https://github.com/arturomoncadatorres/deepsurvk

Implementation of DeepSurv using Keras
https://github.com/arturomoncadatorres/deepsurvk

data-science deep-learning keras survival-analysis tensorflow2

Last synced: 12 days ago
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Implementation of DeepSurv using Keras

• Host: GitHub
• URL: https://github.com/arturomoncadatorres/deepsurvk
• Owner: arturomoncadatorres
• License: mit
• Created: 2020-07-17T15:15:47.000Z (over 4 years ago)
• Default Branch: master
• Last Pushed: 2023-07-06T22:01:18.000Z (over 1 year ago)
• Last Synced: 2024-12-16T00:49:34.827Z (13 days ago)
• Topics: data-science, deep-learning, keras, survival-analysis, tensorflow2
• Language: Python
• Homepage: https://deepsurvk.readthedocs.io/en/latest/
• Size: 2.46 MB
• Stars: 50
• Watchers: 2
• Forks: 18
• Open Issues: 14
• Metadata Files:
  • Readme: README.md
  • Changelog: HISTORY.rst
  • Contributing: CONTRIBUTING.rst
  • License: LICENSE

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 Implementation of DeepSurv using Keras




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  Motivation •

  Features •

  Documentation •

  License •

  References •

  Credits



---

## :pray: Motivation

DeepSurv is a Cox Proportional Hazards deep neural network used for modeling interactions between a patient's covariates and treatment effectiveness. It was originally proposed by [Katzman et. al (2018)](https://bmcmedresmethodol.biomedcentral.com/articles/10.1186/s12874-018-0482-1) and [implemented in Theano (using Lasagne)](https://github.com/jaredleekatzman/DeepSurv).

Unfortunately, [Theano is no longer supported](https://groups.google.com/forum/#!msg/theano-users/7Poq8BZutbY/rNCIfvAEAwAJ). There have been some attempts in recreating DeepSurv in other DL platforms, such as [czifan's `DeepSurv.pytorch`](https://github.com/czifan/DeepSurv.pytorch). However, given its popularity and ease of use, I think TensorFlow 2's Keras is a great option for this task.

[mexchy1000 created `DeepSurv_Keras`](https://github.com/mexchy1000/DeepSurv_Keras). However, it is a very raw prototype: it is not properly documented nor validated. Moreover, it is not being actively supported anymore. Therefore, I used it as a rough starting point for the development of DeepSurvK.

This is my first Python package. I am sure there are many places where it could be improved. Feedback is always welcome!

## :tada: Features

* Implemented using Keras (using TensorFlow 2)

* Includes the original datasets together with a proper description of the variables

* Designed with data as pandas DataFrames in mind

* Visualization tools for the most common plots for fast and easy exploration and prototyping

* Treatment recommender

* (Basic) hyperparameter optimization using grid and randomized search

## :bookmark_tabs: Documentation

You can find the complete package's documentation [here](https://deepsurvk.readthedocs.io). Unfortunately, I haven't had as much time as I would like to work on it. Alternatively, I strongly recommend you take look at the [example notebooks](https://github.com/arturomoncadatorres/deepsurvk/tree/master/examples).

## :page_with_curl: License

This package uses the MIT license

## :black_nib: References

If you are using DeepSurvK, please cite the original DeepSurv paper, as well as the current repository as follows:

> * Katzman, Jared L., et al. ["DeepSurv: personalized treatment recommender system using a Cox proportional hazards deep neural network."](https://link.springer.com/article/10.1186/s12874-018-0482-1) BMC medical research methodology 18.1 (2018): 24. [[BibTeX](https://scholar.googleusercontent.com/scholar.bib?q=info:hG13Z0IGDPkJ:scholar.google.com/&output=citation&scisdr=CgXVK4mOEOOa6e7oHyc:AAGBfm0AAAAAXxbtByd6uXB8fbxpWDom9eCJp71TAtUO&scisig=AAGBfm0AAAAAXxbtB35QPVsdnSAHsADGSX408btb6Gvf&scisf=4&ct=citation&cd=-1&hl=en)]

> * Arturo Moncada-Torres. DeepSurvK. Accessed on [MONTH, 20XX].

## :label: Credits

This package was developed in [Spyder](https://www.spyder-ide.org/) (a fantastic open-source Python IDE) using [Cookiecutter](https://github.com/cookiecutter/cookiecutter) and the [`arturomoncadatorres/cookiecutter-pypackage` project template](https://github.com/arturomoncadatorres/cookiecutter-pypackage).