arXiv subjects

Quanying Liu

Publications and source records attributed to Quanying Liu.

At least 19 recordsLinked to original sources

arXiv2026

BrainTaskonomy: Learning How to Pretrain and What to Transfer in fMRI Foundation Models

fMRI foundation models increasingly aggregate heterogeneous data across brain states, cohorts, and acquisition settings, yet pretraining domains are commonly treated as a flat mixture and downstream tasks are adapted independently. We study whether measured learning relations can organize both stages without modifying the backbone. During pretraining, a lightweight Brain-DiT proxy estimates difficulty and directed facilitation across ten fMRI domains, yielding a priority-guided cumulative domain curriculum combined with high-to-low-noise timestep scheduling and joint consolidation. During adaptation, controlled first- and higher-order transfer across fifteen tasks constructs a directed taskonomy, from which budgeted integer programming (BIP) selects directly supervised source tasks and target-specific routes. The joint priority-domain and high-to-low-timestep curriculum reduces v-NMSE, PSD-NMSE, and FC-MSE by 6.5%, 16.3%, and 10.5%, respectively, relative to uniform sampling over both dimensions, and shows strong downstream performance across six in- and out-of-domain tasks. The taskonomy reveals asymmetric, target-dependent transfer, while exploratory sealed-test evaluation shows larger descriptive gains for BIP policies when higher-order route spaces are available than for matched random controls. Together, these findings support organizing fMRI pretraining and adaptation by measured learning relations rather than treating domains and tasks as independent flat sets.

cs.CV↗

arXiv2026

Complexity and Stability of Neural Activity Across Aging and Neurodegenerative Disease

Objective: EEG signals fluctuate continuously even within a fixed cognitive state, but an important question is whether the brain still reuses similar activity patterns to represent information over time. Methods: To address this, we model EEG as distributions of windowed activity patterns and quantify their temporal stability using Wasserstein distance, while intrinsic dimensionality captures representational complexity. Results: Across multi-task, lifespan, and clinical EEG datasets, we find that neural representations show constrained, condition-specific stability rather than unconstrained drift. Higher intrinsic dimensionality is consistently associated with lower stability, suggesting that richer representational spaces are less reproducible over time. Both measures exhibit reproducible spatial organization, with posterior regions showing higher dimensionality and lower stability than frontal regions. Healthy aging is characterized by increased dimensionality and reduced stability, whereas mild cognitive impairment and Alzheimer's disease show a joint collapse of both. Conclusions: These findings provide a distribution-level framework for understanding neural stability across cognition, aging, and disease. Significance: This framework offers a principled approach to quantifying neural representational stability, with potential utility as a sensitive biomarker for tracking cognitive aging and neurodegeneration in clinical settings.

q-bio.NC↗

arXiv2026

Understanding and Correcting Low-Frequency Bias in EEG Foundation Model

Increasing EEG pretraining data scale or model capacity does not consistently improve downstream performance. We identify a persistent low-frequency bias in representations learned by diverse EEG foundation models, which remains across dataset scales, model capacities, and pretraining objectives. Our analysis links this bias to the interaction between EEG's $1/f^\alpha$-like spectral structure and neural networks' tendency to preferentially learn low-frequency components. In masked autoencoders, the $\ell_2$ reconstruction objective further amplifies this imbalance: under comparable relative reconstruction errors, high-power low-frequency components contribute disproportionately to the loss. To address this issue, we introduce FAME, a frequency-balanced masked autoencoding framework that reconstructs time--frequency activity in predefined EEG bands from masked EEG inputs. FAME independently standardizes the reconstruction targets within each band and assigns equal weight to all band-specific losses, thereby balancing supervision across the EEG spectrum. Evaluated on 41 downstream tasks in OmniEEG-Bench, FAME learns more spectrally balanced representations and achieves state-of-the-art performance on 24 of them. These results underscore the importance of balanced spectral supervision for learning transferable EEG representations.

cs.LG↗

arXiv2026

NeuroOnline: Bridging Pretraining and Online Adaptation for EEG Foundation Models

