arXiv subjects

Dajiang Zhu

Publications and source records attributed to Dajiang Zhu.

At least 37 records · Page 2Linked to original sources

arXiv2025

Bridging Brain Connectomes and Clinical Reports for Early Alzheimer's Disease Diagnosis

Integrating brain imaging data with clinical reports offers a valuable opportunity to leverage complementary multimodal information for more effective and timely diagnosis in practical clinical settings. This approach has gained significant attention in brain disorder research, yet a key challenge remains: how to effectively link objective imaging data with subjective text-based reports, such as doctors' notes. In this work, we propose a novel framework that aligns brain connectomes with clinical reports in a shared cross-modal latent space at both the subject and connectome levels, thereby enhancing representation learning. The key innovation of our approach is that we treat brain subnetworks as tokens of imaging data, rather than raw image patches, to align with word tokens in clinical reports. This enables a more efficient identification of system-level associations between neuroimaging findings and clinical observations, which is critical since brain disorders often manifest as network-level abnormalities rather than isolated regional alterations. We applied our method to mild cognitive impairment (MCI) using the ADNI dataset. Our approach not only achieves state-of-the-art predictive performance but also identifies clinically meaningful connectome-text pairs, offering new insights into the early mechanisms of Alzheimer's disease and supporting the development of clinically useful multimodal biomarkers.

cs.CV↗

arXiv2025

Alignment and Safety in Large Language Models: Safety Mechanisms, Training Paradigms, and Emerging Challenges

Due to the remarkable capabilities and growing impact of large language models (LLMs), they have been deeply integrated into many aspects of society. Thus, ensuring their alignment with human values and intentions has emerged as a critical challenge. This survey provides a comprehensive overview of practical alignment techniques, training protocols, and empirical findings in LLM alignment. We analyze the development of alignment methods across diverse paradigms, characterizing the fundamental trade-offs between core alignment objectives. Our analysis shows that while supervised fine-tuning enables basic instruction-following, preference-based methods offer more flexibility for aligning with nuanced human intent. We discuss state-of-the-art techniques, including Direct Preference Optimization (DPO), Constitutional AI, brain-inspired methods, and alignment uncertainty quantification (AUQ), highlighting their approaches to balancing quality and efficiency. We review existing evaluation frameworks and benchmarking datasets, emphasizing limitations such as reward misspecification, distributional robustness, and scalable oversight. We summarize strategies adopted by leading AI labs to illustrate the current state of practice. We conclude by outlining open problems in oversight, value pluralism, robustness, and continuous alignment. This survey aims to inform both researchers and practitioners navigating the evolving landscape of LLM alignment.

cs.AI↗

arXiv2025

Domain-Adaptive Diagnosis of Lewy Body Disease with Transferability Aware Transformer

Lewy Body Disease (LBD) is a common yet understudied form of dementia that imposes a significant burden on public health. It shares clinical similarities with Alzheimer's disease (AD), as both progress through stages of normal cognition, mild cognitive impairment, and dementia. A major obstacle in LBD diagnosis is data scarcity, which limits the effectiveness of deep learning. In contrast, AD datasets are more abundant, offering potential for knowledge transfer. However, LBD and AD data are typically collected from different sites using different machines and protocols, resulting in a distinct domain shift. To effectively leverage AD data while mitigating domain shift, we propose a Transferability Aware Transformer (TAT) that adapts knowledge from AD to enhance LBD diagnosis. Our method utilizes structural connectivity (SC) derived from structural MRI as training data. Built on the attention mechanism, TAT adaptively assigns greater weights to disease-transferable features while suppressing domain-specific ones, thereby reducing domain shift and improving diagnostic accuracy with limited LBD data. The experimental results demonstrate the effectiveness of TAT. To the best of our knowledge, this is the first study to explore domain adaptation from AD to LBD under conditions of data scarcity and domain shift, providing a promising framework for domain-adaptive diagnosis of rare diseases.

