pathpy 2.2.0

An OpenSource python package for the analysis and visualisation of time series data on complex networks with higher- and multi-order graphical models.

Introduction

pathpy is an OpenSource python package for the analysis of time series data on networks using higher- and multi-order network models.

pathpy is specifically tailored to analyse temporal networks as well as time series and sequence data that capture multiple short, independent paths observed in an underlying graph or network. Examples for data that can be analysed with pathpy include time-stamped social networks, user click streams in information networks, biological pathways, citation networks, or information cascades in social networks.

Unifying the modelling and analysis of path statistics and temporal networks, pathpy provides efficient methods to extract causal or time-respecting paths from time-stamped network data. The current package distributed via the PyPI name pathpy2 supersedes the packages pyTempnets as well as version 1.0 of pathpy.

pathpy facilitates the analysis of temporal correlations in time series data on networks. It uses model selection and statistical learning to generate optimal higher- and multi-order models that capture both topological and temporal characteristics. It can help to answer the important question when a network abstraction of complex systems is justified and when higher-order representations are needed instead.

The theoretical foundation of this package, higher- and multi-order network models, was developed in the following published works:

1. I Scholtes: When is a network a network? Multi-Order Graphical Model Selection in Pathways and Temporal Networks, In KDD’17 - Proceedings of the 23rd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, Halifax, Nova Scotia, Canada, August 13-17, 2017 http://dl.acm.org/citation.cfm?id=3098145

2. I Scholtes, N Wider, A Garas: Higher-Order Aggregate Networks in the Analysis of Temporal Networks: Path structures and centralities In The European Physical Journal B, 89:61, March 2016 http://dx.doi.org/10.1140/epjb/e2016-60663-0

3. I Scholtes, N Wider, R Pfitzner, A Garas, CJ Tessone, F Schweitzer: Causality-driven slow-down and speed-up of diffusion in non-Markovian temporal networks, In Nature Communications, 5, September 2014 http://www.nature.com/ncomms/2014/140924/ncomms6024/full/ncomms6024.html

4. R Pfitzner, I Scholtes, A Garas, CJ Tessone, F Schweitzer: Betweenness preference: Quantifying correlations in the topological dynamics of temporal networks, Phys Rev Lett, 110(19), 198701, May 2013 http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.110.198701

pathpy extends higher-order modelling approaches towards multi-order models for paths that capture temporal correlations at multiple length scales simultaneously. All mathematical details of the framework can be found in the openly available preprint at https://arxiv.org/abs/1702.05499.

A broader view on higher-order models in the analyis of complex systems can be found at https://arxiv.org/abs/1806.05977.

pathpy is fully integrated with jupyter, providing rich and interactive in-line visualisations of networks, temporal networks, higher-, and multi-order models. Visualisations can be exported to HTML5 files that can be shared and published onthe Web.

Download and installation

pathpy is pure python code. It has no platform-specific dependencies and should thus work on all platforms. pathpy requires python 3.x. It builds on numpy and scipy. The latest release version 2.0 of pathpy can be installed by typing:

pip install pathpy2

Please make sure that you use the pyPI name pathpy2 as the package name pathpy is currently blocked.

Tutorial

A comprehensive 3 hour hands-on tutorial that shows how you can use pathpy to analyse data on pathways and temporal networks is available online at:

https://ingoscholtes.github.io/kdd2018-tutorial/

An explanatory video that introduces the science behind pathpy is available here:

https://youtu.be/CxJkVrD2ZlM

A promotional video showcasing some of pathpy’s features is available here:

https://youtu.be/QIPqFaR2Z5c

Documentation

The code is fully documented via docstrings which are accessible through python’s built-in help system. Just type help(SYMBOL_NAME) to see the documentation of a class or method. A reference manual is available here https://ingoscholtes.github.io/pathpy/hierarchy.html

Releases and Versioning

The first public beta release of pathpy (released February 17 2017) is v1.0-beta. Following versions are named MAJOR.MINOR.PATCH according to semantic versioning. The current version is 2.0.0.

Known Issues

• Depending on whether or not scipy has been compiled

  with or without the numerics package MKL, considerable numerical differences can occur, e.g. for eigenvalue centralities, PageRank, and other measures that depend on the eigenvectors and eigenvalues of matrices. Please refer to scipy.show_config() to show compilation flags.

• Interactive visualisations in jupyter are currently only

  supported for juypter notebooks, stand-alone HTML files, and the jupyter display integrated in IDEs like Visual Studio Code (which we highly recommend to work with pathpy). Due to its new widget mechanism, interactive d3js visualisations are currently not available for jupyterLab. Due to the complex document object model generated by jupyter notebooks, visualisation performance is best in stand-alone HTML files and in Visual Studio Code.

• The visualisation of temporal networks currently does

  not support the drawing of edge arrows for directed edges. However, a powerful templating mechanism is available to support custom interactive and dynamic visualizations of temporal networks.

• The visualisation of paths in terms of alluvial diagrams

  within jupyter is currently unstable for networks with large delay. This is due to the asynchronous loading of external scripts.

Acknowledgements

The research behind this data analysis framework was generously funded by the Swiss State Secretariate for Education, Research and Innovation via Grant C14.0036. The development of the predecessor package pyTempNets was further supported by the MTEC Foundation in the context of the project “The Influence of Interaction Patterns on Success in Socio-Technical Systems: From Theory to Practice.”

The further development of pathpy is currently supported by the Swiss National Science Foundation via Grant 176938. See details at:

http://p3.snf.ch/Project-176938

Contributors

Ingo Scholtes (project lead, development) Luca Verginer (development, test suite integration)

Past Contributors

Roman Cattaneo (development) Nicolas Wider (testing)

Copyright

pathpy is licensed under the GNU Affero General Public License. See https://choosealicense.com/licenses/agpl-3.0/

3. ETH Zürich & University of Zurich, 2015 - 2018

History

2.2.0 (2019-09-21)

• Several Bug Fixes for API and visualisations

2.0.0 (2018-08-17)

• PyPi Release of 2.0 release version.

2.0.0a (2018-08-07)

• First public release of 2.0 alpha on PyPI.

1.2.1 (2018-02-23)

• First test release on PyPI.