Gang Qu

Gang Qu, Ziyu Zhou, Vince D. Calhoun et al.

Multimodal neuroimaging modeling has becomes a widely used approach but confronts considerable challenges due to heterogeneity, which encompasses variability in data types, scales, and formats across modalities. This variability necessitates the deployment of advanced computational methods to integrate and interpret these diverse datasets within a cohesive analytical framework. In our research, we amalgamate functional magnetic resonance imaging, diffusion tensor imaging, and structural MRI into a cohesive framework. This integration capitalizes on the unique strengths of each modality and their inherent interconnections, aiming for a comprehensive understanding of the brain's connectivity and anatomical characteristics. Utilizing the Glasser atlas for parcellation, we integrate imaging derived features from various modalities: functional connectivity from fMRI, structural connectivity from DTI, and anatomical features from sMRI within consistent regions. Our approach incorporates a masking strategy to differentially weight neural connections, thereby facilitating a holistic amalgamation of multimodal imaging data. This technique enhances interpretability at connectivity level, transcending traditional analyses centered on singular regional attributes. The model is applied to the Human Connectome Project's Development study to elucidate the associations between multimodal imaging and cognitive functions throughout youth. The analysis demonstrates improved predictive accuracy and uncovers crucial anatomical features and essential neural connections, deepening our understanding of brain structure and function.

Yusong Xiao, Yuxuan Wu, Li Xiao et al.

Convolutional neural networks (CNNs) have achieved exciting performance in joint segmentation of optic disc and optic cup on single-institution datasets. However, their clinical translation is hindered by two major challenges: limited availability of large-scale, high-quality annotations and performance degradation caused by domain shift during deployment across heterogeneous imaging protocols and acquisition platforms. While unsupervised domain adaptation (UDA) provides a way to mitigate these limitations, most existing approaches do not address cross-domain interference and intra-domain generalization within a unified framework. In this paper, we present the Dual-Domain Synergy UDA (DDS-UDA), a novel UDA framework that comprises two key modules. First, a bi-directional cross-domain consistency regularization module is enforced to mitigate cross-domain interference through feature-level semantic information exchange guided by a coarse-to-fine dynamic mask generator, suppressing noise propagation while preserving structural coherence. Second, a frequency-driven intra-domain pseudo label learning module is used to enhance intra-domain generalization by synthesizing spectral amplitude-mixed supervision signals, which ensures high-fidelity feature alignment across domains. Implemented within a teacher-student architecture, DDS-UDA disentangles domain-specific biases from domain-invariant feature-level representations, thereby achieving robust adaptation to heterogeneous imaging environments. We conduct a comprehensive evaluation of our proposed method on two multi-domain fundus image datasets, demonstrating that it outperforms several existing UDA based methods and therefore providing an effective way for optic disc and optic cup segmentation.

Yiting Wang, Wanghao Ye, Ping Guo et al.

Optimizing Register Transfer Level (RTL) code is crucial for improving the power, performance, and area (PPA) of digital circuits in the early stages of synthesis. Manual rewriting, guided by synthesis feedback, can yield high-quality results but is time-consuming and error-prone. Most existing compiler-based approaches have difficulty handling complex design constraints. Large Language Model (LLM)-based methods have emerged as a promising alternative to address these challenges. However, LLM-based approaches often face difficulties in ensuring alignment between the generated code and the provided prompts. This paper presents SymRTLO, a novel neuron-symbolic RTL optimization framework that seamlessly integrates LLM-based code rewriting with symbolic reasoning techniques. Our method incorporates a retrieval-augmented generation (RAG) system of optimization rules and Abstract Syntax Tree (AST)-based templates, enabling LLM-based rewriting that maintains syntactic correctness while minimizing undesired circuit behaviors. A symbolic module is proposed for analyzing and optimizing finite state machine (FSM) logic, allowing fine-grained state merging and partial specification handling beyond the scope of pattern-based compilers. Furthermore, a fast verification pipeline, combining formal equivalence checks with test-driven validation, further reduces the complexity of verification. Experiments on the RTL-Rewriter benchmark with Synopsys Design Compiler and Yosys show that SymRTLO improves power, performance, and area (PPA) by up to 43.9%, 62.5%, and 51.1%, respectively, compared to the state-of-the-art methods.

Ziyu Zhou, Anton Orlichenko, Gang Qu et al.

Both functional and structural magnetic resonance imaging (fMRI and sMRI) are widely used for the diagnosis of mental disorder. However, combining complementary information from these two modalities is challenging due to their heterogeneity. Many existing methods fall short of capturing the interaction between these modalities, frequently defaulting to a simple combination of latent features. In this paper, we propose a novel Cross-Attentive Multi-modal Fusion framework (CAMF), which aims to capture both intra-modal and inter-modal relationships between fMRI and sMRI, enhancing multi-modal data representation. Specifically, our CAMF framework employs self-attention modules to identify interactions within each modality while cross-attention modules identify interactions between modalities. Subsequently, our approach optimizes the integration of latent features from both modalities. This approach significantly improves classification accuracy, as demonstrated by our evaluations on two extensive multi-modal brain imaging datasets, where CAMF consistently outperforms existing methods. Furthermore, the gradient-guided Score-CAM is applied to interpret critical functional networks and brain regions involved in schizophrenia. The bio-markers identified by CAMF align with established research, potentially offering new insights into the diagnosis and pathological endophenotypes of schizophrenia.

Faming Xu, Yiding Wang, Chen Qiao et al.