cs.LG↗

arXiv2025

MolQAE: Quantum Autoencoder for Molecular Representation Learning

We introduce Quantum Molecular Autoencoder (MolQAE), the first quantum autoencoder to leverage the complete molecular structures. MolQAE uniquely maps SMILES strings directly to quantum states using parameterized rotation gates, preserving vital structural information. Its quantum encoder-decoder framework enables latent space compression and reconstruction. A dual-objective strategy optimizes fidelity and minimizes trash state deviation. Our evaluations demonstrate effective capture of molecular characteristics and a remarkable preservation of fidelity, approaching robust molecular reconstruction even with substantial dimensionality reduction. Our model establishes a quantum pathway in cheminformatics by being the first to process complete molecular structural information with a dedicated quantum architecture considering the Noisy Intermediate-Scale Quantum (NISQ)-era development and promising significant advances in drug and materials discovery.

quant-ph↗

arXiv2025

Mechanical Characterization of Brain Tissue: Experimental Techniques, Human Testing Considerations, and Perspectives

Understanding the mechanical behavior of brain tissue is crucial for advancing both fundamental neuroscience and clinical applications. Yet, accurately measuring these properties remains challenging due to the brain unique mechanical attributes and complex anatomical structures. This review provides a comprehensive overview of commonly used techniques for characterizing brain tissue mechanical properties, covering both invasive methods such as atomic force microscopy, indentation, axial mechanical testing, and oscillatory shear testing and noninvasive approaches like magnetic resonance elastography and ultrasound elastography. Each technique is evaluated in terms of working principles, applicability, representative studies, and experimental limitations. We further summarize existing publications that have used these techniques to measure human brain tissue mechanical properties. With a primary focus on invasive studies, we systematically compare their sample preparation, testing conditions, reported mechanical parameters, and modeling strategies. Key sensitivity factors influencing testing outcomes (e.g., sample size, anatomical location, strain rate, temperature, conditioning, and post-mortem interval) are also discussed. Additionally, selected noninvasive studies are reviewed to assess their potential for in vivo characterization. A comparative discussion between invasive and noninvasive methods, as well as in vivo versus ex vivo testing, is included. This review aims to offer practical guidance for researchers and clinicians in selecting appropriate mechanical testing approaches and contributes a curated dataset to support constitutive modeling of human brain tissue.

physics.med-ph↗

arXiv2025

AD-GPT: Large Language Models in Alzheimer's Disease

Large language models (LLMs) have emerged as powerful tools for medical information retrieval, yet their accuracy and depth remain limited in specialized domains such as Alzheimer's disease (AD), a growing global health challenge. To address this gap, we introduce AD-GPT, a domain-specific generative pre-trained transformer designed to enhance the retrieval and analysis of AD-related genetic and neurobiological information. AD-GPT integrates diverse biomedical data sources, including potential AD-associated genes, molecular genetic information, and key gene variants linked to brain regions. We develop a stacked LLM architecture combining Llama3 and BERT, optimized for four critical tasks in AD research: (1) genetic information retrieval, (2) gene-brain region relationship assessment, (3) gene-AD relationship analysis, and (4) brain region-AD relationship mapping. Comparative evaluations against state-of-the-art LLMs demonstrate AD-GPT's superior precision and reliability across these tasks, underscoring its potential as a robust and specialized AI tool for advancing AD research and biomarker discovery.

cs.CL↗

arXiv2025

GyralNet Subnetwork Partitioning via Differentiable Spectral Modularity Optimization

Understanding the structural and functional organization of the human brain requires a detailed examination of cortical folding patterns, among which the three-hinge gyrus (3HG) has been identified as a key structural landmark. GyralNet, a network representation of cortical folding, models 3HGs as nodes and gyral crests as edges, highlighting their role as critical hubs in cortico-cortical connectivity. However, existing methods for analyzing 3HGs face significant challenges, including the sub-voxel scale of 3HGs at typical neuroimaging resolutions, the computational complexity of establishing cross-subject correspondences, and the oversimplification of treating 3HGs as independent nodes without considering their community-level relationships. To address these limitations, we propose a fully differentiable subnetwork partitioning framework that employs a spectral modularity maximization optimization strategy to modularize the organization of 3HGs within GyralNet. By incorporating topological structural similarity and DTI-derived connectivity patterns as attribute features, our approach provides a biologically meaningful representation of cortical organization. Extensive experiments on the Human Connectome Project (HCP) dataset demonstrate that our method effectively partitions GyralNet at the individual level while preserving the community-level consistency of 3HGs across subjects, offering a robust foundation for understanding brain connectivity.

q-bio.NC↗

arXiv2025

Core-Periphery Principle Guided State Space Model for Functional Connectome Classification

