Multimodal Physiological Signals

Protein-protein interaction (PPI) databases do not faithfully reflect biological realities. Instead, they are influenced by study and technical biases that distort certain protein and interaction attributes. Machine learning models can exploit these as learning shortcuts if the negative dataset is not constructed with care. So far, the shortcuts introduced during PPI dataset construction have only been examined in isolation. Here, we systematically characterize both reported and, to our knowledge, previously unreported biases in PPI datasets that lead machine learning models to learn shortcuts instead of biological signal. We analyze HIPPIE, IntAct, and STRING, dedicated PPI databases, as well as two datasets derived from 3D-structural information in the Protein Data Bank (PDB). We show that random data splitting introduces strong topological shortcuts. When train-test protein overlap is removed, the resulting datasets still retain usable shortcuts stemming from self-interactions, taxonomic identity, and functional relatedness, whose prevalence interestingly depends on the data source. We further show that sampling negatives from a set of high-confidence non-interactors, an intuitively appealing choice, can amplify the shortcut stemming from functional relatedness. To detect and mitigate these biases, we provide an open Nextflow pipeline that combines similarity-aware, data-loss-minimizing dataset splitting with bias-minimizing negative sampling, both formulated as integer linear programs. Its key concept of quantifying biases to minimize them through optimization-based negative sampling can, in principle, be extended to any machine learning problem where the pool of negative candidates is much larger than the positives and is thus of interest also beyond PPI prediction.

Cardiac, neural, behavioral, and speech measurements from wearable and mobile devices provide partial, noise-sensitive views of physiological state. BioSync combines these measurements into the \textbf{BioSync Index (BSI)}, a continuous composite digital biomarker defined under the BEST framework. The model applies multi-head self-attention to modality tokens and adds a linear branch whose hypothesis class includes standard feature concatenation. This architecture is motivated by latent-variable measurement theory and by the possibility that joint observations contain information unavailable from individual modalities. We evaluated BioSync on two literature-informed synthetic cohorts: a four-modality cognitive-decline cohort using HRV, EEG, actigraphy, and speech, and a metabolic-autonomic cohort structured around the public AI-READI wearable schema. In the cognitive cohort, BioSync and concatenation obtained AUCs of 0.928 and 0.926, respectively. In the metabolic cohort, BioSync obtained accuracy/F1 of 0.764/0.766, compared with 0.756/0.758 for concatenation. The BSI correlated with latent severity in both cohorts ($r=0.91$ and $r=0.68$). A pure-attention ablation obtained cognitive-cohort AUC 0.911, locating the increase to 0.928 in the combined wide-and-deep architecture. With matched modality-dropout training, BioSync led concatenation at five of six cognitive-cohort corruption rates and at the highest metabolic-cohort rate. Its cognitive-cohort AUC was also higher than five published digital-biomarker reference values, although differences in datasets and tasks preclude a controlled benchmark claim. Comparison with single-modality, early-fusion, and late-fusion designs across six prespecified criteria identifies the model's computational properties; validation on real cohorts remains necessary.

The separation of cardiovascular sounds is a critical task in biomedical signal processing. In this paper, we introduce XVAE-WMT1, an unsupervised explainable generative AI algorithm combining a variational autoencoder (VAE) with explainable AI (XAI), wavelet-based inputs, a post-hoc output mask, and temporal consistency (TC) loss. Unlike existing supervised and VAE-based methods that rely on Short-Time Fourier Transform (STFT) and ignore latent interpretability, XVAE-WMT requires no paired clean recordings and integrates a Continuous Wavelet Transform (CWT) front-end for superior time-frequency localization. We assessed the latent space interpretability via different metrics, with SHAP (SHapley Additive exPlanations) enabling dimensionality reduction to the top 75% of latent features while preserving separation quality. Evaluated across two datasets using Signal-to-Distortion Ratio (SDR), Signal-to-Interference Ratio (SIR), and Signal-to-Artifacts Ratio (SAR), XVAE-WMT attains 26.8 dB SDR, 32.8 dB SIR, and 28.6 dB SAR.