Dynamic effective connectivity networks (dECNs) reveal the changing directed brain activity and the dynamic causal influences among brain regions, which facilitate the identification of individual differences and enhance the understanding of human brain. Although the existing causal discovery methods have shown promising results in effective connectivity network analysis, they often overlook the dynamics of causality, in addition to the incorporation of spatio-temporal information in brain activity data. To address these issues, we propose a deep spatio-temporal fusion architecture, which employs a dynamic causal deep encoder to incorporate spatio-temporal information into dynamic causality modeling, and a dynamic causal deep decoder to verify the discovered causality. The effectiveness of the proposed method is first illustrated with simulated data. Then, experimental results from Philadelphia Neurodevelopmental Cohort (PNC) demonstrate the superiority of the proposed method in inferring dECNs, which reveal the dynamic evolution of directed flow between brain regions. The analysis shows the difference of dECNs between young adults and children. Specifically, the directed brain functional networks transit from fluctuating undifferentiated systems to more stable specialized networks as one grows. This observation provides further evidence on the modularization and adaptation of brain networks during development, leading to higher cognitive abilities observed in young adults.

Anton Orlichenko, Gang Qu, Ziyu Zhou et al.

Objective: fMRI and derived measures such as functional connectivity (FC) have been used to predict brain age, general fluid intelligence, psychiatric disease status, and preclinical neurodegenerative disease. However, it is not always clear that all demographic confounds, such as age, sex, and race, have been removed from fMRI data. Additionally, many fMRI datasets are restricted to authorized researchers, making dissemination of these valuable data sources challenging. Methods: We create a variational autoencoder (VAE)-based model, DemoVAE, to decorrelate fMRI features from demographics and generate high-quality synthetic fMRI data based on user-supplied demographics. We train and validate our model using two large, widely used datasets, the Philadelphia Neurodevelopmental Cohort (PNC) and Bipolar and Schizophrenia Network for Intermediate Phenotypes (BSNIP). Results: We find that DemoVAE recapitulates group differences in fMRI data while capturing the full breadth of individual variations. Significantly, we also find that most clinical and computerized battery fields that are correlated with fMRI data are not correlated with DemoVAE latents. An exception are several fields related to schizophrenia medication and symptom severity. Conclusion: Our model generates fMRI data that captures the full distribution of FC better than traditional VAE or GAN models. We also find that most prediction using fMRI data is dependent on correlation with, and prediction of, demographics. Significance: Our DemoVAE model allows for generation of high quality synthetic data conditioned on subject demographics as well as the removal of the confounding effects of demographics. We identify that FC-based prediction tasks are highly influenced by demographic confounds.

Gang Qu, Anton Orlichenko, Junqi Wang et al.

Functional connectivity (FC) as derived from fMRI has emerged as a pivotal tool in elucidating the intricacies of various psychiatric disorders and delineating the neural pathways that underpin cognitive and behavioral dynamics inherent to the human brain. While Graph Neural Networks (GNNs) offer a structured approach to represent neuroimaging data, they are limited by their need for a predefined graph structure to depict associations between brain regions, a detail not solely provided by FCs. To bridge this gap, we introduce the Gated Graph Transformer (GGT) framework, designed to predict cognitive metrics based on FCs. Empirical validation on the Philadelphia Neurodevelopmental Cohort (PNC) underscores the superior predictive prowess of our model, further accentuating its potential in identifying pivotal neural connectivities that correlate with human cognitive processes.

Gang Qu, Li Xiao, Wenxing Hu et al.

Objective: Multi-modal functional magnetic resonance imaging (fMRI) can be used to make predictions about individual behavioral and cognitive traits based on brain connectivity networks. Methods: To take advantage of complementary information from multi-modal fMRI, we propose an interpretable multi-modal graph convolutional network (MGCN) model, incorporating the fMRI time series and the functional connectivity (FC) between each pair of brain regions. Specifically, our model learns a graph embedding from individual brain networks derived from multi-modal data. A manifold-based regularization term is then enforced to consider the relationships of subjects both within and between modalities. Furthermore, we propose the gradient-weighted regression activation mapping (Grad-RAM) and the edge mask learning to interpret the model, which is used to identify significant cognition-related biomarkers. Results: We validate our MGCN model on the Philadelphia Neurodevelopmental Cohort to predict individual wide range achievement test (WRAT) score. Our model obtains superior predictive performance over GCN with a single modality and other competing approaches. The identified biomarkers are cross-validated from different approaches. Conclusion and Significance: This paper develops a new interpretable graph deep learning framework for cognitive ability prediction, with the potential to overcome the limitations of several current data-fusion models. The results demonstrate the power of MGCN in analyzing multi-modal fMRI and discovering significant biomarkers for human brain studies.

Li Xiao, Biao Cai, Gang Qu et al.

Resting-state functional magnetic resonance imaging (rs-fMRI)-derived functional connectivity patterns have been extensively utilized to delineate global functional organization of the human brain in health, development, and neuropsychiatric disorders. In this paper, we investigate how functional connectivity in males and females differs in an age prediction framework. We first estimate functional connectivity between regions-of-interest (ROIs) using distance correlation instead of Pearson's correlation. Distance correlation, as a multivariate statistical method, explores spatial relations of voxel-wise time courses within individual ROIs and measures both linear and nonlinear dependence, capturing more complex information of between-ROI interactions. Then, a novel non-convex multi-task learning (NC-MTL) model is proposed to study age-related gender differences in functional connectivity, where age prediction for each gender group is viewed as one task. Specifically, in the proposed NC-MTL model, we introduce a composite regularizer with a combination of non-convex $\ell_{2,1-2}$ and $\ell_{1-2}$ regularization terms for selecting both common and task-specific features. Finally, we validate the proposed NC-MTL model along with distance correlation based functional connectivity on rs-fMRI of the Philadelphia Neurodevelopmental Cohort for predicting ages of both genders. The experimental results demonstrate that the proposed NC-MTL model outperforms other competing MTL models in age prediction, as well as characterizing developmental gender differences in functional connectivity patterns.