想知道基因组学里哪个不确定性方法靠谱？这篇实证对比了三种主流方法，贝叶斯网络在类别不平衡时表现最好，还教你怎么用不确定性挑高质量预测。
该研究对基因组学中深度学习模型的不确定性量化方法进行了系统比较，涵盖Deep Ensembles、贝叶斯神经网络和MC-dropout。实验基于序列到活性模型和单细胞表达分析两类任务，评估了不同方法在类别不平衡和分布外数据下的表现。结果显示贝叶斯神经网络在捕获不确定性方面更优，尽管计算成本较高。研究还展示了不确定性分数在蛋白质-RNA相互作用预测中的应用。
Uncertainty-Aware Deep Learning for Genomics Applications: Insights from an Empirical Study
Deep learning models have emerged as the standard computational tool for a wide range of applications in genomics. Yet, uncertainty quantification (UQ) -- and more specifically, the reliability of different uncertainty estimates in this domain -- has received little systematic attention. This work presents an empirical analysis of UQ in deep learning models, focusing on genomics applications. In a series of experiments, we contrast Deep Ensembles, Bayesian Neural Networks, and Monte Carlo-dropout methods. We assess their ability to quantify uncertainty in different scenarios, accounting for common dataset characteristics in two genomic application areas and modalities: sequence-to-activity models, and single-cell expression analysis. Our systematic comparison framework provides guidelines for the applicability and reliability of UQ methods in genomics, highlighting their strengths and limitations in different scenarios. We show that Bayesian Neural Networks are better at capturing uncertainty caused by strong class imbalance and out-of-distribution data in genomics, despite their computational disadvantages. Moreover, we show how uncertainty scores can be used to select high-quality predictions in protein-RNA interactions.