Vision Transformer (ViT) applied to structural magnetic resonance images has demonstrated success in the diagnosis of Alzheimer's disease (AD) and mild cognitive impairment (MCI). However, three key challenges have yet to be well addressed: 1) ViT requires a large labeled dataset to mitigate overfitting while most of the current AD-related sMRI data fall short in the sample sizes. 2) ViT neglects the within-patch feature learning, e.g., local brain atrophy, which is crucial for AD diagnosis. 3) While ViT can enhance capturing local features by reducing the patch size and increasing the number of patches, the computational complexity of ViT quadratically increases with the number of patches with unbearable overhead. To this end, this paper proposes a 3D-convolutional neural network (CNN) Enhanced Multiscale Progressive ViT (3D-CNN-MPVT). First, a 3D-CNN is pre-trained on sMRI data to extract detailed local image features and alleviate overfitting. Second, an MPVT module is proposed with an inner CNN module to explicitly characterize the within-patch interactions that are conducive to AD diagnosis. Third, a stitch operation is proposed to merge cross-patch features and progressively reduce the number of patches. The inner CNN alongside the stitch operation in the MPTV module enhances local feature characterization while mitigating computational costs. Evaluations using the Alzheimer's Disease Neuroimaging Initiative dataset with 6610 scans and the Open Access Series of Imaging Studies-3 with 1866 scans demonstrated its superior performance. With minimal preprocessing, our approach achieved an impressive 90% accuracy and 80% in AD classification and MCI conversion prediction, surpassing recent baselines.

Diffusion-weighted imaging (DWI) enables non-invasive characterization of tissue microstructure, yet acquiring densely sampled q-space data remains time-consuming and impractical in many clinical settings. Existing deep learning methods are typically constrained by fixed q-space sampling, limiting their adaptability to variable sampling scenarios. In this paper, we propose a Q-space Guided Multi-Modal Translation Network (Q-MMTN) for synthesizing multi-shell, high-angular resolution DWI (MS-HARDI) from flexible q-space sampling, leveraging commonly acquired structural data (e.g., T1- and T2-weighted MRI). Q-MMTN integrates the hybrid encoder and multi-modal attention fusion mechanism to effectively extract both local and global complementary information from multiple modalities. This design enhances feature representation and, together with a flexible q-space-aware embedding, enables dynamic modulation of internal features without relying on fixed sampling schemes. Additionally, we introduce a set of task-specific constraints, including adversarial, reconstruction, and anatomical consistency losses, which jointly enforce anatomical fidelity and signal realism. These constraints guide Q-MMTN to accurately capture the intrinsic and nonlinear relationships between directional DWI signals and q-space information. Extensive experiments across four lifespan datasets of children, adolescents, young and older adults demonstrate that Q-MMTN outperforms existing methods, including 1D-qDL, 2D-qDL, MESC-SD, and Q-GAN in estimating parameter maps and fiber tracts with fine-grained anatomical details. Notably, its ability to accommodate flexible q-space sampling highlights its potential as a promising toolkit for clinical and research applications. Our code is available at https://github.com/Idea89560041/Q-MMTN.

Diffusion-weighted imaging (DWI) is a key modality for studying brain microstructure, but its signals are highly susceptible to noise due to the thermal motion of water molecules and interactions with tissue microarchitecture, leading to significant signal attenuation and a low signal-to-noise ratio (SNR). In this paper, we propose a novel approach, a Cycle-Conditional Diffusion Model (Cycle-CDM) using unpaired data learning, aimed at improving DWI quality and reliability through noise correction. Cycle-CDM leverages a cycle-consistent translation architecture to bridge the domain gap between noise-contaminated and noise-free DWIs, enabling the restoration of high-quality images without requiring paired datasets. By utilizing two conditional diffusion models, Cycle-CDM establishes data interrelationships between the two types of DWIs, while incorporating synthesized anatomical priors from the cycle translation process to guide noise removal. In addition, we introduce specific constraints to preserve anatomical fidelity, allowing Cycle-CDM to effectively learn the underlying noise distribution and achieve accurate denoising. Our experiments conducted on simulated datasets, as well as children and adolescents' datasets with strong clinical relevance. Our results demonstrate that Cycle-CDM outperforms comparative methods, such as U-Net, CycleGAN, Pix2Pix, MUNIT and MPPCA, in terms of noise correction performance. We demonstrated that Cycle-CDM can be generalized to DWIs with head motion when they were acquired using different MRI scannsers. Importantly, the denoised DWI data produced by Cycle-CDM exhibit accurate preservation of underlying tissue microstructure, thus substantially improving their medical applicability.

