arXiv:2502.16378q-bio.BMcs.AI2025-02被引 2

用可解释的自动机器学习预测药物毒理性质,提升模型泛化能力。

Auto-ADMET: An Effective and Interpretable AutoML Method for Chemical ADMET Property Prediction

  • 基于语法遗传编程与贝叶斯网络的进化搜索策略
  • 在12个基准数据集上表现优于标准GGP、pkCSM和XGBoost
  • 兼具高预测性能与结果可解释性,适合药学研究者使用

近年来,机器学习在药物发现中扮演重要角色,为化学化合物的(预)筛选提供工具,以减少湿实验成本。其中一项关键任务是构建定量构效关系(QSAR)模型,将分子结构与活性或性质关联。吸收、分布、代谢、排泄和毒性(ADMET)等性质对预测化合物在生物体内的行为至关重要。然而,现有方法缺乏模型个性化,导致在不同化学空间下易出现偏差且泛化能力差,新数据测试时性能下降。自动化机器学习(AutoML)旨在针对具体数据定制最优算法。尽管重要,但其在化学信息学中的应用仍有限。本文提出Auto-ADMET,一种基于语法遗传编程(GGP)与贝叶斯网络的可解释型AutoML方法,用于化学ADMET性质预测。在12个基准数据集上,其性能可媲美或超越标准GGP、pkCSM和XGBoost模型。贝叶斯网络不仅优化了进化搜索过程,还帮助解释模型性能的成因。

原文摘要 · Abstract (English)

Machine learning (ML) has been playing important roles in drug discovery in the past years by providing (pre-)screening tools for prioritising chemical compounds to pass through wet lab experiments. One of the main ML tasks in drug discovery is to build quantitative structure-activity relationship (QSAR) models, associating the molecular structure of chemical compounds with an activity or property. These properties -- including absorption, distribution, metabolism, excretion and toxicity (ADMET) -- are essential to model compound behaviour, activity and interactions in the organism. Although several methods exist, the majority of them do not provide an appropriate model's personalisation, yielding to bias and lack of generalisation to new data since the chemical space usually shifts from application to application. This fact leads to low predictive performance when completely new data is being tested by the model. The area of Automated Machine Learning (AutoML) emerged aiming to solve this issue, outputting tailored ML algorithms to the data at hand. Although an important task, AutoML has not been practically used to assist cheminformatics and computational chemistry researchers often, with just a few works related to the field. To address these challenges, this work introduces Auto-ADMET, an interpretable evolutionary-based AutoML method for chemical ADMET property prediction. Auto-ADMET employs a Grammar-based Genetic Programming (GGP) method with a Bayesian Network Model to achieve comparable or better predictive performance against three alternative methods -- standard GGP method, pkCSM and XGBOOST model -- on 12 benchmark chemical ADMET property prediction datasets. The use of a Bayesian Network model on Auto-ADMET's evolutionary process assisted in both shaping the search procedure and interpreting the causes of its AutoML performance.

AutoML药物发现可解释性ADMET

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