivity-based Graph Convolutional Neural Network (Ex-stGCNN) model for decoding brain states. Here, we consider a developmental dataset, N = 155 (122 children; 3–12 yrs and 33 adults; 18–39 yrs), in which participants watched a short, soundless animated movie, shown to activate Theory-of-Mind (ToM) and pain networs. After scanning, the participants underwent a ToM-related false-belief task, leading to categorization into the pass, fail, and inconsistent groups based on performance. We trained our proposed model using Functional Connectivity (FC) and Inter-Subject Functional Correlations (ISFC) matrices separately. We observed that the stimulus-driven feature set (ISFC) could capture ToM and Pain brain states more accurately with an average accuracy of 94%, whereas it achieved 85% accuracy using FC matrices. We also validated our results using five-fold cross-validation and achieved an average accuracy of 92%. Besides this study, we applied the SHapley Additive exPlanations (SHAP) approach to identify brain fingerprints that contributed the most to predictions. We hypothesized that ToM network brain connectivity could predict individual performance on false-belief tasks. We proposed an Explainable Convolutional Variational Auto-Encoder (Ex-Convolutional VAE) model to predict individual performance on false-belief tasks and trained the model using FC and ISFC matrices separately. ISFC matrices again outperformed the FC matrices in prediction of individual performance. We achieved 93.5% accuracy with an F1-score of 0.94 using ISFC matrices and achieved 90% accuracy with an F1-score of 0.91 using FC matrices.
认知状态解码旨在识别个人的大脑状态和大脑指纹,从而预测行为。深度学习为分析不同发育阶段的大脑信号以了解大脑动态提供了一个重要平台。由于其内部架构和特征提取技术的原因,现有的机器学习和深度学习方法存在分类性能低、可解释性差等问题,必须加以改进。在本研究中,我们假设即使在幼儿阶段(早至 3 岁),大脑区域之间的连接性也能解码大脑状态,并预测虚假信念任务中的行为表现。为此,我们提出了一个可解释的深度学习框架,以解码大脑状态(心智理论和疼痛状态),并预测发育数据集中与心智理论相关的虚假信念任务中的个体表现。我们提出了一种可解释的基于时空连接的图卷积神经网络(Ex-stGCNN)模型,用于解码大脑状态。在这里,我们考虑了一个发育数据集,N = 155(122 名儿童;3-12 岁和 33 名成人;18-39 岁),其中参与者观看了一部无声动画短片,影片显示激活了心智理论(ToM)和疼痛网络。扫描结束后,参与者接受了与 ToM 相关的虚假信念任务,根据表现分为通过组、失败组和不一致组。我们使用功能连接(FC)和受试者间功能相关性(ISFC)矩阵分别训练了我们提出的模型。我们观察到,刺激驱动特征集(ISFC)能更准确地捕捉 ToM 和疼痛的大脑状态,平均准确率为 94%,而使用 FC 矩阵的准确率为 85%。我们还使用五倍交叉验证对结果进行了验证,平均准确率达到 92%。除了这项研究,我们还应用了 SHapley Additive exPlanations(SHAP)方法来识别对预测贡献最大的大脑指纹。我们假设 ToM 网络的大脑连通性可以预测个人在错误信念任务中的表现。我们提出了一个可解释卷积变异自动编码器(Ex-Convolutional VAE)模型来预测个人在虚假信念任务中的表现,并分别使用 FC 和 ISFC 矩阵对该模型进行了训练。在预测个人表现方面,ISFC 矩阵的表现再次优于 FC 矩阵。使用 ISFC 矩阵,我们的准确率达到了 93.5%,F1 分数为 0.94;使用 FC 矩阵,我们的准确率达到了 90%,F1 分数为 0.91。
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引用次数: 0
Identifying discriminative features of brain network for prediction of Alzheimer's disease using graph theory and machine learning. 利用图论和机器学习识别大脑网络的判别特征以预测阿尔茨海默病。
IF 2.5 4区 医学 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2024-06-18 eCollection Date: 2024-01-01 DOI: 10.3389/fninf.2024.1384720
S M Shayez Karim, Md Shah Fahad, R S Rathore

