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Open Source Science

https://github.com/barahona-research-group/ice-node

Integration of Clinical Embeddings with Neural ODEs

https://github.com/barahona-research-group/ice-node

Science Score: 13.0%

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    CITATION.cff file
  • ✓
    codemeta.json file
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    .zenodo.json file
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    Scientific vocabulary similarity
    Low similarity (9.2%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Integration of Clinical Embeddings with Neural ODEs

Basic Info
  • Host: GitHub
  • Owner: barahona-research-group
  • License: gpl-3.0
  • Language: Jupyter Notebook
  • Default Branch: main
  • Homepage:
  • Size: 206 MB
Statistics
  • Stars: 10
  • Watchers: 2
  • Forks: 1
  • Open Issues: 1
  • Releases: 0
Created about 4 years ago · Last pushed over 1 year ago
Metadata Files
Readme License

README.md

Note: If you are referred from ICE-NODE paper, please follow the relevant instructions on the following snapshot of the codebase: MLHC 2022 version.

Roadmap

  • [ ] Pipeline validators.
  • [ ] Integrate consort diagramming in the pipeline.
  • [x] Work with the pytable library directly instead of the pandas library.
  • [ ] Implement packed representations for the tvx_ehr to improve the compressibility of the data.
  • [ ] Implement a scheme manager object to handle schemes and codemaps, instead of using global variables.
  • [x] lib.ehr.tvx* test.
  • [ ] lib.ehr.coding_scheme.CodeMap test.
  • [ ] lib.ehr.* documentation / document edge cases tested.
  • [ ] lib.ehr custom exceptions / adapt tests.
  • [ ] FHIR resources adaptation.
  • [ ] Support for SNOMED-CT.
  • [ ] CLI for running pipelines.
  • [ ] GUI for configuring the dataset and the tvx_ehr.
    • Pipeline 10 + 10 steps.
    • Selection of dataset CodingScheme space.
Coverage

| Branch | Coverage | |--------|------------------------------------------------------------------------------------------------------------------------------------------------------------| | main | main_cov_ehr | | dev | dev_cov_ehr |

Citation

To cite this work, please use the following BibTex entry:

@article{Alaa2022ICENODEIO, title={ICE-NODE: Integration of Clinical Embeddings with Neural Ordinary Differential Equations}, author={Asem Alaa and Erik Mayer and Mauricio Barahona}, journal={ArXiv}, year={2022}, volume={abs/2207.01873} }

Owner

  • Name: Barahona Research - Applied Math - Imperial
  • Login: barahona-research-group
  • Kind: organization
  • Email: m.barahona@imperial.ac.uk

Research codes developed in the Barahona research group - Department of Mathematics - Imperial College London

GitHub Events

Total
  • Push event: 1
Last Year
  • Push event: 1

Dependencies

requirements/analysis-sec.txt pypi
  • UpSetPlot ==0.6.1
  • ipython >=7.31.1
  • jupyter ==1.0.0
  • matplotlib ==3.5.0
  • seaborn ==0.11.2
requirements/common.txt pypi
  • absl-py ==1.0.0
  • dm-haiku ==0.0.5
  • jax ==0.3.13
  • jaxlib ==0.3.10
  • jaxopt ==0.4.2
  • numpy ==1.22.1
  • pandas ==1.3.5
  • scikit-learn ==1.0.2
  • scipy ==1.7.3
  • tqdm ==4.62.3
requirements/hyperopt-sec.txt pypi
  • mlflow >=1.23.1
  • optuna ==2.10.0
.github/workflows/run_tests.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v3 composite
requirements/dev.txt pypi
  • networkx ==2.8.5 development
requirements/mlhc2022.txt pypi
requirements/test.txt pypi