Graph neural networks (GNNs) have proven effective in capturing relationships among nodes in a graph. This study introduces a novel perspective by considering a graph as a simplicial complex, encompassing nodes, edges, triangles, and $k$k-simplices, enabling the definition of graph-structured data on any $k$k-simplex. We design a novel Hodge-Laplacian heterogeneous graph attention network (HL-HGAT) to learn heterogeneous signal representations across $k$k-simplices. The HL-HGAT incorporates three key components: HL convolutional filters (HL-filters), simplicial projection (SP), and simplicial attention pooling (SAP) operators, applied to $k$k-simplices. HL-filters leverage the unique topology of $k$k-simplices encoded by the Hodge-Laplacian (HL) operator, operating within the spectral domain of the $k$k-th HL operator. To address computation challenges, we introduce a polynomial approximation for HL-filters, exhibiting spatial localization properties. Additionally, we propose a pooling operator to coarsen $k$k-simplices, combining features through simplicial attention mechanisms of self-attention and cross-attention via transformers and SP operators, capturing topological interconnections across multiple dimensions of simplices. The HL-HGAT is comprehensively evaluated across diverse graph applications, including NP-hard problems, graph multi-label and classification challenges, and graph regression tasks in logistics, computer vision, biology, chemistry, and neuroscience. The results demonstrate the model's efficacy and versatility in handling a wide range of graph-based scenarios.

The linear mixed-effects model is commonly utilized to interpret longitudinal data, characterizing both the global longitudinal trajectory across all observations and longitudinal trajectories within individuals. However, characterizing these trajectories in high-dimensional longitudinal data presents a challenge. To address this, our study proposes a novel approach, Unsupervised Orthogonal Mixed-Effects Trajectory Modeling (UOMETM), that leverages unsupervised learning to generate latent representations of both global and individual trajectories. We design an autoencoder with a latent space where an orthogonal constraint is imposed to separate the space of global trajectories from individual trajectories. We also devise a cross-reconstruction loss to ensure consistency of global trajectories and enhance the orthogonality between representation spaces. To evaluate UOMETM, we conducted simulation experiments on images to verify that every component functions as intended. Furthermore, we evaluated its performance and robustness using longitudinal brain cortical thickness from two Alzheimer's disease (AD) datasets. Comparative analyses with state-of-the-art methods revealed UOMETM's superiority in identifying global and individual longitudinal patterns, achieving a lower reconstruction error, superior orthogonality, and higher accuracy in AD classification and conversion forecasting. Remarkably, we found that the space of global trajectories did not significantly contribute to AD classification compared to the space of individual trajectories, emphasizing their clear separation. Moreover, our model exhibited satisfactory generalization and robustness across different datasets. The study shows the outstanding performance and potential clinical use of UOMETM in the context of longitudinal data analysis.

Diffuse optical tomography is a rapidly developing imaging technology for biomedical research and clinical studies. A commonly used technique for detecting diffused photons is time correlated single photon counting mechanism, which time stamps the photons while capturing signal. However, time stamping requires an extremely long data acquisition time. Using a spread-spectrum approach, a novel time correlated single photon counting algorithm based on pseudo random bit sequences has been proposed as a solution. This paper describes a FPGA implementation of this pseudo random bit sequence based single photon counter, leveraging the rapid prototyping capabilities of reconfigurable computing. The design consists of a high speed pseudo random number generator and a high speed data reconstruction unit. Furthermore, a demo prototype has been built for experimentation.