Towards Robust Multimodal Physiological Foundation Models: Handling Arbitrary Missing Modalities

Multimodal physiological signals, such as EEG, ECG, EOG, and EMG, are crucial for healthcare and brain-computer interfaces. While existing methods rely on specialized architectures and dataset-specific fusion strategies, they struggle to learn universal representations that generalize across datasets and handle missing modalities at inference time. To address these issues, we propose PhysioOmni, a foundation model for multimodal physiological signal analysis that models both homogeneous and heterogeneous features to decouple multimodal signals and extract generic representations while maintaining compatibility with arbitrary missing modalities. PhysioOmni trains a decoupled multimodal tokenizer, enabling masked signal pre-training via modality-invariant and modality-specific objectives. To ensure adaptability to diverse and incomplete modality combinations, the pre-trained encoders undergo resilient fine-tuning with prototype alignment on downstream datasets. Extensive experiments on four downstream tasks, emotion recognition, sleep stage classification, motor prediction, and mental workload detection, demonstrate that PhysioOmni achieves state-of-the-art performance while maintaining strong robustness to missing modalities. Our code and model weights will be released.

SPD Learning for Covariance-Based Neuroimaging Analysis: Perspectives, Methods, and Challenges

Neuroimaging provides a critical framework for characterizing brain activity by quantifying connectivity patterns and functional architecture across modalities. While modern machine learning has significantly advanced our understanding of neural processing mechanisms through these datasets, decoding task-specific signatures must contend with inherent neuroimaging constraints, for example, low signal-to-noise ratios in raw electrophysiological recordings, cross-session non-stationarity, and limited sample sizes. This review focuses on machine learning approaches for covariance-based neuroimaging data, where often symmetric positive definite (SPD) matrices under full-rank conditions encode inter-channel relationships. By equipping the space of SPD matrices with Riemannian metrics (e.g., affine-invariant or log-Euclidean), their space forms a Riemannian manifold enabling geometric analysis. We unify methodologies operating on this manifold under the SPD learning framework, which systematically leverages the SPD manifold's geometry to process covariance features, thereby advancing brain imaging analytics.

Decoupled Doubly Contrastive Learning for Cross Domain Facial Action Unit Detection

Despite the impressive performance of current vision-based facial action unit (AU) detection approaches, they are heavily susceptible to the variations across different domains and the cross-domain AU detection methods are under-explored. In response to this challenge, we propose a decoupled doubly contrastive adaptation (D$^2$CA) approach to learn a purified AU representation that is semantically aligned for the source and target domains. Specifically, we decompose latent representations into AU-relevant and AU-irrelevant components, with the objective of exclusively facilitating adaptation within the AU-relevant subspace. To achieve the feature decoupling, D$^2$CA is trained to disentangle AU and domain factors by assessing the quality of synthesized faces in cross-domain scenarios when either AU or domain attributes are modified. To further strengthen feature decoupling, particularly in scenarios with limited AU data diversity, D$^2$CA employs a doubly contrastive learning mechanism comprising image and feature-level contrastive learning to ensure the quality of synthesized faces and mitigate feature ambiguities. This new framework leads to an automatically learned, dedicated separation of AU-relevant and domain-relevant factors, and it enables intuitive, scale-specific control of the cross-domain facial image synthesis. Extensive experiments demonstrate the efficacy of D$^2$CA in successfully decoupling AU and domain factors, yielding visually pleasing cross-domain synthesized facial images. Meanwhile, D$^2$CA consistently outperforms state-of-the-art cross-domain AU detection approaches, achieving an average F1 score improvement of 6\%-14\% across various cross-domain scenarios.