Alzheimer's disease (AD) is a challenging neurodegenerative condition, necessitating early diagnosis and intervention. This research leverages machine learning (ML) and graph theory metrics, derived from resting-state functional magnetic resonance imaging (rs-fMRI) data to predict AD. Using Southwest University Adult Lifespan Dataset (SALD, age 21-76 years) and the Open Access Series of Imaging Studies (OASIS, age 64-95 years) dataset, containing 112 participants, various ML models were developed for the purpose of AD prediction. The study identifies key features for a comprehensive understanding of brain network topology and functional connectivity in AD. Through a 5-fold cross-validation, all models demonstrate substantial predictive capabilities (accuracy in 82-92% range), with the support vector machine model standing out as the best having an accuracy of 92%. Present study suggests that top 13 regions, identified based on most important discriminating features, have lost significant connections with thalamus. The functional connection strengths were consistently declined for substantia nigra, pars reticulata, substantia nigra, pars compacta, and nucleus accumbens among AD subjects as compared to healthy adults and aging individuals. The present finding corroborate with the earlier studies, employing various neuroimagining techniques. This research signifies the translational potential of a comprehensive approach integrating ML, graph theory and rs-fMRI analysis in AD prediction, offering potential biomarker for more accurate diagnostics and early prediction of AD.

阿尔茨海默病(AD)是一种具有挑战性的神经退行性疾病,需要早期诊断和干预。这项研究利用从静息态功能磁共振成像(rs-fMRI)数据中得出的机器学习(ML)和图论指标来预测阿尔茨海默病。利用西南大学成人生命期数据集(SALD,21-76 岁)和开放获取系列成像研究数据集(OASIS,64-95 岁)(包含 112 名参与者),开发了各种 ML 模型,用于预测注意力缺失症。该研究确定了全面了解注意力缺失症大脑网络拓扑和功能连接的关键特征。通过 5 倍交叉验证,所有模型都显示出了很强的预测能力(准确率在 82-92% 之间),其中支持向量机模型的准确率高达 92%,是最佳模型。目前的研究表明,根据最重要的判别特征确定的前 13 个区域已经失去了与丘脑的重要联系。与健康成人和老龄人相比,AD 受试者的黑质、网状旁、黑质、紧密旁和伏隔核的功能连接强度持续下降。本研究结果与之前采用各种神经成像技术进行的研究结果相吻合。这项研究表明,将 ML、图论和 rs-fMRI 分析相结合的综合方法在预测注意力缺失症方面具有转化潜力,可为更准确地诊断和早期预测注意力缺失症提供潜在的生物标志物。
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引用次数: 0
Enhancing brain tumor detection in MRI with a rotation invariant Vision Transformer. 利用旋转不变视觉变换器增强核磁共振成像中的脑肿瘤检测。
IF 2.5 4区 医学 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2024-06-18 eCollection Date: 2024-01-01 DOI: 10.3389/fninf.2024.1414925
Palani Thanaraj Krishnan, Pradeep Krishnadoss, Mukund Khandelwal, Devansh Gupta, Anupoju Nihaal, T Sunil Kumar

Background: The Rotation Invariant Vision Transformer (RViT) is a novel deep learning model tailored for brain tumor classification using MRI scans.

Methods: RViT incorporates rotated patch embeddings to enhance the accuracy of brain tumor identification.

Results: Evaluation on the Brain Tumor MRI Dataset from Kaggle demonstrates RViT's superior performance with sensitivity (1.0), specificity (0.975), F1-score (0.984), Matthew's Correlation Coefficient (MCC) (0.972), and an overall accuracy of 0.986.

