Minheng Chen

Jing Zhang, Norman Scheel, Minheng Chen et al.

Understanding how structural connections are associated with tau propagation in Alzheimer's disease (AD) remains a central open question, yet existing computational models either rely heavily on biophysical assumptions or lack neurobiologically interpretable pathway maps. We present SC-TauPath, a structural connectivity (SC) attribution framework that maps tau propagation pathways from in vivo neuroimaging data. SC-TauPath combines a Network Diffusion Model (NDM)-augmented multilayer perceptron with gradient $\times$ input attribution to score each SC edge's contribution to tau prediction, then translates these attribution scores into multi-scale pathway maps (backbone edges, high-traffic routes, and hub ROIs), which validates established Braak staging anatomy. Applied to 234 ADNI participants with paired DTI SC and 18F-Flortaucipir PET, SC-TauPath achieves strong cross-validated tau prediction and yields attribution-based pathway maps consistent with established Braak staging anatomy, demonstrating that SC encode spatially specific information about regional tau distribution in AD.

Tianyang Zhong, Zhengliang Liu, Yi Pan et al.

This comprehensive study evaluates the performance of OpenAI's o1-preview large language model across a diverse array of complex reasoning tasks, spanning multiple domains, including computer science, mathematics, natural sciences, medicine, linguistics, and social sciences. Through rigorous testing, o1-preview demonstrated remarkable capabilities, often achieving human-level or superior performance in areas ranging from coding challenges to scientific reasoning and from language processing to creative problem-solving. Key findings include: -83.3% success rate in solving complex competitive programming problems, surpassing many human experts. -Superior ability in generating coherent and accurate radiology reports, outperforming other evaluated models. -100% accuracy in high school-level mathematical reasoning tasks, providing detailed step-by-step solutions. -Advanced natural language inference capabilities across general and specialized domains like medicine. -Impressive performance in chip design tasks, outperforming specialized models in areas such as EDA script generation and bug analysis. -Remarkable proficiency in anthropology and geology, demonstrating deep understanding and reasoning in these specialized fields. -Strong capabilities in quantitative investing. O1 has comprehensive financial knowledge and statistical modeling skills. -Effective performance in social media analysis, including sentiment analysis and emotion recognition. The model excelled particularly in tasks requiring intricate reasoning and knowledge integration across various fields. While some limitations were observed, including occasional errors on simpler problems and challenges with certain highly specialized concepts, the overall results indicate significant progress towards artificial general intelligence.

Xiaowei Yu, Zhe Huang, Minheng Chen et al.

We investigate the impact of entropy change in deep learning systems by noise injection at different levels, including the embedding space and the image. The series of models that employ our methodology are collectively known as Noisy Neural Networks (NoisyNN), with examples such as NoisyViT and NoisyCNN. Noise is conventionally viewed as a harmful perturbation in various deep learning architectures, such as convolutional neural networks (CNNs) and vision transformers (ViTs), as well as different learning tasks like image classification and transfer learning. However, this work shows noise can be an effective way to change the entropy of the learning system. We demonstrate that specific noise can boost the performance of various deep models under certain conditions. We theoretically prove the enhancement gained from positive noise by reducing the task complexity defined by information entropy and experimentally show the significant performance gain in large image datasets, such as the ImageNet. Herein, we use the information entropy to define the complexity of the task. We categorize the noise into two types, positive noise (PN) and harmful noise (HN), based on whether the noise can help reduce the task complexity. Extensive experiments of CNNs and ViTs have shown performance improvements by proactively injecting positive noise, where we achieved an unprecedented top 1 accuracy of 95$\%$ on ImageNet. Both theoretical analysis and empirical evidence have confirmed that the presence of positive noise, can benefit the learning process, while the traditionally perceived harmful noise indeed impairs deep learning models. The different roles of noise offer new explanations for deep models on specific tasks and provide a new paradigm for improving model performance. Moreover, it reminds us that we can influence the performance of learning systems via information entropy change.

Minheng Chen, Jing Zhang, Tong Chen et al.

