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Recent advancements in machine learning-based signal analysis, coupled with open data initiatives, have fuelled efforts in automatic sleep stage classification. Despite the proliferation of classification models, few have prioritised reducing model complexity, which is a crucial factor for practical applications. In this work, we introduce Multi-Scale and Attention Convolutional Neural Network (MSA-CNN), a lightweight architecture featuring as few as ~10,000 parameters. MSA-CNN leverages a novel multi-scale module employing complementary pooling to eliminate redundant filter parameters and dense convolutions. Model complexity is further reduced by separating temporal and spatial feature extraction and using cost-effective global spatial convolutions. This separation of tasks not only reduces model complexity but also mirrors the approach used by human experts in sleep stage scoring. We evaluated both small and large configurations of MSA-CNN against nine state-of-the-art baseline models across three public datasets, treating univariate and multivariate models separately. Our evaluation, based on repeated cross-validation and re-evaluation of all baseline models, demonstrated that the large MSA-CNN outperformed all baseline models on all three datasets in terms of accuracy and Cohen's kappa, despite its significantly reduced parameter count. Lastly, we explored various model variants and conducted an in-depth analysis of the key modules and techniques, providing deeper insights into the underlying mechanisms. The code for our models, baselines, and evaluation procedures is available at https://github.com/sgoerttler/MSA-CNN.

Electroencephalography (EEG) is a non-invasive technique to measure and record brain electrical activity, widely used in various BCI and healthcare applications. Early EEG decoding methods rely on supervised learning, limited by specific tasks and datasets, hindering model performance and generalizability. With the success of large language models, there is a growing body of studies focusing on EEG foundation models. However, these studies still leave challenges: Firstly, most of existing EEG foundation models employ full EEG modeling strategy. It models the spatial and temporal dependencies between all EEG patches together, but ignores that the spatial and temporal dependencies are heterogeneous due to the unique structural characteristics of EEG signals. Secondly, existing EEG foundation models have limited generalizability on a wide range of downstream BCI tasks due to varying formats of EEG data, making it challenging to adapt to. To address these challenges, we propose a novel foundation model called CBraMod. Specifically, we devise a criss-cross transformer as the backbone to thoroughly leverage the structural characteristics of EEG signals, which can model spatial and temporal dependencies separately through two parallel attention mechanisms. And we utilize an asymmetric conditional positional encoding scheme which can encode positional information of EEG patches and be easily adapted to the EEG with diverse formats. CBraMod is pre-trained on a very large corpus of EEG through patch-based masked EEG reconstruction. We evaluate CBraMod on up to 10 downstream BCI tasks (12 public datasets). CBraMod achieves the state-of-the-art performance across the wide range of tasks, proving its strong capability and generalizability. The source code is publicly available at \url{https://github.com/wjq-learning/CBraMod}.

Accurate sleep stage classification is crucial for diagnosing sleep disorders and evaluating sleep quality. While polysomnography (PSG) remains the gold standard, photoplethysmography (PPG) is more practical due to its affordability and widespread use in wearable devices. However, state-of-the-art sleep staging methods often require prolonged continuous signal acquisition, making them impractical for wearable devices due to high energy consumption. Shorter signal acquisitions are more feasible but less accurate. Our work proposes an adapted sleep staging model based on top-performing state-of-the-art methods and evaluates its performance with different PPG segment sizes. We concatenate 30-second PPG segments over 15-minute intervals to leverage longer segment contexts. This approach achieved an accuracy of 0.75, a Cohen's Kappa of 0.60, an F1-Weighted score of 0.74, and an F1-Macro score of 0.60. Although reducing segment size decreased sensitivity for deep and REM stages, our strategy outperformed single 30-second window methods, particularly for these stages.

This study aims to elucidate the significance of long-range correlations for deep-learning-based sleep staging. It is centered around S4Sleep(TS), a recently proposed model for automated sleep staging. This model utilizes electroencephalography (EEG) as raw time series input and relies on structured state space sequence (S4) models as essential model component. Although the model already surpasses state-of-the-art methods for a moderate number of 15 input epochs, recent literature results suggest potential benefits from incorporating very long correlations spanning hundreds of input epochs. In this submission, we explore the possibility of achieving further enhancements by systematically scaling up the model's input size, anticipating potential improvements in prediction accuracy. In contrast to findings in literature, our results demonstrate that augmenting the input size does not yield a significant enhancement in the performance of S4Sleep(TS). These findings, coupled with the distinctive ability of S4 models to capture long-range dependencies in time series data, cast doubt on the diagnostic relevance of very long-range interactions for sleep staging.

