Tingting Dan

AAAI Conference 2026 Conference Paper

Large Connectome Model: An fMRI Foundation Model of Brain Connectomes Empowered by Brain-Environment Interaction in Multitask Learning Landscape

• Ziquan Wei
• Tingting Dan
• Guorong Wu

A reliable foundation model of functional neuroimages is critical to promote clinical applications where the performance of current AI models is significantly impeded by a limited sample size. To that end, tremendous efforts have been made to pretraining large models on extensive unlabeled fMRI data using scalable self-supervised learning. Since self-supervision is not necessarily aligned with the brain-to-outcome relationship, most foundation models are suboptimal to the downstream task, such as predicting disease outcomes. By capitalizing on rich environmental variables and demographic data along with an unprecedented amount of functional neuroimages, we form the brain modeling as a multitask learning and present a scalable model architecture for (i) multitask pretraining by tokenizing multiple brain-environment interactions (BEI) and (ii) semi-supervised finetuning by assigning pseudo-labels of default BEI. We have evaluated our foundation model on a variety of applications, including sex prediction, human behavior recognition, and disease early diagnosis of Autism, Parkinson's disease, Alzheimer's disease, and Schizophrenia, where promising results indicate the great potential to facilitate current neuroimaging applications in clinical routines.

AAAI Conference 2026 Conference Paper

SyncBrain: Exploring Brain Functional Dynamics Through Neural Oscillatory Synchronization

• Jiaqi Ding
• Tingting Dan
• Zhixuan Zhou
• Guorong Wu

Neural coupling is a fundamental mechanism in neuroscience that facilitates the emergence of cognitive functions through dynamic interactions and synchronization among distributed brain regions. Inspired by this principle, we pose the question: Might the biological mechanism of neural oscillatory synchronization inspire the feature representation learning for neuroscience? By addressing this question through the Kuramoto model, renowned for simulating oscillatory dynamics, we present a novel physics-informed deep model, `SyncBrain`, it models brain regions as interacting oscillatory units and simulates their temporal dynamics and synchronization patterns to distinguish cognitive states. Furthermore, inspired by the brain's inherent ability to dynamically attend to critical temporal information, we incorporate an adaptive control module that introduces an attention-like mechanism to guide information flow. We evaluate our model on multiple functional neuroimaging datasets, it demonstrates promising performance and enhanced interpretability in both cognitive state decoding and early disease diagnosis, outperforming existing computational methods. These results demonstrate the effectiveness of neural oscillatory mechanisms in shaping robust and interpretable machine learning models for neuroscience applications.

NeurIPS Conference 2025 Conference Paper

BrainFlow: A Holistic Pathway of Dynamic Neural System on Manifold

• Zhixuan Zhou
• Tingting Dan
• Guorong Wu

A fundamental challenge in cognitive neuroscience is understanding how cognition emerges from the interplay between structural connectivity (SC) and dynamic functional connectivity (FC) in the brain. Network neuroscience has emerged as a powerful framework to understand brain function through a holistic perspective on structure-function relationships. In this context, current machine learning approaches typically seek to establish direct mappings between structural connectivity (SC) and functional connectivity (FC) associated with specific cognitive states. However, these state-independent methods often yield inconsistent results due to overlapping brain networks across cognitive states. To address this limitation, we conceptualize to uncover the dendritic coupling mechanism between one static SC and multiple FCs by solving a flow problem that bridges the distribution of SC to a mixed distribution of FCs, conditioned on various cognitive states, along a Riemannian manifold of symmetric positive-definite (SPD) manifold. We further prove the equivalence between flow matching on the SPD manifold and on the computationally efficient Cholesky manifold. Since a spare of functional connections is shared across cognitive states, we introduce the notion of consensus control to promote the shared kinetic structures between multiple FC-to-SC pathways via synchronized coordination, yielding a biologically meaningful underpinning on SC-FC coupling mechanism. Together, we present BrainFlow, a reversible generative model that achieves state-of-the-art performance on not only synthetic data but also large-scale neuroimaging datasets from UK Biobank and Human Connectome Project.