EEG foundation models have shown strong potential in learning generalized representations across subjects and tasks. However, most existing approaches follow a pretraining-static deployment paradigm, which suffers from two key limitations: (1) misalignment between pretraining objectives and downstream tasks, and (2) limited adaptability to distribution shifts in online settings. We propose Online Neural Adaptation (NeuroOnline), a unified framework that enables continuous adaptation in online scenarios. NeuroOnline integrates two complementary mechanisms: (1) multi-view consistency learning, which enforces cross-view alignment to promote consistent and task-relevant representations, and (2) context-aware representation modulation, which leverages a learnable context prompt with cross-attention to dynamically adapt representations to evolving data distributions. Together, these mechanisms unify representation alignment and dynamic adaptation. Experiments on multiple EEG benchmarks show that NeuroOnline consistently outperforms strong baselines in online settings, achieving better performance under distribution shifts. Ablation and sensitivity studies further validate the necessity of each component and the effectiveness of the overall design.

cs.LG↗

arXiv2026

Omni-Sleep: A Sleep Foundation Model via Hierarchical Contrastive Learning of CNS-ANS Dynamics

Sleep physiology arises from the coordinated dynamics of the central nervous system (CNS) and autonomic nervous system (ANS), as reflected by multimodal polysomnography signals including EEG, EOG, EMG, ECG, and respiration. However, existing sleep foundation models often fuse heterogeneous biosignals in a topology-agnostic manner, overlooking their physiological organization. We introduce Omni-Sleep, a sleep foundation model that uses the CNS/ANS partition as a physiological prior for topology-constrained representation learning. Omni-Sleep learns structured representations through three objectives: intra-system consistency, which captures shared subsystem-level factors within neural and cardio-respiratory signals; inter-system synchronization, which aligns subsystem trajectories to model brain--body dynamics; and latent-space masked temporal modeling, which captures long-horizon sleep dynamics. Pre-trained on over 100,000 hours of multi-center multimodal PSG data, Omni-Sleep is evaluated on sleep staging and multi-disease classification. Across datasets and modality-ablation settings, Omni-Sleep outperforms strong foundation-model baselines, showing improved label efficiency, cross-dataset generalization, and robustness to missing modalities. These results highlight the value of physiological hierarchy for generalizable sleep representation learning. Code is available at https://github.com/AutoBrain-sleep/OmniSleep.

cs.LG↗

arXiv2026

BrainWorld: A Structural-Prior-Conditioned Generative Model for Whole-Brain 4D fMRI Dynamics

Whole-brain 4D fMRI generation is valuable for modeling functional brain dynamics, yet existing fMRI foundation models mainly target representation learning and downstream prediction rather than conditional predictive generation. We introduce BrainWorld, a structural-prior-conditioned generative model for whole-brain 4D fMRI dynamics. BrainWorld uses sMRI as subject-level anatomical context to guide future fMRI generation, integrating structural information into the denoising process rather than treating it as a parallel modality. Evaluated on 22 datasets spanning diverse cohorts and brain states, BrainWorld generates stable 4D fMRI trajectories up to 400 frames, improves downstream performance through generated-example augmentation, and learns transferable multimodal representations that outperform baselines. Together, these results establish BrainWorld as a condition-aware generative framework for long-horizon brain dynamics modeling and multimodal representation learning.

cs.CV↗

arXiv2026

OpTI-Mouse: Optimization for Targeted Temporal Interference Stimulation in the Mouse Brain

Temporal Interference (TI) stimulation enables deep brain targeting, yet precise optimization tools for mouse models remain limited. We developed a computational optimization tool integrating mouse head modeling with the optimization algorithm to optimize stimulation strategies for predefined target regions. By balancing target intensity and spatial focality, the optimized strategy significantly outperformed empirical baselines. For the CA3-CA1 target, it achieved a 7-fold intensity increase (10.29 vs. 2.89 V/m) under iso-focality conditions. Conversely, for the Dentate Gyrus, it improved spatial confinement ($r_{0.5}$ reduced from 3.99 to 3.54 mm) while maintaining comparable intensity. Cross-model validation on a standardized Sim4Life phantom further confirmed the framework's robustness. This approach offers a powerful tool for enhancing the precision and reproducibility of preclinical TI stimulation studies.

