# Reasoning Instructions Can Break Answer Decoding in Vision--Language Models

arXiv: https://arxiv.org/abs/2609.29278 · HTML: https://mlsanity.com/paper/2609.29278/

## Key facts

- No citing papers in the map yet (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 21 references that are in the map.
- First posted on arXiv 24 Sep 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)

- [LoRA: Low-Rank Adaptation of Large Language Models](https://mlsanity.com/paper/2106.09685/) (2021)
- [Chain-of-Thought Prompting Elicits Reasoning in Large Language Models](https://mlsanity.com/paper/2201.11903/) (2022)
- [Visual Instruction Tuning](https://mlsanity.com/paper/2304.08485/) (2023)
- [Qwen2.5-VL Technical Report](https://mlsanity.com/paper/2502.13923/) (2025)
- [MMBench: Is Your Multi-modal Model an All-around Player?](https://mlsanity.com/paper/2307.06281/) (2023)
- [MMMU: A Massive Multi-discipline Multimodal Understanding and Reasoning Benchmark for Expert AGI](https://mlsanity.com/paper/2311.16502/) (2023)
- [Language Models as Knowledge Bases?](https://mlsanity.com/paper/1909.01066/) (2019)
- [Learn to Explain: Multimodal Reasoning via Thought Chains for Science Question Answering](https://mlsanity.com/paper/2209.09513/) (2022)
- [Calibrate Before Use: Improving Few-Shot Performance of Language Models](https://mlsanity.com/paper/2102.09690/) (2021)
- [Understanding intermediate layers using linear classifier probes](https://mlsanity.com/paper/1610.01644/) (2016)
- [Probing Classifiers: Promises, Shortcomings, and Advances](https://mlsanity.com/paper/2102.12452/) (2021)
- [A Diagram Is Worth A Dozen Images](https://mlsanity.com/paper/1603.07396/) (2016)
- [Designing and Interpreting Probes with Control Tasks](https://mlsanity.com/paper/1909.03368/) (2019)
- [Large Language Models Are Not Robust Multiple Choice Selectors](https://mlsanity.com/paper/2309.03882/) (2023)
- [Judging the Judges: A Systematic Study of Position Bias in LLM-as-a-Judge](https://mlsanity.com/paper/2406.07791/) (2024)
- [Surface Form Competition: Why the Highest Probability Answer Isn't Always Right](https://mlsanity.com/paper/2104.08315/) (2021)
- [Eliminating Position Bias of Language Models: A Mechanistic Approach](https://mlsanity.com/paper/2407.01100/) (2024)
- [More Thought, Less Accuracy? On the Dual Nature of Reasoning in Vision-Language Models](https://mlsanity.com/paper/2509.25848/) (2025)

## Abstract (arXiv)

Chain-of-thought (CoT) instructions can distort multiple-choice VLM evaluation when a scorer appends a reasoning cue but reads answer-label logits before the model generates any rationale. We call this CoT-prefix scoring. On ScienceQA, Qwen2.5-VL-7B drops from 80.76% to 45.48%, and across five option-content permutations 93.54% of CoT-prefix predictions select the first slot. Condition-matched linear probes recover 78.94% from the same hidden states, while free generation restores 75.24%, showing that the answer often survives the prefix and the immediate readout fails. Vocabulary and layer diagnostics explain the mismatch: probability mass moves toward continuation tokens, while answer information remains linearly accessible in late layers. The effect recurs with varying severity across datasets and models, though not universally. These results show that CoT-prefix scoring can confound model knowledge with an evaluation-interface mismatch and should be avoided unless the requested and scored output events are aligned.