Breaking the Chain: A Causal Analysis of LLM Faithfulness to Intermediate Structures

Chain-of-thought (CoT) reasoning improves LLM accuracy on complex tasks, but CoTs are often unfaithful; that is, the model does not rely on the stated reasoning steps to produce its answer. Existing methods to improve faithfulness require human annotations. We propose LIFT, which automatically scores each reasoning step by its causal influence: we replace it with a domain-matched but irrelevant fact and measure the drop in answer log-probability. We fine-tune on high-scoring CoT traces where interventions successfully disrupted reasoning, jointly optimizing for faithfulness and accuracy. LIFT improves faithfulness across three models (Mistral-7B-Instruct, Qwen3-8B, and Qwen3-4B-Instruct) and three benchmarks, with accuracy comparable to a model fine-tuned solely for accuracy.

Deploying large language models in production often requires constraining outputs to structured formats such as JSON or XML, and prior work treats the resulting accuracy loss as an inherent structure tax'. We re-examine this claim by evaluating a battery of models, datasets and schemas, measuring task accuracy, confidence calibration, and hidden-state geometry. The tax turns out to depend on schema design rather than on structure per se: reasoning-first field ordering matches or exceeds free-form accuracy, while answer-first ordering causes steep drops, particularly in smaller models. Format sensitivity scales inversely with a task's own structural constraints, and schemas that preserve reasoning order also improve calibration with CKA showing greater separability between correct and incorrect representations in middle transformer layers. Our findings indicate that properly designed structured formats can match or exceed free-form performance, reframing the critical question from whether to structure' to `how to structure' for optimal reasoning preservation.

Chain-of-thought (CoT) can sound plausible yet be unfaithful to the model's underlying reasoning. Most prior work probes CoT faithfulness through input--output behavior or input attributions, leaving internal computation largely underexplored. We instead cast faithfulness as internal concept grounding: Does a large language model's (LLM) CoT reasoning engage the same internal concepts that support the LLM's direct prediction, and do the shared concepts causally drive its answer? Encoding a prediction pass and a CoT pass with a single shared sparse autoencoder (SAE), a reliable approximator of the latent concepts LLMs use, makes their internal concepts directly comparable. We introduce three correlational metrics of concept-level alignment and a causal metric, $Δp$, which ablates the shared concepts and measures the drop in answer probability. Across five LLMs and four datasets, concept alignment is generally high, as indicated by the correlational metrics; yet these only identify which concepts are shared, not how much they causally contribute. $Δp$ fills this gap: causal faithfulness varies substantially with model depth, peaking at mid-to-late layers rather than the final ones, and model scale reshapes the layer-wise profile. Moreover, causally important shared concepts are not always verbalized in the CoT. These dissociations suggest that faithfulness cannot be reliably assessed from surface-level or representational correspondence alone; assessing it requires causal tests of whether the internal concepts underlying a CoT actually drive the model's prediction.