Latent Confounded Causal Discovery via Lie Bracket Geometry

We study causal discovery from observational and interventional regimes when latent variables may affect the measured system. Our first algorithm, BRIDGE (Bracket Residuals for Interventional Discovery and Geometric Estimation), combines a density-ratio or transport engine with a high-recall geometric screen and passes the retained arrows to a score-based or differentiable discovery method. The main formulation and experiments use known single-node intervention targets; in that regime the screen is designed to retain candidate directed effects, while a downstream learner determines the final graph or equivalence-class representation. Our second algorithm, Spectral Kernel Flow Matching (SKFM), amortizes the response fields, summarizes residual nonclosure by a spectral visible-footprint subspace, and applies an order-dependent graph extractor. Direct extraction succeeds on calibrated chains and selected motifs, but is unstable on harder random DAGs when the order must be learned. On ten-node nonlinear random DAGs, the more reliable hybrid role of the geometry is as a candidate generator: calibrated SKFM/Bridge fields followed by local BIC scoring achieve mean directed F1simeq0.86. Sachs protein signaling provides a real-data stress test and supports a diagnostic, not fully identified, interpretation. The contribution is therefore a practical interventional screening pipeline, explicit guarantees for screen retention and residual-footprint rank under stated assumptions, and a falsifiable account of the boundary between geometric diagnostics and causal identification.