q-bio.NC↗

arXiv2026

FlexiBrain: Resolution-Agnostic Voxel-Level Encoding for Native fMRI

The success of large-scale deep learning models in neuroscience is fundamentally constrained by severe data heterogeneity. Native fMRI data aggregated from diverse sources exhibit substantial variation in both spatial and temporal resolutions. Consequently, most existing frameworks rely on lengthy, rigid preprocessing pipelines that enforce uniformity across datasets. This practice introduces two critical limitations: (1) potential degradation of subject-specific anatomical information; (2) significant computational overhead, often requiring hours of processing per subject. Here, we propose FlexiBrain, a resolution-agnostic voxel-level encoding framework for native fMRI based on Mamba-JEPA. FlexiBrain defines patch sizes in real-world physical units and employs a dynamic patch resizing, thereby bypassing destructive spatial standardization while enabling direct ingestion of data in native space. We instantiate the framework using an efficient Mamba-JEPA backbone to model high-dimensional 4D fMRI signals. Across five diverse downstream neuroscience tasks, FlexiBrain consistently outperforms recent state-of-the-art methods, achieving gains of up to 12 percentage points without external data augmentation. Importantly, FlexiBrain functions as a seamless plug-in module, substantially reducing preprocessing costs and accelerating the development of robust voxel-level fMRI foundation models. Code is available at https://github.com/OneMore1/FlexiBrain.

eess.IV↗

arXiv2026

Behavior-Invariant Task Representation Learning with Transformer-based World Models for Offline Meta-Reinforcement Learning

Offline meta-reinforcement learning leverages static datasets to enable agents to generalize to unseen environments by combining offline efficiency with meta-learning adaptability, yet it faces key challenges from context and policy distribution shifts. These issues hinder agents from adapting to online environments, and are further exacerbated under sparse-reward settings. As a result, agents often become trapped in an inherent pattern dilemma, failing to achieve robust generalization. In this work, we propose a novel framework that integrates information-theoretic task representation learning with a Transformer-based stochastic world model. Our approach extracts task-defining latent variables that are invariant to behavior policy, thereby effectively mitigating the context distribution shift. To further handle policy shift and model exploitation, we apply a conservative value penalty to imagination-based rollouts, preventing the policy from exploiting model inaccuracies while maintaining robust adaptation. Extensive evaluations demonstrate that our method outperforms state-of-the-art approaches, with superior stability and generalization under out-of-distribution and sparse-reward settings.

cs.LG↗

arXiv2026

OmniEEG-Bench: A Standardized Evaluation Benchmark for EEG Foundation Models

Electroencephalography (EEG) supports a variety of brain-computer interface (BCI) tasks ranging from brain-state monitoring to human-LLM interactions. EEG foundation models are emerging, but evaluation remains fragmented due to heterogeneous datasets and nconsistent task protocols. Here, we introduce OmniEEG-Bench, a unified benchmark and downstream task roadmap for EEG foundation models (FMs). It organizes evaluation of EEG FMs into six task families spanning (i) signal reliability, (ii) biometrics and disease, (iii) consciousness and state, (iv) cognition and emotion, (v) naturalistic stimulus decoding, and (vi) motor and interaction, introducing a new generation of tasks not systematically benchmarked in prior EEG FM work. OmniEEG-Bench standardizes model deployment, task definitions, and metrics through a task-card specification, and unifies 54 EEG datasets with consistent evaluation protocols. We benchmark 10 representative EEG foundation models and report a leaderboard that covers diverse evaluation settings. Both pretraining dataset diversity and model size are significantly associated with better average ranks across datasets, revealing scaling-law behavior in EEG foundation models (Figure 1). These results suggest that scaling EEG foundation models requires not only larger architectures but also broader and more diverse pretraining data. The benchmark code is available at https://github.com/ncclab-sustech/omni-eegbench.git.

cs.LG↗

arXiv2026

Pretraining Induces a Reusable Spectral Basis for Downstream Task Adaptation

Finetuning pretrained models occurs in a low-dimensional subspace of the full parameter space. Prior work has focused on characterizing this optimization subspace, but largely ignored the complementary question: why do certain directions remain unexplored during finetuning? Are these stable directions irrelevant to downstream tasks, or do they already encode task-relevant structure that requires no further adjustment? Answering this question is central to understanding how pretrained knowledge transfers. Through systematic spectral analysis across vision and language models, we show that the leading singular vectors of pretrained weight matrices remain highly stable under finetuning and are shared across unrelated downstream tasks, revealing that pretraining establishes a reusable spectral coordinate system. Models pretrained on larger datasets exhibit greater spectral stability under distribution shift or task change, directly linking pretraining scale to geometric transferability. Motivated by these findings, we propose a parameter-efficient method that freezes pretrained singular vectors and optimizes only leading spectral coefficients, achieving competitive performance on GLUE with 0.2% trainable parameters. Our results reveal that the stable directions encode transferable structure rather than irrelevant noise: successful pretraining discovers spectral bases that downstream tasks inherit and operate within.

