WaveGNN: Integrating Graph Neural Networks and Transformers for Decay-Aware Classification of Irregular Clinical Time-Series

Abstract

Clinical time series are often irregularly sampled, with varying sensor frequencies, missing observations, and misaligned timestamps. Prior approaches typically address these irregularities by interpolating data into regular sequences, thereby introducing bias, or by generating inconsistent and uninterpretable relationships across sensor measurements, complicating the accurate learning of both intra-series and inter-series dependencies. We introduce WaveGNN, a model that operates directly on irregular multivariate time series without interpolation or conversion to a regular representation. WaveGNN combines a decay-aware Transformer to capture intra-series dynamics with a sample-specific graph neural network that models both short-term and long-term inter-sensor relationships. Therefore, it generates a single, sparse, and interpretable graph per sample. Across multiple benchmark datasets (P12, P19, MIMIC-III, and PAM), WaveGNN delivers consistently strong performance, whereas other state-of-the-art baselines tend to perform well on some datasets or tasks but poorly on others. While WaveGNN does not necessarily surpass every method in every case, its consistency and robustness across diverse settings set it apart. Moreover, the learned graphs align well with known physiological structures, enhancing interpretability and supporting clinical decision-making.