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https://github.com/atrisovic/space

https://github.com/atrisovic/space

Science Score: 26.0%

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Repository

Basic Info
  • Host: GitHub
  • Owner: atrisovic
  • Language: Shell
  • Default Branch: master
  • Size: 7.81 KB
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Created over 3 years ago · Last pushed over 3 years ago
Metadata Files
Readme

README.md

SpaCE: The Spatial Confounding (Benchmarking) Environment

🚀 Description

SpaCE: The Spatial Confounding Environment is a benchmarking dataset for causal inference that incorporartes spatial confounding. The SpaCE datasets contain real confounder and exposure/treatment data inspired by environmental health studies. The synthetic outcome and counterfactual are generated according to recommended practices for causal evaluation by mimicking the real outcome data distribution learned with machine learning and neural network methods. Spatial confounding is achieved by masking influential confounders in the learned model.

🛰️ Code and methods

The code for source data processing and outcome modeling can be found in the analysis directory. The code for the SpaCE benchmarking data retrieval and sampling is in the data directory. The code benchmarking dataset with all confounders can be viewed on the Harvard Dataverse repository for transparency and reproducibility.

🧑‍🚀 The API

To retrieve and generate the data, run the command below in the Terminal:

sh curl -sSL https://raw.githubusercontent.com/NSAPH-Projects/space/master/data/data.sh | bash -s NN|XGBOOST SEED PATH

The input parameters of the command above are:

| Parameter | Meaning | |--------------------|-------------------| | method | NN or XGBOOST | | random seed | integer | | path (optional) | output file path |

The command downloads the core data and uses it together with the user's input to generate a sample of the potential outcomes (factual and counterfactual) from the core data and the model predictions. The sampling mechanism is tuned to mimic the variability in the observed data.

🔭 Data dictionary

The data dictionary for the SpaCE benchmark data:

| Variable | Values | |--------------------|-------------------| | treatment | | | covariates | | | syntheticoutcome | | | models | xgboost, nnvcnet | | errorgpkernel | | | predictions | | | counterfactuals | | | spatial_smoothness | | | importance | |

👽 Contact

We welcome contributions and feedback about SpaCE. If you have any suggestions or ideas, please open an issue or submit a pull request. Thank you for your interest in our data.

Owner

  • Name: Ana Trisovic
  • Login: atrisovic
  • Kind: user
  • Location: Cambridge, USA
  • Company: Harvard University

Computer Scientist and #Reproducibility Researcher at @HarvardBiostats & @IQSS | previously with @UChicago, @Cambridge_Uni and @LHCbExperiment @CERN

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