Robust causal discovery from observational data under imperfect prior knowledge remains a significant and largely unresolved challenge. Existing methods typically presuppose perfect priors or can only handle specific, pre-identified error types. And their performance degrades substantially when confronted with flawed constraints of unknown location and type. This decline arises because most of them rely on inflexible and biased thresholding strategies that may conflict with the data distribution. To overcome these limitations, we propose to harmonizes knowledge and data through prior alignment and conflict resolution. First, we assess the credibility of imperfect structural constraints through a surrogate model, which then guides a sparse penalization term measuring the loss between the learned and constrained adjacency matrices. We theoretically prove that, under ideal assumption, the knowledge-driven objective aligns with the data-driven objective. Furthermore, to resolve conflicts when this assumption is violated, we introduce a multi-task learning framework optimized via multi-gradient descent, jointly minimizing both objectives. Our proposed method is robust to both linear and nonlinear settings. Extensive experiments, conducted under diverse noise conditions and structural equation model types, demonstrate the effectiveness and efficiency of our method under imperfect structural constraints.

Causal structure learning (CSL) plays a pivotal role in causality and is often formulated as an optimization problem within score-and-search methods. Under the assumption of an infinite dataset and a predefined distribution, several well-established and consistent score functions have been shown to be both optimal and reliable for identifying ground-truth causal graphs. However, in practice, these idealized assumptions are often infeasible, which can result in CSL algorithms learning suboptimal structures. In this paper, we introduce L-SFE, a framework designed to automatically discover effective score functions by exploring the "score function space". L-SFE addresses this task from a bi-level optimization perspective. First, it leverages a Large Language Model (LLM) to interpret the characteristics of score functions and generate the corresponding code implementations. Next, L-SFE employs evolutionary algorithms along with carefully designed operators, to search for solutions with higher fitness. Additionally, we take the BIC as example and prove the consistency of the generated score functions. Experimental evaluations, conducted on discrete, continuous, and real datasets, demonstrate the high stability, generality and effectiveness of L-SFE.

Learning graphical causal models from observational data can effectively elucidate the underlying causal mechanism behind the variables. In the context of limited datasets, modelers often incorporate prior knowledge, which is assumed to be correct, as a penalty in single-objective optimization. However, this approach struggles to adapt complex and uncertain priors effectively. This paper introduces UpCM, which tackles the issue from a multi-objective optimization perspective. Instead of focusing exclusively on the DAG as the optimization goal, UpCM methodically evaluate the effect of uncertain priors on specific structures, merging data-driven and knowledge-driven objectives. Utilizing the MOEA/D framework, it achieve a balanced tradeoff between these objectives. Furthermore, since uncertain priors may introduce erroneous constraints, resulting in PDAGs lacking consistent extensions, the minimal non-consistent extension is explored. This extension, which separately incorporates positive and negative constraints, aims to approximate the true causality of the PDAGs. Experimental results demonstrate that UpCM achieves significant structural accuracy improvements compared to baseline methods. It reduces the SHD by 7.94%, 13.23%, and 12.8% relative to PC stable, GES, and MAHC, respectively, when incorporating uncertain priors. In downstream inference tasks, UpCM outperforms domain-expert knowledge graphs, owing to its ability to learn explainable causal relationships that balance data-driven evidence with prior knowledge