--- a/README.md +++ b/README.md @@ -1,20 +1,18 @@ -# Targeted BEHRT -Repository for publication: Targeted-BEHRT: Deep Learning for Observational Causal Inference on Longitudinal Electronic Health Records<br/> -IEEE Transactions on Neural Networks and Learning Systems; Special Issue on Causality<br/> -https://ieeexplore.ieee.org/document/9804397/<br/> -DOI: 10.1109/TNNLS.2022.3183864.<br/> - - - -How to use:<br/> -In "examples" folder, run the "run_TBEHRT.ipynb" file. A test.csv file is provided to test/play and demonstrate how the vocabulary/year/age/etc function (please read full paper linked above for further methodological details). <br/> -Furthermoree, in the examples folder to run the CV-TMLE estimator, run the "CVTMLE_example.ipynb" file. A host of fake fold data is provided to test/play and demonstrate how the CV-TMLE algorithm works (please read methods publication of CV-TMLE for further details). <br/> - -The files in the "src" folder contain model and data handling packages in addition to other necessary VAE relevant files and helper functions. - -Requirements:<br/> -torch >1.6.0<br/> -numpy 1.19.2<br/> -sklearn 0.23.2<br/> -pandas 1.1.3<br/> -<br/> +# Targeted BEHRT +Repository for publication: Targeted-BEHRT: Deep Learning for Observational Causal Inference on Longitudinal Electronic Health Records<br/> +IEEE Transactions on Neural Networks and Learning Systems; Special Issue on Causality<br/> +https://ieeexplore.ieee.org/document/9804397/<br/> +DOI: 10.1109/TNNLS.2022.3183864.<br/> + +How to use:<br/> +In "examples" folder, run the "run_TBEHRT.ipynb" file. A test.csv file is provided to test/play and demonstrate how the vocabulary/year/age/etc function (please read full paper linked above for further methodological details). <br/> +Furthermoree, in the examples folder to run the CV-TMLE estimator, run the "CVTMLE_example.ipynb" file. A host of fake fold data is provided to test/play and demonstrate how the CV-TMLE algorithm works (please read methods publication of CV-TMLE for further details). <br/> + +The files in the "src" folder contain model and data handling packages in addition to other necessary VAE relevant files and helper functions. + +Requirements:<br/> +torch >1.6.0<br/> +numpy 1.19.2<br/> +sklearn 0.23.2<br/> +pandas 1.1.3<br/> +<br/>