# GrabQC: Graph based Query Contextualization for automated ICD coding

arXiv: https://arxiv.org/abs/2207.06802 · HTML: https://mlsanity.com/paper/2207.06802/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 10 of its 22 references that are in the map.
- First posted on arXiv 14 Jul 2022.

## Builds on (most cited first, 10 of 10)

- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Weisfeiler and Leman Go Neural: Higher-order Graph Neural Networks](https://mlsanity.com/paper/1810.02244/) (2018)
- [ScispaCy: Fast and Robust Models for Biomedical Natural Language Processing](https://mlsanity.com/paper/1902.07669/) (2019)
- [Explainable Prediction of Medical Codes from Clinical Text](https://mlsanity.com/paper/1802.05695/) (2018)
- [ICD Coding from Clinical Text Using Multi-Filter Residual Convolutional Neural Network](https://mlsanity.com/paper/1912.00862/) (2019)
- [BERT-XML: Large Scale Automated ICD Coding Using BERT Pretraining](https://mlsanity.com/paper/2006.03685/) (2020)
- [Towards Automated ICD Coding Using Deep Learning](https://mlsanity.com/paper/1711.04075/) (2017)
- [Inferring Degrees from Incomplete Networks and Nonlinear Dynamics](https://mlsanity.com/paper/2004.10546/) (2020)

## Abstract (arXiv)

Automated medical coding is a process of codifying clinical notes to appropriate diagnosis and procedure codes automatically from the standard taxonomies such as ICD (International Classification of Diseases) and CPT (Current Procedure Terminology). The manual coding process involves the identification of entities from the clinical notes followed by querying a commercial or non-commercial medical codes Information Retrieval (IR) system that follows the Centre for Medicare and Medicaid Services (CMS) guidelines. We propose to automate this manual process by automatically constructing a query for the IR system using the entities auto-extracted from the clinical notes. We propose GrabQC, a Graph based Query Contextualization method that automatically extracts queries from the clinical text, contextualizes the queries using a Graph Neural Network (GNN) model and obtains the ICD Codes using an external IR system. We also propose a method for labelling the dataset for training the model. We perform experiments on two datasets of clinical text in three different setups to assert the effectiveness of our approach. The experimental results show that our proposed method is better than the compared baselines in all three settings.