Cardiovascular AI models can classify clean elec- trocardiogram (ECG) signals, but real wearable signals change because of motion, breathing, posture, sensor contact, and true clinical deterioration. This paper asks when a model should keep its prediction, change it, or flag uncertainty. We propose a physiologic stability framework, called PECS, that compares changes inside the model with measurable changes in the signal. ECG is treated as the main cardiac signal, photoplethysmography (PPG) adds pulse and vascular information, and respiration is used only when ECG and PPG disagree. We test the framework on PTB-XL at pilot and full scales and on synchronized BIDMC and MIMIC waveform cohorts. The PTB-XL pilot and full- scale analyses selected different domain pairs, and the strongest cross-modal pair also changed across BIDMC and MIMIC, showing that adding every available signal is not always the best choice. PECS outperformed the evaluated drift-detection baseline implementations, reaching drift classification accuracy (DCA) of 0.8786 on expanded BIDMC and 0.9560 on MIMIC. The MIMIC results also showed that respiration can help during disagreement cases, but it should be used selectively rather than as an automatic override. Overall, the results support PECS as a candidate monitoring framework for wearable cardiovascular AI while highlighting the need for scale-aware domain selection and interpretable trust routing

Hand gesture recognition via surface electromyography (sEMG) is fundamental to prosthetic control. In this field, deep learning approaches have become the gold standard. However, current architectures struggle to scale; model performance typically decreases as the number of hand movements increases. Performance degradation is tied to the increased statistical complexity of decoding expanded gesture sets and compounded by the limitations of state-of-the-art methods, which primarily rely on low-latency unimodal convolutional architectures. Convolutions operate locally, limiting model's ability to capture long-range sequential patterns. Unimodal setups cannot leverage complementary information from coordinated signals characterizing movement execution, such as inertial and eye-tracking data. These limitations motivate architectures that integrate local and global features across multimodal physiological sequences. To bridge this gap, this study introduces EMG-CrossFormer, an end-to-end hybrid convolutional-transformer for seamless multimodal integration. EMG-CrossFormer combines representations from an arbitrary number of unimodal encoders through cascaded cross-attention fusion layers, and decodes the fused representations using learnable gesture queries. EMG-CrossFormer was evaluated on four NinaPro datasets (DB2, DB3, DB7, and DB10) and benchmarked against six state-of-the-art models using an increasing number of modalities. Using only sEMG, EMG-CrossFormer achieved mean accuracies of 72.33%, 52.48%, 79.16%, and 73.49% on DB2, DB3, DB7, and DB10, respectively. Incorporating inertial signals improved performance to 90.66%, 80.40%, 92.79%, and 92.06%. These results show that joint local-global feature modeling improves sEMG-only decoding and that multimodal fusion substantially amplifies this benefit, underscoring the value of both design principles for complex hand gesture recognition.

Low-power event-based Analog Front-Ends (AFEs) are essential for building efficient, end-to-end neuromorphic signal processing systems. In this paper, we present an event-based AFE Application-Specific Integrated Circuit (ASIC) optimized for biomedical signal acquisition and encoding. The chip features 32 independently programmable input channels with dual-mode encoding mechanism outputs, comprising Pulse Frequency Modulation (PFM) and adaptive Asynchronous Delta Modulator (aADM) circuits. The aADM encoder provides an auto-scaling mechanism that adapts the encoding data-rate based on the input signal envelope in real-time, enabling very high data compression for low-power information transmission. This approach paves the way toward adaptive wireless communication of neural signals for on-line processing in brain-computer interfaces. Fabricated in a 180 nm CMOS process, the proposed ASIC offers a highly configurable interface compatible with state-of-the-art Spiking Neural Network (SNN) neuromorphic processors.

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.

Clinical time series prediction in intensive care units remains challenging due to heterogeneous physiological variables and informative missingness. The presence or absence of a measurement can reflect clinical decisions and patient severity, and thus missingness can serve as a predictive signal rather than a simple data artifact. This work presents CISM, a Channel-Independent Spectrogram framework with a Missingness stream for clinical multivariate time series prediction. CISM converts each clinical variable into a variable-wise time-frequency spectrogram, preserves variable identity through variable-aligned encoding, and aligns an explicit missingness stream with the spectrogram representation. Experiments on an in-hospital mortality task derived from MIMIC-IV show that CISM achieves the highest mean AUROC (0.7225), AUPRC (0.3308), and F1 (0.3808) among the compared time series, missingness-aware, vision, and time-frequency baselines. Ablation studies further show that observation patterns provide a meaningful informative signal. Pixel-level mask injection improves performance over plain spectrogram inputs and recovers much of this predictive value. The aligned missingness stream contributes a further, complementary gain in both AUROC and AUPRC. These results highlight the importance of modeling observation patterns as structured signals in clinical time series prediction.

