Integrated Brain Connectivity Analysis with fMRI, DTI, and sMRI Powered by Interpretable Graph Neural Networks

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.

A Demographic-Conditioned Variational Autoencoder for fMRI Distribution Sampling and Removal of Confounds

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.

Dual-Scale Transformer for Large-Scale Single-Pixel Imaging

Single-pixel imaging (SPI) is a potential computational imaging technique which produces image by solving an illposed reconstruction problem from few measurements captured by a single-pixel detector. Deep learning has achieved impressive success on SPI reconstruction. However, previous poor reconstruction performance and impractical imaging model limit its real-world applications. In this paper, we propose a deep unfolding network with hybrid-attention Transformer on Kronecker SPI model, dubbed HATNet, to improve the imaging quality of real SPI cameras. Specifically, we unfold the computation graph of the iterative shrinkagethresholding algorithm (ISTA) into two alternative modules: efficient tensor gradient descent and hybrid-attention multiscale denoising. By virtue of Kronecker SPI, the gradient descent module can avoid high computational overheads rooted in previous gradient descent modules based on vectorized SPI. The denoising module is an encoder-decoder architecture powered by dual-scale spatial attention for high- and low-frequency aggregation and channel attention for global information recalibration. Moreover, we build a SPI prototype to verify the effectiveness of the proposed method. Extensive experiments on synthetic and real data demonstrate that our method achieves the state-of-the-art performance. The source code and pre-trained models are available at https://github.com/Gang-Qu/HATNet-SPI.

An Interpretable Cross-Attentive Multi-modal MRI Fusion Framework for Schizophrenia Diagnosis

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.

LLM4SecHW: Leveraging Domain Specific Large Language Model for Hardware Debugging

This paper presents LLM4SecHW, a novel framework for hardware debugging that leverages domain specific Large Language Model (LLM). Despite the success of LLMs in automating various software development tasks, their application in the hardware security domain has been limited due to the constraints of commercial LLMs and the scarcity of domain specific data. To address these challenges, we propose a unique approach to compile a dataset of open source hardware design defects and their remediation steps, utilizing version control data. This dataset provides a substantial foundation for training machine learning models for hardware. LLM4SecHW employs fine tuning of medium sized LLMs based on this dataset, enabling the identification and rectification of bugs in hardware designs. This pioneering approach offers a reference workflow for the application of fine tuning domain specific LLMs in other research areas. We evaluate the performance of our proposed system on various open source hardware designs, demonstrating its efficacy in accurately identifying and correcting defects. Our work brings a new perspective on automating the quality control process in hardware design.

Exploring General Intelligence via Gated Graph Transformer in Functional Connectivity Studies

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.

Fooling the Eyes of Autonomous Vehicles: Robust Physical Adversarial Examples Against Traffic Sign Recognition Systems

Adversarial Examples (AEs) can deceive Deep Neural Networks (DNNs) and have received a lot of attention recently. However, majority of the research on AEs is in the digital domain and the adversarial patches are static, which is very different from many real-world DNN applications such as Traffic Sign Recognition (TSR) systems in autonomous vehicles. In TSR systems, object detectors use DNNs to process streaming video in real time. From the view of object detectors, the traffic sign`s position and quality of the video are continuously changing, rendering the digital AEs ineffective in the physical world. In this paper, we propose a systematic pipeline to generate robust physical AEs against real-world object detectors. Robustness is achieved in three ways. First, we simulate the in-vehicle cameras by extending the distribution of image transformations with the blur transformation and the resolution transformation. Second, we design the single and multiple bounding boxes filters to improve the efficiency of the perturbation training. Third, we consider four representative attack vectors, namely Hiding Attack, Appearance Attack, Non-Target Attack and Target Attack. We perform a comprehensive set of experiments under a variety of environmental conditions, and considering illuminations in sunny and cloudy weather as well as at night. The experimental results show that the physical AEs generated from our pipeline are effective and robust when attacking the YOLO v5 based TSR system. The attacks have good transferability and can deceive other state-of-the-art object detectors. We launched HA and NTA on a brand-new 2021 model vehicle. Both attacks are successful in fooling the TSR system, which could be a life-threatening case for autonomous vehicles. Finally, we discuss three defense mechanisms based on image preprocessing, AEs detection, and model enhancing.

Don't Forget to Sign the Gradients!

Engineering a top-notch deep learning model is an expensive procedure that involves collecting data, hiring human resources with expertise in machine learning, and providing high computational resources. For that reason, deep learning models are considered as valuable Intellectual Properties (IPs) of the model vendors. To ensure reliable commercialization of deep learning models, it is crucial to develop techniques to protect model vendors against IP infringements. One of such techniques that recently has shown great promise is digital watermarking. However, current watermarking approaches can embed very limited amount of information and are vulnerable against watermark removal attacks. In this paper, we present GradSigns, a novel watermarking framework for deep neural networks (DNNs). GradSigns embeds the owner's signature into the gradient of the cross-entropy cost function with respect to inputs to the model. Our approach has a negligible impact on the performance of the protected model and it allows model vendors to remotely verify the watermark through prediction APIs. We evaluate GradSigns on DNNs trained for different image classification tasks using CIFAR-10, SVHN, and YTF datasets. Experimental results show that GradSigns is robust against all known counter-watermark attacks and can embed a large amount of information into DNNs.

Meta Federated Learning

Due to its distributed methodology alongside its privacy-preserving features, Federated Learning (FL) is vulnerable to training time adversarial attacks. In this study, our focus is on backdoor attacks in which the adversary's goal is to cause targeted misclassifications for inputs embedded with an adversarial trigger while maintaining an acceptable performance on the main learning task at hand. Contemporary defenses against backdoor attacks in federated learning require direct access to each individual client's update which is not feasible in recent FL settings where Secure Aggregation is deployed. In this study, we seek to answer the following question, Is it possible to defend against backdoor attacks when secure aggregation is in place?, a question that has not been addressed by prior arts. To this end, we propose Meta Federated Learning (Meta-FL), a novel variant of federated learning which not only is compatible with secure aggregation protocol but also facilitates defense against backdoor attacks. We perform a systematic evaluation of Meta-FL on two classification datasets: SVHN and GTSRB. The results show that Meta-FL not only achieves better utility than classic FL, but also enhances the performance of contemporary defenses in terms of robustness against adversarial attacks.

Ensemble manifold based regularized multi-modal graph convolutional network for cognitive ability prediction

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.