# SynCABEL: Synthetic Contextualized Augmentation for Biomedical Entity Linking

arXiv: https://arxiv.org/abs/2601.19667 · HTML: https://mlsanity.com/paper/2601.19667/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 17 of its 36 references that are in the map.
- First posted on arXiv 27 Jan 2026.

## Builds on (most cited first, 17 of 17)

- [The Llama 3 Herd of Models](https://mlsanity.com/paper/2407.21783/) (2024)
- [Autoregressive Entity Retrieval](https://mlsanity.com/paper/2010.00904/) (2020)
- [Multilingual Translation with Extensible Multilingual Pretraining and Finetuning](https://mlsanity.com/paper/2008.00401/) (2020)
- [ScispaCy: Fast and Robust Models for Biomedical Natural Language Processing](https://mlsanity.com/paper/1902.07669/) (2019)
- [Self-Alignment Pretraining for Biomedical Entity Representations](https://mlsanity.com/paper/2010.11784/) (2020)
- [Exploiting Asymmetry for Synthetic Training Data Generation: SynthIE and the Case of Information Extraction](https://mlsanity.com/paper/2303.04132/) (2023)
- [MedMentions: A Large Biomedical Corpus Annotated with UMLS Concepts](https://mlsanity.com/paper/1902.09476/) (2019)
- [CODER: Knowledge infused cross-lingual medical term embedding for term normalization](https://mlsanity.com/paper/2011.02947/) (2020)
- [Generative Biomedical Entity Linking via Knowledge Base-Guided Pre-training and Synonyms-Aware Fine-tuning](https://mlsanity.com/paper/2204.05164/) (2022)
- [Knowledge-Rich Self-Supervision for Biomedical Entity Linking](https://mlsanity.com/paper/2112.07887/) (2021)
- [Learning Domain-Specialised Representations for Cross-Lingual Biomedical Entity Linking](https://mlsanity.com/paper/2105.14398/) (2021)
- [Entity Linking and Discovery via Arborescence-based Supervised Clustering](https://mlsanity.com/paper/2109.01242/) (2021)
- [LLMAEL: Large Language Models are Good Context Augmenters for Entity Linking](https://mlsanity.com/paper/2407.04020/) (2024)
- [Instructed Language Models with Retrievers Are Powerful Entity Linkers](https://mlsanity.com/paper/2311.03250/) (2023)
- [Improving Broad-Coverage Medical Entity Linking with Semantic Type Prediction and Large-Scale Datasets](https://mlsanity.com/paper/2005.00460/) (2020)
- [Learning from Negative Samples in Biomedical Generative Entity Linking](https://mlsanity.com/paper/2408.16493/) (2024)
- [Contextual Augmentation for Entity Linking using Large Language Models](https://mlsanity.com/paper/2510.18888/) (2025)

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

- [LongBEL: Long-Context and Document-Consistent Biomedical Entity Linking](https://mlsanity.com/paper/2605.13451/) (2026)

## Abstract (arXiv)

We present SynCABEL (Synthetic Contextualized Augmentation for Biomedical Entity Linking), a framework that addresses a central bottleneck in supervised biomedical entity linking (BEL): the scarcity of expert-annotated training data. SynCABEL leverages large language models to generate context-rich synthetic training examples for all candidate concepts in a target knowledge base, providing broad supervision without manual annotation. We demonstrate that SynCABEL, when combined with decoder-only models and guided inference, establishes new state-of-the-art results across three widely used multilingual benchmarks: MedMentions for English, QUAERO for French, and SPACCC for Spanish. Evaluating data efficiency, we show that SynCABEL reaches the performance of full human supervision using up to 60% less annotated data, substantially reducing reliance on labor-intensive and costly expert labeling. Finally, acknowledging that standard evaluation based on exact code matching often underestimates clinically valid predictions due to ontology redundancy, we introduce an LLM-as-a-judge protocol. This analysis reveals that SynCABEL significantly improves the rate of clinically valid predictions. Our synthetic datasets, models, and code are released to support reproducibility and future research.