In this document, we describe characteristics and technical details of the multimodal biosignal dataset DOSE-I of procedural sedation for endoscopy published on zenodo. The DOSE-I dataset includes 78.5 hours of recording in 171 records ranging from 6.7 to 70.8 minutes (mean: 27.5, SD: 11.6) of 281 endoscopic procedures. 1129 (median: 6 per record) transitions of consciousness and 7328 (median: 39 per record) individual sedation depth labels were recorded. In addition to clinically annotated biosignals, the DOSE-I dataset provides detailed static data about the respective study subject and metadata about the respective recordings. To further support future research, we provide details about artifact detection and preprocessed pEEG features, too. C code used for this preprocessing is provided separately via Github.

Modeling long-sequence medical time series data, such as electrocardiograms (ECG), poses significant challenges due to high sampling rates, multichannel signal complexity, inherent noise, and limited labeled data. While recent self-supervised learning (SSL) methods, based on various encoder architectures such as convolutional neural networks, have been proposed to learn representations from unlabeled data, they often fall short in capturing long-range dependencies and noise-invariant features. Structured state space models (S4) excel at long-sequence modeling, but existing S4 architectures fail to capture the unique characteristics of multichannel physiological waveforms. In this work, we propose SL-S4Wave, a self-supervised learning framework that combines contrastive learning with a tailored encoder built on structured state space models. The encoder incorporates multi-layer global convolution using multiscale subkernels, enabling the capture of both fine-grained local patterns and long-range temporal dependencies in noisy, high-resolution multichannel waveforms. Extensive experiments on real-world datasets demonstrate that SL-S4Wave (1) consistently outperforms state-of-the-art supervised and self-supervised baselines in a challenging arrhythmia detection task, (2) achieves high performance with significantly fewer labeled examples, showcasing strong label efficiency, and (3) maintains robust performance on long waveform segments, highlighting its capacity to model complex temporal dynamics in long sequences that most existing approaches fail to efficiently model, and (4) transfers effectively to unseen arrhythmia types, underscoring its robust cross-domain generalization. We additionally evaluate SL-S4Wave on multiple EEG tasks, achieving superior performance over strong baselines, demonstrating generalizability of our approach beyond cardiac waveforms.

Nanopores are versatile single-molecular sensors, but their utility is fundamentally constrained by stochastic translocation dynamics warping any encoded information. We resolve it by shifting from time-domain analysis to a learned latent-space mapping via a contrastive encoder trained exclusively on simulated signals from a physics-informed model. This encoder maps solid-state nanopore signals of engineered DNA barcodes into an interpretable molecular coordinate system. The learned representation is responsive to structural barcode parameters while remaining invariant to acquisition conditions and translocation conformation, allowing data pooling across devices. Molecule identification requires a single pass through the encoder, reducing computational cost by three orders of magnitude relative to alignment-based methods. We experimentally validate through mixture quantification, rare-variant detection, consensus barcode reconstruction, and real-time signal acquisition. This shift from temporal analysis to mapping structural coordinates into a latent space changes the paradigm behind analyzing stochastic sensor signals by linking classification to interpretable encoded molecular information.

Foundation models offer a promising route to compress multi-modal physiological signals into compact representations of human health, with broad applications across sleep medicine, cardiology, neurology and other healthcare domains. Existing models have typically been trained with masked-reconstruction or contrastive objectives. However, masked reconstruction may be poorly suited to the stochastic nature of these signals, while contrastive approaches rely on positive-pair definitions despite the semantic invariances of physiological signals being poorly understood. In this work, we show that next-token prediction is a simple and scalable alternative. We develop Hypnos, a multi-modal sleep foundation model trained using eight different sensing modalities (e.g. EEG, ECG, respiratory signals) drawn from over 20,000 overnight polysomnography recordings. We tokenize each modality into streams of discrete tokens using residual vector quantization, then train a large auto-regressive RQ-Transformer to jointly predict the next token across all modalities in parallel. After training, Hypnos can be applied to continuous streams of sensor data from any subset of supported modalities, generating embeddings for downstream tasks. Across a range of benchmarks, Hypnos significantly outperforms existing foundation models. In sleep stage classification, we match the performance of strong supervised baselines on held-out test sets whilst using $100\times$ less labelled data. Hypnos even generalises to daytime physiology, surpassing a dedicated ECG foundation model at detecting atrial fibrillation. Our results demonstrate that next-token prediction is a strong self-supervised objective for representation learning from multi-modal physiological signals.

