Not Just the Destination, But the Journey: Reasoning Traces Causally Shape Generalization Behaviors

Chain-of-thought (CoT) reasoning is widely used to improve both the performance and interpretability of large language models (LLMs), yet the generated reasoning may not faithfully support the final answer. We study this problem from a causal perspective, where a faithful CoT process should follow the chain $Z\rightarrow X\rightarrow Y$, with $Z$, $X$, and $Y$ denoting the instruction, reasoning chain, and final answer, respectively. In this process, the instruction should affect the answer only through the reasoning chain. However, conventional autoregressive LLMs condition answer generation on both the instruction and the CoT, which still allows a direct instruction-to-answer shortcut. To address this issue, we propose CASE, a framework that combines training-time causal alignment and inference-time structural enforcement. During training, CASE builds counterfactual-CoT, biased-instruction, and empty-instruction datasets, and applies selective-loss fine-tuning to strengthen CoT-to-answer dependence while suppressing instruction shortcuts. During inference, CASE masks direct attention from instruction tokens to answer tokens, preventing the model from bypassing the generated CoT. We provide an information-theoretic analysis showing how these components promote faithful chains. Experiments on three models and four benchmarks show that CASE achieves a 37% average per-setting relative improvement in overall CoT faithfulness over the strongest baselines, exhibits stronger cross-dataset faithfulness transfer, and maintains competitive average accuracy. Code is available at https://github.com/oddwang/CASE.

As chain of thought (CoT) has become central to scaling reasoning capabilities in large language models (LLMs), it has also emerged as a promising tool for interpretability, suggesting the opportunity to understand model decisions through verbalized reasoning. However, the utility of CoT toward interpretability depends upon its faithfulness---whether the model's stated reasoning reflects the underlying decision process. We provide mechanistic evidence that instruction-tuned models often determine their answer before generating CoT. Training linear probes on residual stream activations at the last token before CoT, we can predict the model's final answer with >0.9 AUC on most tasks. We find that these directions are not only predictive, but also causal: steering activations along the probe direction often flips model answers, with flip rates substantially exceeding norm-matched orthogonal baselines across most model-dataset pairs. When steering induces incorrect answers, we observe two distinct failure modes: confabulation (fabricating false premises) and non-entailment (stating correct premises but drawing unsupported conclusions). While post-hoc reasoning may be instrumentally useful when the model has a correct pre-CoT belief, these failure modes suggest it can result in undesirable behaviors when reasoning from a false belief.

Chain-of-thought (CoT) traces often serve as a proxy for how Large Language Models (LLMs) arrive at their answers. However, growing evidence shows that models' CoT often fails to reflect their internal computations and can be changed without affecting their final answers. In this work, we measure and improve the alignment between the reasoning described in an LLM's CoT and what it computes internally. We propose CoT-Interpretability Alignment (CIA), a metric that measures the agreement between a model's CoT traces and its internal reasoning strategies as detected by interpretability tools. We evaluate CIA on three tasks (two-hop question answering, hint intervention, and integer multiplication) across three LLMs, finding that LLMs exhibit limited alignment across all tasks (44.8-75.9%). We then experiment with improving CIA via post-training, setting both the task accuracy and parametric faithfulness signals as a reward. Experiments show that we can substantially improve CoT parametric faithfulness while maintaining or improving the task accuracy. We provide rich analysis, such as their generalization patterns. Our work provides both a framework for auditing CoT parametric faithfulness and a pathway toward making models' explicit reasoning more trustworthy. Code and data are available at https://github.com/yihuaihong/CIA-minimal-repro.