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Recently, an intriguing class of non-convex optimization problems has emerged in the context of learning directed acyclic graphs (DAGs). These problems involve minimizing a given loss or score function, subject to a non-convex continuous constraint that penalizes the presence of cycles in a graph. In this work, we delve into the optimality challenges associated with this class of non-convex programs. To address these challenges, we propose a bi-level algorithm that leverages the non-convex constraint in a novel way. The outer level of the algorithm optimizes over topological orders by iteratively swapping pairs of nodes within the topological order of a DAG. A key innovation of our approach is the development of an effective method for generating a set of candidate swapping pairs for each iteration. At the inner level, given a topological order, we utilize off-the-shelf solvers that can handle linear constraints. The key advantage of our proposed algorithm is that it is guaranteed to find a local minimum or a KKT point under weaker conditions compared to previous work and finds solutions with lower scores. Extensive experiments demonstrate that our method outperforms state-of-the-art approaches in terms of achieving a better score. Additionally, our method can also be used as a post-processing algorithm to significantly improve the score of other algorithms. Code implementing the proposed method is available at https://github.com/duntrain/topo. 

Recently, a new class of non-convex optimization problems motivated by the statistical problem of learning an acyclic directed graphical model from data has attracted significant interest. While existing work uses standard first-order optimization schemes to solve this problem, proving the global optimality of such approaches has proven elusive. The difficulty lies in the fact that unlike other non-convex problems in the literature, this problem is not "benign", and possesses multiple spurious solutions that standard approaches can easily get trapped in. In this paper, we prove that a simple path-following optimization scheme globally converges to the global minimum of the population loss in the bivariate setting. 

Structural causal models (SCMs) are widely used in various disciplines to represent causal relationships among variables in complex systems. Unfortunately, the true underlying directed acyclic graph (DAG) structure is often unknown, and determining it from observational or interventional data remains a challenging task. However, in many situations, the end goal is to identify changes (shifts) in causal mechanisms between related SCMs rather than recovering the entire underlying DAG structure. Examples include analyzing gene regulatory network structure changes between healthy and cancerous individuals or understanding variations in biological pathways under different cellular contexts. This paper focuses on identifying functional mechanism shifts in two or more related SCMs over the same set of variables -- without estimating the entire DAG structure of each SCM. Prior work under this setting assumed linear models with Gaussian noises; instead, in this work we assume that each SCM belongs to the more general class of nonlinear additive noise models (ANMs). A key contribution of this work is to show that the Jacobian of the score function for the mixture distribution allows for identification of shifts in general non-parametric functional mechanisms. Once the shifted variables are identified, we leverage recent work to estimate the structural differences, if any, for the shifted variables. Experiments on synthetic and real-world data are provided to showcase the applicability of this approach. 

Structural causal models (SCMs) are widely used in various disciplines to repre- sent causal relationships among variables in complex systems. Unfortunately, the underlying causal structure is often unknown, and estimating it from data remains a challenging task. In many situations, however, the end goal is to localize the changes (shifts) in the causal mechanisms between related datasets instead of learn- ing the full causal structure of the individual datasets. Some applications include root cause analysis, analyzing gene regulatory network structure changes between healthy and cancerous individuals, or explaining distribution shifts. This paper focuses on identifying the causal mechanism shifts in two or more related datasets over the same set of variables—without estimating the entire DAG structure of each SCM. Prior work under this setting assumed linear models with Gaussian noises; instead, in this work we assume that each SCM belongs to the more general class of nonlinear additive noise models (ANMs). A key technical contribution of this work is to show that the Jacobian of the score function for the mixture distribution allows for the identification of shifts under general non-parametric functional mechanisms. Once the shifted variables are identified, we leverage recent work to estimate the structural differences, if any, for the shifted variables. Experiments on synthetic and real-world data are provided to showcase the applicability of this approach. Code implementing the proposed method is open-source and publicly available at https://github.com/kevinsbello/iSCAN. 

The combinatorial problem of learning directed acyclic graphs (DAGs) from data was recently framed as a purely continuous optimization problem by leveraging a differentiable acyclicity characterization of DAGs based on the trace of a matrix exponential function. Existing acyclicity characterizations are based on the idea that powers of an adjacency matrix contain information about walks and cycles. In this work, we propose a new acyclicity characterization based on the log-determinant (log-det) function, which leverages the nilpotency property of DAGs. To deal with the inherent asymmetries of a DAG, we relate the domain of our log-det characterization to the set of $$\textit{M-matrices}$$, which is a key difference to the classical log-det function defined over the cone of positive definite matrices. Similar to acyclicity functions previously proposed, our characterization is also exact and differentiable. However, when compared to existing characterizations, our log-det function: (1) Is better at detecting large cycles; (2) Has better-behaved gradients; and (3) Its runtime is in practice about an order of magnitude faster. From the optimization side, we drop the typically used augmented Lagrangian scheme and propose DAGMA ($$\textit{Directed Acyclic Graphs via M-matrices for Acyclicity}$$), a method that resembles the central path for barrier methods. Each point in the central path of DAGMA is a solution to an unconstrained problem regularized by our log-det function, then we show that at the limit of the central path the solution is guaranteed to be a DAG. Finally, we provide extensive experiments for $$\textit{linear}$$ and $$\textit{nonlinear}$$ SEMs and show that our approach can reach large speed-ups and smaller structural Hamming distances against state-of-the-art methods.