A Reproducible Optimisation Protocol for Calibrating Prompt-Based Large Language Model Workflows in Evidence Synthesis

Abstract: This methods article presents a reproducible calibration workflow for prompt-based LLMs in structured evidence-synthesis tasks. The method separates the rules that define the scientific task from the mutable prompt harness that frames and applies them. It optimises that harness against labelled or reference examples and an explicit task metric, then preserves the calibrated workflow as an inspectable artefact with its specification, metric, settings, and evaluation traces. The example code instantiates the protocol with DSPy and GEPA tools, but the underlying logic can transfer to other prompt-optimisation frameworks that support structured task definitions, metric-guided search, and artefact reuse. Title and abstract screening is the worked validation case because it provides labelled benchmark data and clear evaluation metrics. The demonstrated workflow uses a smaller student LLM for performing the scientific task execution and a larger reflection LLM to steer the prompt optimisation process during calibration. This work shows compilation, artefact round-tripping, and how optimisation budget affects a smaller student model.