arXiv:2512.05386cs.LGcs.AI2025-12被引 2

测试蛋白-配体评分函数在新靶点上的泛化能力,发现现有基准不真实。

Generalization Beyond Benchmarks: Evaluating Learnable Protein-Ligand Scoring Functions on Unseen Targets

  • 用模拟少结构、少数据的新靶点数据集评估评分函数。
  • 主流基准无法反映真实泛化挑战,性能在新靶点上大幅下降。
  • 小样本自监督预训练和少量测试数据可提升预测效果,适合药物设计者。

随着机器学习在分子设计中日益重要,确保可学习的蛋白-配体评分函数在新蛋白靶点上的可靠性至关重要。尽管许多评分函数在标准基准上表现良好,其在训练数据之外的泛化能力仍是重大挑战。本文评估了前沿评分函数在模拟新靶点(仅有少量已知结构和实验亲和力数据)的数据集分割上的表现。分析表明,常用基准未能反映真实泛化难度。我们进一步研究大规模自监督预训练是否能缩小这一差距,初步显示其潜力。此外,我们探索了利用少量测试靶点数据提升性能的简单方法。结果强调需要更严格的评估协议,并为设计具备新靶点预测能力的评分函数提供了实用指导。

原文摘要 · Abstract (English)

As machine learning becomes increasingly central to molecular design, it is vital to ensure the reliability of learnable protein-ligand scoring functions on novel protein targets. While many scoring functions perform well on standard benchmarks, their ability to generalize beyond training data remains a significant challenge. In this work, we evaluate the generalization capability of state-of-the-art scoring functions on dataset splits that simulate evaluation on targets with a limited number of known structures and experimental affinity measurements. Our analysis reveals that the commonly used benchmarks do not reflect the true challenge of generalizing to novel targets. We also investigate whether large-scale self-supervised pretraining can bridge this generalization gap and we provide preliminary evidence of its potential. Furthermore, we probe the efficacy of simple methods that leverage limited test-target data to improve scoring function performance. Our findings underscore the need for more rigorous evaluation protocols and offer practical guidance for designing scoring functions with predictive power extending to novel protein targets.

蛋白-配体泛化能力药物设计机器学习

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