SEPO: Evidence-Grounded Prompt Optimization via Structural Editing

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%).

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.

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.