cs.LG↗

arXiv2026

A geometry aware framework enhances noninvasive mapping of whole human brain dynamics

Non-invasive electrophysiology lacks methods that accurately reconstruct whole-brain spatiotemporal dynamics while incorporating individual cortical geometry, leaving current electroencephalography and magnetoencephalography source imaging limited by simplistic or biologically implausible priors. Here, we show that embedding participant-specific Geometric Basis Functions (GBFs), eigenmodes derived from each individual's cortical surface, provides a powerful anatomic constraint that resolves the inverse problem and improves reconstruction fidelity. The method reconstructs neural sources as linear combinations of geometric basis functions, thereby aligning source estimates with the geometric organization of neural dynamics. We validate GBF across the Meta-Source Benchmark, task-evoked data, resting-state networks, intracranial stimulation, and epilepsy data. The results demonstrate that GBF yields high localization accuracy and captures fast spatiotemporal dynamics consistent with anatomical pathways. These findings suggest that both spontaneous and evoked whole-brain activity can be described by hundreds of geometric modes, providing a compact yet accurate representation of neural sources. By linking cortical geometry to electrophysiological dynamics, GBF offers a versatile source imaging tool for both scientific and clinical applications.

q-bio.NC↗

arXiv2026

Brain-DiT: A Universal Multi-state fMRI Foundation Model with Metadata-Conditioned Pretraining

Current fMRI foundation models primarily rely on a limited range of brain states and mismatched pretraining tasks, restricting their ability to learn generalized representations across diverse brain states. We present Brain-DiT, a universal multi-state fMRI foundation model pretrained on 349,898 sessions from 24 datasets spanning resting, task, naturalistic, disease, and sleep states. Unlike prior fMRI foundation models that rely on masked reconstruction in the raw-signal space or a latent space, Brain-DiT adopts metadata-conditioned diffusion pretraining with a Diffusion Transformer (DiT), enabling the model to learn multi-scale representations that capture both fine-grained functional structure and global semantics. Across extensive evaluations and ablations on 7 downstream tasks, we find consistent evidence that diffusion-based generative pretraining is a stronger proxy than reconstruction or alignment, with metadata-conditioned pretraining further improving downstream performance by disentangling intrinsic neural dynamics from population-level variability. We also observe that downstream tasks exhibit distinct preferences for representational scale: ADNI classification benefits more from global semantic representations, whereas age/sex prediction comparatively relies more on fine-grained local structure.

cs.CV↗

arXiv2026

Forecasting Epileptic Seizures from Contactless Camera via Cross-Species Transfer Learning

Epileptic seizure forecasting is a clinically important yet challenging problem in epilepsy research. Existing approaches predominantly rely on neural signals such as electroencephalography (EEG), which require specialized equipment and limit long-term deployment in real-world settings. In contrast, video data provide a non-invasive and accessible alternative, yet existing video-based studies mainly focus on post-onset seizure detection, leaving seizure forecasting largely unexplored. In this work, we formulate a novel task of video-based epileptic seizure forecasting, where short pre-ictal video segments (3-10 seconds) are used to predict whether a seizure will occur within the subsequent 5 seconds. To address the scarcity of annotated human epilepsy videos, we propose a cross-species transfer learning framework that leverages large-scale rodent video data for auxiliary pretraining. This enables the model to capture seizure-related behavioral dynamics that generalize across species. Experimental results demonstrate that our approach achieves over 70% prediction accuracy under a strictly video-only setting and outperforms existing baselines. These findings highlight the potential of cross-species learning for building non-invasive, scalable early-warning systems for epilepsy.

cs.CV↗

arXiv2026

Inferring brain plasticity rule under long-term stimulation with structured recurrent dynamics

