Two-Stage Prompt Optimization for Few-Shot Relation Extraction: From Reasoning-Guided Search to Gradient-Guided Refinement

Prompt optimization methods either analyze individual failures in isolation or compare prompt variants across examples, operating on single execution traces with no access to the reasoning process distinguishing success from failure on the same input. We introduce ContraPrompt, built on the observation that when a model fails but succeeds on a retry with feedback, the difference between its two chain-of-thought traces constitutes an optimization signal not captured by prior methods. Unlike prior contrastive methods, we compare complete intermediate reasoning processes: the two traces share model, input, and base prompt, so remaining differences reflect reasoning strategy and appended error feedback -- we call this dyadic reasoning trace analysis. The multi-attempt solving phase is an instrumented agentic retry loop that generates contrastive data automatically without human annotation. Extracted rules are organized into an input-aware decision tree routing instructions by observable input characteristics. On four reasoning and compliance benchmarks, ContraPrompt outperforms GEPA (Agrawal et al., 2026) on all four, with absolute gains of +8.29 pp on HotPotQA (+20.8% rel.), +2.21 pp on GDPR-Bench (+18.2% rel.), +7.14 pp on GPQA Diamond (+10.6% rel.), and +0.74 pp on BBH (+0.85% rel.). Ablations confirm dyadic trace contrastivity is the critical component, with a -16% relative average drop upon its removal. On 53 EvalSet black-box optimization problems, ContraPrompt beats GEPA on 11, ties on 41, and loses on 1 at equal budget. On FiNER-139 financial named entity recognition (Loukas et al., 2022), ContraPrompt achieves +7.77 pp over the unoptimized baseline (+11.6% rel.) and +1.94 pp over GEPA (+2.66% rel.), with branch conditions aligning with standard US GAAP financial-instrument categories.

Biomedical relation extraction (BioRE) is a key step in transforming biomedical literature into structured knowledge. However, most existing approaches rely on supervised models trained on costly annotated datasets, limiting their scalability and adaptability across relation types and domains. We investigate few-shot BioRE using prompt-based learning with large language models (LLMs) and compare two task formulations: pairwise classification, which predicts relations for individual entity pairs, and joint generation, which extracts multiple relations in a single model call. Experiments on the BioREDirect dataset reveal a clear precision-recall trade-off. Pairwise classification achieves higher recall, whereas joint generation is more precise and computationally efficient. The best-performing model achieves a micro-F1 score of 0.44, substantially outperforming previous few-shot results (0.34) while remaining below the supervised baseline (0.56). Much of this gap is attributable to a single ambiguously defined relation type. When evaluated using macro-F1, which better captures performance across relation types in an imbalanced setting, prompt-based approaches outperform the supervised baseline (0.45 vs. 0.38), particularly on rare relation types. These findings highlight the potential of LLMs for BioRE in low-resource settings and underscore the importance of well-defined relation schemas.

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.