# Diagnosing Pathological Chain-of-Thought in Reasoning Models

arXiv: https://arxiv.org/abs/2602.13904 · HTML: https://mlsanity.com/paper/2602.13904/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Placed in Prompting and chain-of-thought reasoning, one of 17 directions in LLM reasoning.
- Builds on 18 of its 23 references that are in the map.
- First posted on arXiv 14 Feb 2026.

## Placed in

- LLM reasoning / [Prompting and chain-of-thought reasoning](https://mlsanity.com/lr/prompting-and-chain-of-thought-reasoning/)

## Builds on (most cited first, 18 of 18)

- [DeepSeek-R1: Incentivizing Reasoning Capability in LLMs via Reinforcement Learning](https://mlsanity.com/paper/2501.12948/) (2025)
- [OpenAI o1 System Card](https://mlsanity.com/paper/2412.16720/) (2024)
- [Language Models Don't Always Say What They Think: Unfaithful Explanations in Chain-of-Thought Prompting](https://mlsanity.com/paper/2305.04388/) (2023)
- [Training Large Language Models to Reason in a Continuous Latent Space](https://mlsanity.com/paper/2412.06769/) (2024)
- [Measuring Faithfulness in Chain-of-Thought Reasoning](https://mlsanity.com/paper/2307.13702/) (2023)
- [Reasoning Models Don't Always Say What They Think](https://mlsanity.com/paper/2505.05410/) (2025)
- [Monitoring Reasoning Models for Misbehavior and the Risks of Promoting Obfuscation](https://mlsanity.com/paper/2503.11926/) (2025)
- [Chain of Thought Monitorability: A New and Fragile Opportunity for AI Safety](https://mlsanity.com/paper/2507.11473/) (2025)
- [AI Control: Improving Safety Despite Intentional Subversion](https://mlsanity.com/paper/2312.06942/) (2023)
- [Let's Think Dot by Dot: Hidden Computation in Transformer Language Models](https://mlsanity.com/paper/2404.15758/) (2024)
- [ROSCOE: A Suite of Metrics for Scoring Step-by-Step Reasoning](https://mlsanity.com/paper/2212.07919/) (2022)
- [MME-CoT: Benchmarking Chain-of-Thought in Large Multimodal Models for Reasoning Quality, Robustness, and Efficiency](https://mlsanity.com/paper/2502.09621/) (2025)
- [Stress Testing Deliberative Alignment for Anti-Scheming Training](https://mlsanity.com/paper/2509.15541/) (2025)
- [Preventing Language Models From Hiding Their Reasoning](https://mlsanity.com/paper/2310.18512/) (2023)
- [Monitoring Monitorability](https://mlsanity.com/paper/2512.18311/) (2025)
- [CoT Red-Handed: Stress Testing Chain-of-Thought Monitoring](https://mlsanity.com/paper/2505.23575/) (2025)
- [Measuring Chain of Thought Faithfulness by Unlearning Reasoning Steps](https://mlsanity.com/paper/2502.14829/) (2025)
- [Large language models can learn and generalize steganographic chain-of-thought under process supervision](https://mlsanity.com/paper/2506.01926/) (2025)

## Built on by (most cited first, 2 of 2)

- [Do Androids Dream of Breaking the Game? Systematically Auditing AI Agent Benchmarks with BenchJack](https://mlsanity.com/paper/2605.12673/) (2026)
- [ThinkProbe: Beyond Accuracy -- Structural Profiling of Open-Ended LLM Reasoning Traces via Non-Generative Thought Graphs](https://mlsanity.com/paper/2606.29067/) (2026)

## Abstract (arXiv)

Chain-of-thought (CoT) reasoning is fundamental to modern LLM architectures and represents a critical intervention point for AI safety. However, CoT reasoning may exhibit failure modes that we note as pathologies, which prevent it from being useful for monitoring. Prior work has identified three distinct pathologies: post-hoc rationalization, where models generate plausible explanations backwards from predetermined answers; encoded reasoning, where intermediate steps conceal information within seemingly interpretable text; and internalized reasoning, where models replace explicit reasoning with meaningless filler tokens while computing internally. To better understand and discriminate between these pathologies, we create a set of concrete metrics that are simple to implement, computationally inexpensive, and task-agnostic. To validate our approach, we develop model organisms deliberately trained to exhibit specific CoT pathologies. Our work provides a practical toolkit for assessing CoT pathologies, with direct implications for training-time monitoring.