polyDAG: Polynomial Acyclicity Constraints for Efficient Continuous Causal Discovery in Visual Semantic Graphs

Inferring the structure of directed acyclic graphs (DAGs) from data is a central challenge in causal discovery, particularly in modern high-dimensional settings where large-scale interventional data are increasingly available. While interventional data can improve identifiability, existing methods remain limited by soft acyclicity constraints, leading to optimization over invalid cyclic graphs, numerical instability, and reduced scalability. We introduce PACER (Perturbation-driven Acyclic Causal Edge Recovery), a scalable framework for causal discovery that guarantees acyclicity by construction. PACER parameterizes a distribution over DAGs through a joint model of variable permutations and edge probabilities, enabling direct optimization over valid causal structures without surrogate penalties. The framework supports a unified likelihood-based treatment of observational and interventional data, flexible conditional density models, and the incorporation of structural prior knowledge. For linear-Gaussian mechanisms, we derive closed-form expressions for the expected interventional log-likelihood and its gradients, yielding substantial computational gains. Empirically, PACER matches or exceeds state-of-the-art methods on protein signaling and large-scale genetic perturbation benchmarks, while scaling efficiently to networks with thousands of variables and achieving up to two orders of magnitude speedups over penalty-based differentiable approaches. These results demonstrate that exact and scalable causal discovery from high-dimensional perturbation data is achievable through principled search space design.

This work addresses the problem of learning directed acyclic graphs (DAGs) from nodal observations generated by a linear structural equation model. DAG learning is a central task in signal processing, machine learning, and causal inference, but it remains challenging because acyclicity is a global combinatorial property. Continuous acyclicity constraints have led to important algorithmic advances by replacing the discrete DAG constraint with smooth equality constraints. However, existing formulations still involve difficult non-convex optimization landscapes and may suffer from degenerate first-order optimality conditions. Here, we restrict attention to DAGs with non-negative edge weights and exploit this additional structure to obtain a simpler characterization of acyclicity. Building on this characterization, we formulate a regularized non-negative DAG learning problem and develop an algorithm based on the method of multipliers. We further analyze the benign optimization landscape induced by non-negativity. In the population regime, we show that the true DAG is the unique global minimizer of the proposed augmented-Lagrangian formulation; moreover, the landscape contains no spurious interior stationary points, and the true DAG is the only acyclic KKT point. Numerical experiments on synthetic and real-world data show that the proposed method improves over state-of-the-art continuous DAG-learning alternatives.

Continuous optimization methods for learning Directed Acyclic Graphs (DAGs) operate on weighted adjacency matrices and are therefore limited to pairwise causal relationships. We propose a framework for learning Directed Acyclic Hypergraphs (DAHGs) from observational data, capturing joint parental influences that pairwise models cannot represent. Our approach rests on three components: (i) a generalized linear structural equation model (SEM) with multiplicative interaction terms whose non-zero weights correspond one-to-one with directed hyperedges; (ii) a weighted adjacency tensor representation whose acyclicity is characterized via nilpotency under the tensor t-product; and (iii) a differentiable acyclicity constraint derived through the Fourier decomposition of the t-product, which reduces tensor nilpotency to slice-wise matrix nilpotency and enables least-squares learning via the augmented Lagrangian method.