In healthcare, multimodal time series tasks often operate on incomplete observations in practice, for example when ECG segments are lost because electrodes detach or an entire respiratory channel is unavailable during overnight monitoring. Such missingness typically appears in two structurally distinct patterns: within-modality missing, where values are absent within an otherwise observed modality, and modality-level missing, where an entire modality is unavailable. Existing methods typically represent unobserved data implicitly through masks or missing embeddings, without learning instance-specific missing information, and most are designed for only one missingness pattern. A natural approach is to explicitly estimate the missing data; however, existing imputation methods treat missingness uniformly despite their different structural priors, and the imputation process is often isolated from downstream tasks, preventing downstream tasks from guiding imputation toward more informative representations. To address these limitations, we present PAMF, a multimodal time-series framework that explicitly handles different missingness patterns while coupling imputation with downstream prediction through prior-aware flow matching and weight sharing. Specifically, the method initializes the flow-matching source state with type-specific priors to distinguish two missing types. It further connects imputation and classification through architecturally matched encoders with weight sharing, transferring task-relevant representations into the imputation process. Experiments on multiple multimodal healthcare time-series benchmarks show that the proposed method achieves the strongest overall downstream performance across diverse datasets and missing settings compared with existing baselines.

In recent years, emotion recognition based on physiological signals such as electroencephalogram (EEG) has gained considerable attention, as internal physiological data offer greater objectivity and reliability compared to external behavioral data like facial expressions. However, due to distribution shifts caused by individual and contextual differences, along with variations in sample quality across modalities, constructing a cross-domain multimodal emotion recognition model with high generalization and robustness remains a key challenge. In this study, we propose a Unified Framework with Adaptive Multimodal Alignment (UF-AMA) to address cross-subject and cross-session emotion recognition using multimodal physiological signals. First, we construct a cross-modal feature fusion network comprising Transformer encoders and multi-head cross-attention modules, enabling the deep integration of EEG signals and eye-tracking data. Subsequently, we introduce a confidence-aware screening mechanism that dynamically assesses the predictive reliability of each modality branch on target domain samples, partitions samples into different quality subsets, and accordingly applies global consistency alignment and cross-modal distillation. Finally, we propose a multi-level domain adaptation framework that jointly optimizes the marginal and conditional distributions of both local modality-specific and global fusion features, thereby reducing cross-domain distribution shifts at multiple granularities. Extensive experiments on the SEED and SEED-IV datasets demonstrate that UF-AMA achieves state-of-the-art (SOTA) performance in both cross-subject and cross-session tasks. The source code is available at: https://github.com/BetterCoderLab/UF-AMA.

Electrocardiograms (ECGs) are widely used non-invasive measurements of cardiac activity and play a central role in clinical diagnosis. Recent multimodal approaches align ECG signals with clinical reports to incorporate diagnostic semantics, but clinical reports often fail to preserve the rich physiological structure of ECG waveforms, particularly across multiple levels of abstraction ranging from coarse diagnostic categories to fine-grained morphology. To address this limitation, we formulate ECG representation learning from an information-theoretic perspective and derive a tractable objective that jointly preserves signal structure and integrates clinical semantics. Based on this principle, we propose \textbf{MERIT} (Multimodal ECG Representation via Information Theory), a dual-branch pretraining framework combining masked ECG modeling with ECG--text contrastive alignment. Extensive experiments on PTB-XL and additional benchmarks demonstrate consistent improvements over prior methods, including gains exceeding $3$ F1 on PTB-XL All and $5$ F1 on SubClass classification. In zero-shot evaluation, MERIT further improves performance by up to $+2.66\%$ AUC and $+2.11\%$ F1 on PTB-XL SubClass, while also demonstrating robustness under multiple distribution-shift settings. Moreover, leveraging the learned ECG representations for ECG-conditioned clinical text generation with large language models improves text quality across several metrics, including ROUGE and METEOR. Together, these results demonstrate that MERIT learns more informative and clinically meaningful ECG representations, particularly for fine-grained clinical applications.

