Collaborative Agent Reasoning Engineering (CARE): A Three-Party Design Methodology for Systematically Engineering AI Agents with Subject Matter Experts, Developers, and Helper Agents

Large language models are rapidly moving towards closing the development cycle, transitioning from simple assistive companions to autonomous contributors deeply embedded into collaborative development environments. Despite their accelerated adoption, existing evaluation techniques are limited due to their fragmented nature and distorted projection of true model capabilities, often obtained from hypothetical syntactic scenarios. This research aims to bridge this gap by providing a comprehensive evaluation methodology for LLM-powered agents that is grounded in real-world software development practice. Our evaluation approach focuses on contamination-awareness, in-the-wild agentic behavior assessment, and trajectory-aware benchmarks and metrics capturing realistic coding contexts, human-aligned behavior, and model failure modes.

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.

Agentic systems are becoming more capable: agents define strategies, take actions, and interact with different environments. This autonomy poses serious challenges for overseeing and assessing agent behavior. Most current tools are limited, focusing on observability with basic evaluation capabilities or imposing static, hand-crafted error taxonomies that cannot adapt to new domains. To address this gap, we present Agentic CLEAR, an automatic, dynamic, and easy-to-use evaluation framework. It produces textual insights into the agent behavior on three levels of granularity: system, trace, and node. Agentic CLEAR operates above the observability layer, enabling seamless integration and featuring an intuitive UI that makes agent evaluation highly accessible. In our experiments on four benchmarks, seven agentic settings, and tens of thousands of LLM calls, we show that Agentic CLEAR produces high-quality, data-driven, insightful feedback. Our analysis shows strong alignment with human-annotated errors and the ability to predict task success rate.