Beyond Overfitting: Doubly Adaptive Dropout for Generalizable AU Detection

Facial Action Units (AUs) are essential for conveying psychological states and emotional expressions. While automatic AU detection systems leveraging deep learning have progressed, they often overfit to specific datasets and individual features, limiting their cross-domain applicability. To overcome these limitations, we propose a doubly adaptive dropout approach for cross-domain AU detection, which enhances the robustness of convolutional feature maps and spatial tokens against domain shifts. This approach includes a Channel Drop Unit (CD-Unit) and a Token Drop Unit (TD-Unit), which work together to reduce domain-specific noise at both the channel and token levels. The CD-Unit preserves domain-agnostic local patterns in feature maps, while the TD-Unit helps the model identify AU relationships generalizable across domains. An auxiliary domain classifier, integrated at each layer, guides the selective omission of domain-sensitive features. To prevent excessive feature dropout, a progressive training strategy is used, allowing for selective exclusion of sensitive features at any model layer. Our method consistently outperforms existing techniques in cross-domain AU detection, as demonstrated by extensive experimental evaluations. Visualizations of attention maps also highlight clear and meaningful patterns related to both individual and combined AUs, further validating the approach's effectiveness.

Decoding Human Attentive States from Spatial-temporal EEG Patches Using Transformers

Learning the spatial topology of electroencephalogram (EEG) channels and their temporal dynamics is crucial for decoding attention states. This paper introduces EEG-PatchFormer, a transformer-based deep learning framework designed specifically for EEG attention classification in Brain-Computer Interface (BCI) applications. By integrating a Temporal CNN for frequency-based EEG feature extraction, a pointwise CNN for feature enhancement, and Spatial and Temporal Patching modules for organizing features into spatial-temporal patches, EEG-PatchFormer jointly learns spatial-temporal information from EEG data. Leveraging the global learning capabilities of the self-attention mechanism, it captures essential features across brain regions over time, thereby enhancing EEG data decoding performance. Demonstrating superior performance, EEG-PatchFormer surpasses existing benchmarks in accuracy, area under the ROC curve (AUC), and macro-F1 score on a public cognitive attention dataset. The code can be found via: https://github.com/yi-ding-cs/EEG-PatchFormer .

EmT: A Novel Transformer for Generalized Cross-subject EEG Emotion Recognition

Integrating prior knowledge of neurophysiology into neural network architecture enhances the performance of emotion decoding. While numerous techniques emphasize learning spatial and short-term temporal patterns, there has been limited emphasis on capturing the vital long-term contextual information associated with emotional cognitive processes. In order to address this discrepancy, we introduce a novel transformer model called emotion transformer (EmT). EmT is designed to excel in both generalized cross-subject EEG emotion classification and regression tasks. In EmT, EEG signals are transformed into a temporal graph format, creating a sequence of EEG feature graphs using a temporal graph construction module (TGC). A novel residual multi-view pyramid GCN module (RMPG) is then proposed to learn dynamic graph representations for each EEG feature graph within the series, and the learned representations of each graph are fused into one token. Furthermore, we design a temporal contextual transformer module (TCT) with two types of token mixers to learn the temporal contextual information. Finally, the task-specific output module (TSO) generates the desired outputs. Experiments on four publicly available datasets show that EmT achieves higher results than the baseline methods for both EEG emotion classification and regression tasks. The code is available at https://github.com/yi-ding-cs/EmT.

EEG-Deformer: A Dense Convolutional Transformer for Brain-computer Interfaces

Effectively learning the temporal dynamics in electroencephalogram (EEG) signals is challenging yet essential for decoding brain activities using brain-computer interfaces (BCIs). Although Transformers are popular for their long-term sequential learning ability in the BCI field, most methods combining Transformers with convolutional neural networks (CNNs) fail to capture the coarse-to-fine temporal dynamics of EEG signals. To overcome this limitation, we introduce EEG-Deformer, which incorporates two main novel components into a CNN-Transformer: (1) a Hierarchical Coarse-to-Fine Transformer (HCT) block that integrates a Fine-grained Temporal Learning (FTL) branch into Transformers, effectively discerning coarse-to-fine temporal patterns; and (2) a Dense Information Purification (DIP) module, which utilizes multi-level, purified temporal information to enhance decoding accuracy. Comprehensive experiments on three representative cognitive tasks consistently verify the generalizability of our proposed EEG-Deformer, demonstrating that it either outperforms existing state-of-the-art methods or is comparable to them. Visualization results show that EEG-Deformer learns from neurophysiologically meaningful brain regions for the corresponding cognitive tasks. The source code can be found at https://github.com/yi-ding-cs/EEG-Deformer.

