不改模型结构,用新优化方法提升蛋白质稳定性预测的鲁棒性。
Constraint-Aware Optimization for Robust Protein Stability Prediction

- 引入约束感知优化框架,结合三种损失函数改进训练过程。
- 在S669数据集上斯皮尔曼相关系数提升至0.540,优于原基线0.50。
- 对罕见稳定突变和分布外数据表现更好,适合蛋白工程研究者。
融合蛋白质语言模型与逆折叠表征的多模态ΔΔG预测器在Megascale数据集上表现出色,但在分布外(OOD)蛋白上鲁棒性不足,且在成对突变基准上存在持续的正反向偏差,稀有稳定突变被低估。现有方法主要依赖额外架构组件,优化层面干预较少。本文提出一种无需修改SPURS骨干网络的约束感知优化框架,结合平衡均方误差、孪生反对称正则化项及新型位置级特征表示的OOD边界一致性损失。在十一项基准测试中,该框架将S669的斯皮尔曼相关系数从0.486提升至0.540(三组随机种子下σ=0.002),匹配已发表的SPURS基线(0.50);在S461上从0.653提升至0.711,并在五个额外的OOD数据集上取得一致增益。对Ssym的控制诊断显示,反对称训练无法消除系统性正反向偏差,表明性能提升源于隐式正则化而非精确热力学约束强制。
原文摘要 · Abstract (English)
Multimodal $ΔΔG$ predictors integrating protein language models with inverse-folding representations achieve strong in-distribution accuracy on the Megascale dataset but exhibit limited robustness on out-of-distribution (OOD) proteins, persistent forward-reverse bias on paired-mutation benchmarks, and under-representation of rare stabilizing mutations. Existing approaches address these limitations primarily through additional architectural components, leaving optimization-level intervention comparatively underexplored. We introduce a constraint-aware optimization framework combining Balanced Mean Squared Error, a Siamese anti-symmetric regularizer, and a novel OOD-margin consistency loss on the per-position feature representation, requiring no architectural changes to the SPURS backbone. Across eleven benchmarks and three random seeds, the framework improves Spearman correlation on S669 from 0.486 to 0.540 ($σ=0.002$ across seeds), matching the published SPURS baseline (0.50) without architectural modification, and on S461 from 0.653 to 0.711, with consistent smaller gains on five additional OOD datasets. A controlled diagnostic on Ssym reveals that anti-symmetric training does not eliminate systematic forward-reverse bias, indicating that gains arise through implicit regularization rather than exact thermodynamic constraint enforcement.
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