arXiv subjects

Kaining Peng

Publications and source records attributed to Kaining Peng.

5 recordsLinked to original sources

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↗

arXiv2025

SLIM-Brain: A Data- and Training-Efficient Foundation Model for fMRI Data Analysis

Foundation models are emerging as a powerful paradigm for fMRI analysis, but current approaches face a dual bottleneck of data- and training-efficiency. Atlas-based methods aggregate voxel signals into fixed regions of interest, reducing data dimensionality but discarding fine-grained spatial details, and requiring extremely large cohorts to train effectively as general-purpose foundation models. Atlas-free methods, on the other hand, operate directly on voxel-level information - preserving spatial fidelity but are prohibitively memory- and compute-intensive, making large-scale pre-training infeasible. We introduce SLIM-Brain (Sample-efficient, Low-memory fMRI Foundation Model for Human Brain), a new atlas-free foundation model that simultaneously improves both data- and training-efficiency. SLIM-Brain adopts a two-stage adaptive design: (i) a lightweight temporal extractor captures global context across full sequences and ranks data windows by saliency, and (ii) a 4D hierarchical encoder (Hiera-JEPA) learns fine-grained voxel-level representations only from the top-$k$ selected windows, while deleting about 70% masked patches. Extensive experiments across seven public benchmarks show that SLIM-Brain establishes new state-of-the-art performance on diverse tasks, while requiring only 4 thousand pre-training sessions and approximately 30% of GPU memory comparing to traditional voxel-level methods.

cs.CV↗

arXiv2025

DCA: Graph-Guided Deep Embedding Clustering for Brain Atlases

Brain atlases are essential for reducing the dimensionality of neuroimaging data and enabling interpretable analysis. However, most existing atlases are predefined, group-level templates with limited flexibility and resolution. We present Deep Cluster Atlas (DCA), a graph-guided deep embedding clustering framework for generating individualized, voxel-wise brain parcellations. DCA combines a pretrained autoencoder with spatially regularized deep clustering to produce functionally coherent and spatially contiguous regions. Our method supports flexible control over resolution and anatomical scope, and generalizes to arbitrary brain structures. We further introduce a standardized benchmarking platform for atlas evaluation, using multiple large-scale fMRI datasets. Across multiple datasets and scales, DCA outperforms state-of-the-art atlases, improving functional homogeneity by 98.8% and silhouette coefficient by 29%, and achieves superior performance in downstream tasks such as autism diagnosis and cognitive decoding. We also observe that a fine-tuned pretrained model achieves superior results on the corresponding task. Codes and models are available at https://github.com/ncclab-sustech/DCA .

q-bio.NC↗

arXiv2024

Uncovering cognitive taskonomy through transfer learning in masked autoencoder-based fMRI reconstruction

Data reconstruction is a widely used pre-training task to learn the generalized features for many downstream tasks. Although reconstruction tasks have been applied to neural signal completion and denoising, neural signal reconstruction is less studied. Here, we employ the masked autoencoder (MAE) model to reconstruct functional magnetic resonance imaging (fMRI) data, and utilize a transfer learning framework to obtain the cognitive taskonomy, a matrix to quantify the similarity between cognitive tasks. Our experimental results demonstrate that the MAE model effectively captures the temporal dynamics patterns and interactions within the brain regions, enabling robust cross-subject fMRI signal reconstruction. The cognitive taskonomy derived from the transfer learning framework reveals the relationships among cognitive tasks, highlighting subtask correlations within motor tasks and similarities between emotion, social, and gambling tasks. Our study suggests that the fMRI reconstruction with MAE model can uncover the latent representation and the obtained taskonomy offers guidance for selecting source tasks in neural decoding tasks for improving the decoding performance on target tasks.

q-bio.NC↗

arXiv2022

Mapping effective connectivity by virtually perturbing a surrogate brain

Effective connectivity (EC), indicative of the causal interactions between brain regions, is fundamental to understanding information processing in the brain. Traditional approaches, which infer EC from neural responses to stimulations, are not suited for mapping whole-brain EC in humans due to being invasive and having limited spatial coverage of stimulations. To address this gap, we present Neural Perturbational Inference (NPI), a data-driven framework designed to map EC across the entire brain. NPI employs an artificial neural network trained to learn large-scale neural dynamics as a computational surrogate of the brain. NPI maps EC by perturbing each region of the surrogate brain and observing the resulting responses in all other regions. NPI captures the directionality, strength, and excitatory/inhibitory properties of brain-wide EC. Our validation of NPI, using models having ground-truth EC, shows its superiority over Granger causality and dynamic causal modeling. Applying NPI to resting-state fMRI data from diverse datasets reveals consistent and structurally supported EC. Further validation using a cortico-cortical evoked potentials dataset reveals a significant correlation between NPI-inferred EC and real stimulation propagation pathways. By transitioning from correlational to causal understandings of brain functionality, NPI marks a stride in decoding the brain's functional architecture and facilitating both neuroscience research and clinical applications.

q-bio.NC↗