Causal Discovery with LLMs

LLM agents can now run causal discovery algorithms on a dataset and report what comes out. Whether they do more than that, such as noticing where an algorithm went wrong and fixing it with further tests, is hard to tell from current benchmarks. Most of them give the variables meaningful names, and an LLM shown only the names of the Tübingen cause-effect pairs already gets 99% of the directions right. With the names removed, the data are usually clean enough that picking a better algorithm than PC closes most of the gap. We introduce Heuresis, a benchmark of anonymous simulated datasets whose mechanisms range from linear Gaussian to heavy-tailed. For each family of datasets it separates what a better existing algorithm can gain from what only a closer look at the data can gain, and it traces every edge an agent changes. Every family leaves a gap that none of the algorithms, the router and the two causal-discovery foundation models we ran can close, so a score above the best chosen algorithm has to come from using the data. We instantiate the benchmark with an agent harness and three LLMs, GPT-6.1 Sol, Claude Opus 5.5 and Qwen 3.8 Flash. GPT-6.1 Sol surpasses the best chosen algorithm on all six families, by 14% adjacency F1 on the most difficult one, and Claude Opus 5.5 does so by 7.4% there. A third of the true edges the two agents restore on the two hardest families appear in no algorithm's output. The code and data will be publicly released to facilitate future work.

Interpretive Structural Modeling (ISM) is a well-known process for multi-criteria decision making. The success of ISM over other methodologies is its ability to model causal relationships, the binary scale of factors, and resulting hierarchical representation. Traditionally, the modeling process is performed by repeated interactions with subject matter experts until consensus is reached. This process is tedious, labor-intense, and most importantly limits the ability of ISM to scale to studies with hundreds of variables. Drawing on existing work of causal graph discovery with large language models (LLM) as imperfect experts, this work explores an integrated LLM-ISM approach for ISM. Pairwise, k-wise, rowwise, and full graph discovery methodologies are compared and evaluated. It is shown that causal graph discovery methods for ISM perform best using rowwise (SHD=160, F1-score=0.77) and full graph methods (SHD=135, F1-score=0.73).

Causal AI is a branch of Artificial Intelligence which helps understand and reason about cause and effect relationships, not just patterns or correlations. Causal discovery aims to infer elements of the underlying causal structure--often represented as a directed graph--from observational and, when available, interventional data. While causal discovery is the fundamental step for moving beyond mere associations toward genuine understanding, and thus the basic building block of causal AI, it becomes intrinsically difficult when causal relations must be inferred from single observations. In such situations, standard causal discovery methods cannot be used and one has to identify causal relations from limited amount of information. This is typically the case for, e.g., sequences of events produced by different alarms which need to be analyzed on the fly to detect abnormal phenomena, which are usually rare. We show in this study that it is possible to leverage the predictive power of Large Language Models (LLMs) to infer causal relations between only two sequences of events. This approach, which is validated on both synthetic and real data, provides better results than standard causal discovery algorithms on several time series data, even though these data were converted into smaller, single observed sequences.

Large language models (LLMs) have been applied to causal discovery, but candidate-graph generation rarely treats premature omission of potentially relevant causal relations as an explicit design objective. We propose MaSCoD, a multi-agent framework that organizes candidate third variables and local structural patterns before direct-edge judgment. We evaluate MaSCoD on Auto-MPG, DWD, and Sachs using GPT-5.4 as the primary backbone and GPT-4o for replication. MaSCoD exhibits a dataset- and backbone-dependent retention-selectivity profile rather than uniform superiority. Across all six dataset-backbone settings, Full, which supplies structural hypotheses before direct-edge judgment, achieved higher mean Recall and F1 than No Phase 1, which instead constructs them within the judgment procedure, while also increasing false-positive rates. Additional reference-edge retention over all evaluated baselines was observed on DWD with GPT-5.4 and on Sachs with GPT-4o, rather than uniformly across settings. Partial ablations showed that supplying both information components did not always outperform supplying only one. For GPT-5.4, stage-wise analysis showed that the Full-No Phase 1 retention gap was already present after direct-edge judgment, while reconciliation introduced additional reference-edge loss for Full on Sachs. These findings support structural pre-organization as an explicit design and evaluation target for omission control and motivate evaluating context construction jointly with its utilization in judgment.

