Tatsuyoshi Ikenoue

Masayuki Takayama, Tadahisa Okuda, Thong Pham et al.

In practical statistical causal discovery (SCD), embedding domain expert knowledge as constraints into the algorithm is important for reasonable causal models reflecting the broad knowledge of domain experts, despite the challenges in the systematic acquisition of background knowledge. To overcome these challenges, this paper proposes a novel method for causal inference, in which SCD and knowledge-based causal inference (KBCI) with a large language model (LLM) are synthesized through ``statistical causal prompting (SCP)'' for LLMs and prior knowledge augmentation for SCD. The experiments in this work have revealed that the results of LLM-KBCI and SCD augmented with LLM-KBCI approach the ground truths, more than the SCD result without prior knowledge. These experiments have also revealed that the SCD result can be further improved if the LLM undergoes SCP. Furthermore, with an unpublished real-world dataset, we have demonstrated that the background knowledge provided by the LLM can improve the SCD on this dataset, even if this dataset has never been included in the training data of the LLM. For future practical application of this proposed method across important domains such as healthcare, we also thoroughly discuss the limitations, risks of critical errors, expected improvement of techniques around LLMs, and realistic integration of expert checks of the results into this automatic process, with SCP simulations under various conditions both in successful and failure scenarios. The careful and appropriate application of the proposed approach in this work, with improvement and customization for each domain, can thus address challenges such as dataset biases and limitations, illustrating the potential of LLMs to improve data-driven causal inference across diverse scientific domains. The code used in this work is publicly available at: www.github.com/mas-takayama/LLM-and-SCD

Tadahisa Okuda, Shohei Shimizu, Thong Pham et al.

Causal discovery has achieved substantial theoretical progress, yet its deployment in large-scale longitudinal systems remains limited. A key obstacle is that operational data are generated under institutional workflows whose induced partial orders are rarely formalized, enlarging the admissible graph space in ways inconsistent with the recording process. We characterize a workflow-induced constraint class for longitudinal causal discovery that restricts the admissible directed acyclic graph space through protocol-derived structural masks and timeline-aligned indexing. Rather than introducing a new optimization algorithm, we show that explicitly encoding workflow-consistent partial orders reduces structural ambiguity, especially in mixed discrete--continuous panels where within-time orientation is weakly identified. The framework combines workflow-derived admissible-edge constraints, measurement-aligned time indexing and block structure, bootstrap-based uncertainty quantification for lagged total effects, and a dynamic representation supporting intervention queries. In a nationwide annual health screening cohort in Japan with 107,261 individuals and 429,044 person-years, workflow-constrained longitudinal LiNGAM yields temporally consistent within-time substructures and interpretable lagged total effects with explicit uncertainty. Sensitivity analyses using alternative exposure and body-composition definitions preserve the main qualitative patterns. We argue that formalizing workflow-derived constraint classes improves structural interpretability without relying on domain-specific edge specification, providing a reproducible bridge between operational workflows and longitudinal causal discovery under standard identifiability assumptions.