The identifiability analysis of linear Ordinary Differential Equation (ODE) systems is a necessary prerequisite for making reliable causal inferences about these systems. While identifiability has been well studied in scenarios where the system is fully observable, the conditions for identifiability remain unexplored when latent variables interact with the system. This paper aims to address this gap by presenting a systematic analysis of identifiability in linear ODE systems incorporating hidden confounders. Specifically, we investigate two cases of such systems. In the first case, latent confounders exhibit no causal relationships, yet their evolution adheres to specific functional forms, such as polynomial functions of time t. Subsequently, we extend this analysis to encompass scenarios where hidden confounders exhibit causal dependencies, with the causal structure of latent variables described by a Directed Acyclic Graph (DAG). The second case represents a more intricate variation of the first case, prompting a more comprehensive identifiability analysis. Accordingly, we conduct detailed identifiability analyses of the second system under various observation conditions, including both continuous and discrete observations from single or multiple trajectories. To validate our theoretical results, we perform a series of simulations, which support and substantiate our findings.
We study identifiability in continuous-time linear stationary stochastic differential equations with a known causal structure. Unlike existing approaches, we relax the assumption of a known diffusion matrix, thereby respecting the model's intrinsic scale invariance. Therefore, rather than recovering drift coefficients themselves, we introduce edge-sign identifiability: for a given causal structure, we ask whether the sign of a given drift entry is uniquely determined across all observational covariance matrices induced by parametrisations compatible with that structure. This leads to a trichotomy of edge-sign identifiability: identifiable, non-identifiable, and partially identifiable. This trichotomy introduces the new notion of partial identifiability to the literature, which we show is a genuine category in our setting. Under a notion of faithfulness, we derive criteria to identify membership of each category for general graphs. Applying our criteria to specific causal structures, both analogous to classical causal settings (e.g., instrumental variables) and novel cyclic settings, we determine their edge-sign identifiability and, in some cases, obtain explicit expressions for the sign of a target edge in terms of the observational covariance matrix.
Causal inference in continuous-time sequential decision problems is challenged by hidden confounding and partially observed states. We show that, under explicit structural assumptions, observability of the latent state enables identification of dynamic treatment effects through a continuous-time conditional front-door adjustment, even in the presence of hidden confounding. We derive a general adjustment formula and show that it reduces to a tractable state-space formula when unobserved contemporaneous disturbances are temporally uncorrelated. This formula expresses potential-outcome distributions under alternative treatment trajectories through the measurement model, latent dynamics, and the filtering distribution over latent states. We propose Observable Neural ODEs (ObsNODEs), Neural ODE models in observable normal form that implement this tractable adjustment for causal forecasting. ObsNODEs learn continuous-time dynamics with states reconstructible from observations, enabling outcome prediction under alternative treatment paths. Experiments on synthetic, semi-synthetic, and real-world clinical data demonstrate strong performance over recent sequence models, including external validation.
Jennifer Wendland, Nicolas Freitag, Maik Kschischo
Department of Computer Science University of Koblenz 53424 Koblenz, Germany
Causal discovery aims to recover causal relationships from observed data. In various fields, exploring causal relationships among variables remains an important topic, but this task becomes challenging due to the existence of latent confounders. Ignoring such confounders can lead to false associations and incorrect edge directions. In this paper, we study the linear structural equation model with latent confounders. We propose an algorithm that iteratively identifies terminal (observed) nodes and reconstructs the directed acyclic graph of the observed variables. To do this, we recover the precision matrix of the observed variables as a sparse plus low-rank matrix: a sparse matrix captures the conditional dependencies among observed variables, while a low-rank matrix captures the combined influence of a few latent confounders. We establish that for p observed variables, r latent confounders and s edges, our procedure correctly identifies the directed causal relationship among observed variables, for n≳max{slogp,rp} samples. Experimental results validate our theoretical contributions.