论文标题

PYABC:高效且易于使用的易用近似贝叶斯计算

pyABC: Efficient and robust easy-to-use approximate Bayesian computation

论文作者

Schälte, Yannik, Klinger, Emmanuel, Alamoudi, Emad, Hasenauer, Jan

论文摘要

Python软件包PYABC为近似贝叶斯计算(ABC)提供了一个框架,这是一种在许多研究领域流行的可能性参数推理方法。从本质上讲,它实现了一个顺序的蒙特卡洛(SMC)方案,并具有各种算法以适应问题结构并自动调整超参数。为了扩展到计算昂贵的问题,它为多核和分布式系统提供了有效的并行化策略。该软件包是高度模块化的,并且设计为易于使用。在对PYABC的重大更新中,我们实施了几种高级算法,这些算法促进了广泛的数据和模型类型的有效且可靠的推断。特别是,我们实施算法来说明噪声,适应尺度差异距离指标,以稳健的处理数据异常值,通过回归模型阐明信息性数据点,通过基于最佳传输的距离来规避汇总统计,并通过基于接收率率策展人来避免局部最佳端口。此外,除了先前对Python和R的支持外,我们还提供了尤其是与Julia语言,Copasi Simulator和PETAB标准的接口。

The Python package pyABC provides a framework for approximate Bayesian computation (ABC), a likelihood-free parameter inference method popular in many research areas. At its core, it implements a sequential Monte-Carlo (SMC) scheme, with various algorithms to adapt to the problem structure and automatically tune hyperparameters. To scale to computationally expensive problems, it provides efficient parallelization strategies for multi-core and distributed systems. The package is highly modular and designed to be easily usable. In this major update to pyABC, we implement several advanced algorithms that facilitate efficient and robust inference on a wide range of data and model types. In particular, we implement algorithms to account for noise, to adaptively scale-normalize distance metrics, to robustly handle data outliers, to elucidate informative data points via regression models, to circumvent summary statistics via optimal transport based distances, and to avoid local optima in acceptance threshold sequences by predicting acceptance rate curves. Further, we provide, besides previously existing support of Python and R, interfaces in particular to the Julia language, the COPASI simulator, and the PEtab standard.

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