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Life sciences · Preprint
arXiv · October 2, 2026
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Causal representation learning for time-series data aims to identify latent states and their causal relations from observations. In this setting, an important challenge is to model both lagged causal relations across observation intervals and faster causal effects that appear as instantaneous relations within an interval, while accounting for nonstationarity in time-series data. However, methods that jointly handle these causal relations and nonstationarity remain limited. To address this gap, we establish sufficient conditions for identifying latent states up to component permutation and component-wise invertible transformations, and their instantaneous and lagged causal structures up to the same permutation, using an observed auxiliary variable, such as time or a condition label, associated with changes in transition-noise distributions. Based on these results, we propose iCReN, a framework that uses contrastive learning with discrete or continuous auxiliary variables to learn latent representations and estimate their instantaneous and lagged causal structures. Experiments demonstrate accurate recovery of latent states and both instantaneous and lagged causal structures on synthetic data and the utility of the learned representations for downstream forecasting on real-world data.