Alzheimer's disease (AD) and Lewy body dementia (LBD) present overlapping clinical features yet require distinct diagnostic strategies. While neuroimaging-based brain network analysis is promising, atlas-based representations may obscure individualized anatomy. Gyral folding-based networks using three-hinge gyri provide a biologically grounded alternative, but inter-individual variability in cortical folding results in inconsistent landmark correspondence and highly irregular network sizes, violating the fixed-topology and node-alignment assumptions of most existing graph learning methods, particularly in clinical datasets where pathological changes further amplify anatomical heterogeneity. We therefore propose a probability-invariant random-walk-based framework that classifies individualized gyral folding networks without explicit node alignment. Cortical similarity networks are built from local morphometric features and represented by distributions of anonymized random walks, with an anatomy-aware encoding that preserves permutation invariance. Experiments on a large clinical cohort of AD and LBD subjects show consistent improvements over existing gyral folding and atlas-based models, demonstrating robustness and potential for dementia diagnosis.

Minheng Chen, Zhirun Zhang, Shuheng Gu et al.

We present a novel deep learning-based framework: Embedded Feature Similarity Optimization with Specific Parameter Initialization (SOPI) for 2D/3D medical image registration which is a most challenging problem due to the difficulty such as dimensional mismatch, heavy computation load and lack of golden evaluation standard. The framework we design includes a parameter specification module to efficiently choose initialization pose parameter and a fine-registration module to align images. The proposed framework takes extracting multi-scale features into consideration using a novel composite connection encoder with special training techniques. We compare the method with both learning-based methods and optimization-based methods on a in-house CT/X-ray dataset as well as simulated data to further evaluate performance. Our experiments demonstrate that the method in this paper has improved the registration performance, and thereby outperforms the existing methods in terms of accuracy and running time. We also show the potential of the proposed method as an initial pose estimator. The code is available at https://github.com/m1nhengChen/SOPI

Minheng Chen, Chao Cao, Jing Zhang et al.

Functional connectivity (FC) derived from resting-state fMRI is widely used to characterize large-scale brain network alterations in neurological and psychiatric disorders. However, FC construction critically depends on the choice of brain atlas, and different parcellations may emphasize distinct organizational features, leading to heterogeneous and sometimes inconsistent representations. Existing multi-atlas approaches partially alleviate this issue but often fuse atlas-derived features or predictions at a relatively shallow level, while single-atlas disentanglement methods do not explicitly address cross-atlas heterogeneity. We propose Multi-Atlas Disentangled Connectivity LEarning (MADCLE), a multi-branch representation learning framework that jointly encodes FC matrices derived from different brain atlases. Rather than introducing a single explicitly shared latent variable across parcellations, MADCLE learns atlas-wise disease-related representations and encourages them to be cross-atlas consistent through distributional alignment. Meanwhile, covariate-related and atlas-dependent residual factors are modeled separately using covariate similarity supervision, atlas-specific reconstruction, and decorrelation constraints, thereby reducing the leakage of non-disease and parcellation-dependent information into the disease-related embeddings. Experiments on the ADNI and ADHD-200 datasets suggest that MADCLE achieves competitive or improved performance compared with single-atlas baselines, multi-atlas GNN/Transformer models, and recent multi-atlas consistency frameworks. These results support the potential value of structured disentanglement for FC-based disorder identification under heterogeneous parcellation schemes.

Minheng Chen, Tonglong Li, Zhirun Zhang et al.

A robust and efficient optimization-based 2D/3D registration framework is crucial for the navigation system of orthopedic surgical robots. It can provide precise position information of surgical instruments and implants during surgery. While artificial intelligence technology has advanced rapidly in recent years, traditional optimization-based registration methods remain indispensable in the field of 2D/3D registration.he exceptional precision of this method enables it to be considered as a post-processing step of the learning-based methods, thereby offering a reliable assurance for registration. In this paper, we present a coarse-to-fine registration framework based on the CMA-ES algorithm. We conducted intensive testing of our method using data from different parts of the spine. The results shows the effectiveness of the proposed framework on real orthopedic spine surgery clinical data. This work can be viewed as an additional extension that complements the optimization-based methods employed in our previous studies.

Jing Zhang, Xiaowei Yu, Yanjun Lyu et al.

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.

Minheng Chen, Zhirun Zhang, Shuheng Gu et al.

Image-based rigid 2D/3D registration is a critical technique for fluoroscopic guided surgical interventions. In recent years, some learning-based fully differentiable methods have produced beneficial outcomes while the process of feature extraction and gradient flow transmission still lack controllability and interpretability. To alleviate these problems, in this work, we propose a novel fully differentiable correlation-driven network using a dual-branch CNN-transformer encoder which enables the network to extract and separate low-frequency global features from high-frequency local features. A correlation-driven loss is further proposed for low-frequency feature and high-frequency feature decomposition based on embedded information. Besides, a training strategy that learns to approximate a convex-shape similarity function is applied in our work. We test our approach on a in-house datasetand show that it outperforms both existing fully differentiable learning-based registration approaches and the conventional optimization-based baseline.

