How Robustly do LLMs Understand Execution Semantics?

Standard accuracy metrics cannot explain why LLMs handle variable tracking but fail on semantically equivalent loops. We study an internal lifecycle of code reasoning in which models first brew the answer, making it linearly recoverable many layers before it becomes self-decodable, and then diverge into one of four resolution outcomes: Resolved, Overprocessed, Misresolved, or Unresolved. Understanding this lifecycle matters because similar task accuracies can mask fundamentally different failure modes that surface-level evaluation cannot detect. We introduce a dual diagnostic framework pairing layer-wise linear probing with Context-Stripped Decoding (CSD) and apply it to six code-reasoning task families across 16 models spanning Qwen, Llama, and DeepSeek architectures. All four outcomes carry substantial mass in every task family: overall Resolved is only 41.5%, with multiple tasks below 30%. Controlled sweeps over structure, depth, and operators expose task-specific failure bottlenecks: Function Call Resolved plunges from 61.1% to 2.5% as call depth increases from one to three. Across architectures and scales, the brewing scaffold remains stable, with normalized brewing duration 24-42% across all 16 models, while resolution success varies with capability. This indicates that the scaffold is a stable empirical regularity across the tested decoder-only Transformer families, whereas resolution success covaries with capability, scale, and training. Code: https://github.com/euyis1019/llm-brewing

Large language models (LLMs) have shown proficiency in various software engineering tasks, such as code generation and translation. However, a key limitation in their performance may be their (lack of) understanding of programming-language semantics. Even when explicit semantics are given, it remains unclear whether LLMs apply those rules or lean on priors learned during pre-training instead. We study if LLMs lean on priors or given semantics with a novel task--Program Executability Prediction (PrEx)--that asks models to predict whether a program is semantically valid or invalid (and, if invalid, which formal rule it violates) given the program's syntax and operational semantics. Because PrEx requires both valid and invalid programs, we build a dataset with systematically generated invalid transformations derived from valid programs. We evaluate open-source coding LLMs under two semantic formalisms and two semantic shifts across Human-Written, LLM-Translated, and Fuzzer-Generated program splits. Our findings show that LLMs lean on pre-training priors rather than systematically applying the given rules, performing especially poorly on modified semantics and degrading further as program complexity increases. PrEx is available at https://github.com/EngineeringSoftware/prex.

Code language models are now trusted collaborators in production workflows for debugging, refactoring, and iterative repair, and every benchmark that evaluates them assumes the instructions they act on are correct. We study what happens when that assumption breaks. We evaluate code language models across four experiments designed to assess whether models resist or obey incorrect instructions in single-pass and iterative repair settings, using the RunBugRun dataset of algorithmic Python problems with deterministic test cases. Our findings reveal a striking behavioral pattern: models correctly identify an incorrect instruction as wrong, then follow it anyway. This compliance unknowingly introduces errors beyond the original bug, and the corrupted code state cannot be recovered through subsequent self-guided iterative repair, which fails to converge across passes. We term this Blind Obedience, characterize the Ghost (Unknown) Errors it introduces, quantify the proportion of cases where semantic corruption proves irrecoverable, and show that extended reasoning cannot reverse it. These findings surface behavioral properties invisible to pass-rate evaluation, with direct consequences for code language models deployed in production settings.