# BELXTR: Biomedical Entity Linking via Contextualized Token Retrieval

arXiv: https://arxiv.org/abs/2609.25859 · HTML: https://mlsanity.com/paper/2609.25859/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 41 of its 81 references that are in the map.
- First posted on arXiv 22 Sep 2026.

## Builds on (most cited first, 30 of 41)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [GPT-4o System Card](https://mlsanity.com/paper/2410.21276/) (2024)
- [BEIR: A Heterogenous Benchmark for Zero-shot Evaluation of Information Retrieval Models](https://mlsanity.com/paper/2104.08663/) (2021)
- [ColBERT: Efficient and Effective Passage Search via Contextualized Late Interaction over BERT](https://mlsanity.com/paper/2004.12832/) (2020)
- [Efficient and robust approximate nearest neighbor search using Hierarchical Navigable Small World graphs](https://mlsanity.com/paper/1603.09320/) (2016)
- [DSPy: Compiling Declarative Language Model Calls into Self-Improving Pipelines](https://mlsanity.com/paper/2310.03714/) (2023)
- [Smarter, Better, Faster, Longer: A Modern Bidirectional Encoder for Fast, Memory Efficient, and Long Context Finetuning and Inference](https://mlsanity.com/paper/2412.13663/) (2024)
- [Understanding the Behaviour of Contrastive Loss](https://mlsanity.com/paper/2012.09740/) (2020)
- [Autoregressive Entity Retrieval](https://mlsanity.com/paper/2010.00904/) (2020)
- [Self-Alignment Pretraining for Biomedical Entity Representations](https://mlsanity.com/paper/2010.11784/) (2020)
- [Opportunities and Challenges for ChatGPT and Large Language Models in Biomedicine and Health](https://mlsanity.com/paper/2306.10070/) (2023)
- [PLAID: An Efficient Engine for Late Interaction Retrieval](https://mlsanity.com/paper/2205.09707/) (2022)
- [BioRED: A Rich Biomedical Relation Extraction Dataset](https://mlsanity.com/paper/2204.04263/) (2022)
- [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)
- [BERN2: an advanced neural biomedical named entity recognition and normalization tool](https://mlsanity.com/paper/2201.02080/) (2022)
- [Understanding Hard Negatives in Noise Contrastive Estimation](https://mlsanity.com/paper/2104.06245/) (2021)
- [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)
- [Rethinking the Role of Token Retrieval in Multi-Vector Retrieval](https://mlsanity.com/paper/2304.01982/) (2023)
- [PubTator 3.0: an AI-powered Literature Resource for Unlocking Biomedical Knowledge](https://mlsanity.com/paper/2401.11048/) (2024)
- [Entity Linking and Discovery via Arborescence-based Supervised Clustering](https://mlsanity.com/paper/2109.01242/) (2021)
- [Highly Parallel Autoregressive Entity Linking with Discriminative Correction](https://mlsanity.com/paper/2109.03792/) (2021)
- [Generative Relevance Feedback with Large Language Models](https://mlsanity.com/paper/2304.13157/) (2023)
- [PyLate: Flexible Training and Retrieval for Late Interaction Models](https://mlsanity.com/paper/2508.03555/) (2025)
- [WARP: An Efficient Engine for Multi-Vector Retrieval](https://mlsanity.com/paper/2501.17788/) (2025)
- [AIONER: All-in-one scheme-based biomedical named entity recognition using deep learning](https://mlsanity.com/paper/2211.16944/) (2022)
- [Overview of BioASQ 2025: The Thirteenth BioASQ Challenge on Large-Scale Biomedical Semantic Indexing and Question Answering](https://mlsanity.com/paper/2508.20554/) (2025)

## Abstract (arXiv)

Biomedical Entity Linking disambiguates mentions to entities in a knowledge base (KB), making it the cornerstone of information extraction pipelines. While embedding-based models are a popular approach for the task, they suffer from a key limitation. They compress mentions (and entities) into a single vector, forcing the model to average away crucial fine-grained differences. We present BELXTR, a novel embedding model based on the multi-vector (a.k.a. late interaction) architecture, which allows to leverage token-level matching information. BELXTR extends the original XTR model to biomedical entity linking by integrating an existing task-specific training objective and exploring active query expansion. Experiments across ten corpora and five KBs show that BELXTR improves upon current state-of-the-art in half of the corpora with an average improvement of 5pp recall@1. The largest gains are reported on the challenging cross-species gene disambiguation subtask, where BELXTR outperforms an LLM-powered retrieve-and-rerank pipeline and closely approaches a specialized rule-based system. Our results highlight multi-vector models as a practical alternative to hard-to-maintain rule-based systems or in scenarios where LLM-based reranking is too costly as in PubMed-scale mining. The code to reproduce our experiments can be found at: https://github.com/sg-wbi/belxtr.