# Generative Biomedical Entity Linking via Knowledge Base-Guided Pre-training and Synonyms-Aware Fine-tuning

arXiv: https://arxiv.org/abs/2204.05164 · HTML: https://mlsanity.com/paper/2204.05164/

## Key facts

- Cited by 35 papers in the map (data through 14 Oct 2026).
- Builds on 20 of its 39 references that are in the map.
- First posted on arXiv 11 Apr 2022.

## Builds on (most cited first, 20 of 20)

- [BART: Denoising Sequence-to-Sequence Pre-training for Natural Language Generation, Translation, and Comprehension](https://mlsanity.com/paper/1910.13461/) (2019)
- [Rethinking the Inception Architecture for Computer Vision](https://mlsanity.com/paper/1512.00567/) (2015)
- [Sequence to Sequence Learning with Neural Networks](https://mlsanity.com/paper/1409.3215/) (2014)
- [Pre-train, Prompt, and Predict: A Systematic Survey of Prompting Methods in Natural Language Processing](https://mlsanity.com/paper/2107.13586/) (2021)
- [Autoregressive Entity Retrieval](https://mlsanity.com/paper/2010.00904/) (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)
- [Scalable Zero-shot Entity Linking with Dense Entity Retrieval](https://mlsanity.com/paper/1911.03814/) (2019)
- [MedMentions: A Large Biomedical Corpus Annotated with UMLS Concepts](https://mlsanity.com/paper/1902.09476/) (2019)
- [Biomedical Entity Representations with Synonym Marginalization](https://mlsanity.com/paper/2005.00239/) (2020)
- [CODER: Knowledge infused cross-lingual medical term embedding for term normalization](https://mlsanity.com/paper/2011.02947/) (2020)
- [COMETA: A Corpus for Medical Entity Linking in the Social Media](https://mlsanity.com/paper/2010.03295/) (2020)
- [Multilingual Autoregressive Entity Linking](https://mlsanity.com/paper/2103.12528/) (2021)
- [Entity Linking and Discovery via Arborescence-based Supervised Clustering](https://mlsanity.com/paper/2109.01242/) (2021)
- [Fast and Effective Biomedical Entity Linking Using a Dual Encoder](https://mlsanity.com/paper/2103.05028/) (2021)
- [Cross-Domain Data Integration for Named Entity Disambiguation in Biomedical Text](https://mlsanity.com/paper/2110.08228/) (2021)
- [BERT might be Overkill: A Tiny but Effective Biomedical Entity Linker based on Residual Convolutional Neural Networks](https://mlsanity.com/paper/2109.02237/) (2021)
- [Efficient Symptom Inquiring and Diagnosis via Adaptive Alignment of Reinforcement Learning and Classification](https://mlsanity.com/paper/2112.00733/) (2021)
- [Deep Neural Models for Medical Concept Normalization in User-Generated Texts](https://mlsanity.com/paper/1907.07972/) (2019)
- [Biomedical Entity Linking with Contrastive Context Matching](https://mlsanity.com/paper/2106.07583/) (2021)