Time series classification (TSC) of biological signals has progressed from handcrafted, modality-specific approaches to deep architectures capable of representing the diverse waveform structures of underlying physiological processes (i.e., morphology). This review introduces a unified morphology--modality framework that connects waveform structure to a methodological design, revealing how spikes, bursts, oscillations, slow drift, and hierarchical rhythms inform model design. By analyzing electroencephalography, electromyography, electrocardiography, photoplethysmography, and ocular modalities (electrooculography, pupillometry, eye-tracking), the review demonstrates how morphology determines preprocessing and modeling strategies. Integrating evidence across these biological signals, the framework reveals that morphology, not model class, most strongly determines performance and interpretability. This provides insight into why deep models succeed when their inductive biases align with underlying waveform dynamics. This review also identifies future work including morphological data augmentation and evaluation metrics to improve generalization. Together, these insights position morphology-aware modeling as a unifying principle for developing generalizable, interpretable, and physiologically meaningful TSC models across biological signals.

Proteins encode diverse functions within complex three-dimensional structures, yet most deep learning representations remain highly entangled, obscuring the biophysical signals that underlie function. Here we introduce ProtDiS, a knowledge-guided framework that decomposes pretrained protein micro-environment embeddings into biologically grounded and task-relevant dimensions. Inspired by the information bottleneck principle, ProtDiS learns representations that balance informativeness and compression, yielding structural features that are more specific, independent, and information-efficient, and achieving consistent improvements across twelve downstream tasks, with the largest gains under structure-based splits. Protein- and residue-level analyses further show that ProtDiS differentiates proteins with similar folds but divergent functions and captures fine-grained biophysical signals critical. These findings suggest that knowledge-guided decomposition provides a general and interpretable approach for structuring latent spaces in protein structural modeling. The source code and implementation details are publicly available at https://github.com/AI-HPC-Research-Team/ProtDiS.

Cardiovascular disease remains the leading cause of global mortality, yet scalable cardiac monitoring is hindered by the gap between diagnostic-rich ECG and ubiquitous wearable PPG. Bridging this gap requires representations that are compact, transferable across modalities and devices, and deployable without task-specific retraining. Here we introduce biosignal fingerprints: compact latent representations of cardiovascular state derived from a cross-modal foundation model, the Multi-modal Masked Autoencoder (M2AE), trained on over 3.4 million paired ECG and PPG signals. M2AE integrates modality-specific encoders with a shared bottleneck and dual decoders, jointly optimized using reconstruction and cross-modal contrastive objectives, yielding generalizable fingerprints that retain intra- and inter-modality features. Like a biometric fingerprint, these representations uniquely encode an individual's cardiovascular state in a modality-agnostic, privacy-preserving form reusable across clinical tasks without exposing raw waveform data or requiring model retraining. Across 7 downstream tasks, spanning cross-modal reconstruction, cardiovascular disease classification, hypertension detection, mortality prediction, and demographic inference, biosignal fingerprints achieve competitive or superior performance compared to leading domain-specialist foundation models in frozen settings, including an AUROC of 0.974 for five-class CVD classification and 0.877 for hypertension detection, with a maximum improvement of 27.7% in AUROC across 5 classification tasks. Critically, strong performance is maintained with only a single modality, enabling deployment in resource-constrained, single-sensor environments typical of real-world wearable monitoring, with direct implications for continuous cardiovascular monitoring across clinical and consumer health settings.

