论文标题
NETRD:用于网络重建和图形距离的库
netrd: A library for network reconstruction and graph distances
论文作者
论文摘要
在过去的二十年中,随着大型网络数据集的可用性的增加,我们目睹了网络科学的迅速增长。但是,对于许多系统,我们可以访问的数据不是基础网络的直接描述。越来越多的是,我们看到研究了已从非网络数据推断或重建的网络的动力,尤其是使用系统中节点的时间序列数据来推断它们之间可能的连接。在网络科学中,为此任务选择最合适的技术是一个具有挑战性的问题。不同的重建技术通常具有不同的假设,其性能因现实世界中的系统而异。解决此问题的一种方法可能是使用几种不同的重建技术并比较结果网络。但是,网络比较也不是一个容易的问题,因为这并不明显如何最好地量化两个网络之间的差异,部分原因是这样做的工具多样性。 NetRD Python软件包试图通过提供网络重建技术和网络比较技术(通常称为图形距离)(https://github.com.com/github.com/netsiphd/netrd)中最广泛的网络重建技术和网络比较技术(通常称为图形距离)来解决网络科学中的这两个平行问题。在本文中,我们详细介绍了NetRD软件包的两个主要功能。在此过程中,我们描述了其其他一些有用的功能。该软件包以常用的Python软件包为基础,并且已经是网络科学家和其他多学科研究人员的广泛使用的资源。随着开源开发的持续,我们将其视为一种工具,将继续被各种研究人员使用。
Over the last two decades, alongside the increased availability of large network datasets, we have witnessed the rapid rise of network science. For many systems, however, the data we have access to is not a direct description of the underlying network. More and more, we see the drive to study networks that have been inferred or reconstructed from non-network data---in particular, using time series data from the nodes in a system to infer likely connections between them. Selecting the most appropriate technique for this task is a challenging problem in network science. Different reconstruction techniques usually have different assumptions, and their performance varies from system to system in the real world. One way around this problem could be to use several different reconstruction techniques and compare the resulting networks. However, network comparison is also not an easy problem, as it is not obvious how best to quantify the differences between two networks, in part because of the diversity of tools for doing so. The netrd Python package seeks to address these two parallel problems in network science by providing, to our knowledge, the most extensive collection of both network reconstruction techniques and network comparison techniques (often referred to as graph distances) in a single library (https://github.com/netsiphd/netrd). In this article, we detail the two main functionalities of the netrd package. Along the way, we describe some of its other useful features. This package builds on commonly used Python packages and is already a widely used resource for network scientists and other multidisciplinary researchers. With ongoing open-source development, we see this as a tool that will continue to be used by all sorts of researchers to come.