We introduce the Active Causal Discovery Benchmark (ACDB), an SCM-grounded environment for evaluating whether LLM agents recover causal graph structure from observations and budget-constrained hard interventions. ACDB pairs a linear-Gaussian world generator with a fixed observe-intervene-submit API and a three-layer scoring contract that separates skeleton recovery, DAG recovery, and intervention efficiency. On the current six-level ladder, PC with a greedy active orientation heuristic is the strongest non-oracle method (directed F1 42.7%, SHD 4.79), ahead of Claude Sonnet 4.6 raw active (31.7%, 7.25) and GPT-5.4 raw active (22.9%, 9.27). The most informative diagnostic is the precision-recall decomposition: PC under-commits with high precision, LLMs over-commit with lower precision, and statistical-tool access often increases abstention rather than useful intervention. A structure-blind random DAG baseline reaches 23.6% directed F1 on this dense v0 ladder; a density probe lowers this floor to 16.9%, motivating the v1 calibration pass. The current results should therefore be read as a benchmark audit and calibration report, not as evidence that current LLMs solve active causal discovery.

Physical Activity (PA) is consistently associated with lower risk of dementia, yet the mechanism linking PA to dementia prevention remain incomopletely understood. Here, we integrate large language model (LLM)-guided causal discovery with mediation analysis in 42,293 older adults aged 60 years or older from the UK Biobank to systematically identify pathways connecting objectively measured moderate-to-vigorous physical activity (MVPA) to dementia risk. Across behavioral, psychological, functional, and clinical domains, causal discovery consistently identified interconnected pathways linking higher MVPA to lower dementia risk through depression, functional capacity, smoking behavior, hypertension, cardiovascular disease, chronic kidney disease, and brain injury. Chain mediation analyses further identified depression as a central pathway, accounting for 15.1% of the overall association between MVPA and dementia risk. Sex-stratified analyses revealed distinct mechanistic patterns, with females exhibiting predominantly metabolic and functional pathways, while males showed behavioral and cardiometabolic cascades involving smoking and cardiovascular disease. Together, these findings suggest that the protective association between PA and dementia is mediated through interconnected behavioral, psychological, and cardiometabolic processes rather than a single pathway. Depression emerged as a prominent and potentially modifiable pathway, highlighting opportunities for integrating dementia prevention strategies that combine PA promotion with mental health and cardiovascular risk management.

Adverse Pregnancy Outcomes (APOs) such as preterm birth and gestational diabetes can have long-term consequences for both the mother and child, yet an understanding of their causes remains elusive. Causal discovery in this domain is especially challenging due to a paucity of data and incomplete domain knowledge. As a result, pure data-driven methods fail, and Large Language Model (LLM) outputs remain inconsistent or contradictory. We introduce a neurosymbolic framework for generating plausible causal hypotheses that iteratively combines the broad prior knowledge of LLMs with empirical scoring on data. Our method treats the LLM as an adaptive proposal distribution, generating hypotheses that are scored against empirical data; the resulting high-scoring graphs are then used to update the LLM's context, steering subsequent generations toward more promising regions of the hypothesis space. We evaluate our approach on a real-world clinical dataset for modeling APOs and their risk factors, comparing our results against an expert-constructed causal graph. Our method recovers all expert-validated edges and identifies additional plausible causal relations not previously listed by experts, potentially providing new insights for targeted interventions.