Understanding how long-term stimulation reshapes neural circuits requires uncovering the rules of brain plasticity. While short-term synaptic modifications have been extensively characterized, the principles that drive circuit-level reorganization across hours to weeks remain unknown. Here, we formalize these principles as a latent dynamical law that governs how recurrent connectivity evolves under repeated interventions. To capture this law, we introduce the Stimulus-Evoked Evolution Recurrent dynamics (STEER) framework, a dual-timescale model that disentangles fast neural activity from slow plastic changes. STEER represents plasticity as low-dimensional latent coefficients evolving under a learnable recurrence, enabling testable inference of plasticity rules rather than absorbing them into black-box parameters. We validate STEER with four benchmarks: synthetic Lorenz systems with controlled parameter shifts, BCM-based networks with biologically grounded plasticity, a task learning setting with adaptively optimized external stimulation and longitudinal recordings from Parkinsonian rats receiving closed-loop DBS. Our results demonstrate that STEER recovers interpretable update equations, predicts network adaptation under unseen stimulation schedules, and supports the design of improved intervention protocols. By elevating long-term plasticity from a hidden confound to an identifiable dynamical object, STEER provides a data-driven foundation for both mechanistic insight and principled optimization of brain stimulation.

q-bio.NC↗

arXiv2026

MindPilot: Closed-loop Visual Stimulation Optimization for Brain Modulation with EEG-guided Diffusion

Whereas most brain-computer interface research has focused on decoding neural signals into behavior or intent, the reverse challenge-using controlled stimuli to steer brain activity-remains far less understood, particularly in the visual domain. However, designing images that consistently elicit desired neural responses is difficult: subjective states lack clear quantitative measures, and EEG feedback is both noisy and non-differentiable. We introduce MindPilot, the first closed-loop framework that uses EEG signals as optimization feedback to guide naturalistic image generation. Unlike prior work limited to invasive settings or low-level flicker stimuli, MindPilot leverages non-invasive EEG with natural images, treating the brain as a black-box function and employing a pseudo-model guidance mechanism to iteratively refine images without requiring explicit rewards or gradients. We validate MindPilot in both simulation and human experiments, demonstrating (i) efficient retrieval of semantic targets, (ii) closed-loop optimization of EEG features, and (iii) human-subject validations in mental matching and emotion regulation tasks. Our results establish the feasibility of EEG-guided image synthesis and open new avenues for non-invasive closed-loop brain modulation, bidirectional brain-computer interfaces, and neural signal-guided generative modeling.

cs.NE↗

arXiv2026

Local Intrinsic Dimension of Representations Predicts Alignment and Generalization in AI Models and Human Brain

Recent work has found that neural networks with stronger generalization tend to exhibit higher representational alignment with one another across architectures and training paradigms. In this work, we show that models with stronger generalization also align more strongly with human neural activity. Moreover, generalization performance, model--model alignment, and model--brain alignment are all significantly correlated with each other. We further show that these relationships can be explained by a single geometric property of learned representations: the local intrinsic dimension of embeddings. Lower local dimension is consistently associated with stronger model--model alignment, stronger model--brain alignment, and better generalization, whereas global dimension measures fail to capture these effects. Finally, we find that increasing model capacity and training data scale systematically reduces local intrinsic dimension, providing a geometric account of the benefits of scaling. Together, our results identify local intrinsic dimension as a unifying descriptor of representational convergence in artificial and biological systems.

cs.LG↗

arXiv2026

Understanding Generalization from Embedding Dimension and Distributional Convergence

Deep neural networks often generalize well despite heavy over-parameterization, challenging classical parameter-based analyses. We study generalization from a representation-centric perspective and analyze how the geometry of learned embeddings controls predictive performance for a fixed trained model. We show that population risk can be bounded by two factors: (i) the intrinsic dimension of the embedding distribution, which determines the convergence rate of empirical embedding distribution to the population distribution in Wasserstein distance, and (ii) the sensitivity of the downstream mapping from embeddings to predictions, characterized by Lipschitz constants. Together, these yield an embedding-dependent error bound that does not rely on parameter counts or hypothesis class complexity. At the final embedding layer, architectural sensitivity vanishes and the bound is dominated by embedding dimension, explaining its strong empirical correlation with generalization performance. Experiments across architectures and datasets validate the theory and demonstrate the utility of embedding-based diagnostics.

cs.LG↗