From Monolithic to Modular: Segment-level Automatic Prompt Optimization

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.

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%).

System prompt optimization improves agent behavior without modifying the underlying model, yielding human-readable, model-agnostic instructions. Existing methods build a prompt agent that refines task agents' system prompts, yet leave the prompt agent's own system prompt hand-engineered and fixed. We propose Self-Evolving Prompt Optimization (SePO), which treats the prompt agent's own system prompt as an optimization target alongside task agents' system prompts. SePO adopts a self-referential design. A single prompt agent improves both task agents' system prompts and its own under an open-ended evolutionary search that maintains an archive of candidate prompts as stepping stones. Training proceeds in two stages: pre-training evolves the prompt agent on a multi-task pool, and fine-tuning then applies it to a target task. Across five benchmarks spanning math (AIME'25), abstract reasoning (ARC-AGI-1), graduate-level science (GPQA), code generation (MBPP), and logic puzzles (Sudoku), SePO consistently outperforms Manual-CoT, TextGrad, and MetaSPO, improving the average accuracy by 4.49 points compared to Manual-CoT. The prompt optimization skill from pre-training also generalizes to tasks beyond the pre-training mixture, rather than memorizing per-task prompts.