Deep learning in neuroimaging data analysis: Applications, challenges, and solutions

Deep Learning Radiomics Analysis of CT Imaging for Differentiating Between Crohn's Disease and Intestinal Tuberculosis

This study aimed to develop and evaluate a CT-based deep learning radiomics model for differentiating between Crohn's disease (CD) and intestinal tuberculosis (ITB). A total of 330 patients with pathologically confirmed as CD or ITB from the First Affiliated Hospital of Zhengzhou University were divided into the validation dataset one (CD: 167; ITB: 57) and validation dataset two (CD: 78; ITB: 28). Based on the validation dataset one, the synthetic minority oversampling technique (SMOTE) was adopted to create balanced dataset as training data for feature selection and model construction. The handcrafted and deep learning (DL) radiomics features were extracted from the arterial and venous phases images, respectively. The interobserver consistency analysis, Spearman's correlation, univariate analysis, and the least absolute shrinkage and selection operator (LASSO) regression were used to select features. Based on extracted multi-phase radiomics features, six logistic regression models were finally constructed. The diagnostic performances of different models were compared using ROC analysis and Delong test. The arterial-venous combined deep learning radiomics model for differentiating between CD and ITB showed a high prediction quality with AUCs of 0.885, 0.877, and 0.800 in SMOTE dataset, validation dataset one, and validation dataset two, respectively. Moreover, the deep learning radiomics model outperformed the handcrafted radiomics model in same phase images. In validation dataset one, the Delong test results indicated that there was a significant difference in the AUC of the arterial models (p = 0.037), while not in venous and arterial-venous combined models (p = 0.398 and p = 0.265) as comparing deep learning radiomics models and handcrafted radiomics models. In our study, the arterial-venous combined model based on deep learning radiomics analysis exhibited good performance in differentiating between CD and ITB.

Dense attention network identifies EEG abnormalities during working memory performance of patients with schizophrenia

Introduction

Patients with schizophrenia typically exhibit deficits in working memory (WM) associated with abnormalities in brain activity. Alterations in the encoding, maintenance and retrieval phases of sequential WM tasks are well established. However, due to the heterogeneity of symptoms and complexity of its neurophysiological underpinnings, differential diagnosis remains a challenge. We conducted an electroencephalographic (EEG) study during a visual WM task in fifteen schizophrenia patients and fifteen healthy controls. We hypothesized that EEG abnormalities during the task could be identified, and patients successfully classified by an interpretable machine learning algorithm.

Methods

We tested a custom dense attention network (DAN) machine learning model to discriminate patients from control subjects and compared its performance with simpler and more commonly used machine learning models. Additionally, we analyzed behavioral performance, event-related EEG potentials, and time-frequency representations of the evoked responses to further characterize abnormalities in patients during WM.

Results

The DAN model was significantly accurate in discriminating patients from healthy controls, ACC = 0.69, SD = 0.05. There were no significant differences between groups, conditions, or their interaction in behavioral performance or event-related potentials. However, patients showed significantly lower alpha suppression in the task preparation, memory encoding, maintenance, and retrieval phases F(1,28) = 5.93, p = 0.022, η2 = 0.149. Further analysis revealed that the two highest peaks in the attention value vector of the DAN model overlapped in time with the preparation and memory retrieval phases, as well as with two of the four significant time-frequency ROIs.

Discussion

These results highlight the potential utility of interpretable machine learning algorithms as an aid in diagnosis of schizophrenia and other psychiatric disorders presenting oscillatory abnormalities.

GDNet-EEG: An attention-aware deep neural network based on group depth-wise convolution for SSVEP stimulation frequency recognition

Background

Steady state visually evoked potentials (SSVEPs) based early glaucoma diagnosis requires effective data processing (e.g., deep learning) to provide accurate stimulation frequency recognition. Thus, we propose a group depth-wise convolutional neural network (GDNet-EEG), a novel electroencephalography (EEG)-oriented deep learning model tailored to learn regional characteristics and network characteristics of EEG-based brain activity to perform SSVEPs-based stimulation frequency recognition.

Method

Group depth-wise convolution is proposed to extract temporal and spectral features from the EEG signal of each brain region and represent regional characteristics as diverse as possible. Furthermore, EEG attention consisting of EEG channel-wise attention and specialized network-wise attention is designed to identify essential brain regions and form significant feature maps as specialized brain functional networks. Two publicly SSVEPs datasets (large-scale benchmark and BETA dataset) and their combined dataset are utilized to validate the classification performance of our model.

Results

Based on the input sample with a signal length of 1 s, the GDNet-EEG model achieves the average classification accuracies of 84.11, 85.93, and 93.35% on the benchmark, BETA, and combination datasets, respectively. Compared with the average classification accuracies achieved by comparison baselines, the average classification accuracies of the GDNet-EEG trained on a combination dataset increased from 1.96 to 18.2%.

Conclusion

Our approach can be potentially suitable for providing accurate SSVEP stimulation frequency recognition and being used in early glaucoma diagnosis.

Data management strategy for a collaborative research center

The importance of effective research data management (RDM) strategies to support the generation of Findable, Accessible, Interoperable, and Reusable (FAIR) neuroscience data grows with each advance in data acquisition techniques and research methods. To maximize the impact of diverse research strategies, multidisciplinary, large-scale neuroscience research consortia face a number of unsolved challenges in RDM. While open science principles are largely accepted, it is practically difficult for researchers to prioritize RDM over other pressing demands. The implementation of a coherent, executable RDM plan for consortia spanning animal, human, and clinical studies is becoming increasingly challenging. Here, we present an RDM strategy implemented for the Heidelberg Collaborative Research Consortium. Our consortium combines basic and clinical research in diverse populations (animals and humans) and produces highly heterogeneous and multimodal research data (e.g., neurophysiology, neuroimaging, genetics, behavior). We present a concrete strategy for initiating early-stage RDM and FAIR data generation for large-scale collaborative research consortia, with a focus on sustainable solutions that incentivize incremental RDM while respecting research-specific requirements.