Sheng Zhang, Minheng Chen, Junxian Wu et al.

Vertebrae identification in arbitrary fields-of-view plays a crucial role in diagnosing spine disease. Most spine CT contain only local regions, such as the neck, chest, and abdomen. Therefore, identification should not depend on specific vertebrae or a particular number of vertebrae being visible. Existing methods at the spine-level are unable to meet this challenge. In this paper, we propose a three-stage method to address the challenges in 3D CT vertebrae identification at vertebrae-level. By sequentially performing the tasks of vertebrae localization, segmentation, and identification, the anatomical prior information of the vertebrae is effectively utilized throughout the process. Specifically, we introduce a dual-factor density clustering algorithm to acquire localization information for individual vertebra, thereby facilitating subsequent segmentation and identification processes. In addition, to tackle the issue of interclass similarity and intra-class variability, we pre-train our identification network by using a supervised contrastive learning method. To further optimize the identification results, we estimated the uncertainty of the classification network and utilized the message fusion module to combine the uncertainty scores, while aggregating global information about the spine. Our method achieves state-of-the-art results on the VerSe19 and VerSe20 challenge benchmarks. Additionally, our approach demonstrates outstanding generalization performance on an collected dataset containing a wide range of abnormal cases.

Jing Zhang, Yanjun Lyu, Xiaowei Yu et al.

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.

Minheng Chen, Xiaowei Yu, Jing Zhang et al.

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.

Minheng Chen, Tong Chen, Yan Zhuang et al.

Cortical folding exhibits substantial inter-individual variability while preserving stable anatomical landmarks that enable fine-scale characterization of cortical organization. Among these, the three-hinge gyrus (3HG) serves as a key folding primitive, showing consistent topology yet meaningful variations in morphology, connectivity, and function. Existing landmark-based methods typically model each 3HG independently, ignoring that 3HGs form higher-order folding communities that capture mesoscale structure. This simplification weakens anatomical representation and makes one-to-one matching sensitive to positional variability and noise. We propose a spectral graph representation learning framework that models community-level folding units rather than isolated landmarks. Each 3HG is encoded using a dual-profile representation combining surface topology and structural connectivity. Subject-specific spectral clustering identifies coherent folding communities, followed by topological refinement to preserve anatomical continuity. For cross-subject correspondence, we introduce Joint Morphological-Geometric Matching, jointly optimizing geometric and morphometric similarity. Across over 1000 Human Connectome Project subjects, the resulting communities show reduced morphometric variance, stronger modular organization, improved hemispheric consistency, and superior alignment compared with atlas-based and landmark-based or embedding-based baselines. These findings demonstrate that community-level modeling provides a robust and anatomically grounded framework for individualized cortical characterization and reliable cross-subject correspondence.

Xiaowei Yu, Jing Zhang, Tong Chen et al.

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.

Minheng Chen, Chao Cao, Tong Chen et al.

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.

Minheng Chen, Youyong Kong

Intraoperative 2D/3D registration aligns preoperative 3D volumes with real-time 2D radiographs, enabling accurate localization of instruments and implants. A recent fully differentiable similarity learning framework approximates geodesic distances on SE(3), expanding the capture range of registration and mitigating the effects of substantial disturbances, but existing Euclidean approximations distort manifold structure and slow convergence. To address these limitations, we explore similarity learning in non-Euclidean spherical feature spaces to better capture and fit complex manifold structure. We extract feature embeddings using a CNN-Transformer encoder, project them into spherical space, and approximate their geodesic distances with Riemannian distances in the bi-invariant SO(4) space. This enables a more expressive and geometrically consistent deep similarity metric, enhancing the ability to distinguish subtle pose differences. During inference, we replace gradient descent with fully differentiable Levenberg-Marquardt optimization to accelerate convergence. Experiments on real and synthetic datasets show superior accuracy in both patient-specific and patient-agnostic scenarios.

Jing Zhang, Xiaowei Yu, Minheng Chen et al.

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.

Yan Zhuang, Minheng Chen, Chao Cao et al.

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.