arXiv:2604.12350cs.LGcs.AI2026-04

用化学约束的三元组训练大模型,实现骨架保留的分子优化

Scaffold-Conditioned Preference Triplets for Controllable Molecular Optimization with Large Language Models

  • 构建骨架约束的优劣三元组,引导模型生成合理分子
  • 在多目标优化中提升属性改善幅度,同时保持更高骨架相似度
  • 支持可控数据构建,适用于不同药物研发场景

分子属性优化是药物发现的核心,但现有深度学习方法依赖黑箱评分,难以控制骨架保留,常生成不稳定或生物上不合理结构。尽管大语言模型(LLM)在分子生成方面前景广阔,其优化仍受限于缺乏基于化学知识的偏好监督和系统化数据构建。本文提出骨架条件偏好三元组(SCPT),通过骨架对齐与化学驱动的过滤器构建相似性约束三元组⟨骨架,更好,更差⟩,确保生成结果在有效性、可合成性和属性提升上均合理。利用这些偏好,我们将预训练分子LLM对齐为条件编辑器,实现属性提升且保留原始骨架的修改。在单目标和多目标基准测试中,SCPT显著提升优化成功率与属性增益,同时保持高于基线的骨架相似度。相较于代表性非LLM方法,经SCPT训练的LLM更适配骨架约束和多目标优化任务;此外,单属性与双属性监督训练的模型能有效泛化至三属性任务,表明在有限高阶监督下具备良好外推能力。SCPT还提供可调控的数据构建机制,可预测地实现相似度-收益权衡,支持多样化优化场景的系统性适配。

原文摘要 · Abstract (English)

Molecular property optimization is central to drug discovery, yet many deep learning methods rely on black-box scoring and offer limited control over scaffold preservation, often producing unstable or biologically implausible edits. While large language models (LLMs) are promising molecular generators, optimization remains constrained by the lack of chemistry-grounded preference supervision and principled data curation. We introduce \textbf{Scaffold-Conditioned Preference Triplets (SCPT)}, a pipeline that constructs similarity-constrained triplets $\langle\text{scaffold}, \text{better}, \text{worse}\rangle$ via scaffold alignment and chemistry-driven filters for validity, synthesizability, and meaningful property gains. Using these preferences, we align a pretrained molecular LLM as a conditional editor, enabling property-improving edits that retain the scaffold. Across single- and multi-objective benchmarks, SCPT improves optimization success and property gains while maintaining higher scaffold similarity than competitive baselines. Compared with representative non-LLM molecular optimization methods, SCPT-trained LLMs are better suited to scaffold-constrained and multi-objective optimization. In addition, models trained on single-property and two-property supervision generalize effectively to three-property tasks, indicating promising extrapolative generalization under limited higher-order supervision. SCPT also provides controllable data-construction knobs that yield a predictable similarity-gain frontier, enabling systematic adaptation to diverse optimization regimes.

分子生成大模型药物发现可控优化

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