Aligning Language Models with Observational Data: Opportunities and Risks from a Causal Perspective

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, \emph{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

Offline evaluation of language models from usage logs is biased when model choice is confounded: the same user-side factors that influence which model is used can also influence how its output is judged, so raw comparisons of logged scores mix self-selected populations rather than estimating a common quantity of interest. A small randomized experiment can break this bias by overriding model choice, but in practice such experiments are scarce and costly. We study a three-source design that combines a large confounded observational log (OBS) for scale, a small randomized experiment (EXP) for unconfounded scoring, and an offline simulator (SIM) that replays candidate models on cached contexts. Our main result is an identification theorem showing that the randomized experiment and the simulator are together enough to recover causal model values; the observational log enters only afterward, to reduce estimation error rather than to make the causal comparison valid. Six estimator families are evaluated in a controlled semi-synthetic validation and in two real-task cached benchmarks for summarization and coding. No family dominates every regime; relative performance depends on the amount of unbiased EXP supervision and on how closely the target reward aligns with OBS-derived structure.

Large language model (LLM) development is currently driven by large-scale empirical iteration over data mixtures, reward models, routing strategies, and evaluation pipelines. Here, we argue that many central questions in LLM development and evaluation are inherently causal: What is the effect of adding a data domain during pretraining? How do annotator preferences change when LLMs generate text in a different style? Should a prompt be routed to a larger or smaller model given inference cost constraints? In general, causal methods are well-suited to such settings where interventions change outcomes but, surprisingly, are underrepresented in LLM development. Our contribution is threefold: (1) We explain how causal methods can help develop modern LLM development and evaluation: LLM development relies heavily on logged data, which are often subject to confounding and distribution shifts; evaluation uses learned but potentially biased judges; and deployment environments are non-stationary. These conditions make purely predictive approaches fragile and create opportunities for principled identification and estimation methods from causal inference. (2) We further map opportunities for causal methods in the entire LLM development pipeline, including pretraining, alignment, routing, agentic workflows, and evaluation. (3) We discuss new research opportunities around leveraging causal methods for LLM development and evaluation. Overall, we argue that causal methods are potentially underutilized for the LLM development and evaluation pipeline, despite the fact that such methods can ensure a reliable and scientifically grounded design.