NeurIPS Conference 2025 Conference Paper

BrainMoE: Cognition Joint Embedding via Mixture-of-Expert Towards Robust Brain Foundation Model

• Ziquan Wei
• Tingting Dan
• Tianlong Chen
• Guorong Wu

Given the large scale of public functional Magnetic Resonance Imaging (fMRI), e. g. , UK Biobank (UKB) and Human Connectome Projects (HCP), brain foundation models are emerging. Although the amount of samples under rich environmental variables is unprecedented, existing brain foundation models learn from fMRI derived from a narrow range of cognitive states stimulated by similar environments, causing the limited robustness demonstrated in various applications and datasets acquired with different pipelines and limited sample size. By capitalizing on the variety of cognitive status as subjects performing explicit tasks, we present the mixture of brain experts, namely BrainMoE, pre-training on tasking fMRI with rich behavioral tasks in addition to resting fMRI for a robust brain foundation model. Brain experts are designed to produce embeddings for different behavioral tasks related to cognition. Afterward, these cognition embeddings are mixed by a cognition adapter via cross-attention so that BrainMoE can handle orthogonal embeddings and be robust on those boutique downstream datasets. We have pre-trained two existing self-regressive architectures and one new supervised architecture as brain experts on 68, 251 fMRI scans among UKB and HCP, containing 12 different cognitive states. Then, BrainMoE is evaluated on a variety of applications, including sex, age prediction, human behavior recognition, disease early diagnosis of Autism, Parkinson's disease, Alzheimer's disease, and Schizophrenia, and fMRI-EEG multimodal applications, where promising results in eight datasets from three different pipelines indicate great potential to facilitate current neuroimaging applications in clinical routines.

ICLR Conference 2025 Conference Paper

Conditional Diffusion with Ordinal Regression: Longitudinal Data Generation for Neurodegenerative Disease Studies

• Hyuna Cho
• Ziquan Wei
• Seungjoo Lee
• Tingting Dan
• Guorong Wu 0001
• Won Hwa Kim

Modeling the progression of neurodegenerative diseases such as Alzheimer’s disease (AD) is crucial for early detection and prevention given their irreversible nature. However, the scarcity of longitudinal data and complex disease dynamics make the analysis highly challenging. Moreover, longitudinal samples often contain irregular and large intervals between subject visits, which underscore the necessity for advanced data generation techniques that can accurately simulate disease progression over time. In this regime, we propose a novel conditional generative model for synthesizing longitudinal sequences and present its application to neurodegenerative disease data generation conditioned on multiple time-dependent ordinal factors, such as age and disease severity. Our method sequentially generates continuous data by bridging gaps between sparse data points with a diffusion model, ensuring a realistic representation of disease progression. The synthetic data are curated to integrate both cohort-level and individual-specific characteristics, where the cohort-level representations are modeled with an ordinal regression to capture longitudinally monotonic behavior. Extensive experiments on four AD biomarkers validate the superiority of our method over nine baseline approaches, highlighting its potential to be applied to a variety of longitudinal data generation.

NeurIPS Conference 2025 Conference Paper

Explore In-Context Message Passing Operator for Graph Neural Networks in A Mean Field Game

• Tingting Dan
• Xinwei Huang
• Won Hwa Kim
• Guorong Wu

In typical graph neural networks (GNNs), feature representation learning naturally evolves through iteratively updating node features and exchanging information based on graph topology. In this context, we conceptualize that the learning process in GNNs is a mean-field game (MFG), where each graph node is an agent, interacting with its topologically connected neighbors. However, current GNNs often employ the identical MFG strategy across different graph datasets, regardless of whether the graph exhibits homophilic or heterophilic characteristics. To address this challenge, we propose to formulate the learning mechanism into a variational framework of the MFG inverse problem, introducing an in-context selective message passing paradigm for each agent, which promotes the best overall outcome for the graph. Specifically, we seek for the application-adaptive transportation function (controlling information exchange throughout the graph) and reaction function (controlling feature representation learning on each agent), \textit{on the fly}, which allows us to uncover the most suitable selective mechanism of message passing by solving an MFG variational problem through the lens of Hamiltonian flows. Taken together, our variational framework unifies existing GNN models into various mean-field games with distinct equilibrium states, each characterized by the learned in-context message passing operators. Furthermore, we present an agnostic end-to-end deep model, coined \textit{Game-of-GNN}, to jointly identify the message passing mechanism and fine-tune the GNN hyper-parameters on top of the elucidated message passing operators. \textit{Game-of-GNN} has achieved SOTA performance on diverse graph data, including popular benchmark datasets and human connectomes. More importantly, the mathematical insight of MFG framework provides a new window to understand the foundational principles of graph learning as an interactive dynamical system, which allows us to reshape the idea of designing next-generation GNN models.

