Causal Inference for Sequential Settings under Interference and Latent Confounding

We study causal inference under outcome interference for sequential, observational settings. Specifically, we consider settings where the binary outcomes over N units are Markovian across T time steps. At each time step, the outcomes of N units have dependencies captured through an Ising model; each outcome is also impacted through an external field capturing the effects of its treatment as well as latent confounders. Similar to panel data literature, these latent confounders are modeled to have a low-rank factor structure. Our data is a single sample from this high-dimensional distribution. To estimate causal quantities of interest, we provide a computationally efficient method based on Maximum Pseudo-Likelihood Estimation (MPLE) for learning the model parameters. Under mild assumptions, we establish non-asymptotic consistency for parameter estimation and show this translates to faithful estimation of causal quantities of interest after sampling from the learned model. We demonstrate the efficacy of the method through synthetic experiments as well as a real-world case-study investigating causal effects of vaccine rates on COVID-19 death rates within US counties nationwide.

The Spectral Structure of Latent Treatment Effects

Identifying heterogeneous treatment effects under unobserved confounding is central in observational causal inference. In proxy models with a discrete latent confounder, prior Synthetic Potential Outcomes (SPO) [Mazaheri-Squires-Uhler '25] recover the mixture of treatment effects through recursively constructed scalar moments. We show that this sequence is one projection of a more fundamental object. Under the same population factorization assumptions, there is an exact compressed observable operator: after projecting onto the shared proxy signal subspace, the difference of two treatment-arm quotient operators is similar to the diagonal matrix of latent treatment effects. Its eigenvalues are the latent effects; its lifted left eigenvectors, after anchor normalization, recover the target-proxy feature matrix and then the latent mixture proportions. Every scalar SPO moment is a bilinear functional of a power of this operator. The resulting estimator handles overcomplete proxy systems, replaces high-order scalar inversion with finite-dimensional spectral analysis, and admits high-probability first-order perturbation bounds for treatment effects, feature rows, and simplex-projected mixture weights.

How Does Bayesian Causal Discovery Fail? Characterising Structural Consequences in Linear Gaussian Networks under Latent Confounding

Bayesian causal discovery is widely used for its ability to quantify epistemic uncertainty over directed acyclic graphs (DAGs) through posterior inference. However, its behaviour under latent confounding remains poorly understood, as existing work typically notes that confounding breaks identifiability without characterising how the posterior distribution over DAGs responds. In this work, we analyse posterior behaviour under latent confounding in linear Gaussian causal models, focusing on additive latent confounding between exactly two observed variables. We derive a critical correlation threshold above which the score function favours graphs with a spurious edge between the confounded variables, and show that this threshold decreases with sample size -- more data lowers the correlation required for the spurious edge to be favoured. Beyond this threshold, we characterize two distinct posterior failure regimes determined by the local structure around the confounded variables. Our findings are supported by exact posterior computations on multiple graph structures, demonstrating both the predicted failure regimes.

FoundCause: Causal Discovery with Latent Confounders from Observational Data

Causal discovery from observational data remains challenging due to the need to recover directed structure and latent confounding without interventions. We propose FoundCause, an amortized causal discovery model trained entirely on synthetic data that maps datasets directly to causal graphs in a single forward pass. By learning from large collections of simulated structural causal models, FoundCause captures transferable statistical patterns that generalize beyond individual datasets. The architecture incorporates several key inductive biases for causal discovery. It uses a permutation-invariant transformer encoder with alternating attention over samples and variables to jointly model cross-variable dependence and per-variable distributions. Pairwise statistical features derived from classical asymmetry measures are injected through statistics-conditioned attention, guiding the model toward known causal signals. A factorized decoder separates edge existence from direction, while a triangular refinement module enables reasoning over higher-order causal motifs such as chains and colliders. In addition, a dedicated confounder module based on learnable latent tokens explicitly models hidden common causes, and the model explicitly handles missing data via its masked input representation. To our knowledge, FoundCause is the first amortized causal discovery approach to explicitly model latent confounding. FoundCause outperforms 11 classical non-amortized methods (e.g., PC, GES, NOTEARS-style optimization) and 4 amortized causal discovery methods on 15 real-world datasets, achieving +9.6% improvement in $F_1$, +1.2% in AUROC, and an 18.9% reduction in structural Hamming distance relative to the strongest non-amortized methods, while performing inference in a single forward pass.