icdcodex

This is experimental software and a stable API is not expected until version 1.0

What is it?

A python library for building vector representations of ICD-9 and ICD-10 codes. Because it takes advantage of the hierarchical nature of ICD codes, it also provides these hierarchies in a networkx format.

Motivation

icdcodex was the first prize winner in the Data Driven Healthcare Track of John Hopkins' MedHacks 2020. It was hacked together to address the problem of ICD miscodes, which is a major issue for health insurance in the United States. Indeed, while ICD coding is tedious and labour intensive, it is not obvious how to automate because the output space is enourmous. For example, ICD-10 CM (clinical modification) has over 70,000 codes and growing.

There are many strategies for target encoding that address these issues. icdcodex has two features that make ICD classification more amenable to modeling:

• Access to a networkx tree representation of the ICD-9 and ICD-10 hierarchies
• Vector embeddings of ICD codes using the node2vec algorithm (including pre-computed embeddings and an interface to create new embeddings)

Example Code

from icdcodex import icd2vec, hierarchy
embedder = icd2vec.Icd2Vec(num_embedding_dimensions=64)
embedder.fit(*hierarchy.icd9())
X = get_patient_covariates()
y = embedder.to_vec(["0010"])  # 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, Website, Code, Alternate Code
• Learning Low-Dimensional Representations of Medical Concepts: Paper, Code

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/

Contributions

Contributions are always welcome!

History

0.4.9, 0.5.0 and 0.5.1 (2024-01-08)

• Added 2024 ICD-10-CM
• Fixed a bug where the node descriptions were being discarded
• Regenerated the hierarchy files with the descriptions

0.4.8 (2023-05-02)

• Use the newer scikit-learn PyPI location
• Deprecate the Python 3.6 version
• Add 2023 ICD-10-CM

0.4.6 (2022-10-13)

• Add 2022 ICD-10-CM (thank you @keithcallenberg!)

0.4.4 and 0.4.5 (2020-10-18)

• Add the code descriptions for ICD9
• Add usage on how to recapitulate functionality of sirrice/icd9
• Make the hierarchy directed to allow simpler and more intuitive traversal
• Fix issue where edges were not being formed between "Diseases Of The Blood And Blood-Forming Organs" and "Congenital Anomalies" and their children

0.4.3 (2020-10-04)

• Fix issue where hierarchy jsons were not being shipped with the pypi distribution

0.4.2 (2020-10-03)

• Add support for python <= 3.8 in the hierarchy module by using the importlib.resources backport

0.4.1 (2020-09-11)

• Update PyPI metadata

0.4.0 (2020-09-11)

• ICD-10-CM (2019 to 2020) codes are now fully present (whereas hackathon version missed certain codes)
• Versions of the ICD 9 and ICD-10-CM hierarchies are now cached to the data module
• Changed the hierarchy API: hierarchy.icd9hierarchy() is now hierarchy.icd9(). Ditto for ICD-10-CM.

0.3.0 (2020-09-05)

• Finesse API, now consistent between documentation and implementation

0.1.0 (2020-09-04)

• First release on PyPI, testing the waters during hackathon