SL-S4Wave: Self-Supervised Learning of Physiological Waveforms with Structured State Space Models

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.

G-Transformer: Counterfactual Outcome Prediction under Dynamic and Time-varying Treatment Regimes

In the context of medical decision making, counterfactual prediction enables clinicians to predict treatment outcomes of interest under alternative courses of therapeutic actions given observed patient history. Prior machine learning approaches for counterfactual predictions under time-varying treatments focus on static time-varying treatment regimes where treatments do not depend on previous covariate history. In this work, we present G-Transformer, a Transformer-based framework supporting g-computation for counterfactual prediction under dynamic and time-varying treatment strategies. G-Transfomer captures complex, long-range dependencies in time-varying covariates using a Transformer architecture. G-Transformer estimates the conditional distribution of relevant covariates given covariate and treatment history at each time point using an encoder architecture, then produces Monte Carlo estimates of counterfactual outcomes by simulating forward patient trajectories under treatment strategies of interest. We evaluate G-Transformer extensively using two simulated longitudinal datasets from mechanistic models, and a real-world sepsis ICU dataset from MIMIC-IV. G-Transformer outperforms both classical and state-of-the-art counterfactual prediction models in these settings. To the best of our knowledge, this is the first Transformer-based architecture for counterfactual outcome prediction under dynamic and time-varying treatment strategies. Code will be released upon publication of the paper.