Adaptive Prompt Structure Factorization: A Framework for Self-Discovering and Optimizing Compositional Prompt Programs

Large language models (LLMs) have become increasingly capable of following instructions and complex reasoning, making prompting a flexible interface for adapting models without parameter updates. Yet prompt design remains labor-intensive and highly sensitive to formatting, phrasing, and instruction order, motivating automated prompt optimization methods that reduce manual effort while preserving inference-time flexibility. However, existing methods often search over prompt candidates or use fixed critique-refine pipelines driven by individual examples or small batches, limiting their ability to capture systematic error patterns and make targeted edits grounded in failure history. We propose Reflective Prompt Tuning (RPT), a framework that uses LLM function calling to simulate the iterative workflow of human prompt engineers. An LLM optimizer calls a diagnostic function that evaluates the target model over an entire optimization set, summarizes recurring failure modes, and returns a structured diagnostic report. The optimizer uses this report, together with an accumulated memory of prior reports, to revise the prompt for the next iteration. RPT further supports confidence-aware optimization by using calibration signals in diagnostic feedback and final prompt selection. Across three reasoning tasks, RPT improves over initial prompts by up to 12.9 points, remains competitive with state of the art, and improves confidence calibration. Our analyses show that RPT is especially effective on multi-hop and mathematical reasoning, producing targeted prompt revisions that align with diagnosed failure patterns and lead to gains in task performance and calibration.

Prompt optimization has become a practical way to improve the performance of Large Language Models (LLMs) without retraining. However, most existing frameworks treat evaluation as a black box, relying solely on outcome scores without explaining why prompts succeed or fail. Moreover, they involve repetitive trial-and-error refinements that remain implicit, offering limited interpretability or actionable guidance for systematic improvement. In this paper, we propose MA-SAPO: a new Multi-Agent Reasoning for Score Aware Prompt Optimization framework that links evaluation outcomes directly to targeted refinements. Specifically, in the Training Phase, multiple agents interpret evaluation scores, diagnose weaknesses, and generate concrete revision directives, which are stored as reusable reasoning assets. In the Test Phase, an analyzer agent retrieves relevant exemplars and assets for a new prompt, and a refiner agent applies evidence-based edits to improve the prompt and its response. By grounding optimization in structured reasoning, MA-SAPO ensures edits are interpretable, auditable, and controllable. Experiments on the HelpSteer1/2 benchmarks show that our framework consistently outperforms single-pass prompting, retrieval-augmented generation, and prior multi-agent methods across multiple evaluation metrics.

Multi-step LLM pipelines fail through interactions among retrieval, reasoning, and formatting steps, so prompt-only optimization can miss bottlenecks in the chain. We present Fully Automated Prompt Optimization (FAPO), a framework that lets Claude Code optimize an LLM pipeline inside a standardized codebase. FAPO evaluates a pipeline, inspects intermediate steps, diagnoses failures, proposes scoped changes, and validates variants repeatedly to optimize against a score function. It first tries prompt edits and, only when prompt optimization appears insufficient, changes chain structure within the permitted scope when attribution identifies a structural bottleneck. Across six benchmarks and three task models, FAPO beats the baseline GEPA in 15 of 18 model-benchmark comparisons. In 11 model-benchmark comparisons, FAPO wins with non-overlapping mean $\pm$ trial-standard-deviation ranges, and the mean FAPO-GEPA gain is +14.1 pp. In the six HoVer and IFBench comparisons where prompt-first search escalated to structural changes, FAPO wins all six with a mean gain of +33.8 pp. FAPO also improves performance on security tasks: on CTIBench-RCM, a security CVE-to-CWE task, prompt-only FAPO lifts test accuracy by +4.0 pp on GPT-5, +7.1 pp on Foundation-Sec-8B-Instruct, and +2.0 pp on Foundation-Sec-8B-Reasoning. These results position FAPO as a state-of-the-art pipeline optimization technique for both general-purpose and security-focused tasks.