Recent attempts to combine large language models (LLMs) with causal discovery ask models to infer pairwise directions, propose graph structures, or inject language-model outputs as priors and constraints. These approaches promise faster analysis, but they also obscure whether a causal evidence is supported by data and assumptions or by textual associations, prompt artifacts and hallucinated mechanisms. We argue for a different role for agents in causal discovery. Agents should inspect data, retrieve context, explain method assumptions and clarify graph outputs, but they should not supply edges, orientations, priors, constraints or causal conclusions. We propose the principle that agents assist the workflow, while causal claims remain grounded in data, explicit assumptions, formal algorithms, diagnostics and user or domain-expert decisions. We instantiate this principle in causal-learn+, an online platform that coordinates data analysis, preprocessing, method recommendation, expert-knowledge incorporation, formal discovery and interpretation around the algorithmic ecosystem of causal-learn. A case study on Big Five personality data illustrates agent-assisted pipeline of causal discovery without turning language-model unreliability into causal evidence. The platform is available at causallearn.com.

Because large language models (LLMs) are impressively successful in predicting text, it appears that they must have access to a 'world model' representing causal and definitional structure. However, the dominant formalisms of modern causal inference -- Judea Pearl's interventionist approach and the Neyman-Rubin potential outcomes framework -- struggle to illuminate how LLMs learn causal structure. I resolve this puzzle by arguing that LLMs employ a specific inductive approach based on a difference-making logic -- sometimes called variational induction. I demonstrate how central aspects of this logic are realized during training, where LLMs require enormous amounts of text data from a wide range of contexts to identify difference- and indifference-makers within word sequences. Furthermore, I analyze specific architectural features of LLMs -- such as token embeddings and self-attention -- to determine their roles in variational induction. The difference-making logic of LLMs fundamentally parallels the experimental method, where causal relations are derived by systematically varying individual circumstances to determine their influence on a phenomenon.

Causal discovery aims to uncover causal structures from observational data, which is crucial for real-world decision-making. However, different causal discovery algorithms can produce divergent results that conflict with each other, complicating the identification of accurate causal graphs. Traditional approaches rely on numerical values and statistical assumptions, often ignoring rich domain-specific information, such as feature descriptions, which could also help structure learning. While recent works explore using Large Language Models (LLMs) to infer causal relations via direct queries, such methods can be unreliable due to a lack of alignment with the actual data. To address these limitations, we propose Causal Ensemble Agent (CEA), a novel framework that aggregates structural insights from statistical discovery experts across different graph levels via linear opinion pooling, and uses an LLM as a meta-referee to dynamically reweight experts when the aggregated confidence is close to the decision boundary, thereby composing an improved and more complete causal graph. Extensive experiments on both synthetic and real-world datasets demonstrate that CEA achieves the strongest overall performance across a wide range of causal discovery methods, highlighting the effectiveness of using LLMs for meta-analysis in causal discovery.

Textual event records, such as alarm logs, have become an increasingly common data source in engineering and manufacturing systems. Beyond identifying correlations or recurring patterns, engineers are often interested in understanding which types of events causally trigger or influence other events during system operation. Textual event descriptions may contain semantic clues about such causal relationships, and recent large language models (LLMs) provide a promising tool for extracting these signals. However, relying solely on LLM-encoded textual information is insufficient for accurate causal discovery, since semantic patterns do not directly reveal causal mechanisms and may confuse causation with correlation or frequent sequential patterns. To address these challenges, we propose LMT, a Bayesian causal discovery framework for engineering event data that jointly leverages textual descriptions and timestamps. Specifically, LMT first uses LLMs to extract semantic causal signals from event descriptions and constructs a prior distribution over causal graphs among event types or event clusters. It then incorporates temporal evidence through a Poisson-process-based likelihood, allowing the LLM-informed prior to be refined by timestamp-based statistical evidence. By integrating the textual and temporal information, LMT produces a causal graph that is both interpretable and data-supported. Simulation studies show that the proposed framework is effective across different settings and is especially advantageous in small-sample alarm-event scenarios.

