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

Large Language Models (LLMs) have demonstrated strong capabilities in complex reasoning tasks, while recent prompting strategies such as Chain-of-Thought (CoT) have further elevated their performance in handling complex logical problems. Despite these advances, high-quality reasoning remains heavily reliant on manual static prompts and is sensitive to decoding configurations and task distributions, leading to performance fluctuations and limited transferability. Existing automatic prompt optimization methods typically adopt single-agent local search, failing to simultaneously optimize prompts and decoding hyperparameters within a unified framework to achieve stable global improvements. To address this limitation, we propose Agent-GWO, a dynamic prompt optimization framework for complex reasoning. Specifically, we unify prompt templates and decoding hyperparameters as inheritable agent configurations. By leveraging the leader-follower mechanism of the Grey Wolf Optimizer (GWO), we automatically select three leader agents ($α$, $β$, and $δ$) to guide the collaborative updates of the remaining agents, enabling iterative convergence toward robust optimal reasoning configurations that can be seamlessly integrated for inference. Extensive experiments on multiple mathematical and hybrid reasoning benchmarks across diverse LLM backbones show that Agent-GWO consistently improves accuracy and stability over existing prompt optimization methods. The code will be released publicly.

Large language model (LLM)-based systems are increasingly deployed to conduct scientific research autonomously, yet whether their reasoning adheres to the epistemic norms that make scientific inquiry self-correcting is poorly understood. Here, we evaluate LLM-based scientific agents across eight domains, spanning workflow execution to hypothesis-driven inquiry, through more than 25,000 agent runs and two complementary lenses: (i) a systematic performance analysis that decomposes the contributions of the base model and the agent scaffold, and (ii) a behavioral analysis of the epistemological structure of agent reasoning. We observe that the base model is the primary determinant of both performance and behavior, accounting for 41.4% of explained variance versus 1.5% for the scaffold. Across all configurations, evidence is ignored in 68% of traces, refutation-driven belief revision occurs in 26%, and convergent multi-test evidence is rare. The same reasoning pattern appears whether the agent executes a computational workflow or conducts hypothesis-driven inquiry. They persist even when agents receive near-complete successful reasoning trajectories as context, and the resulting unreliability compounds across repeated trials in epistemically demanding domains. Thus, current LLM-based agents execute scientific workflows but do not exhibit the epistemic patterns that characterize scientific reasoning. Outcome-based evaluation cannot detect these failures, and scaffold engineering alone cannot repair them. Until reasoning itself becomes a training target, the scientific knowledge produced by such agents cannot be justified by the process that generated it.

Large language models (LLMs) have recently shown strong progress on scientific reasoning, yet two major bottlenecks remain. First, explicit retrieval fragments reasoning, imposing a hidden "tool tax" of extra tokens and steps. Second, multi-agent pipelines often dilute strong solutions by averaging across all candidates. We address these challenges with a unified framework that combines implicit retrieval and structured collaboration. At its foundation, a Monitor-based retrieval module operates at the token level, integrating external knowledge with minimal disruption to reasoning. On top of this substrate, Hierarchical Solution Refinement (HSR) iteratively designates each candidate as an anchor to be repaired by its peers, while Quality-Aware Iterative Reasoning (QAIR) adapts refinement to solution quality. On Humanity's Last Exam (HLE) Bio/Chem Gold, our framework achieves 48.3% accuracy - the highest reported to date, surpassing the strongest agent baseline by 13.4 points and leading frontier LLMs by up to 18.1 points, while simultaneously reducing token usage by 53.5% and agent steps by 43.7%. Results on SuperGPQA and TRQA confirm robustness across domains. Error analysis shows that reasoning failures and knowledge gaps co-occur in over 85% of cases, while diversity analysis reveals a clear dichotomy: retrieval tasks benefit from solution variety, whereas reasoning tasks favor consensus. Together, these findings demonstrate how implicit augmentation and structured refinement overcome the inefficiencies of explicit tool use and uniform aggregation. The code is available at https://github.com/tangxiangru/Eigen-1.