## Built on by (most cited first, 30 of 35)

- [A Comprehensive Evaluation of Large Language Models on Benchmark Biomedical Text Processing Tasks](https://mlsanity.com/paper/2310.04270/) (2023)
- [Summarization as Indirect Supervision for Relation Extraction](https://mlsanity.com/paper/2205.09837/) (2022)
- [Evaluation of ChatGPT on Biomedical Tasks: A Zero-Shot Comparison with Fine-Tuned Generative Transformers](https://mlsanity.com/paper/2306.04504/) (2023)
- [Multi-label Few-shot ICD Coding as Autoregressive Generation with Prompt](https://mlsanity.com/paper/2211.13813/) (2022)
- [HunFlair2 in a cross-corpus evaluation of biomedical named entity recognition and normalization tools](https://mlsanity.com/paper/2402.12372/) (2024)
- [BELB: a Biomedical Entity Linking Benchmark](https://mlsanity.com/paper/2308.11537/) (2023)
- [Learning from Negative Samples in Biomedical Generative Entity Linking](https://mlsanity.com/paper/2408.16493/) (2024)
- [CoRTEx: Contrastive Learning for Representing Terms via Explanations with Applications on Constructing Biomedical Knowledge Graphs](https://mlsanity.com/paper/2312.08036/) (2023)
- [Optimal Transport Guided Correlation Assignment for Multimodal Entity Linking](https://mlsanity.com/paper/2406.01934/) (2024)
- [BELHD: Improving Biomedical Entity Linking with Homonoym Disambiguation](https://mlsanity.com/paper/2401.05125/) (2024)
- [xMEN: A Modular Toolkit for Cross-Lingual Medical Entity Normalization](https://mlsanity.com/paper/2310.11275/) (2023)
- [ClinLinker: Medical Entity Linking of Clinical Concept Mentions in Spanish](https://mlsanity.com/paper/2404.06367/) (2024)
- [Disease Entity Recognition and Normalization is Improved with Large Language Model Derived Synthetic Normalized Mentions](https://mlsanity.com/paper/2410.07951/) (2024)
- [Exploring Partial Knowledge Base Inference in Biomedical Entity Linking](https://mlsanity.com/paper/2303.10330/) (2023)
- [Biomedical Entity Linking with Triple-aware Pre-Training](https://mlsanity.com/paper/2308.14429/) (2023)
- [Improving Biomedical Entity Linking with Retrieval-enhanced Learning](https://mlsanity.com/paper/2312.09806/) (2023)
- [Biomedical Entity Linking as Multiple Choice Question Answering](https://mlsanity.com/paper/2402.15189/) (2024)
- [RxSafeBench: Identifying Medication Safety Issues of Large Language Models in Simulated Consultation](https://mlsanity.com/paper/2511.04328/) (2025)
- [Biomedical Entity Linking for Dutch: Fine-tuning a Self-alignment BERT Model on an Automatically Generated Wikipedia Corpus](https://mlsanity.com/paper/2405.11941/) (2024)
- [Explainable ICD Coding via Entity Linking](https://mlsanity.com/paper/2503.20508/) (2025)
- [MedPath: Multi-Domain Cross-Vocabulary Hierarchical Paths for Biomedical Entity Linking](https://mlsanity.com/paper/2511.10887/) (2025)
- [SynCABEL: Synthetic Contextualized Augmentation for Biomedical Entity Linking](https://mlsanity.com/paper/2601.19667/) (2026)
- [Sem4SAP: Synonymous Expression Mining From Open Knowledge Graph For Language Model Synonym-Aware Pretraining](https://mlsanity.com/paper/2303.14425/) (2023)
- [Iteratively Improving Biomedical Entity Linking and Event Extraction via Hard Expectation-Maximization](https://mlsanity.com/paper/2305.14645/) (2023)
- [Efficient Biomedical Entity Linking: Clinical Text Standardization with Low-Resource Techniques](https://mlsanity.com/paper/2405.15134/) (2024)
- [Boosting Biomedical Concept Extraction by Rule-Based Data Augmentation](https://mlsanity.com/paper/2407.02719/) (2024)
- [Hybrid X-Linker: Automated Data Generation and Extreme Multi-label Ranking for Biomedical Entity Linking](https://mlsanity.com/paper/2407.06292/) (2024)
- [Unified Representation of Genomic and Biomedical Concepts through Multi-Task, Multi-Source Contrastive Learning](https://mlsanity.com/paper/2410.10144/) (2024)
- [LongBEL: Long-Context and Document-Consistent Biomedical Entity Linking](https://mlsanity.com/paper/2605.13451/) (2026)
- [BioELX: Context-Aware Cross-lingual Biomedical Entity Linking without Task-Specific Supervision](https://mlsanity.com/paper/2605.27380/) (2026)

## Abstract (arXiv)

Entities lie in the heart of biomedical natural language understanding, and the biomedical entity linking (EL) task remains challenging due to the fine-grained and diversiform concept names. Generative methods achieve remarkable performances in general domain EL with less memory usage while requiring expensive pre-training. Previous biomedical EL methods leverage synonyms from knowledge bases (KB) which is not trivial to inject into a generative method. In this work, we use a generative approach to model biomedical EL and propose to inject synonyms knowledge in it. We propose KB-guided pre-training by constructing synthetic samples with synonyms and definitions from KB and require the model to recover concept names. We also propose synonyms-aware fine-tuning to select concept names for training, and propose decoder prompt and multi-synonyms constrained prefix tree for inference. Our method achieves state-of-the-art results on several biomedical EL tasks without candidate selection which displays the effectiveness of proposed pre-training and fine-tuning strategies.