According to the theory of constructed emotion, the brain actively forms emotion categories by integrating multimodal bodily signals, and constructs emotional experiences by using these categories to predict and interpret sensory inputs. While research has advanced in modeling individual emotion construction, the social process of co-construction-how a shared understanding of emotions emerges between individuals-remains computationally underexplored. This study investigates this process by modeling emergent communication between two embodied agents using the Metropolis-Hastings Naming Game (MHNG), grounded in the Collective Predictive Coding (CPC) framework. Our experiments, using visual, auditory, and simulated interoceptive inputs, yield two main findings. First, MHNG-based communication significantly improves the alignment, clarity, and inter-agent agreement of the learned emotion categories compared to non-communicative and non-selective baselines, with the alignment effect concentrated at the symbolic layer rather than the perceptual latent representation. Second, even when the two agents have systematically divergent interoceptive dynamics, communication still produces robust categorical alignment, with distinct, category-specific reshaping patterns of each agent's emotion categories-consistent with the constructed-emotion view that interoceptive heterogeneity is constitutive of, rather than an obstacle to, shared emotional meaning. These findings provide computational support for the co-constructionist view of emotion and extend the CPC framework from physical to socially-grounded domains.

Discovering structure in biological signals without supervision is a fundamental problem in computational intelligence, yet existing bioacoustic methods assume vocal production models or predefined semantic units, leaving non-vocal species poorly served. This work introduces BeeVe, an unsupervised framework for acoustic state discovery in collective honey bee buzzing. BeeVe uses the self-supervised Patchout Spectrogram Transformer (PaSST) as a frozen feature extractor, then trains a Vector-Quantized Variational Autoencoder (VQ-VAE) without labels on those embeddings, learning a finite discrete codebook of acoustic tokens directly from unlabelled hive audio. No labels, pretext tasks, or contrastive objectives are used at any stage. Post-hoc evaluation against known queen status reveals that the learned tokens separate queenright and queenless conditions with Jensen-Shannon Divergence values between 0.609 and 0.688, and that the queenless condition further decomposes into three internally coherent sub-states stable across experiments with different codebook sizes and random seeds. Token transition analysis confirms non-random sequential structure (p << 0.001) across all experiments. Generalisation to unseen recordings preserves both token overlap (Jaccard = 0.947) and global manifold topology. These results demonstrate that unsupervised discrete codebook learning can recover repeatable acoustic structure from a non-vocal biological signal without annotation, opening a path toward non-invasive acoustic hive health monitoring.

An interpretable and scalable framework for decoding driving behaviors from multimodal physiological signals is proposed in this study. We utilize multimodal physiological driving behavior large-scale dataset comprising synchronized electroencephalogram (EEG), electromyography (EMG), and galvanic skin response (GSR) signals. Our approach involves rigorous preprocessing followed by a domain-specific feature extraction pipeline targeting time-domain, frequency-domain, and derived physiological indices. To address high dimensionality, we employ SHAP-based elite feature selection, retaining the top 250 features to reduce computational overhead while preserving predictive power. Hyperparameter optimization for extreme gradient boosting (XGBoost) and light gradient boosting machine (LightGBM) models is conducted using Bayesian optimization via Optuna. Finally, a weighted soft-voting ensemble is constructed to leverage the complementary strengths of both gradient boosting frameworks. The results demonstrate that the proposed ensemble achieves a test accuracy of 80.91% and a macro-F1 score of 0.79, significantly outperforming single-modality baselines and traditional machine learning models. Ablation studies confirm an 8% performance gain over the best single modality (EEG), validating the necessity of multimodal fusion. SHAP analysis further validates the physiological plausibility of the model, revealing that the EEG contributes the majority of predictive weight, GSR and EMG features provide critical discriminatory signals for high-arousal and motor-intensive maneuvers.

Sleep foundation models have recently demonstrated strong performance on in-domain polysomnography tasks, including sleep staging, apnea detection, and disease risk prediction. In this work, we investigate whether sleep biosignals can serve as an effective pretraining distribution for learning representations that transfer beyond sleep to adjacent domains. Following sleep foundation models, we perform sleep-only multimodal contrastive pretraining (with a leave-one-out objective) and evaluate transfer to non-sleep EEG and ECG, two well-benchmarked biosignal modalities with heterogeneous datasets and clinically meaningful downstream tasks. Across eight downstream tasks spanning multiple EEG and ECG datasets, sleep pretraining consistently improves performance relative to training from scratch. Moreover, on several tasks, we achieve performance competitive with or surpassing prior specialized state-of-the-art and foundation models.