Understanding the organization of human brain networks has become a central focus in neuroscience, particularly in the study of functional connectivity, which plays a crucial role in diagnosing neurological disorders. Advances in functional magnetic resonance imaging and machine learning techniques have significantly improved brain network analysis. However, traditional machine learning approaches struggle to capture the complex relationships between brain regions, while deep learning methods, particularly Transformer-based models, face computational challenges due to their quadratic complexity in long-sequence modeling. To address these limitations, we propose a Core-Periphery State-Space Model (CP-SSM), an innovative framework for functional connectome classification. Specifically, we introduce Mamba, a selective state-space model with linear complexity, to effectively capture long-range dependencies in functional brain networks. Furthermore, inspired by the core-periphery (CP) organization, a fundamental characteristic of brain networks that enhances efficient information transmission, we design CP-MoE, a CP-guided Mixture-of-Experts that improves the representation learning of brain connectivity patterns. We evaluate CP-SSM on two benchmark fMRI datasets: ABIDE and ADNI. Experimental results demonstrate that CP-SSM surpasses Transformer-based models in classification performance while significantly reducing computational complexity. These findings highlight the effectiveness and efficiency of CP-SSM in modeling brain functional connectivity, offering a promising direction for neuroimaging-based neurological disease diagnosis.

q-bio.NC↗

arXiv2025

BrainNet-MoE: Brain-Inspired Mixture-of-Experts Learning for Neurological Disease Identification

The Lewy body dementia (LBD) is the second most common neurodegenerative dementia after Alzheimer's disease (AD). Early differentiation between AD and LBD is crucial because they require different treatment approaches, but this is challenging due to significant clinical overlap, heterogeneity, complex pathogenesis, and the rarity of LBD. While recent advances in artificial intelligence (AI) demonstrate powerful learning capabilities and offer new hope for accurate diagnosis, existing methods primarily focus on designing "neural-level networks". Our work represents a pioneering effort in modeling system-level artificial neural network called BrainNet-MoE for brain modeling and diagnosing. Inspired by the brain's hierarchical organization of bottom-up sensory integration and top-down control, we design a set of disease-specific expert groups to process brain sub-network under different condition, A disease gate mechanism guides the specializa-tion of expert groups, while a transformer layer enables communication be-tween all sub-networks, generating a comprehensive whole-brain represen-tation for downstream disease classification. Experimental results show superior classification accuracy with interpretable insights into how brain sub-networks contribute to different neurodegenerative conditions.

cs.LG↗

arXiv2025

Using Structural Similarity and Kolmogorov-Arnold Networks for Anatomical Embedding of Cortical Folding Patterns

The 3-hinge gyrus (3HG) is a newly defined folding pattern, which is the conjunction of gyri coming from three directions in cortical folding. Many studies demonstrated that 3HGs can be reliable nodes when constructing brain networks or connectome since they simultaneously possess commonality and individuality across different individual brains and populations. However, 3HGs are identified and validated within individual spaces, making it difficult to directly serve as the brain network nodes due to the absence of cross-subject correspondence. The 3HG correspondences represent the intrinsic regulation of brain organizational architecture, traditional image-based registration methods tend to fail because individual anatomical properties need to be fully respected. To address this challenge, we propose a novel self-supervised framework for anatomical feature embedding of the 3HGs to build the correspondences among different brains. The core component of this framework is to construct a structural similarity-enhanced multi-hop feature encoding strategy based on the recently developed Kolmogorov-Arnold network (KAN) for anatomical feature embedding. Extensive experiments suggest that our approach can effectively establish robust cross-subject correspondences when no one-to-one mapping exists.

cs.CV↗

arXiv2025

Classification of Mild Cognitive Impairment Based on Dynamic Functional Connectivity Using Spatio-Temporal Transformer

