FAPO: Fully Automated Prompt Optimization of Multi-Step LLM Pipelines

Automatic Prompt Optimization (APO) often rewrites prompts monolithically, which can improve one behavior while degrading others. We present SAPO, a segment-level APO method that decomposes prompts into role, context, tasks, and output format, then applies targeted improvements based on top-5 and bottom-5 examples. The optimization loop uses one LLM with static meta-prompts and structured outputs for segmentation, weakness analysis, and candidate generation. We describe a train/validation protocol and a two-stage generation process: (1) segment-level diagnosis and recommendation extraction, (2) candidate synthesis constrained by weak/strong segment signals. Using the evaluation setup across SQuADv2, TweetEval, XSUM, CommonGen, and GSM8K on GPT-3.5-Turbo and GPT-4o-mini, SAPO achieves the best average score against Zero-shot and strong APO baselines including APE, OPRO, EvoPrompt, GEPA, and StraGO.

Evolutionary prompt optimizers such as GEPA suffer from prompt bloat: each iteration appends rules and caveats, producing prompts up to 3$\times$ longer yet no more accurate. We trace this to three deficiencies - incomplete error observation, limited search diversity, and unreliable selection - and propose ESPO (Error-Structured Prompt Optimization), which decomposes prompt optimization into three phases: Diagnose clusters all training errors into structural patterns in one round; Propose generates candidates via four complementary strategies with independent biases; Select applies bootstrap stability selection. On seven public NLP benchmarks - Tweet, MMLU, GSM8K, HotpotQA, ScoNe, HoVer, and PUPA - ESPO improves average accuracy by $+$3.76 pp over the state-of-the-art (74.67% vs 70.91% for GEPA), matching or exceeding GEPA on every dataset while producing prompts 47% shorter (1,004 vs 1,878 chars) and faster at inference. Cross-model experiments across four additional student models (Gemma 3 12B, Mistral 14B, Qwen3 32B, Claude Haiku 4.5) show ESPO yields the best average accuracy on every model tested, with the largest gap on Qwen3 GSM8K (15.00% $\to$ 91.40%). A generalization bound (Appendix) grounds each phase in a corresponding term of the test-time gap, and the ablation confirms a key prediction: adding diversity without bootstrap selection actually hurts performance ($-$1.20%).

Large language models (LLMs) achieve strong performance across a wide range of tasks but are highly sensitive to prompt design, motivating the need for automatic prompt optimization. Existing methods predominantly focus on performance alone, ignoring competing objectives such as inference cost or latency. At the same time, existing work on multi-objective prompt optimization relies on off-the-shelf NSGA-II, ignoring optimization efficiency. As a remedy, we introduce MO-CAPO, a novel multi-objective prompt optimization algorithm that jointly optimizes performance and inference cost while leveraging budget allocation for cost-efficient optimization. We further propose a deployment-oriented cost objective that captures the full computational profile of LLM inference. We evaluate our approach across four tasks and three LLMs and compare it to an NSGA-II-based multi-objective method and state-of-the-art single-objective prompt optimizers. Results show that MO-CAPO consistently identifies strong, robust, and diverse Pareto front approximations while maintaining cost-efficiency. It outperforms the NSGA-II baseline on 8 out of 12 cases in terms of the noisy R2 metric and achieves competitive performances often already at a considerably lower budget. The discovered solution sets span diverse performance-cost trade-offs that are omitted by single-objective optimizers, yet the top-performance candidates remain competitive with single-objective solutions. Additionally, we conduct the first evaluation of multi-objective machine learning experiments that considers generalization and robustness through noisy R2 and approximation gap, enabling a more realistic assessment of solution quality. MO-CAPO enables practitioners to select from an efficiently discovered set of multiple prompts offering different trade-offs between performance and cost.