# A Natural Language Processing Approach to Support Biomedical Data Harmonization: Leveraging Large Language Models

arXiv: https://arxiv.org/abs/2411.02730 · HTML: https://mlsanity.com/paper/2411.02730/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 18 of its 78 references that are in the map.
- First posted on arXiv 5 Nov 2024.

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

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Distilling the Knowledge in a Neural Network](https://mlsanity.com/paper/1503.02531/) (2015)
- [Retrieval-Augmented Generation for Knowledge-Intensive NLP Tasks](https://mlsanity.com/paper/2005.11401/) (2020)
- [Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks](https://mlsanity.com/paper/1908.10084/) (2019)
- [SimCSE: Simple Contrastive Learning of Sentence Embeddings](https://mlsanity.com/paper/2104.08821/) (2021)
- [MS MARCO: A Human Generated MAchine Reading COmprehension Dataset](https://mlsanity.com/paper/1611.09268/) (2016)
- [MiniLM: Deep Self-Attention Distillation for Task-Agnostic Compression of Pre-Trained Transformers](https://mlsanity.com/paper/2002.10957/) (2020)
- [Model soups: averaging weights of multiple fine-tuned models improves accuracy without increasing inference time](https://mlsanity.com/paper/2203.05482/) (2022)
- [Text Embeddings by Weakly-Supervised Contrastive Pre-training](https://mlsanity.com/paper/2212.03533/) (2022)
- [BEIR: A Heterogenous Benchmark for Zero-shot Evaluation of Information Retrieval Models](https://mlsanity.com/paper/2104.08663/) (2021)
- [MPNet: Masked and Permuted Pre-training for Language Understanding](https://mlsanity.com/paper/2004.09297/) (2020)
- [MTEB: Massive Text Embedding Benchmark](https://mlsanity.com/paper/2210.07316/) (2022)
- [All Models are Wrong, but Many are Useful: Learning a Variable's Importance by Studying an Entire Class of Prediction Models Simultaneously](https://mlsanity.com/paper/1801.01489/) (2018)
- [Detect and Correct Bias in Multi-Site Neuroimaging Datasets](https://mlsanity.com/paper/2002.05049/) (2020)
- [BioLORD: Learning Ontological Representations from Definitions (for Biomedical Concepts and their Textual Descriptions)](https://mlsanity.com/paper/2210.11892/) (2022)
- [Automatic Glossary of Clinical Terminology: a Large-Scale Dictionary of Biomedical Definitions Generated from Ontological Knowledge](https://mlsanity.com/paper/2306.00665/) (2023)
- [Boosting Adverse Drug Event Normalization on Social Media: General-Purpose Model Initialization and Biomedical Semantic Text Similarity Benefit Zero-Shot Linking in Informal Contexts](https://mlsanity.com/paper/2308.00157/) (2023)

## Built on by (most cited first, 1 of 1)

- [Beyond Correctness: Evaluating Semantic Knowledge in Cross-Table Transfer](https://mlsanity.com/paper/2609.34098/) (2026)

## Abstract (arXiv)

Biomedical research requires large, diverse samples to produce unbiased results. Automated methods for matching variables across datasets can accelerate this process. Research in this area has been limited, primarily focusing on lexical matching and ontology based semantic matching. We aimed to develop new methods, leveraging large language models (LLM) and ensemble learning, to automate variable matching. Methods: We utilized data from two GERAS cohort (European and Japan) studies to develop variable matching methods. We first manually created a dataset by matching 352 EU variables with 1322 candidate JP variables, where matched variable pairs were positive and unmatched pairs were negative instances. Using this dataset, we developed and evaluated two types of natural language processing (NLP) methods, which matched variables based on variable labels and definitions from data dictionaries: (1) LLM-based and (2) fuzzy matching. We then developed an ensemble-learning method, using the Random Forest model, to integrate individual NLP methods. RF was trained and evaluated on 50 trials. Each trial had a random split (4:1) of training and test sets, with the model's hyperparameters optimized through cross-validation on the training set. For each EU variable, 1322 candidate JP variables were ranked based on NLP-derived similarity scores or RF's probability scores, denoting their likelihood to match the EU variable. Ranking performance was measured by top-n hit ratio (HRn) and mean reciprocal rank (MRR). Results:E5 performed best among individual methods, achieving 0.90 HR-30 and 0.70 MRR. RF performed better than E5 on all metrics over 50 trials (P less than 0.001) and achieved an average HR 30 of 0.98 and MRR of 0.73. LLM-derived features contributed most to RF's performance. One major cause of errors in automatic variable matching was ambiguous variable definitions within data dictionaries.