# A Multi-View Joint Learning Framework for Embedding Clinical Codes and Text Using Graph Neural Networks

arXiv: https://arxiv.org/abs/2301.11608 · HTML: https://mlsanity.com/paper/2301.11608/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 18 of its 33 references that are in the map.
- First posted on arXiv 27 Jan 2023.

## Builds on (most cited first, 18 of 18)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [Distributed Representations of Words and Phrases and their Compositionality](https://mlsanity.com/paper/1310.4546/) (2013)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [Modeling Relational Data with Graph Convolutional Networks](https://mlsanity.com/paper/1703.06103/) (2017)
- [Deeper Insights into Graph Convolutional Networks for Semi-Supervised Learning](https://mlsanity.com/paper/1801.07606/) (2018)
- [Publicly Available Clinical BERT Embeddings](https://mlsanity.com/paper/1904.03323/) (2019)
- [ClinicalBERT: Modeling Clinical Notes and Predicting Hospital Readmission](https://mlsanity.com/paper/1904.05342/) (2019)
- [On Deep Multi-View Representation Learning: Objectives and Optimization](https://mlsanity.com/paper/1602.01024/) (2016)
- [Deep EHR: A Survey of Recent Advances in Deep Learning Techniques for Electronic Health Record (EHR) Analysis](https://mlsanity.com/paper/1706.03446/) (2017)
- [Learning the Graphical Structure of Electronic Health Records with Graph Convolutional Transformer](https://mlsanity.com/paper/1906.04716/) (2019)
- [ICD Coding from Clinical Text Using Multi-Filter Residual Convolutional Neural Network](https://mlsanity.com/paper/1912.00862/) (2019)
- [Enhancing Clinical Concept Extraction with Contextual Embeddings](https://mlsanity.com/paper/1902.08691/) (2019)
- [Clinical XLNet: Modeling Sequential Clinical Notes and Predicting Prolonged Mechanical Ventilation](https://mlsanity.com/paper/1912.11975/) (2019)
- [Heterogeneous Similarity Graph Neural Network on Electronic Health Records](https://mlsanity.com/paper/2101.06800/) (2021)
- [Deep Learning under Privileged Information Using Heteroscedastic Dropout](https://mlsanity.com/paper/1805.11614/) (2018)
- [Towards BERT-based Automatic ICD Coding: Limitations and Opportunities](https://mlsanity.com/paper/2104.06709/) (2021)

## Abstract (arXiv)

Learning to represent free text is a core task in many clinical machine learning (ML) applications, as clinical text contains observations and plans not otherwise available for inference. State-of-the-art methods use large language models developed with immense computational resources and training data; however, applying these models is challenging because of the highly varying syntax and vocabulary in clinical free text. Structured information such as International Classification of Disease (ICD) codes often succinctly abstracts the most important facts of a clinical encounter and yields good performance, but is often not as available as clinical text in real-world scenarios. We propose a multi-view learning framework that jointly learns from codes and text to combine the availability and forward-looking nature of text and better performance of ICD codes. The learned text embeddings can be used as inputs to predictive algorithms independent of the ICD codes during inference. Our approach uses a Graph Neural Network (GNN) to process ICD codes, and Bi-LSTM to process text. We apply Deep Canonical Correlation Analysis (DCCA) to enforce the two views to learn a similar representation of each patient. In experiments using planned surgical procedure text, our model outperforms BERT models fine-tuned to clinical data, and in experiments using diverse text in MIMIC-III, our model is competitive to a fine-tuned BERT at a tiny fraction of its computational effort.