Automatic sleep staging is essential for sleep assessment and disorder diagnosis. Most existing methods depend on one specific dataset and are limited to be generalized to other unseen datasets, for which the training data and testing data are from the same dataset. In this paper, we introduce domain generalization into automatic sleep staging and propose the task of generalizable sleep staging which aims to improve the model generalization ability to unseen datasets. Inspired by existing domain generalization methods, we adopt the feature alignment idea and propose a framework called SleepDG to solve it. Considering both of local salient features and sequential features are important for sleep staging, we propose a Multi-level Feature Alignment combining epoch-level and sequence-level feature alignment to learn domain-invariant feature representations. Specifically, we design an Epoch-level Feature Alignment to align the feature distribution of each single sleep epoch among different domains, and a Sequence-level Feature Alignment to minimize the discrepancy of sequential features among different domains. SleepDG is validated on five public datasets, achieving the state-of-the-art performance.

Background: Injection drug use (IDU) is a dangerous health behavior that increases mortality and morbidity. Identifying IDU early and initiating harm reduction interventions can benefit individuals at risk. However, extracting IDU behaviors from patients' electronic health records (EHR) is difficult because there is no International Classification of Disease (ICD) code and the only place IDU information can be indicated is unstructured free-text clinical notes. Although natural language processing can efficiently extract this information from unstructured data, there are no validated tools. Methods: To address this gap in clinical information, we design and demonstrate a question-answering (QA) framework to extract information on IDU from clinical notes. Our framework involves two main steps: (1) generating a gold-standard QA dataset and (2) developing and testing the QA model. We utilize 2323 clinical notes of 1145 patients sourced from the VA Corporate Data Warehouse to construct the gold-standard dataset for developing and evaluating the QA model. We also demonstrate the QA model's ability to extract IDU-related information on temporally out-of-distribution data. Results: Here we show that for a strict match between gold-standard and predicted answers, the QA model achieves 51.65% F1 score. For a relaxed match between the gold-standard and predicted answers, the QA model obtains 78.03% F1 score, along with 85.38% Precision and 79.02% Recall scores. Moreover, the QA model demonstrates consistent performance when subjected to temporally out-of-distribution data. Conclusions: Our study introduces a QA framework designed to extract IDU information from clinical notes, aiming to enhance the accurate and efficient detection of people who inject drugs, extract relevant information, and ultimately facilitate informed patient care.

Accurate sleep stage classification is significant for sleep health assessment. In recent years, several machine-learning based sleep staging algorithms have been developed , and in particular, deep-learning based algorithms have achieved performance on par with human annotation. Despite improved performance, a limitation of most deep-learning based algorithms is their black-box behavior, which have limited their use in clinical settings. Here, we propose a cross-modal transformer, which is a transformer-based method for sleep stage classification. The proposed cross-modal transformer consists of a novel cross-modal transformer encoder architecture along with a multi-scale one-dimensional convolutional neural network for automatic representation learning. Our method outperforms the state-of-the-art methods and eliminates the black-box behavior of deep-learning models by utilizing the interpretability aspect of the attention modules. Furthermore, our method provides considerable reductions in the number of parameters and training time compared to the state-of-the-art methods. Our code is available at https://github.com/Jathurshan0330/Cross-Modal-Transformer. A demo of our work can be found at https://bit.ly/Cross_modal_transformer_demo.

In many machine learning applications on signals and biomedical data, especially electroencephalogram (EEG), one major challenge is the variability of the data across subjects, sessions, and hardware devices. In this work, we propose a new method called Convolutional Monge Mapping Normalization (CMMN), which consists in filtering the signals in order to adapt their power spectrum density (PSD) to a Wasserstein barycenter estimated on training data. CMMN relies on novel closed-form solutions for optimal transport mappings and barycenters and provides individual test time adaptation to new data without needing to retrain a prediction model. Numerical experiments on sleep EEG data show that CMMN leads to significant and consistent performance gains independent from the neural network architecture when adapting between subjects, sessions, and even datasets collected with different hardware. Notably our performance gain is on par with much more numerically intensive Domain Adaptation (DA) methods and can be used in conjunction with those for even better performances.

Scoring sleep stages in polysomnography recordings is a time-consuming task plagued by significant inter-rater variability. Therefore, it stands to benefit from the application of machine learning algorithms. While many algorithms have been proposed for this purpose, certain critical architectural decisions have not received systematic exploration. In this study, we meticulously investigate these design choices within the broad category of encoder-predictor architectures. We identify robust architectures applicable to both time series and spectrogram input representations. These architectures incorporate structured state space models as integral components, leading to statistically significant advancements in performance on the extensive SHHS dataset. These improvements are assessed through both statistical and systematic error estimations. We anticipate that the architectural insights gained from this study will not only prove valuable for future research in sleep staging but also hold relevance for other time series annotation tasks.