The Causal Discovery Foundation Model (CDFM) is formulated as a unified, general-purpose framework for zero-shot structural inference, and a principled variational framework that treats unknown causal mechanisms as latent variables and mathematically decomposes the intractable marginal likelihood into distinct, tractable learning modules is formulated.
Abstract
Causal discovery, the process of recovering underlying causal structures from observational data, is a fundamental pursuit across scientific disciplines. Over the past decades, numerous algorithms have been developed to tackle this challenge through workflows tailored to the specific causal mechanisms underlying each type of dataset, demonstrating effectiveness across a wide range of applications. However, as the volume and heterogeneity of real-world data continue to grow, this dataset-specific approach inevitably leads to a fragmented, test-driven paradigm that struggles to scale to the demands of modern scientific discovery. To address this, we formulate the Causal Discovery Foundation Model (CDFM) as a unified, general-purpose framework for zero-shot structural inference. To ensure reliable generalization across unknown domains, we first investigate the theoretical boundaries of causal identifiability, revealing the indispensable role of causal prior mechanisms in this process. Building on these insights, we formulate a principled variational framework that treats unknown causal mechanisms as latent variables and mathematically decomposes the intractable marginal likelihood into distinct, tractable learning modules. The variational decomposition provides a conceptual design principle for the architecture design of CDFM, while comprehensive causal knowledge guides the large-scale synthesis of our pretraining data. By pretraining on a massive, highly diverse space of synthetic structural causal models, CDFM successfully internalizes complex statistical asymmetries. Extensive experiments demonstrate that CDFM consistently outperforms traditional algorithms, driving a paradigm shift toward a general-purpose causal discovery foundation model.
This work considers the task of conditional causal discovery as a Bayesian inference problem, in which the posterior is targeted over causal graphs and parameters conditional on an event such as a causal-effect constraint, and adapts rare-event estimation techniques to perform inference the joint graph-parameter space.
Cixuan Zhang, Guy Van den Broeck, Benjie Wang· 0 citations
Causal discovery aims to uncover causal structures from data and is fundamental to scientific reasoning and intervention-based decision making. Its evaluation relies heavily on structural causal models (SCMs), which specify a causal graph together with the mechanisms that generate data, yet existing studies differ substantially in graph families, mechanisms, and evaluation protocols. The emergence of causal discovery foundation models (CDFMs) further complicates evaluation: performance may reflect not only causal discovery ability, but also overlap between pretraining environments and test SCMs, making results on fixed synthetic benchmarks difficult to interpret. We introduce CausalArena, a unified and evolvable benchmark for causal discovery under a common protocol. Synthetic SCMs supply controlled breadth over structures and mechanisms; semantic operational SCMs provide human-auditable, semantically grounded environments beyond standard synthetic generators; and formula-grounded SCMs test discovery under explicit scientific mechanisms. Public real-world datasets provide an additional external-validity check. Experiments across classical, neural, and pretrained methods reveal substantial ranking shifts across SCM families and protocols, showing that strong performance in one benchmark regime does not reliably transfer to others. These results highlight benchmark diversity and pretraining--evaluation overlap as central challenges for evaluating causal discovery in the foundation model era.
Zi-Rong Li, Si-Zhuang Liu, Tian-Zuo Wang et al.· 0 citations
Causal Discovery (CD) from observational data faces two fundamental challenges. First, purely statistical methods often lack the power to resolve structural ambiguities in low-sample regimes. Second, although LLM-assisted hybrid approaches improve structure recovery through semantic reasoning, the influence of that reasoning on individual edge decisions remains largely opaque. Consequently, existing hybrid methods fail to satisfy a fundamental requirement: explaining why a particular edge is included or excluded in the learned directed acyclic graph (DAG). This is critical in real-world applications, where no ground-truth DAG exists and every structural decision must be independently justified. We formalize this requirement as decision traceability, requiring every inferred edge to be supported by auditable statistical evidence, Markov Blanket consistency, or explicit domain reasoning. We propose GENESIS, an explainable hybrid CD framework that decomposes graph construction into interpretable decision points. GENESIS first identifies and scores three-node structural motifs, including chains, forks, and colliders, to establish transparent structural priors, then progressively refines the graph by integrating these priors with observational evidence, invoking domain knowledge only when statistical evidence is insufficient. By design, every edge decision is resolved through an auditable source of evidence. Experiments show that GENESIS achieves 100% decision traceability across all settings, establishing explainability as a first-class objective in causal discovery. Despite this additional requirement, GENESIS consistently outperforms purely statistical CD methods on the majority of benchmark datasets across all sample regimes in terms of Structural Hamming Distance (SHD), while achieving performance comparable to state-of-the-art LLM-assisted approaches.
A. Thorat, Ravi Kolla, Vishak K Bhat et al.· 0 citations
Causal inference is the practice of estimating the effect of a treatment or intervention from data. It traditionally requires a bespoke pipeline for every new problem: first proposing a causal mechanism, selecting a compatible estimator, and finally training it. Meanwhile, across diverse settings and modalities, much of machine learning has shifted to the paradigm of foundation models: networks pretrained once at scale and applied to new tasks without fine-tuning. Causal foundation models (CFMs) bring this paradigm to causal inference. CFMs are pretrained neural networks that estimate causal quantities, such as the average treatment effect, on entirely new datasets using in-context learning without requiring model updates. This work provides a practical introduction to this emerging area. We summarize the necessary background in causal inference and machine learning before discussing CFMs. Throughout, we include example code and Jupyter notebooks.
Christopher Stith, Hossein Rahmani, Jesse C. Cresswell· 0 citations
LoCaLS is proposed, a local causal structure learning algorithm that is sound and complete under standard assumptions and identifies the same direct causes and effects of a target variable as those identifiable by global causal discovery methods, while allowing for latent variables and selection bias.
Zheng Li, Hao Zhang, Ruxin Wang et al.· arXiv.org· 1 citation
SVI-DAG is proposed, a structured variational inference approach to Bayesian causal discovery using observational data and prior beliefs that uses normalizing flows to model dependencies between edges, supporting expressive and multimodal posterior learning over DAGs.
Shrenik Zinage· 0 citations
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