Contrastive Representation-Guided Genetic Minority Oversampling for Imbalanced Time-Series Classification

Synthetic medical time-series generation can alleviate data scarcity and support the development of reliable clinical prediction models. However, existing methods mainly focus on matching the overall distribution and temporal dynamics of real data, which does not necessarily ensure strong downstream utility on imbalanced medical datasets. Clinically informative patterns often occur at heterogeneous temporal scales, while rare minority-class characteristics can be obscured by dominant population patterns. To address these challenges, we propose MedFlow, a class-aware multi-scale flow matching framework for medical time-series synthesis. MedFlow employs a vector-quantized multi-scale tokenizer to represent medical sequences at complementary temporal resolutions, capturing both coarse clinical trends and fine-grained dynamics. We further introduce Token Marginal Guidance, which incorporates class-conditional token statistics directly into the flow matching process to steer generation toward class-specific regions of the learned tokens. This mechanism strengthens minority-class patterns, while preserving the global and tail distributions of real data. Experiments on four public datasets covering electronic health records, EEG, and ECG signals demonstrate that MedFlow consistently outperforms recent state-of-the-art diffusion-based baselines across downstream prediction tasks. On average, it improves AUPRC by 5.8%, reduces Context-FID by 88.6%, and achieves 3.8$\times$ higher sampling throughput.

Class imbalance complicates probabilistic classification because standard training objectives emphasize majority-class performance. Synthetic oversampling can reduce imbalance, but discrepancies between the synthetic and target minority distributions may bias the fitted classifier, especially because synthetic samples depend on the observed data. We propose a bias-correction procedure that estimates the generator-induced loss discrepancy from a held-out subset of majority observations and transfers this correction to the minority class under a uniform bias-transfer condition. We establish finite-sample bounds for bias transfer and for the excess balanced risk of the resulting empirical risk minimizer, and characterize a regime in which SMOTE induces non-negligible loss bias. The framework can also be implemented in imbalanced multi-task learning and propensity-score estimation, with details provided in the Supplementary Material. Real data analyses show that the correction is most useful when synthetic distortion is appreciable.

Supervised learning demands large quantities of labeled data, a bottleneck that is expensive and reliant on domain-specific expertise. Self-supervised learning, particularly contrastive learning, has emerged as a compelling alternative, enabling rich representation learning directly from unlabeled data. Yet its success hinges critically on the design of positive and negative sample pairs. Existing approaches for time series rely on hand-crafted augmentations and masking heuristics that embed strong domain assumptions, often limiting generalization across diverse temporal patterns and potentially introducing spurious correlations. In this work, we challenge this paradigm by demonstrating that explicitly encoding temporal shift invariance through a simple, deterministic view construction is sufficient to learn strong representations for time series classification. By exploiting temporal structure, our method, Shift Invariant Feature Training (ShiFT), achieves state-of-the-art performance on six diverse real-world time series benchmark datasets, as well as the UCR and UEA archives, while reducing training time. Beyond empirical performance, we present a systematic analysis of contrastive learning dynamics in time series settings, examining the effects of batch size and the number of negatives on downstream performance. Our findings provide practical insights for designing efficient contrastive learning frameworks for time series representation learning. The source code is publicly available at https://github.com/sfi-norwai/ShiFT.