Beyond Missing Data Imputation: Information-Theoretic Coupling of Missingness and Class Imbalance for Optimal Irregular Time Series Classification

Irregular time series (IRTS) are prevalent in real-world applications, where uneven sampling and missing data pose fundamental challenges to deep learning-based feature modeling. Although existing methods attempt to retain timestamp information, they often overlook the structured patterns embedded within the missingness itself, and tend to perform poorly when confronted with class imbalance exacerbated by data incompleteness. Specifically, temporal irregularity hinders the modeling of long-range dependencies and local patterns, while sparse observations limit representational capacity, disproportionately impairing minority classes and leading to severe classification bias. To address these deeply coupled challenges, we propose SPECTRA (Structured Pattern and Enriched Context-aware Temporal Representation Architecture), a unified framework for robust IRTS classification. SPECTRA introduces a frequency-guided observation encoder that reconstructs temporal dependencies in a stable manner, mitigating spectral distortion and information corruption. Complementarily, a missingness pattern encoder explicitly captures the dynamic evolution of missing data and leverages it as a discriminative signal. In addition, a prototype-constrained classification paradigm directly optimizes the geometric structure of the feature space, enhancing intra-class compactness and alleviating generalization bottlenecks caused by class imbalance. Extensive experiments on three public IRTS datasets-P12, P19, and PAM-demonstrate the superior performance of SPECTRA under both missing and imbalanced conditions.