NeurIPS Conference 2025 Conference Paper

GeoDynamics: A Geometric State‑Space Neural Network for Understanding Brain Dynamics on Riemannian Manifolds

• Tingting Dan
• Jiaqi Ding
• Guorong Wu

State‑space models (SSMs) have become a cornerstone for unraveling brain dynamics, capturing how latent neural states evolve over time and give rise to observed signals. By combining deep learning’s flexibility with SSMs’ principled dynamical structure, recent studies have achieved powerful fits to functional neuroimaging data. However, most approaches still view the brain as a set of loosely connected regions or impose oversimplified network priors, falling short of a truly holistic, self‐organized dynamical system perspective. Brain functional connectivity (FC) at each time point naturally forms a symmetric positive definite (SPD) matrix, which lives on a curved Riemannian manifold rather than in Euclidean space. Capturing the trajectories of these SPD matrices is key to understanding how coordinated networks support cognition and behavior. To this end, we introduce GeoDynamics, a geometric state space neural network that tracks latent brain state trajectories directly on the high‑dimensional SPD manifold. GeoDynamics embeds each connectivity matrix into a manifold‑aware recurrent framework, learning smooth, geometry‑respecting transitions that reveal task‐driven state changes and early markers of Alzheimer’s, Parkinson’s, and autism. Beyond neuroscience, we validate GeoDynamics on human action recognition benchmarks (UTKinect, Florence, HDM05), demonstrating its scalability and robustness in modeling complex spatiotemporal dynamics across diverse domains.

NeurIPS Conference 2025 Conference Paper

Let Brain Rhythm Shape Machine Intelligence for Connecting Dots on Graphs

• Jiaqi Ding
• Tingting Dan
• Zhixuan Zhou
• Guorong Wu

In both neuroscience and artificial intelligence (AI), it is well-established that neural “coupling” gives rise to dynamically distributed systems. These systems exhibit self-organized spatiotemporal patterns of synchronized neural oscillations, enabling the representation of abstract concepts. By capitalizing on the unprecedented amount of human neuroimaging data, we propose that advancing the theoretical understanding of rhythmic coordination in neural circuits can offer powerful design principles for the next generation of machine learning models with improved efficiency and robustness. To this end, we introduce a physics-informed deep learning framework for \underline{B}rain \underline{R}hythm \underline{I}dentification by \underline{K}uramoto and \underline{C}ontrol (coined \textit{BRICK}) to characterize the synchronization of neural oscillations that shapes the dynamics of evolving cognitive states. Recognizing that brain networks are structurally connected yet behaviorally dynamic, we further conceptualize rhythmic neural activity as an artificial dynamical system of coupled oscillators, offering a shared mechanistic bridge to brain-inspired machine intelligence. By treating each node as an oscillator interacting with its neighbors, this approach moves beyond the conventional paradigm of graph heat diffusion and establishes a new regime of representation compression through oscillatory synchronization. Empirical evaluations demonstrate that this synchronization-driven mechanism not only mitigates over-smoothing in deep GNNs but also enhances the model’s capacity for reasoning and solving complex graph-based problems.

NeurIPS Conference 2025 Conference Paper

Uncover Governing Law of Pathology Propagation Mechanism Through A Mean-Field Game

