CoRA: Confidence-Rationale Alignment for Reliable Chain-of-Thought Reasoning

Long chains of thought (CoT) from current language models frequently contain logical gaps and unjustified leaps, limiting the gains from additional test-time compute. Improving reasoning quality directly would require process reward models, but the step-level annotations needed to train them are expensive and scarce. We find such a signal in how the model's confidence evolves during reasoning: premature confidence, the tendency to commit to an answer early and use the remaining tokens to rationalize it, strongly predicts flawed reasoning across tasks and model scales. We exploit this in progressive confidence shaping, a reinforcement learning objective that trains models to update their confidence as they reason rather than commit early -- rewarding gradual confidence growth and penalizing early commitment, with no external labels or reward models. The method improves accuracy and reasoning quality from 1.5B to 8B parameters across arithmetic (Countdown), math (DAPO, AIME), and science (ScienceQA): on Countdown, accuracy improves 3.2x (+42.0pp) and flawed reasoning drops 48pp; on AIME, Pass@64 improves 6.6pp. Consistent with this mechanism, the method also improves faithfulness: on a safety benchmark, our models more transparently surface misleading content in their reasoning traces rather than concealing it. Controlled experiments reveal that the problem and its remedy scale together: premature confidence grows with model size and task difficulty, and so do the gains from addressing it.

Large reasoning models often reach correct answers through flawed intermediate steps, creating a gap between final accuracy and reasoning reliability. Existing alignment strategies address this with external verifiers or massive sampling, limiting scalability. In this work, we introduce CASPO (Confidence-Aware Step-wise Preference Optimization), a framework that aligns token-level confidence with step-wise logical correctness through iterative Direct Preference Optimization, without training a separate reward model. During inference, we propose Confidence-aware Thought (CaT), which leverages this calibrated confidence to dynamically prune uncertain reasoning branches with negligible O(V) latency. Experiments across ten benchmarks and multiple model families show that CASPO consistently improves reasoning reliability and inference efficiency. CASPO scales to Qwen3-8B-Base and surpasses tree-search baselines on AIME'24 and AIME'25 without using reward-model data. We also release a step-wise dataset with confidence annotations to support fine-grained analysis of reasoning reliability. Code is available at https://github.com/Thecommonirin/CASPO.

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.