Spatio-temporal signals arising from event-driven biological processes, such as surface electromyography (sEMG), exhibit asynchronous and highly structured activation patterns that are challenging to model using conventional discrete or purely real-valued representations. In this work, we propose a continuous temporal modeling framework based on interference-based wave representations. The approach maps event-like input signals into a complex-valued latent wave field, where temporal structure is encoded through phase modulation and interactions between latent components. By projecting the resulting wave field onto an energy domain, the model induces structured activation patterns that capture both temporal localization and relational dependencies within finite observation windows, without relying on explicit recurrence or causal state propagation. The proposed formulation is particularly suited for event-driven biosignals, where continuous representations enable efficient gradient-based optimization and robust feature extraction. In particular, the method is designed to support learning from sEMG data for downstream control tasks in biomechanical systems, such as prosthetic devices and exoskeletons. Experimental results demonstrate that the proposed interference-based wave model provides improved representation quality compared to purely real-valued representations, while maintaining computational efficiency suitable for practical deployment.

Biosignals acquired from different locations on the body often provide temporally ordered views of the same underlying physiological process. However, most existing self supervised learning methods treat these signals as interchangeable views, overlooking the directional temporal dynamics that link them. A canonical example is the relationship between electrocardiography (ECG), which captures the electrical activation initiating each heartbeat, and photoplethysmography (PPG), which records the resulting peripheral pulse delayed by vascular dynamics. To capture this structured relationship, we introduce xMAE, a biosignal pretraining framework that leverages masked cross modal reconstruction across temporally ordered biosignals as a training time constraint to encourage physiologically meaningful timing structure in the learned representations. We show that pretraining with xMAE yields representations that outperform both unimodal and multimodal baselines on 15 of 19 downstream tasks, including cardiovascular outcome prediction, abnormal laboratory test detection, sleep staging, and demographic inference, while generalizing across devices, body locations, and acquisition settings. Further analysis suggests that the ECG PPG timing structure is reflected in the learned PPG representations. More broadly, xMAE demonstrates the effectiveness of incorporating temporal structure into multimodal pretraining when signals observe different stages of a shared underlying process. Code is available at https://github.com/hzhou3/xMAE.

Learning meaningful representations from medical time series (MedTS) such as ECG or EEG signals is a critical challenge. These signals are often high-dimensional, variable-length and rife with noise. Existing self-supervised approaches, such as Masked Autoencoders (MAEs) are highly effective for pre-training general-purpose encoders. However, they do not explicitly learn compact and semantically interpretable latent representations, typically relying on heuristic aggregation strategies such as global average pooling or a designated [CLS] token. We propose a novel framework that compresses a variable-length MedTS into a fixed-size set of $k$ latent Fingerprint Tokens. Our architecture employs a cross-attention bottleneck to generate these tokens and is trained with a dual-objective function. The first objective is a reconstruction loss, which ensures the tokens are \textit{sufficient statistics} for the original data. The second, a diversity penalty based on the Total Coding Rate (TCR), explicitly minimizes the redundancy between tokens, encouraging them to become statistically \textit{disentangled} representations. We present the theoretical justification for our method, framing it as a novel \textbf{Disentangled Rate-Distortion} problem. This approach produces a low-dimensional, interpretable, and sample-efficient representation, where each token is encouraged to capture an independent factor of variation, paving the way for more robust digital biomarkers.

Multivariate time series classification (MTSC) plays a crucial role in various domains, including biomedical signal analysis and motion monitoring. However, existing approaches, particularly deep learning models, often require high computational resources, making them unsuitable for real-time applications or deployment on low-cost hardware, such as IoT devices and wearable systems. In this paper, we propose the Univariate Channel Fusion (UCF) method to deal with MTSC efficiently. UCF transforms multivariate time series into a univariate representation through simple channel fusion strategies such as the mean, median, or dynamic time warping barycenter. This transformation enables the use of any classifier originally designed for univariate time series, providing a flexible and computationally lightweight alternative to complex models. We evaluate UCF in five case studies covering diverse application domains, including chemical monitoring, brain-computer interfaces, and human activity analysis. The results demonstrate that UCF often outperforms baseline methods and state-of-the-art algorithms tailored for MTSC, while achieving substantial gains in computational efficiency, being particularly effective in problems with high inter-channel correlation.

