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Causal analyses of longitudinal data generally assume that the qualitative causal structure relating variables remains invariant over time. In structured systems that transition between qualitatively differ- ent states in discrete time steps, such an approach is deficient on two fronts. First, time-varying variables may have state-specific causal relationships that need to be captured. Second, an intervention can result in state transitions downstream of the intervention different from those actually observed in the data. In other words, interventions may counter- factually alter the subsequent temporal evolution of the system. We introduce a generalization of causal graphical models, Path Dependent Structural Equation Models (PDSEMs), that can describe such systems. We show how causal inference may be performed in such models and illustrate its use in simulations and data obtained from a septoplasty surgical procedure. 

The data drawn from biological, economic, and social systems are often confounded due to the presence of unmeasured variables. Prior work in causal discovery has focused on discrete search procedures for selecting acyclic directed mixed graphs (ADMGs), specifically ancestral ADMGs, that encode ordinary conditional independence constraints among the observed variables of the system. However, confounded systems also exhibit more general equality restrictions that cannot be represented via these graphs, placing a limit on the kinds of structures that can be learned using ancestral ADMGs. In this work, we derive differentiable algebraic constraints that fully characterize the space of ancestral ADMGs, as well as more general classes of ADMGs, arid ADMGs and bow-free ADMGs, that capture all equality restrictions on the observed variables. We use these constraints to cast causal discovery as a continuous optimization problem and design differentiable procedures to find the best fitting ADMG when the data comes from a confounded linear system of equations with correlated errors. We demonstrate the efficacy of our method through simulations and application to a protein expression dataset. Code implementing our methods is open-source and publicly available at https: //gitlab.com/rbhatta8/dcd and will be incorporated into the Ananke package.