• Tingting Dan
• Zhihao Fan
• Guorong Wu

Alzheimer’s disease (AD) is marked by cognitive decline along with the widespread of tau aggregates across the brain cortex. Due to the challenges of imaging pathology spreading flows \textit{in vivo}, however, quantitative analysis on the cortical pathways of tau propagation and its interaction with the cascade of amyloid-beta (A$\beta$) plaques lags behind the experimental insights of underlying pathophysiological mechanisms. To address this challenge, we present a physics-informed neural network, empowered by mean-field theory, to uncover the biologically meaningful spreading pathways of tau aggregates between two longitudinal snapshots. Following the notion of `prion-like' mechanism in AD, we first formulate the dynamics of tau propagation as a mean-field game (MFG), where the spread of tau aggregate at each location (aka. agent) depends on the collective behavior of the surrounding agents as well as the potential field formed by amyloid burden. Given the governing equation of propagation dynamics, MFG reaches an equilibrium that allows us to model the evolution of tau aggregates as an optimal transport with the lowest cost in \textit{Wasserstein} space. By leveraging the variational primal-dual structure in MFG, we propose a \textit{Wasserstein}-1 Lagrangian generative adversarial network (GAN), in which a Lipschitz critic seeks the appropriate transport cost at the population level and a generator parameterizes the flow fields of optimal transport across individuals. Additionally, we incorporate a symbolic regression module to derive an explicit formulation capturing the A$\beta$-tau crosstalk. Experimental results on public neuroimaging datasets demonstrate that our explainable deep model not only yields precise and reliable predictions of future tau progression for unseen new subjects but also provides a new window to uncover new understanding of pathology propagation in AD through learning-based approaches.

NeurIPS Conference 2024 Conference Paper

$\textit{NeuroPath}$: A Neural Pathway Transformer for Joining the Dots of Human Connectomes

• Ziquan Wei
• Tingting Dan
• Jiaqi Ding
• Guorong Wu

Although modern imaging technologies allow us to study connectivity between two distinct brain regions $\textit{in-vivo}$, an in-depth understanding of how anatomical structure supports brain function and how spontaneous functional fluctuations emerge remarkable cognition is still elusive. Meanwhile, tremendous efforts have been made in the realm of machine learning to establish the nonlinear mapping between neuroimaging data and phenotypic traits. However, the absence of neuroscience insight in the current approaches poses significant challenges in understanding cognitive behavior from transient neural activities. To address this challenge, we put the spotlight on the coupling mechanism of structural connectivity (SC) and functional connectivity (FC) by formulating such network neuroscience question into an expressive graph representation learning problem for high-order topology. Specifically, we introduce the concept of $\textit{topological detour}$ to characterize how a ubiquitous instance of FC (direct link) is supported by neural pathways (detour) physically wired by SC, which forms a cyclic loop interacted by brain structure and function. In the clich\'e of machine learning, the multi-hop detour pathway underlying SC-FC coupling allows us to devise a novel multi-head self-attention mechanism within Transformer to capture multi-modal feature representation from paired graphs of SC and FC. Taken together, we propose a biological-inspired deep model, coined as $\textit{NeuroPath}$, to find putative connectomic feature representations from the unprecedented amount of neuroimages, which can be plugged into various downstream applications such as task recognition and disease diagnosis. We have evaluated $\textit{NeuroPath}$ on large-scale public datasets including Human Connectome Project (HCP) and UK Biobank (UKB) under different experiment settings of supervised and zero-shot learning, where the state-of-the-art performance by our $\textit{NeuroPath}$ indicates great potential in network neuroscience.

AIIM Journal 2024 Journal Article

Corrigendum to “DeepGA for automatically estimating fetal gestational age through ultrasound imaging” [Artif. Intell. Med. 135 (2023) 102453]

• Tingting Dan
• Xijie Chen
• Miao He
• Hongmei Guo
• Xiaoqin He
• Jiazhou Chen
• Jianbo Xian
• Yu Hu

ICML Conference 2024 Conference Paper

Exploring the Enigma of Neural Dynamics Through A Scattering-Transform Mixer Landscape for Riemannian Manifold

• Tingting Dan
• Ziquan Wei
• Won Hwa Kim
• Guorong Wu 0001

The human brain is a complex inter-wired system that emerges spontaneous functional fluctuations. In spite of tremendous success in the experimental neuroscience field, a system-level understanding of how brain anatomy supports various neural activities remains elusive. Capitalizing on the unprecedented amount of neuroimaging data, we present a physics-informed deep model to uncover the coupling mechanism between brain structure and function through the lens of data geometry that is rooted in the widespread wiring topology of connections between distant brain regions. Since deciphering the puzzle of self-organized patterns in functional fluctuations is the gateway to understanding the emergence of cognition and behavior, we devise a geometric deep model to uncover manifold mapping functions that characterize the intrinsic feature representations of evolving functional fluctuations on the Riemannian manifold. In lieu of learning unconstrained mapping functions, we introduce a set of graph-harmonic scattering transforms to impose the brain-wide geometry on top of manifold mapping functions, which allows us to cast the manifold-based deep learning into a reminiscent of MLP-Mixer architecture (in computer vision) for Riemannian manifold. As a proof-of-concept approach, we explore a neural-manifold perspective to understand the relationship between (static) brain structure and (dynamic) function, challenging the prevailing notion in cognitive neuroscience by proposing that neural activities are essentially excited by brain-wide oscillation waves living on the geometry of human connectomes, instead of being confined to focal areas.

