Layer-Informed Fine-Tuning via Three-Stage Functional Segmentation of LLMs

Understanding how LLMs reason is hindered by a practical asymmetry: while their generated outputs are observable, the underlying reasoning patterns remain opaque. Relying on single probes, such as Mutual Information Peak (MIP) or Deep-Thinking Ratio (DTR), risks underestimating the genuine inferential structure. To response this deficiency, we present an Integrated, cross-Architecture Reasoning (IAR) framework, designed to provide a unified approach to LLM reasoning interpretability. Specifically, we first propose to use bandwidth-calibrated MIP coupled with Tukey IQR peak-detection to isolate reasoning-crucial tokens at the output layer. Second, we performed an overlap analysis between MIP-picked tokens and DTR-deep tokens to trace the cross-layer trajectories of those tokens. This also discloses whether reasoning-crucial tokens are computation-intensive as well, further facilitating to understand how reasoning patterns evolve across model layers. Finally, we apply a Jaccard stability metric over multi-domain problems to verify if the MIP-identified tokens are reasoning quality-guaranteed. Extensive experiments on six models across four domains (mathematics, code, logic, and common sense) demonstrate IAR's generalizable interpretation capabilities across architectures. Our code is available at https://github.com/LeonardoMatthew/IAR.

Large Language Models (LLMs) increasingly rely on intermediate reasoning, yet explicit Chain-of-Thought (CoT) suffers from a linguistic space bottleneck: each thought must be decoded into tokens, causing high inference overhead. Latent reasoning moves deliberation into continuous space, but existing methods mostly learn deterministic or reward-maximizing paths, lacking a principled way to allocate probability across trajectories with different correctness and costs. We propose Latent Thought Flow (LTF), which models reasoning as variable-length continuous trajectories and trains a sampler to match a reward-induced posterior over answer quality and computation cost. We instantiate this with a continuous GFlowNet using stochastic latent transitions. To handle sparse answer supervision, we introduce an Entropy-Weighted Subtrajectory Balance objective for intermediate rewards and a reference-prior regularizer to anchor exploration. Experiments under finetuning and transfer learning settings show that LTF outperforms explicit CoT and latent reasoning baselines, improving accuracy by 9.5% while reducing reasoning length by 27.2% on average compared with strong latent reasoning baselines.

Explicit chain-of-thought (CoT) reasoning substantially improves the reasoning ability of large language models (LLMs), but incurs high inference cost due to lengthy autoregressive traces. Existing latent reasoning methods offer a promising alternative, yet they often treat reasoning as uniformly compressible, causing precision-critical intermediate steps to be overly compressed and thereby degrading reasoning accuracy. In this work, we propose Selective Latent Thinking (SLT), a framework that selectively compresses redundant reasoning spans into latent representations while preserving precision-critical spans as explicit CoT within the same reasoning trajectory. Specifically, SLT first uses a lightweight decoder to anticipate a short upcoming reasoning span, and then applies confidence-based gating to determine the longest span that can be reliably compressed. The accepted span is encoded into a compact latent representation to improve reasoning efficiency, while uncertain or precision-critical reasoning remains in explicit CoT form to preserve accuracy. To learn this selective compression policy, SLT adopts a three-stage training strategy that combines span-level latent compression, reliability-aware future reasoning prediction, and trajectory-level reinforcement learning to optimize the trade-off between answer correctness and reasoning cost. Extensive experiments across four mathematical reasoning benchmarks demonstrate that SLT achieves 22.7% higher accuracy than latent reasoning baselines at comparable compression ratios, while reducing reasoning chain length by 58.4% with only 2.8% accuracy degradation compared to explicit CoT,Our code can be found in https://github.com/hunshi34/SLT.