icdcodex 0.4.0

icd embedding for machine learning

[](https://pypi.python.org/pypi/icdcodex/) [](http://icd-codex.readthedocs.io/?badge=latest) [](https://github.com/psf/black) [](https://github.com/icd-codex/icd-codex/blob/master/LICENSE)

icdcodex was the first prize winner in the Data Driven Healthcare Track of John Hopkins’ [MedHacks 2020](https://medhacks2020.devpost.com).

`{admonition} Experimental This is experimental software and a stable API is not expected until version 1.0 `

## Motivation Thousands of Americans are misquoted on their health insurance yearly due to ICD miscodes. While ICD coding is manual and laborous, it is difficult to automate by machine learning because the output space is enormous. For example, ICD-10 CM (clinical modification) has over 70,000 codes and growing. There are [many strategies](https://maxhalford.github.io/blog/target-encoding/) for label embedding that address these issues.

icdcodex has two features that make ICD classification more amenable to modeling: - Access to a networkx tree representation of the ICD9 and ICD10 hierarchies - Vector embeddings of ICD codes (including pre-computed embeddings and an interface to create new embeddings)

## Example Code `python from icdcodex import icd2vec, hierarchy embedder = icd2vec.Icd2Vec(num_embedding_dimensions=64) embedder.fit(*hierarchy.icd9()) X = get_patient_covariates() y = embedder.to_vec(["001.0"]) # Cholera due to vibrio cholerae ` In this case, y is a 64-dimensional vector close to other Infectious And Parasitic Diseases codes.

## Related Work - node2vec [Paper](https://cs.stanford.edu/people/jure/pubs/node2vec-kdd16.pdf), [Website](https://snap.stanford.edu/node2vec/), [Code](https://github.com/snap-stanford/snap/tree/master/examples/node2vec), [Alternate Code](https://github.com/eliorc/node2vec) - Learning Low-Dimensional Representations of Medical Concepts: [Paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5001761/), [Code](https://github.com/clinicalml/embeddings) - Projection Word Embedding Model With Hybrid Sampling Training for Classifying ICD-10-CM Codes [Paper](https://pubmed.ncbi.nlm.nih.gov/31339103/)

## The Hackathon Team - Jeremy Fisher (Maintainer) - Alhusain Abdalla - Natasha Nehra - Tejas Patel - Hamrish Saravanakumar

## Documentation

See the full documentation: [https://icd-codex.readthedocs.io/en/latest/](https://icd-codex.readthedocs.io/en/latest/)

## Contributions

[Contributions are always welcome!](https://icd-codex.readthedocs.io/en/latest/contributing.html)

History

0.1.0 (2020-09-04)

• First release on PyPI.

0.3.0 (2020-09-05)

• Finesse API, now consistent between documentation and implementation