论文标题

CausalBench:单细胞扰动数据的网络推断的大规模基准

CausalBench: A Large-scale Benchmark for Network Inference from Single-cell Perturbation Data

论文作者

Chevalley, Mathieu, Roohani, Yusuf, Mehrjou, Arash, Leskovec, Jure, Schwab, Patrick

论文摘要

因果推论是多个科学学科的重要方面,通常应用于医学等高影响力应用。但是,由于需要在介入和控制条件下进行观察,评估现实世界环境中因果推理方法的性能是具有挑战性的。在合成数据集上进行的传统评估并不能反映现实世界中的性能。为了解决这个问题,我们介绍了Causalbench,这是一个基准套件,用于评估来自大型单细胞扰动实验的现实世界介入数据的网络推断方法。 Causalbench结合了生物动机的性能指标,包括新的基于分布的介入指标。使用我们的CausalBench套件对最新因果推理方法进行系统评估,突显了当前方法的可扩展性差会限制性能。此外,使用介入信息的方法与仅使用观察数据的方法不优于与合成基准相反的方法。因此,Causalbench在因果网络推理研究中开辟了新的途径,并提供了一种原则可靠的方式来跟踪利用现实世界介入数据的进度。

Causal inference is a vital aspect of multiple scientific disciplines and is routinely applied to high-impact applications such as medicine. However, evaluating the performance of causal inference methods in real-world environments is challenging due to the need for observations under both interventional and control conditions. Traditional evaluations conducted on synthetic datasets do not reflect the performance in real-world systems. To address this, we introduce CausalBench, a benchmark suite for evaluating network inference methods on real-world interventional data from large-scale single-cell perturbation experiments. CausalBench incorporates biologically-motivated performance metrics, including new distribution-based interventional metrics. A systematic evaluation of state-of-the-art causal inference methods using our CausalBench suite highlights how poor scalability of current methods limits performance. Moreover, methods that use interventional information do not outperform those that only use observational data, contrary to what is observed on synthetic benchmarks. Thus, CausalBench opens new avenues in causal network inference research and provides a principled and reliable way to track progress in leveraging real-world interventional data.

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