# Lost in the Flow with Code Talkers: Unveiling the Instruction-Tuning Tax of Large Language Models in Code Tasks

arXiv: https://arxiv.org/abs/2606.08676 · HTML: https://mlsanity.com/paper/2606.08676/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 23 of its 40 references that are in the map.
- First posted on arXiv 7 Jun 2026.

## Builds on (most cited first, 23 of 23)

- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [Training language models to follow instructions with human feedback](https://mlsanity.com/paper/2203.02155/) (2022)
- [Evaluating Large Language Models Trained on Code](https://mlsanity.com/paper/2107.03374/) (2021)
- [Program Synthesis with Large Language Models](https://mlsanity.com/paper/2108.07732/) (2021)
- [SWE-bench: Can Language Models Resolve Real-World GitHub Issues?](https://mlsanity.com/paper/2310.06770/) (2023)
- [Self-Instruct: Aligning Language Models with Self-Generated Instructions](https://mlsanity.com/paper/2212.10560/) (2022)
- [Is Your Code Generated by ChatGPT Really Correct? Rigorous Evaluation of Large Language Models for Code Generation](https://mlsanity.com/paper/2305.01210/) (2023)
- [OpenHands: An Open Platform for AI Software Developers as Generalist Agents](https://mlsanity.com/paper/2407.16741/) (2024)
- [CodeT5: Identifier-aware Unified Pre-trained Encoder-Decoder Models for Code Understanding and Generation](https://mlsanity.com/paper/2109.00859/) (2021)
- [CodeXGLUE: A Machine Learning Benchmark Dataset for Code Understanding and Generation](https://mlsanity.com/paper/2102.04664/) (2021)
- [An Empirical Study of Catastrophic Forgetting in Large Language Models During Continual Fine-tuning](https://mlsanity.com/paper/2308.08747/) (2023)
- [BigCodeBench: Benchmarking Code Generation with Diverse Function Calls and Complex Instructions](https://mlsanity.com/paper/2406.15877/) (2024)
- [StarCoder 2 and The Stack v2: The Next Generation](https://mlsanity.com/paper/2402.19173/) (2024)
- [InCoder: A Generative Model for Code Infilling and Synthesis](https://mlsanity.com/paper/2204.05999/) (2022)
- [DS-1000: A Natural and Reliable Benchmark for Data Science Code Generation](https://mlsanity.com/paper/2211.11501/) (2022)
- [UniXcoder: Unified Cross-Modal Pre-training for Code Representation](https://mlsanity.com/paper/2203.03850/) (2022)
- [Efficient Training of Language Models to Fill in the Middle](https://mlsanity.com/paper/2207.14255/) (2022)
- [How Abilities in Large Language Models are Affected by Supervised Fine-tuning Data Composition](https://mlsanity.com/paper/2310.05492/) (2023)
- [Grounded Copilot: How Programmers Interact with Code-Generating Models](https://mlsanity.com/paper/2206.15000/) (2022)
- [ClassEval: A Manually-Crafted Benchmark for Evaluating LLMs on Class-level Code Generation](https://mlsanity.com/paper/2308.01861/) (2023)
- [Evaluation of LLMs on Syntax-Aware Code Fill-in-the-Middle Tasks](https://mlsanity.com/paper/2403.04814/) (2024)
- [Out of Distribution, Out of Luck: How Well Can LLMs Trained on Vulnerability Datasets Detect Top 25 CWE Weaknesses?](https://mlsanity.com/paper/2507.21817/) (2025)
- [RAG or Fine-tuning? A Comparative Study on LCMs-based Code Completion in Industry](https://mlsanity.com/paper/2505.15179/) (2025)

## Abstract (arXiv)

AI coding assistants have significantly improved developer productivity by automatically suggesting code that aligns with user intent, and many of these tools are now integrated directly into Integrated Development Environments (IDEs). Developers interact with code in two distinct cognitive modes: Flow and Command. While developers require tools that directly complete or infill code in unfinished programs during Flow mode, they also need tools that can comprehend intentions expressed as natural-language instructions and convert them into executable code in Command mode. Although instruction-tuned Large Language Models (LLMs) dominate many application scenarios due to their abilities to infer and fulfill developers' intents, it remains unclear whether the same paradigm is equally suitable for different code-related tasks. Therefore, it is necessary to understand how instruction tuning affects the feasibility of CodeLLMs as coding assistants. To fill this gap, we conduct the first empirical study that uncovers a key trade-off caused by instruction tuning across programming modes, which we term the Instruction-Tuning Tax. Our results show that instruction tuning is not a free lunch: although instruction-tuned models are more capable of following instructions and leveraging structured guidance, these gains often come at the cost of weaker infilling performance. We further extend our study through both qualitative and quantitative analyses, including manual failure categorization, behavioral metrics that capture generation fidelity, and intermediate-checkpoint evaluation throughout the tuning process. Summarizing our results into seven findings and four implications, our study offers a new perspective on the development of AI-powered coding tools and highlights the need to carefully balance instruction-following ability with effective code generation assistance.