arXivDaily arXiv每日学术速递 周一至周五更新
arXiv 2407.06015stat.MLcs.LGstat.AP
收藏

基因扰动实验中因果结构学习的基于模拟的基准评测

Simulation-based Benchmarking for Causal Structure Learning in Gene Perturbation Experiments

MRC Biostatistics Unit(MRC生物统计学单元);University of Cambridge(剑桥大学);DZNE(德国神经退行性疾病研究中心);University of Bonn(波恩大学)

Luka Kovačević, Izzy Newsham, Sach Mukherjee, John Whittaker

AI总结:

本文提出 CausalRegNet 乘性效应结构因果模型,用于生成贴合基因扰动情境的观测与干预数据,以支持因果结构学习方法的基准评测。

摘要:

因果结构学习(CSL)是指从数据中学习因果关系的任务。CSL 的进展如今使得在多种应用领域中学习因果图成为可能,这有望促进数据驱动的因果决策。现实世界中的 CSL 性能取决于许多“情境特定”因素,包括在实际用例中非常重要的情境特定数据分布和非线性依赖关系。然而,我们对于如何在特定情境中评估和选择 CSL 方法的理解仍然有限。为弥补这一空白,我们提出了 CausalRegNet,这是一种乘性效应结构因果模型,能够生成融合情境特定属性的观测数据和干预数据,并聚焦于基因扰动实验场景。利用真实世界的基因扰动数据,我们表明 CausalRegNet 能够生成准确的分布,并且其可扩展性远优于现有模拟框架。我们展示了 CausalRegNet 在生物学干预实验情境下评估 CSL 方法的用途。

英文摘要:

Causal structure learning (CSL) refers to the task of learning causal relationships from data. Advances in CSL now allow learning of causal graphs in diverse application domains, which has the potential to facilitate data-driven causal decision-making. Real-world CSL performance depends on a number of $\textit{context-specific}$ factors, including context-specific data distributions and non-linear dependencies, that are important in practical use-cases. However, our understanding of how to assess and select CSL methods in specific contexts remains limited. To address this gap, we present $\textit{CausalRegNet}$, a multiplicative effect structural causal model that allows for generating observational and interventional data incorporating context-specific properties, with a focus on the setting of gene perturbation experiments. Using real-world gene perturbation data, we show that CausalRegNet generates accurate distributions and scales far better than current simulation frameworks. We illustrate the use of CausalRegNet in assessing CSL methods in the context of interventional experiments in biology.

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。

↑