Lost in the Flow with Code Talkers: Unveiling the Instruction-Tuning Tax of Large Language Models in Code Tasks
Authors: Shi Ying Chang, Chiok Yew Ho, Yichen Li, Yintong Huo
Abstract
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.
Instruction tuning is meant to make language models follow user requests, yet it is unclear whether small models comply when an instruction conflicts with their usual task behavior. We study this across three tasks - multiple-choice question answering (MCQA), sentiment classification, and mathematical question answering - by pairing a standard instruction with a conflicting non-standard one (select an incorrect option, output the opposite sentiment, or return twice the answer). This cross-task design allows us to test whether resistance to conflicting instructions is tied to specific task characteristics or reflects a broader behavioral tendency. As all predictions are scored against the original ground truth, a model that ignores the non-standard instruction still appears accurate. Using standard accuracy, non-standard accuracy, and an Instruction-Following Failure Rate (IFFR), we evaluate instruction-tuned Qwen models across sizes. Both standard accuracy and instruction following generally improve with scale, although the pattern is not consistent across all tasks and datasets. Small models stay competent yet routinely ignore the non-standard instruction, while larger models show a clear gap between the two settings. These findings suggest that gains in task capability do not automatically provide reliable control over model behavior. Task competence and instruction following are therefore distinct abilities, and reporting only standard accuracy hides instruction-following failures.
Instruction tuning is commonly assumed to endow language models with a domain-general ability to follow instructions, yet the underlying mechanism remains poorly understood. Does instruction-following rely on a universal mechanism or compositional skill deployment? We investigate this through diagnostic probing across nine diverse tasks in three instruction-tuned models. Our analysis provides converging evidence against a universal mechanism. First, general probes trained across all tasks show selective rather than uniform deficits relative to task-specific specialists, indicating that representational sharing is partial and structured rather than global. Second, cross-task transfer is weak and clustered by skill similarity. Third, causal ablation reveals sparse asymmetric dependencies rather than shared representations. Tasks also stratify by complexity across layers, with structural constraints emerging early and semantic tasks emerging late. Finally, temporal analysis shows that the constraint signal becomes decodable only once generation is under way, and remains so throughout the response. These findings indicate that instruction-following is better characterized as skillful coordination of diverse linguistic capabilities rather than deployment of a single abstract constraint-checking process.
Recently, the rapid development of large language models (LLMs) has reshaped software engineering by enabling autonomous code agents that plan, execute, and utilize external tools iteratively to tackle complex tasks. Beyond achieving functional correctness, these agents must faithfully follow process instructions and constraints throughout the development lifecycle. However, existing benchmarks typically focus on final functional correctness or confine instruction-following evaluation to single-turn, general chat or simple code generation scenarios, leaving instruction-following in multi-turn agentic coding underexplored. To bridge this gap, we propose MTAC-IFBench, a comprehensive benchmark for this critical capability. It features multi-turn progressive software development instructions with diverse constraints spanning 6 primary and 18 secondary categories. With an average of 7.04 turns and 91.33 constraints per instance, it poses a rigorous challenge to current LLMs. To make the evaluation reliable, we construct a checklist for each constraint and functional requirement, and integrate verification scripts and judge agents to verify each checklist item. MTAC-IFBench identifies significant deficiencies in existing code agents in multi-turn instruction-following, with their performance degrading rapidly as the interaction session grows longer.