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arXiv 2409.02644stat.MLcs.LGq-bio.QM
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动态生物系统中的保形预测

Conformal Prediction in Dynamic Biological Systems

MBG-CSIC, Spanish National Research Council(西班牙国家研究委员会MBG-CSIC);Harvard University(哈佛大学)

Alberto Portela, Julio R. Banga, Marcos Matabuena

AI总结:

针对非线性常微分方程生物动态模型中贝叶斯UQ依赖先验、小样本受限且计算昂贵的问题,提出两种具非渐近保证的保形推断算法,提升稳健性与可扩展性。

摘要:

不确定性量化(UQ)是系统性地确定并刻画计算模型预测置信程度的过程。在系统生物学中,尤其是在动态模型方面,UQ至关重要,因为它应对非线性和参数敏感性带来的挑战,使我们能够正确理解并外推复杂生物系统的行为。本文聚焦于由确定性非线性常微分方程表示的动态模型。该领域当前的许多UQ方法依赖贝叶斯统计方法。这些方法虽然强大,但通常需要强先验设定,并作出在生物系统中未必始终成立的参数假设。此外,在样本量有限且统计推断受到约束的领域,这些方法面临挑战;在生物系统的大型模型中,计算速度也成为瓶颈。作为替代方案,我们提出使用保形推断方法,引入两种新颖算法;它们在某些情况下提供非渐近保证,从而增强多种应用中的稳健性和可扩展性。我们通过若干场景展示所提算法的有效性,突出其相对于传统贝叶斯方法的优势。所提方法在多样的生物数据结构和场景中展现出良好结果,为量化生物系统动态模型的不确定性提供了一个通用框架。用于该方法及结果复现的软件可在 https://zenodo.org/doi/10.5281/zenodo.13644870 获取。

英文摘要:

Uncertainty quantification (UQ) is the process of systematically determining and characterizing the degree of confidence in computational model predictions. In the context of systems biology, especially with dynamic models, UQ is crucial because it addresses the challenges posed by nonlinearity and parameter sensitivity, allowing us to properly understand and extrapolate the behavior of complex biological systems. Here, we focus on dynamic models represented by deterministic nonlinear ordinary differential equations. Many current UQ approaches in this field rely on Bayesian statistical methods. While powerful, these methods often require strong prior specifications and make parametric assumptions that may not always hold in biological systems. Additionally, these methods face challenges in domains where sample sizes are limited, and statistical inference becomes constrained, with computational speed being a bottleneck in large models of biological systems. As an alternative, we propose the use of conformal inference methods, introducing two novel algorithms that, in some instances, offer non-asymptotic guarantees, enhancing robustness and scalability across various applications. We demonstrate the efficacy of our proposed algorithms through several scenarios, highlighting their advantages over traditional Bayesian approaches. The proposed methods show promising results for diverse biological data structures and scenarios, offering a general framework to quantify uncertainty for dynamic models of biological systems.The software for the methodology and the reproduction of the results is available at https://zenodo.org/doi/10.5281/zenodo.13644870.

机构、总结、中文摘要均由AI分析而来,可能存在错误,请以论文正文为准。

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