arXiv:2503.20767cs.LGq-bio.QM2025-03ICML被引 2

为机器学习辅助设计选择可靠算法,确保产出满足目标的新型分子。

Reliable algorithm selection for machine learning-guided design

  • 基于预测值与留出数据结合,预测不同算法生成的设计分布特性。
  • 在高概率下选出能使至少10%设计达标的成功算法(或返回空集)。
  • 适用于蛋白和RNA设计,支持已知或估算的密度比场景。

机器学习辅助设计算法利用模型预测来提出具有特定性质的新对象。面对新任务(如设计与治疗靶点高亲和力结合的新蛋白质),需选择合适的设计算法、超参数及预测/生成模型。本文提出一种设计算法选择方法,旨在挑选出能生成满足用户指定成功标准的设计标签分布的算法——例如,至少10%的设计标签超过某阈值。该方法通过结合设计预测值与保留的带标签数据,可靠地预测不同算法产生的标签分布特征,基于预测驱动推断技术。若已知设计数据与标签数据之间的密度比,则该方法以高概率返回能产生成功标签分布的算法(或空集)。我们在模拟的蛋白质与RNA设计任务中验证了该方法的有效性,涵盖密度比已知或估计的情况。

原文摘要 · Abstract (English)

Algorithms for machine learning-guided design, or design algorithms, use machine learning-based predictions to propose novel objects with desired property values. Given a new design task -- for example, to design novel proteins with high binding affinity to a therapeutic target -- one must choose a design algorithm and specify any hyperparameters and predictive and/or generative models involved. How can these decisions be made such that the resulting designs are successful? This paper proposes a method for design algorithm selection, which aims to select design algorithms that will produce a distribution of design labels satisfying a user-specified success criterion -- for example, that at least ten percent of designs' labels exceed a threshold. It does so by combining designs' predicted property values with held-out labeled data to reliably forecast characteristics of the label distributions produced by different design algorithms, building upon techniques from prediction-powered inference. The method is guaranteed with high probability to return design algorithms that yield successful label distributions (or the null set if none exist), if the density ratios between the design and labeled data distributions are known. We demonstrate the method's effectiveness in simulated protein and RNA design tasks, in settings with either known or estimated density ratios.

算法选择机器学习设计蛋白质设计预测推断

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