Dynamic functional connectivity (dFC) using resting-state functional magnetic resonance imaging (rs-fMRI) is an advanced technique for capturing the dynamic changes of neural activities, and can be very useful in the studies of brain diseases such as Alzheimer's disease (AD). Yet, existing studies have not fully leveraged the sequential information embedded within dFC that can potentially provide valuable information when identifying brain conditions. In this paper, we propose a novel framework that jointly learns the embedding of both spatial and temporal information within dFC based on the transformer architecture. Specifically, we first construct dFC networks from rs-fMRI data through a sliding window strategy. Then, we simultaneously employ a temporal block and a spatial block to capture higher-order representations of dynamic spatio-temporal dependencies, via mapping them into an efficient fused feature representation. To further enhance the robustness of these feature representations by reducing the dependency on labeled data, we also introduce a contrastive learning strategy to manipulate different brain states. Experimental results on 345 subjects with 570 scans from the Alzheimer's Disease Neuroimaging Initiative (ADNI) demonstrate the superiority of our proposed method for MCI (Mild Cognitive Impairment, the prodromal stage of AD) prediction, highlighting its potential for early identification of AD.

eess.IV↗

arXiv2025

Brain-Adapter: Enhancing Neurological Disorder Analysis with Adapter-Tuning Multimodal Large Language Models

Understanding brain disorders is crucial for accurate clinical diagnosis and treatment. Recent advances in Multimodal Large Language Models (MLLMs) offer a promising approach to interpreting medical images with the support of text descriptions. However, previous research has primarily focused on 2D medical images, leaving richer spatial information of 3D images under-explored, and single-modality-based methods are limited by overlooking the critical clinical information contained in other modalities. To address this issue, this paper proposes Brain-Adapter, a novel approach that incorporates an extra bottleneck layer to learn new knowledge and instill it into the original pre-trained knowledge. The major idea is to incorporate a lightweight bottleneck layer to train fewer parameters while capturing essential information and utilize a Contrastive Language-Image Pre-training (CLIP) strategy to align multimodal data within a unified representation space. Extensive experiments demonstrated the effectiveness of our approach in integrating multimodal data to significantly improve the diagnosis accuracy without high computational costs, highlighting the potential to enhance real-world diagnostic workflows.

eess.IV↗

arXiv2025

Large Language Models for Bioinformatics

With the rapid advancements in large language model (LLM) technology and the emergence of bioinformatics-specific language models (BioLMs), there is a growing need for a comprehensive analysis of the current landscape, computational characteristics, and diverse applications. This survey aims to address this need by providing a thorough review of BioLMs, focusing on their evolution, classification, and distinguishing features, alongside a detailed examination of training methodologies, datasets, and evaluation frameworks. We explore the wide-ranging applications of BioLMs in critical areas such as disease diagnosis, drug discovery, and vaccine development, highlighting their impact and transformative potential in bioinformatics. We identify key challenges and limitations inherent in BioLMs, including data privacy and security concerns, interpretability issues, biases in training data and model outputs, and domain adaptation complexities. Finally, we highlight emerging trends and future directions, offering valuable insights to guide researchers and clinicians toward advancing BioLMs for increasingly sophisticated biological and clinical applications.

q-bio.QM↗

arXiv2024

Analyzing Nobel Prize Literature with Large Language Models

This study examines the capabilities of advanced Large Language Models (LLMs), particularly the o1 model, in the context of literary analysis. The outputs of these models are compared directly to those produced by graduate-level human participants. By focusing on two Nobel Prize-winning short stories, 'Nine Chapters' by Han Kang, the 2024 laureate, and 'Friendship' by Jon Fosse, the 2023 laureate, the research explores the extent to which AI can engage with complex literary elements such as thematic analysis, intertextuality, cultural and historical contexts, linguistic and structural innovations, and character development. Given the Nobel Prize's prestige and its emphasis on cultural, historical, and linguistic richness, applying LLMs to these works provides a deeper understanding of both human and AI approaches to interpretation. The study uses qualitative and quantitative evaluations of coherence, creativity, and fidelity to the text, revealing the strengths and limitations of AI in tasks typically reserved for human expertise. While LLMs demonstrate strong analytical capabilities, particularly in structured tasks, they often fall short in emotional nuance and coherence, areas where human interpretation excels. This research underscores the potential for human-AI collaboration in the humanities, opening new opportunities in literary studies and beyond.