In this paper, a learning framework is introduced which incorporates principles of probabilistic inference, variational optimization, and geometry-preserving operations inspired by quantum transformations. The central innovation of this quantum-inspired variational convolution (QiVC) lies in its quantum-inspired rotated ensemble (QiRE) mechanism. QiRE performs differentiable low-dimensional subspace rotations of convolutional weights. By drawing a mathematical analogy from unitary evolution, this approach enables structured uncertainty modeling that respects the intrinsic geometry of the parameter space. To demonstrate its practical potential, the concept is instantiated in a QiVC-based convolutional network (QiVC-Net) and evaluated in the context of biosignal classification, focusing on phonocardiogram (PCG) recordings. The proposed QiVC-Net integrates an architecture in which the QiVC layer does not introduce additional parameters, instead performing an ensemble rotation of the convolutional weights through a structured mechanism ensuring robustness without added highly computational burden. Experiments on two benchmark datasets, PhysioNet CinC 2016 and PhysioNet CirCor DigiScope 2022, show that QiVC-Net achieves state-of-the-art performance, reaching accuracies of 97.84% and 97.89%, respectively. These findings highlight the versatility of the QiVC framework and its promise for advancing uncertainty-aware modeling in real-world biomedical signal analysis. The implementation of the QiVConv layer is available in GitHub for public use.

Cardiovascular diseases (CVDs) are the leading cause of death worldwide, accounting for approximately 17.9 million deaths each year. Early detection is critical, creating a demand for accurate and inexpensive pre-screening methods. Deep learning has recently been applied to classify abnormal heart sounds indicative of CVDs using synchronised phonocardiogram (PCG) and electrocardiogram (ECG) signals, as well as multichannel PCG (mPCG). However, state-of-the-art architectures remain underutilised due to the limited availability of synchronised and multichannel datasets. Augmented datasets and pre-trained models provide a pathway to overcome these limitations, enabling transformer-based architectures to be trained effectively. This work combines traditional signal processing with denoising diffusion models, WaveGrad and DiffWave, to create an augmented dataset to fine-tune a Wav2Vec 2.0-based classifier on multimodal and multichannel heart sound datasets. The approach achieves state-of-the-art performance. On the Computing in Cardiology (CinC) 2016 dataset of single channel PCG, accuracy, unweighted average recall (UAR), sensitivity, specificity and Matthew's correlation coefficient (MCC) reach 92.48%, 93.05%, 93.63%, 92.48%, 94.93% and 0.8283, respectively. Using the synchronised PCG and ECG signals of the training-a dataset from CinC, 93.14%, 92.21%, 94.35%, 90.10%, 95.12% and 0.8380 are achieved for accuracy, UAR, sensitivity, specificity and MCC, respectively. Using a wearable vest dataset consisting of mPCG data, the model achieves 77.13% accuracy, 74.25% UAR, 86.47% sensitivity, 62.04% specificity, and 0.5082 MCC. These results demonstrate the effectiveness of transformer-based models for CVD detection when supported by augmented datasets, highlighting their potential to advance multimodal and multichannel heart sound classification.

Purpose: Uncertainty Quantification (UQ) has gained traction in an attempt to improve the interpretability and robustness of machine learning predictions. Specifically (medical) biosignals such as electroencephalography (EEG), electrocardiography (ECG), electrooculography (EOG), and electromyography (EMG) could benefit from good UQ, since these suffer from a poor signal-to-noise ratio, and good human interpretability is pivotal for medical applications. To determine how uncertainty estimation can be used for biosignal tasks, we investigate current methods, use cases, applications, evaluations, and uncertainty measures. Methods: In this paper, we systematically review the state of the art of applying Uncertainty Quantification to Machine Learning tasks in the biosignal domain. All works from Web of Science, Scopus, IEEE XPlore and PsycINFO that discuss uncertainty in Machine Learning on one of the aforementioned biosignals is included. Results: We present various methods, shortcomings, uncertainty measures and theoretical frameworks that currently exist in this application domain based on the 53 reviewed papers and related literature. We address misconceptions in the field, provide recommendations for future work, and discuss gaps in the literature in relation to diagnostic implementations as well as control for prostheses or brain-computer interfaces. Conclusion: Overall it can be concluded that promising UQ methods are available, but that research is needed on how people and systems may interact with an uncertainty-model in a (clinical) environment.