Causal discovery from observational data remains challenging due to the fundamental limitations of purely statistical methods, such as statistical distinguishability within equivalence classes and sensitivity to finite sample sizes. While large language models (LLMs) offer a promising source of domain knowledge to complement statistical inference, existing LLM-augmented methods are vulnerable to LLM errors and incur high token costs. Moreover, reliance on a single data-centric algorithm can make results sensitive to algorithm-specific biases. To address these limitations, we propose CauTion, a framework that reliably integrates LLM domain knowledge into an ensemble of statistical causal discovery algorithms through consensus filtering and LLM reliability estimation. CauTion proceeds in three stages. First, an algorithm ensemble utilizes a consensus voting to resolve up to 96% of edges on which algorithms agree, achieving near-perfect accuracy on the filtered consensus edges. Second, a trust-calibrated arbitration mechanism estimates the relative reliability of the LLM and the algorithms via an annotation-free trust calibration procedure, which is then utilized to govern a trust-weighted voting process that restricts LLM arbitration exclusively to edges with unreliable algorithmic evidence. Third, a cycle repair step is applied to guarantee the final causal graph is validly acyclic. Experiments on six datasets demonstrate that CauTion consistently outperforms both data-centric and LLM-augmented baselines, with larger gains on larger graphs and strong robustness to LLM errors. Code is available at https://github.com/OpenCausaLab/CauTion.

Causal discovery is a cornerstone of scientific reasoning, yet whether large language models can perform it reliably remains an open question. Recent benchmarks show that even fine-tuned models plateau on simple causal graphs and degrade as complexity grows, but why they fail has not been established. We prove the failure is fundamental: supervised fine-tuning, direct preference optimization, and in-context learning all produce predictors that cannot distinguish between causal graphs generating similar observational data, and any attempt to do so requires the model's internal representations to grow unboundedly, violating the very conditions under which these methods work. We formalize this as a kernel obstruction theorem, establishing that the limitation is intrinsic to the learning paradigm, not any particular model or dataset. We propose Agentic Causal Bayesian Optimization (A-CBO), wherein a frozen language model serves as an interventional oracle answering targeted queries about intervention effects, while an external Bayesian loop concentrates beliefs over candidate graphs in logarithmically many rounds. Because the decision operates outside the space where the obstruction applies, A-CBO provably converges while the underlying model remains unchanged. On Corr2Cause, A-CBO matches fine-tuned baselines without any training. On Extended Corr2Cause, a new benchmark scaling to 24 variables with 18K test samples, A-CBO significantly outperforms both fine-tuning and preference optimization, with the advantage growing

We introduce CausaLab, a scalable environment for evaluating interactive causal discovery by LLM agents. Unlike prior evaluations, CausaLab evaluates both whether an agent can solve a problem using causal evidence and whether its answer is grounded in a faithful recovered causal mechanism. Each episode places an agent in a synthetic laboratory: it receives prior measurement records, intervenes on a manipulator crystal, and predicts the resonance frequency of a held-out reactor crystal governed by the same mechanism. The hidden data-generating process is a randomly sampled structural causal model (SCM), so success requires recovering both a causal graph and structural equations rather than recalling prior knowledge. Experiments show a persistent gap between prediction and mechanism recovery: in the purely observational 6-node setting, GPT-5.2-high reaches 92% task accuracy but only 0.471 all-edge $F_1$. Mixed observation-intervention strategies improve structural fidelity, while pure intervention remains difficult even for strong agents. We identify premature stopping as a major weakness and show that consistency verification mitigates it. CausaLab therefore separates predictive success from causal understanding and exposes current LLM agents' limits as experimental causal reasoners.

Causal graphs in text are typically populated by observable, predefined events. In contrast, we study implicit causal graph construction from text by treating each described cause-effect pair as the begin- and endpoint of an underlying latent causal graph and using large language models (LLMs) to infer intermediate causal events. We compare end-to-end graph construction with methods that frame the task as causal chain discovery. In the latter, graphs are built either by aggregating inferred chains or by progressively expanding partial chains through an iterative search process. We further explore Wisdom of the Crowd extensions that access causal knowledge from multiple LLMs in post-hoc aggregation and collaborative inference settings. We analyze trade-offs among these approaches and evaluate the validity of inferred causal relations using a manually curated database of 1,560 scientifically validated causal pairs. This database-based evaluation is proposed as reliable, resource-efficient, and transferable to settings where ground-truth graphs are unavailable.

