Collaborative Agent Reasoning Engineering (CARE): A Structured Methodology for Systematically Engineering AI Agents for Science

We present Collaborative Agent Reasoning Engineering (CARE), a disciplined methodology for engineering Large Language Model (LLM) agents in scientific domains. Unlike ad-hoc trial-and-error approaches, CARE specifies behavior, grounding, tool orchestration, and verification through reusable artifacts and systematic, stage-gated phases. The methodology employs a three-party workflow involving Subject-Matter Experts (SMEs), developers, and LLM-based helper agents. These helper agents function as facilitation infrastructure, transforming informal domain intent into structured, reviewable specifications for human approval at defined gates. CARE addresses the "jagged technological frontier", characterized by uneven LLM performance, by bridging the gap between novice and expert analysts regarding domain constraints and verification practices. By generating concrete artifacts, including interaction requirements, reasoning policies, and evaluation criteria, CARE ensures agent behavior is specifiable, testable, and maintainable. Evaluation results from a scientific use case demonstrate that this stage-gated, artifact-driven methodology yields measurable improvements in development efficiency and complex-query performance.