Code and real data for the paper "Counterfactual Temporal Point Processes", available at arXiv.

Overview

counterfactual-tpp

This is a repository containing code and real data for the paper Counterfactual Temporal Point Processes.

Pre-requisites

This code depends on the following packages:

  1. networkx
  2. numpy
  3. pandas
  4. matplotlib

to generate map plots:

  1. GeoPandas
  2. geoplot

Code structure

  • src/counterfactual_tpp.py: Contains the code to sample rejected events using the superposition property and the algorithm to calculate the counterfactuals.
  • src/gumbel.py: Contains the utility functions for the Gumbel-Max SCM.
  • src/sampling_utils.py: Contains the code for the Lewis' thinning algorithm (thinning_T function) and some other sampling utilities.
  • src/hawkes/hawkes.py: Contains the code for sampling from the hawkes process using the superposition property of tpps. It also includes the algorithm for sampling a counterfactual sequence of events given a sequence of observed events for a Hawkes process.
  • src/hawkes/hawkes_example.ipynb: Contains an example of running algorithm 3 (in the paper) for both cases where we have (1) both observed and un-observed events, and (2) the case that we have only the observed events.
  • ebola/graph_generation.py: Contains code to build the Ebola network based on the network of connected districts. This code is adopted from the disease-control project.
  • ebola/dynamics.py: Contains code for sampling counterfactual sequence of infections given a sequence of observed infections from the SIR porcess (the calculate_counterfactual function). The rest of the code is adopted from the disease-control project, which simulates continuous-time SIR epidemics with exponentially distributed inter-event times.

The directory ebola/data/ebola contains the information about the Ebola network adjanceny matrix and the cleaned ebola outbreak data adopted from the disease-control project.

The directory ebola/map/geojson contains the geographical information of the districts studied in the Ebola outbreak dataset. The geojson files are obtained from Nominatim.

The directory ebola/map/overall_data contains data for generating the geographical maps in the paper, and includs the overall number of infection under applying different interventions.

The directories src/data_hawkes and src/data_inhomogeneous contain observational data used to generate Synthetic plots in the paper. You can use this data to re-generate paper's plots. Otherwise, you can simply generate new random samples by the code.

Experiments

Synthetic

Epidemiological

Citation

If you use parts of the code in this repository for your own research, please consider citing:

@article{noorbakhsh2021counterfactual,
        title={Counterfactual Temporal Point Processes},
        author={Noorbakhsh, Kimia and Gomez-Rodriguez, Manuel},
        journal={arXiv preprint arXiv:2111.07603},
        year={2021}
}
Owner
Networks Learning
Networks Learning group at MPI-SWS
Networks Learning
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