Conclusion: RViT outperforms the standard Vision Transformer model and several existing techniques, highlighting its efficacy in medical imaging. The study confirms that integrating rotational patch embeddings improves the model's capability to handle diverse orientations, a common challenge in tumor imaging. The specialized architecture and rotational invariance approach of RViT have the potential to enhance current methodologies for brain tumor detection and extend to other complex imaging tasks.

背景旋转不变视觉变换器(RViT)是一种新型深度学习模型,专为使用核磁共振扫描进行脑肿瘤分类而定制:RViT结合了旋转补丁嵌入,以提高脑肿瘤识别的准确性:在 Kaggle 的脑肿瘤 MRI 数据集上进行的评估表明,RViT 的灵敏度 (1.0)、特异度 (0.975)、F1-分数 (0.984)、马修相关系数 (MCC) (0.972) 和总体准确度 (0.986) 均表现优异:RViT 优于标准视觉变换器模型和几种现有技术,突出了其在医学成像中的功效。研究证实,集成旋转补丁嵌入提高了模型处理不同方向的能力,这是肿瘤成像中的一个常见挑战。RViT 的专业架构和旋转不变性方法有望增强当前的脑肿瘤检测方法,并扩展到其他复杂的成像任务。
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引用次数: 0
Frontiers | Neuroimaging article reexecution and reproduction assessment system 神经影像学前沿》文章重发与转载评估系统
IF 3.5 4区 医学 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2024-06-11 DOI: 10.3389/fninf.2024.1376022
Horea-Ioan Ioanas, Austin Macdonald, Yaroslav O. Halchenko
The value of research articles is increasingly contingent on complex data analysis results which substantiate their claims. Compared to data production, data analysis more readily lends itself to a higher standard of transparency and repeated operator-independent execution. This higher standard can be approached via fully reexecutable research outputs, which contain the entire instruction set for automatic end-to-end generation of an entire article from the earliest feasible provenance point. In this study, we make use of a peer-reviewed neuroimaging article which provides complete but fragile reexecution instructions, as a starting point to draft a new reexecution system which is both robust and portable. We render this system modular as a core design aspect, so that reexecutable article code, data, and environment specifications could potentially be substituted or adapted. In conjunction with this system, which forms the demonstrative product of this study, we detail the core challenges with full article reexecution and specify a number of best practices which permitted us to mitigate them. We further show how the capabilities of our system can subsequently be used to provide reproducibility assessments, both via simple statistical metrics and by visually highlighting divergent elements for human inspection. We argue that fully reexecutable articles are thus a feasible best practice, which can greatly enhance the understanding of data analysis variability and the trust in results. Lastly, we comment at length on the outlook for reexecutable research outputs and encourage re-use and derivation of the system produced herein.
研究文章的价值越来越取决于能够证实其主张的复杂数据分析结果。与数据生产相比,数据分析更容易达到更高的透明度标准,并可独立于操作员重复执行。这种更高的标准可以通过完全可重复执行的研究成果来实现,这些成果包含从最早的可行出处点开始端到端自动生成整篇文章的全部指令集。在本研究中,我们以一篇同行评议的神经影像学文章为起点,起草了一个既稳健又可移植的全新重执行系统,该文章提供了完整但脆弱的重执行指令。我们将这一系统模块化作为设计的核心内容,这样,可重新执行的文章代码、数据和环境规格就有可能被替换或调整。该系统是本研究的示范产品,结合该系统,我们详细介绍了完整文章重执行所面临的核心挑战,并具体介绍了一些最佳实践,这些实践使我们能够减轻这些挑战。我们还进一步展示了如何利用我们系统的能力,通过简单的统计指标和直观地突出差异元素,为人类检查提供可重复性评估。我们认为,完全可重新执行的文章是一种可行的最佳实践,它能极大地增强对数据分析变异性的理解和对结果的信任。最后,我们详细评论了可重新执行研究成果的前景,并鼓励重新使用和衍生本文中的系统。
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引用次数: 0
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Frontiers in Neuroinformatics
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