cs.CL↗

arXiv2024

Artificial General Intelligence for Medical Imaging Analysis

Large-scale Artificial General Intelligence (AGI) models, including Large Language Models (LLMs) such as ChatGPT/GPT-4, have achieved unprecedented success in a variety of general domain tasks. Yet, when applied directly to specialized domains like medical imaging, which require in-depth expertise, these models face notable challenges arising from the medical field's inherent complexities and unique characteristics. In this review, we delve into the potential applications of AGI models in medical imaging and healthcare, with a primary focus on LLMs, Large Vision Models, and Large Multimodal Models. We provide a thorough overview of the key features and enabling techniques of LLMs and AGI, and further examine the roadmaps guiding the evolution and implementation of AGI models in the medical sector, summarizing their present applications, potentialities, and associated challenges. In addition, we highlight potential future research directions, offering a holistic view on upcoming ventures. This comprehensive review aims to offer insights into the future implications of AGI in medical imaging, healthcare, and beyond.

cs.AI↗

arXiv2024

Towards Next-Generation Medical Agent: How o1 is Reshaping Decision-Making in Medical Scenarios

Artificial Intelligence (AI) has become essential in modern healthcare, with large language models (LLMs) offering promising advances in clinical decision-making. Traditional model-based approaches, including those leveraging in-context demonstrations and those with specialized medical fine-tuning, have demonstrated strong performance in medical language processing but struggle with real-time adaptability, multi-step reasoning, and handling complex medical tasks. Agent-based AI systems address these limitations by incorporating reasoning traces, tool selection based on context, knowledge retrieval, and both short- and long-term memory. These additional features enable the medical AI agent to handle complex medical scenarios where decision-making should be built on real-time interaction with the environment. Therefore, unlike conventional model-based approaches that treat medical queries as isolated questions, medical AI agents approach them as complex tasks and behave more like human doctors. In this paper, we study the choice of the backbone LLM for medical AI agents, which is the foundation for the agent's overall reasoning and action generation. In particular, we consider the emergent o1 model and examine its impact on agents' reasoning, tool-use adaptability, and real-time information retrieval across diverse clinical scenarios, including high-stakes settings such as intensive care units (ICUs). Our findings demonstrate o1's ability to enhance diagnostic accuracy and consistency, paving the way for smarter, more responsive AI tools that support better patient outcomes and decision-making efficacy in clinical practice.

cs.CL↗

arXiv2024

EG-SpikeFormer: Eye-Gaze Guided Transformer on Spiking Neural Networks for Medical Image Analysis

Neuromorphic computing has emerged as a promising energy-efficient alternative to traditional artificial intelligence, predominantly utilizing spiking neural networks (SNNs) implemented on neuromorphic hardware. Significant advancements have been made in SNN-based convolutional neural networks (CNNs) and Transformer architectures. However, neuromorphic computing for the medical imaging domain remains underexplored. In this study, we introduce EG-SpikeFormer, an SNN architecture tailored for clinical tasks that incorporates eye-gaze data to guide the model's attention to the diagnostically relevant regions in medical images. Our developed approach effectively addresses shortcut learning issues commonly observed in conventional models, especially in scenarios with limited clinical data and high demands for model reliability, generalizability, and transparency. Our EG-SpikeFormer not only demonstrates superior energy efficiency and performance in medical image prediction tasks but also enhances clinical relevance through multi-modal information alignment. By incorporating eye-gaze data, the model improves interpretability and generalization, opening new directions for applying neuromorphic computing in healthcare.

eess.IV↗

arXiv2024

Large Language Models for Manufacturing

The rapid advances in Large Language Models (LLMs) have the potential to transform manufacturing industry, offering new opportunities to optimize processes, improve efficiency, and drive innovation. This paper provides a comprehensive exploration of the integration of LLMs into the manufacturing domain, focusing on their potential to automate and enhance various aspects of manufacturing, from product design and development to quality control, supply chain optimization, and talent management. Through extensive evaluations across multiple manufacturing tasks, we demonstrate the remarkable capabilities of state-of-the-art LLMs, such as GPT-4V, in understanding and executing complex instructions, extracting valuable insights from vast amounts of data, and facilitating knowledge sharing. We also delve into the transformative potential of LLMs in reshaping manufacturing education, automating coding processes, enhancing robot control systems, and enabling the creation of immersive, data-rich virtual environments through the industrial metaverse. By highlighting the practical applications and emerging use cases of LLMs in manufacturing, this paper aims to provide a valuable resource for professionals, researchers, and decision-makers seeking to harness the power of these technologies to address real-world challenges, drive operational excellence, and unlock sustainable growth in an increasingly competitive landscape.

cs.AI↗