Large language models (LLMs) are increasingly used to provide prior causal knowledge for structural causal discovery, yet whether their direct-edge judgments and confidence can be trusted remains unclear.
We systematically evaluate 12 instruction-tuned open-weight models across six benchmark causal graphs, five prompting strategies, and four confidence sources: verbalized, logit-based, cross-prompt agreement, and cross-model agreement.
Under our language-only pairwise protocol, our evaluation yields three key findings.
- (i) LLM-based causal judgments are strongly recall-dominant: models predict overly dense graphs with many false-positive edges, while prompting mainly shifts the precision-recall trade-off rather than resolving overprediction. Gains from model scale diminish on the largest graphs and do not eliminate miscalibration.
- (ii) LLMs often capture causal relatedness without reliably identifying directness or orientation. Relative to published reference graphs, models misclassify 40.0% of indirect and 36.0% of reversed non-edges as direct edges, versus 28.2% of other non-edges. Moreover, 80.8% and 84.6% of these false positives receive verbalized confidence of at least 80%, revealing substantial overconfidence in structurally incorrect predictions.
- (iii) Conventional confidence estimates are unreliable, whereas agreement offers a more promising signal. Logit-based confidence frequently collapses near 1.0 regardless of correctness, while cross-prompt and cross-model agreement achieve better mean calibration and discrimination, though their advantages are not statistically significant after Holm correction.
A benchmark-familiarity audit further identifies potential familiarity in five model-dataset pairs, all involving AsiaM.
Overall, our results suggest LLMs are better viewed as sources of externally validated soft causal priors than as direct evidence of causal structure.