用多样评分器组合,让化学逆合成更可靠不瞎编。
Trustworthy Retrosynthesis: Eliminating Hallucinations with a Diverse Ensemble of Reaction Scorers
- 用多个不同原理的打分模型组合,识别不同类型的错误反应。
- 在32个新药靶标上,成功过滤所有幻觉反应并产出最多优质路径。
- 适合关注药物合成可靠性与评估方法的研究者参考。
逆合成是生成模型改变的重要领域,但错误输出(幻觉)问题尤为严重:人工评估耗时,自动方法又不足。本文提出RetroTrim系统,在一组具有挑战性的类药物目标上有效避免了不合理合成路径。相比主流基线,该系统不仅是唯一能完全过滤幻觉反应的方法,且整体产出高质量路径数量最高。核心思路是结合基于机器学习模型和现有化学数据库的多样化反应评分策略。通过分析标注的逆合成中间体数据集,我们发现这些评分策略可捕获不同类别的幻觉。该方法成为我们赢得100万美元标准工业逆合成挑战赛的解决方案。为评估逆合成系统,我们提出基于专家结构化评审的新评测协议,用于32个反映当前药物结构趋势的新靶标。尽管方法原理具广泛适用性,但聚焦于类药物目标。通过发布基准靶标和评测协议细节,我们希望推动更可靠的逆合成研究。
原文摘要 · Abstract (English)
Retrosynthesis is one of the domains transformed by the rise of generative models, and it is one where the problem of nonsensical or erroneous outputs (hallucinations) is particularly insidious: reliable assessment of synthetic plans is time-consuming, with automatic methods lacking. In this work, we present RetroTrim, a retrosynthesis system that successfully avoids nonsensical plans on a set of challenging drug-like targets. Compared to common baselines in the field, our system is not only the sole method that succeeds in filtering out hallucinated reactions, but it also results in the highest number of high-quality paths overall. The key insight behind RetroTrim is the combination of diverse reaction scoring strategies, based on machine learning models and existing chemical databases. We show that our scoring strategies capture different classes of hallucinations by analyzing them on a dataset of labeled retrosynthetic intermediates. This approach formed the basis of our winning solution to the Standard Industries \$1 million Retrosynthesis Challenge. To measure the performance of retrosynthesis systems, we propose a novel evaluation protocol for reactions and synthetic paths based on a structured review by expert chemists. Using this protocol, we compare systems on a set of 32 novel targets, curated to reflect recent trends in drug structures. While the insights behind our methodology are broadly applicable to retrosynthesis, our focus is on targets in the drug-like domain. By releasing our benchmark targets and the details of our evaluation protocol, we hope to inspire further research into reliable retrosynthesis.
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