Background: Brain–computer interfaces (BCIs) based on motor imagery (MI) offer promising solutions for motor rehabilitation and communication. However, electroencephalography (EEG) signals are often characterized by low signal-to-noise ratios, strong non-stationarity, and significant inter-subject variability, which pose significant challenges for accurate decoding. Existing methods often struggle to simultaneously model the spatial interactions between EEG channels, the local fine-grained features within signals, and global semantic patterns. Methods: To address this, we propose the graph attention-based hierarchical temporal network (GAH-TNet), which integrates spatial graph attention modeling with hierarchical temporal feature encoding. Specifically, we design the graph attention temporal encoding block (GATE). The graph attention mechanism is used to model spatial dependencies between EEG channels and encode short-term temporal dynamic features. Subsequently, a hierarchical attention-guided deep temporal feature encoding block (HADTE) is introduced, which extracts local fine-grained and global long-term dependency features through two-stage attention and temporal convolution. Finally, a fully connected classifier is used to obtain the classification results. The proposed model is evaluated on two publicly available MI-EEG datasets. Results: Our method outperforms multiple existing state-of-the-art methods in classification accuracy. On the BCI IV 2a dataset, the average classification accuracy reaches 86.84%, and on BCI IV 2b, it reaches 89.15%. Ablation experiments validate the complementary roles of GATE and HADTE in modeling. Additionally, the model exhibits good generalization ability across subjects. Conclusions: This framework effectively captures the spatio-temporal dynamic characteristics and topological structure of MI-EEG signals. This hierarchical and interpretable framework provides a new approach for improving decoding performance in EEG motor imagery tasks.

Functional near-infrared spectroscopy (fNIRS) offers a safe and portable signal source for brain–computer interface (BCI) applications, particularly in motor imagery (MI) decoding. However, its low sampling rate and hemodynamic delay pose challenges for temporal modeling and dynamic brain network analysis. To address these limitations in temporal dynamics, static graph modeling, and feature fusion interpretability, we propose TopoTempNet, an innovative topology-enhanced temporal network for biomedical signal decoding. TopoTempNet integrates multi-level graph features with temporal modeling through three key innovations: (1) multi-level topological feature construction using local and global functional connectivity metrics (e.g., connection strength, density, global efficiency); (2) a graph-modulated attention mechanism combining Transformer and Bi-LSTM to dynamically model key connections; and (3) a multimodal fusion strategy uniting raw signals, graph structures, and temporal representations into a high-dimensional discriminative space. Evaluated on three public fNIRS datasets (MA, WG, UFFT), TopoTempNet achieves superior accuracy (up to 90.04% ± 3.53%) and Kappa scores compared to state-of-the-art models. The ROC curves and t-SNE visualizations confirm its excellent feature discrimination and structural clarity. Furthermore, the statistical analysis of graph features reveals the model’s ability to capture task-specific functional connectivity patterns, enhancing the interpretability of decoding outcomes. TopoTempNet provides a novel pathway for building interpretable and high-performance BCI systems based on fNIRS.