Causal Chain of Thought: Mitigating Attention Leakage via Context Isolation

Chain-of-thought (CoT) prompting is widely used as a reasoning aid and is often treated as a transparency mechanism. Yet behavioral gains under CoT do not imply that the model's internal computation causally depends on the emitted reasoning text, i.e. models may produce fluent rationales while routing decision-critical computation through latent pathways. We introduce a causal, layerwise audit of CoT faithfulness based on activation patching. Our key metric, the CoT Mediation Index (CMI), isolates CoT-specific causal influence by comparing performance degradation from patching CoT-token hidden states against matched control patches. Across multiple model families (Phi, Qwen, DialoGPT) and scales, we find that CoT-specific influence is typically depth-localized into narrow ''reasoning windows,'' and we identify bypass regimes where CMI is near-zero despite plausible CoT text. We further observe that models tuned explicitly for reasoning tend to exhibit stronger and more structured mediation than larger untuned counterparts, while Mixture-of-Experts models show more distributed mediation consistent with routing-based computation. Overall, our results show that CoT faithfulness varies substantially across models and tasks and cannot be inferred from behavior alone, motivating causal, layerwise audits when using CoT as a transparency signal.

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.

Understanding the causal structure of a language model's thought process is a problem of significant importance for both transparency and safety. In this work, we take a local approach toward this goal by analyzing the causal relationships among individual components, termed units, of a given, specific chain-of-thought trace. We construct a structural causal model on these units and relate each unit to the log probability of generating (subsequent) output units. Our algorithm, termed AttriCoT, is a black-box method that performs attribution by estimating importance parameters in the structural causal model using $O(U)$ forward passes through the model, where $U$ is the number of units. Evaluation of perturbation curves across 5 datasets and 4 reasoning models shows that AttriCoT produces attributions that are more faithful to the model's behavior than alternative methods. The attribution results also reveal notable differences in thought structure between models and domains.