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

Last update: Dec 9, 2022

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:

networkx
numpy
pandas
matplotlib

to generate map plots:

GeoPandas
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}
}

Comments

Bump numpy from 1.20.2 to 1.22.0
Bumps numpy from 1.20.2 to 1.22.0.

Release notes

Sourced from numpy's releases.

v1.22.0

NumPy 1.22.0 Release Notes

NumPy 1.22.0 is a big release featuring the work of 153 contributors spread over 609 pull requests. There have been many improvements, highlights are:

Annotations of the main namespace are essentially complete. Upstream is a moving target, so there will likely be further improvements, but the major work is done. This is probably the most user visible enhancement in this release.

A preliminary version of the proposed Array-API is provided. This is a step in creating a standard collection of functions that can be used across application such as CuPy and JAX.

NumPy now has a DLPack backend. DLPack provides a common interchange format for array (tensor) data.

New methods for quantile, percentile, and related functions. The new methods provide a complete set of the methods commonly found in the literature.

A new configurable allocator for use by downstream projects.

These are in addition to the ongoing work to provide SIMD support for commonly used functions, improvements to F2PY, and better documentation.

The Python versions supported in this release are 3.8-3.10, Python 3.7 has been dropped. Note that 32 bit wheels are only provided for Python 3.8 and 3.9 on Windows, all other wheels are 64 bits on account of Ubuntu, Fedora, and other Linux distributions dropping 32 bit support. All 64 bit wheels are also linked with 64 bit integer OpenBLAS, which should fix the occasional problems encountered by folks using truly huge arrays.

Expired deprecations

Deprecated numeric style dtype strings have been removed

Using the strings "Bytes0", "Datetime64", "Str0", "Uint32", and "Uint64" as a dtype will now raise a TypeError.

(gh-19539)

Expired deprecations for loads, ndfromtxt, and mafromtxt in npyio

numpy.loads was deprecated in v1.15, with the recommendation that users use pickle.loads instead. ndfromtxt and mafromtxt were both deprecated in v1.17 - users should use numpy.genfromtxt instead with the appropriate value for the usemask parameter.

(gh-19615)

... (truncated)

Commits

4adc87d Merge pull request #20685 from charris/prepare-for-1.22.0-release

fd66547 REL: Prepare for the NumPy 1.22.0 release.

125304b wip

c283859 Merge pull request #20682 from charris/backport-20416

5399c03 Merge pull request #20681 from charris/backport-20954

f9c45f8 Merge pull request #20680 from charris/backport-20663

794b36f Update armccompiler.py

d93b14e Update test_public_api.py

7662c07 Update init.py

311ab52 Update armccompiler.py

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Related tags

Overview

counterfactual-tpp

Pre-requisites

Code structure

Experiments

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Epidemiological

Citation

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Comments

Bump numpy from 1.20.2 to 1.22.0

v1.22.0

NumPy 1.22.0 Release Notes

Expired deprecations

Deprecated numeric style dtype strings have been removed

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Owner

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PyTorch reimplementation of the Smooth ReLU activation function proposed in the paper "Real World Large Scale Recommendation Systems Reproducibility and Smooth Activations" [arXiv 2022].

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

Related tags

Overview

counterfactual-tpp

Pre-requisites

Code structure

Experiments

Synthetic

Epidemiological

Citation

You might also like...

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Comments

Bump numpy from 1.20.2 to 1.22.0

v1.22.0

NumPy 1.22.0 Release Notes

Expired deprecations

Deprecated numeric style dtype strings have been removed

Expired deprecations for loads, ndfromtxt, and mafromtxt in npyio

Owner

Networks Learning

Listing arxiv - Personalized list of today's articles from ArXiv

Arxiv harvester - Poor man's simple harvester for arXiv resources

The LaTeX and Python code for generating the paper, experiments' results and visualizations reported in each paper is available (whenever possible) in the paper's directory

PyTorch reimplementation of the Smooth ReLU activation function proposed in the paper "Real World Large Scale Recommendation Systems Reproducibility and Smooth Activations" [arXiv 2022].

Official repository with code and data accompanying the NAACL 2021 paper "Hurdles to Progress in Long-form Question Answering" (https://arxiv.org/abs/2103.06332).

Source code for models described in the paper "AudioCLIP: Extending CLIP to Image, Text and Audio" (https://arxiv.org/abs/2106.13043)

Code for our method RePRI for Few-Shot Segmentation. Paper at http://arxiv.org/abs/2012.06166

Supplementary code for the paper "Meta-Solver for Neural Ordinary Differential Equations" https://arxiv.org/abs/2103.08561

Code for paper "A Critical Assessment of State-of-the-Art in Entity Alignment" (https://arxiv.org/abs/2010.16314)

Code for the paper: Learning Adversarially Robust Representations via Worst-Case Mutual Information Maximization (https://arxiv.org/abs/2002.11798)

Expired deprecations for `loads`, `ndfromtxt`, and `mafromtxt` in npyio