# BioBridge: Unified Bio-Embedding with Bridging Modality in Code-Switched EMR

arXiv: https://arxiv.org/abs/2412.11671 · HTML: https://mlsanity.com/paper/2412.11671/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 24 of its 82 references that are in the map.
- First posted on arXiv 16 Dec 2024.

## Builds on (most cited first, 24 of 24)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
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- [Efficient Estimation of Word Representations in Vector Space](https://mlsanity.com/paper/1301.3781/) (2013)
- [Unsupervised Cross-lingual Representation Learning at Scale](https://mlsanity.com/paper/1911.02116/) (2019)
- [ViLBERT: Pretraining Task-Agnostic Visiolinguistic Representations for Vision-and-Language Tasks](https://mlsanity.com/paper/1908.02265/) (2019)
- [HuggingFace's Transformers: State-of-the-art Natural Language Processing](https://mlsanity.com/paper/1910.03771/) (2019)
- [LXMERT: Learning Cross-Modality Encoder Representations from Transformers](https://mlsanity.com/paper/1908.07490/) (2019)
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- [Aligning Books and Movies: Towards Story-like Visual Explanations by Watching Movies and Reading Books](https://mlsanity.com/paper/1506.06724/) (2015)
- [Publicly Available Clinical BERT Embeddings](https://mlsanity.com/paper/1904.03323/) (2019)
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- [Unified Vision-Language Pre-Training for Image Captioning and VQA](https://mlsanity.com/paper/1909.11059/) (2019)
- [Med-BERT: pre-trained contextualized embeddings on large-scale structured electronic health records for disease prediction](https://mlsanity.com/paper/2005.12833/) (2020)
- [GatorTron: A Large Clinical Language Model to Unlock Patient Information from Unstructured Electronic Health Records](https://mlsanity.com/paper/2203.03540/) (2022)
- [Dynamic Fusion with Intra- and Inter- Modality Attention Flow for Visual Question Answering](https://mlsanity.com/paper/1812.05252/) (2018)
- [Unsupervised Learning of Sentence Embeddings using Compositional n-Gram Features](https://mlsanity.com/paper/1703.02507/) (2017)
- [Multi-layer Representation Learning for Medical Concepts](https://mlsanity.com/paper/1602.05568/) (2016)
- [BioSentVec: creating sentence embeddings for biomedical texts](https://mlsanity.com/paper/1810.09302/) (2018)
- [Modality Shifting Attention Network for Multi-modal Video Question Answering](https://mlsanity.com/paper/2007.02036/) (2020)
- [KR-BERT: A Small-Scale Korean-Specific Language Model](https://mlsanity.com/paper/2008.03979/) (2020)

## Abstract (arXiv)

Pediatric Emergency Department (PED) overcrowding presents a significant global challenge, prompting the need for efficient solutions. This paper introduces the BioBridge framework, a novel approach that applies Natural Language Processing (NLP) to Electronic Medical Records (EMRs) in written free-text form to enhance decision-making in PED. In non-English speaking countries, such as South Korea, EMR data is often written in a Code-Switching (CS) format that mixes the native language with English, with most code-switched English words having clinical significance. The BioBridge framework consists of two core modules: "bridging modality in context" and "unified bio-embedding." The "bridging modality in context" module improves the contextual understanding of bilingual and code-switched EMRs. In the "unified bio-embedding" module, the knowledge of the model trained in the medical domain is injected into the encoder-based model to bridge the gap between the medical and general domains. Experimental results demonstrate that the proposed BioBridge significantly performance traditional machine learning and pre-trained encoder-based models on several metrics, including F1 score, area under the receiver operating characteristic curve (AUROC), area under the precision-recall curve (AUPRC), and Brier score. Specifically, BioBridge-XLM achieved enhancements of 0.85% in F1 score, 0.75% in AUROC, and 0.76% in AUPRC, along with a notable 3.04% decrease in the Brier score, demonstrating marked improvements in accuracy, reliability, and prediction calibration over the baseline XLM model. The source code will be made publicly available.