# Beyond the Answer: Decoding the Behavior of LLMs as Scientific Reasoners

arXiv: https://arxiv.org/abs/2603.28038 · HTML: https://mlsanity.com/paper/2603.28038/

## 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 14 of its 17 references that are in the map.
- First posted on arXiv 30 Mar 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, 14 of 14)

- [Distilling the Knowledge in a Neural Network](https://mlsanity.com/paper/1503.02531/) (2015)
- [DeepSeek-R1: Incentivizing Reasoning Capability in LLMs via Reinforcement Learning](https://mlsanity.com/paper/2501.12948/) (2025)
- [GPQA: A Graduate-Level Google-Proof Q&A Benchmark](https://mlsanity.com/paper/2311.12022/) (2023)
- [Program of Thoughts Prompting: Disentangling Computation from Reasoning for Numerical Reasoning Tasks](https://mlsanity.com/paper/2211.12588/) (2022)
- [Large Language Models as Optimizers](https://mlsanity.com/paper/2309.03409/) (2023)
- [DSPy: Compiling Declarative Language Model Calls into Self-Improving Pipelines](https://mlsanity.com/paper/2310.03714/) (2023)
- [Towards Reasoning in Large Language Models: A Survey](https://mlsanity.com/paper/2212.10403/) (2022)
- [GSM-Symbolic: Understanding the Limitations of Mathematical Reasoning in Large Language Models](https://mlsanity.com/paper/2410.05229/) (2024)
- [GEPA: Reflective Prompt Evolution Can Outperform Reinforcement Learning](https://mlsanity.com/paper/2507.19457/) (2025)
- [LeanDojo: Theorem Proving with Retrieval-Augmented Language Models](https://mlsanity.com/paper/2306.15626/) (2023)
- [The Reversal Curse: LLMs trained on "A is B" fail to learn "B is A"](https://mlsanity.com/paper/2309.12288/) (2023)
- [MiniF2F: a cross-system benchmark for formal Olympiad-level mathematics](https://mlsanity.com/paper/2109.00110/) (2021)
- [Epistemological Fault Lines Between Human and Artificial Intelligence](https://mlsanity.com/paper/2512.19466/) (2025)
- [Do explanations generalize across large reasoning models?](https://mlsanity.com/paper/2601.11517/) (2026)

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

- [More Than Can Be Said: A Benchmark and Framework for Pre-Question Scientific Ideation](https://mlsanity.com/paper/2605.06345/) (2026)
- [RCCM: Diagnosing Gains and Harms in Reasoning-Prompt Transfer](https://mlsanity.com/paper/2610.19872/) (2026)

## Abstract (arXiv)

As Large Language Models (LLMs) achieve increasingly sophisticated performance on complex reasoning tasks, current architectures serve as critical proxies for the internal heuristics of frontier models. Characterizing emergent reasoning is vital for long-term interpretability and safety. Furthermore, understanding how prompting modulates these processes is essential, as natural language will likely be the primary interface for interacting with AGI systems. In this work, we use a custom variant of Genetic Pareto (GEPA) to systematically optimize prompts for scientific reasoning tasks, and analyze how prompting can affect reasoning behavior. We investigate the structural patterns and logical heuristics inherent in GEPA-optimized prompts, and evaluate their transferability and brittleness. Our findings reveal that gains in scientific reasoning often correspond to model-specific heuristics that fail to generalize across systems, which we call "local" logic. By framing prompt optimization as a tool for model interpretability, we argue that mapping these preferred reasoning structures for LLMs is an important prerequisite for effectively collaborating with superhuman intelligence.