Large language models (LLMs) are trained on enormous amounts of data and encode knowledge in their parameters. We propose a pipeline to elicit causal relationships from LLMs. Specifically, (i) we sample many documents from LLMs on a given topic, (ii) we extract an event list from from each document, (iii) we group events that appear across documents into canonical events, (iv) we construct a binary indicator vector for each document over canonical events, and (v) we estimate candidate causal graphs using causal discovery methods. Our approach does not guarantee real-world causality. Rather, it provides a framework for presenting the set of causal hypotheses that LLMs can plausibly assume, as an inspectable set of variables and candidate graphs.

We present DMCD (DataMap Causal Discovery), a two-phase causal discovery framework that integrates LLM-based semantic drafting from variable metadata with statistical validation on observational data. In Phase I, a large language model proposes a sparse draft DAG, serving as a semantically informed prior over the space of possible causal structures. In Phase II, this draft is audited and refined via conditional independence testing, with detected discrepancies guiding targeted edge revisions. We evaluate our approach on three metadata-rich real-world benchmarks spanning industrial engineering, environmental monitoring, and IT systems analysis. Across these datasets, DMCD achieves competitive or leading performance against diverse causal discovery baselines, with particularly large gains in recall and F1 score. Probing and ablation experiments suggest that these improvements arise from semantic reasoning over metadata rather than memorization of benchmark graphs. Overall, our results demonstrate that combining semantic priors with principled statistical verification yields a high-performing and practically effective approach to causal structure learning.

Causal discovery seeks to uncover causal relations from data, typically represented as causal graphs, and is essential for predicting the effects of interventions. While expert knowledge is required to construct principled causal graphs, many statistical methods have been proposed to leverage observational data with varying formal guarantees. Causal Assumption-based Argumentation (ABA) is a framework that uses symbolic reasoning to ensure correspondence between input constraints and output graphs, while offering a principled way to combine data and expertise. We explore the use of large language models (LLMs) as imperfect experts for Causal ABA, eliciting semantic structural priors from variable names and descriptions and integrating them with conditional-independence evidence. Experiments on standard benchmarks and semantically grounded synthetic graphs demonstrate state-of-the-art performance, and we additionally introduce an evaluation protocol to mitigate memorisation bias when assessing LLMs for causal discovery.

Revealing hidden causal variables alongside the underlying causal mechanisms is essential to the development of science. Despite the progress in the past decades, existing practice in causal discovery (CD) heavily relies on high-quality measured variables, which are usually given by human experts. In fact, the lack of well-defined high-level variables behind unstructured data has been a longstanding roadblock to a broader real-world application of CD. This procedure can naturally benefit from an automated process that can suggest potential hidden variables in the system. Interestingly, Large language models (LLMs) are trained on massive observations of the world and have demonstrated great capability in processing unstructured data. To leverage the power of LLMs, we develop a new framework termed Causal representatiOn AssistanT (COAT) that incorporates the rich world knowledge of LLMs to propose useful measured variables for CD with respect to high-value target variables on their paired unstructured data. Instead of directly inferring causality with LLMs, COAT constructs feedback from intermediate CD results to LLMs to refine the proposed variables. Given the target variable and the paired unstructured data, we first develop COAT-MB that leverages the predictivity of the proposed variables to iteratively uncover the Markov Blanket of the target variable. Built upon COAT-MB, COAT-PAG further extends to uncover a more complete causal graph, i.e., Partial Ancestral Graph, by iterating over the target variables and actively seeking new high-level variables. Moreover, the reliable CD capabilities of COAT also extend the debiased causal inference to unstructured data by discovering an adjustment set. We establish theoretical guarantees for the CD results and verify their efficiency and reliability across realistic benchmarks and real-world case studies.