MASA-TCN: Multi-anchor Space-aware Temporal Convolutional Neural Networks for Continuous and Discrete EEG Emotion Recognition

Emotion recognition using electroencephalogram (EEG) mainly has two scenarios: classification of the discrete labels and regression of the continuously tagged labels. Although many algorithms were proposed for classification tasks, there are only a few methods for regression tasks. For emotion regression, the label is continuous in time. A natural method is to learn the temporal dynamic patterns. In previous studies, long short-term memory (LSTM) and temporal convolutional neural networks (TCN) were utilized to learn the temporal contextual information from feature vectors of EEG. However, the spatial patterns of EEG were not effectively extracted. To enable the spatial learning ability of TCN towards better regression and classification performances, we propose a novel unified model, named MASA-TCN, for EEG emotion regression and classification tasks. The space-aware temporal layer enables TCN to additionally learn from spatial relations among EEG electrodes. Besides, a novel multi-anchor block with attentive fusion is proposed to learn dynamic temporal dependencies. Experiments on two publicly available datasets show MASA-TCN achieves higher results than the state-of-the-art methods for both EEG emotion regression and classification tasks. The code is available at https://github.com/yi-ding-cs/MASA-TCN.

Aggregating Intrinsic Information to Enhance BCI Performance through Federated Learning

Insufficient data is a long-standing challenge for Brain-Computer Interface (BCI) to build a high-performance deep learning model. Though numerous research groups and institutes collect a multitude of EEG datasets for the same BCI task, sharing EEG data from multiple sites is still challenging due to the heterogeneity of devices. The significance of this challenge cannot be overstated, given the critical role of data diversity in fostering model robustness. However, existing works rarely discuss this issue, predominantly centering their attention on model training within a single dataset, often in the context of inter-subject or inter-session settings. In this work, we propose a hierarchical personalized Federated Learning EEG decoding (FLEEG) framework to surmount this challenge. This innovative framework heralds a new learning paradigm for BCI, enabling datasets with disparate data formats to collaborate in the model training process. Each client is assigned a specific dataset and trains a hierarchical personalized model to manage diverse data formats and facilitate information exchange. Meanwhile, the server coordinates the training procedure to harness knowledge gleaned from all datasets, thus elevating overall performance. The framework has been evaluated in Motor Imagery (MI) classification with nine EEG datasets collected by different devices but implementing the same MI task. Results demonstrate that the proposed frame can boost classification performance up to 16.7% by enabling knowledge sharing between multiple datasets, especially for smaller datasets. Visualization results also indicate that the proposed framework can empower the local models to put a stable focus on task-related areas, yielding better performance. To the best of our knowledge, this is the first end-to-end solution to address this important challenge.

SemiGNN-PPI: Self-Ensembling Multi-Graph Neural Network for Efficient and Generalizable Protein-Protein Interaction Prediction

Protein-protein interactions (PPIs) are crucial in various biological processes and their study has significant implications for drug development and disease diagnosis. Existing deep learning methods suffer from significant performance degradation under complex real-world scenarios due to various factors, e.g., label scarcity and domain shift. In this paper, we propose a self-ensembling multigraph neural network (SemiGNN-PPI) that can effectively predict PPIs while being both efficient and generalizable. In SemiGNN-PPI, we not only model the protein correlations but explore the label dependencies by constructing and processing multiple graphs from the perspectives of both features and labels in the graph learning process. We further marry GNN with Mean Teacher to effectively leverage unlabeled graph-structured PPI data for self-ensemble graph learning. We also design multiple graph consistency constraints to align the student and teacher graphs in the feature embedding space, enabling the student model to better learn from the teacher model by incorporating more relationships. Extensive experiments on PPI datasets of different scales with different evaluation settings demonstrate that SemiGNN-PPI outperforms state-of-the-art PPI prediction methods, particularly in challenging scenarios such as training with limited annotations and testing on unseen data.