AIIM Journal 2023 Journal Article

DeepGA for automatically estimating fetal gestational age through ultrasound imaging

• Tingting Dan
• Xijie Chen
• Miao He
• Hongmei Guo
• Xiaoqin He
• Jiazhou Chen
• Jianbo Xian
• Yu Hu

NeurIPS Conference 2023 Conference Paper

Re-Think and Re-Design Graph Neural Networks in Spaces of Continuous Graph Diffusion Functionals

• Tingting Dan
• Jiaqi Ding
• Ziquan Wei
• Shahar Kovalsky
• Minjeong Kim
• Won Hwa Kim
• Guorong Wu

Graphs are ubiquitous in various domains, such as social networks and biological systems. Despite the great successes of graph neural networks (GNNs) in modeling and analyzing complex graph data, the inductive bias of locality assumption, which involves exchanging information only within neighboring connected nodes, restricts GNNs in capturing long-range dependencies and global patterns in graphs. Inspired by the classic Brachistochrone problem, we seek how to devise a new inductive bias for cutting-edge graph application and present a general framework through the lens of variational analysis. The backbone of our framework is a two-way mapping between the discrete GNN model and continuous diffusion functional, which allows us to design application-specific objective function in the continuous domain and engineer discrete deep model with mathematical guarantees. First, we address over-smoothing in current GNNs. Specifically, our inference reveals that the existing layer-by-layer models of graph embedding learning are equivalent to a ${\ell _2}$-norm integral functional of graph gradients, which is the underlying cause of the over-smoothing problem. Similar to edge-preserving filters in image denoising, we introduce the total variation (TV) to promote alignment of the graph diffusion pattern with the global information present in community topologies. On top of this, we devise a new selective mechanism for inductive bias that can be easily integrated into existing GNNs and effectively address the trade-off between model depth and over-smoothing. Second, we devise a novel generative adversarial network (GAN) to predict the spreading flows in the graph through a neural transport equation. To avoid the potential issue of vanishing flows, we tailor the objective function to minimize the transportation within each community while maximizing the inter-community flows. Our new GNN models achieve state-of-the-art (SOTA) performance on graph learning benchmarks such as Cora, Citeseer, and Pubmed.

AAAI Conference 2021 Conference Paper

Savable but Lost Lives when ICU Is Overloaded: a Model from 733 Patients in Epicenter Wuhan, China

• Tingting Dan
• Yang Li
• Ziwei Zhu
• Xijie Chen
• Wuxiu Quan
• Yu Hu
• Guihua Tao
• Lei Zhu

Coronavirus Disease 2019 (COVID-19) causes a sudden turnover to bad at some checkpoints and thus needs the intervention of intensive care unit (ICU). This resulted in urgent and large needs of ICUs posed great risks to the medical system. Estimating the mortality of critical in-patients who were not admitted into the ICU will be valuable to optimize the management and assignment of ICU. Retrospective, 733 in-patients diagnosed with COVID-19 at a local hospital (Wuhan, China), as of March 18, 2020. Demographic, clinical and laboratory results were collected and analyzed using machine learning to build a predictive model. Considering the shortage of ICU beds at the beginning of disease emergence, we defined the mortality for those patients who were predicted to be in needing ICU care yet they did not as Missing-ICU (MI)-mortality. To estimate MI-mortality, a prognostic classification model was built to identify the in-patients who may need ICU care. Its predictive accuracy was 0. 8288, with an AUC of 0. 9119. On our cohort of 733 patients, 25 in-patients who have been predicted by our model that they should need ICU, yet they did not enter ICU due to lack of shorting ICU wards. Our analysis had shown that the MI-mortality is 41%, yet the mortality of ICU is 32%, implying that enough bed of ICU in treating patients in critical conditions.