# Neighborhood-Aware Dual Biomedical Entity Linking

arXiv: https://arxiv.org/abs/2608.04144 · HTML: https://mlsanity.com/paper/2608.04144/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 22 of its 43 references that are in the map.
- First posted on arXiv 4 Aug 2026.

## Builds on (most cited first, 22 of 22)

- [BART: Denoising Sequence-to-Sequence Pre-training for Natural Language Generation, Translation, and Comprehension](https://mlsanity.com/paper/1910.13461/) (2019)
- [Lost in the Middle: How Language Models Use Long Contexts](https://mlsanity.com/paper/2307.03172/) (2023)
- [Precise Zero-Shot Dense Retrieval without Relevance Labels](https://mlsanity.com/paper/2212.10496/) (2022)
- [Document Ranking with a Pretrained Sequence-to-Sequence Model](https://mlsanity.com/paper/2003.06713/) (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)
- [Multi-Stage Document Ranking with BERT](https://mlsanity.com/paper/1910.14424/) (2019)
- [RankZephyr: Effective and Robust Zero-Shot Listwise Reranking is a Breeze!](https://mlsanity.com/paper/2312.02724/) (2023)
- [RankT5: Fine-Tuning T5 for Text Ranking with Ranking Losses](https://mlsanity.com/paper/2210.10634/) (2022)
- [Beyond Yes and No: Improving Zero-Shot LLM Rankers via Scoring Fine-Grained Relevance Labels](https://mlsanity.com/paper/2310.14122/) (2023)
- [MedMentions: A Large Biomedical Corpus Annotated with UMLS Concepts](https://mlsanity.com/paper/1902.09476/) (2019)
- [Large Language Models Know Your Contextual Search Intent: A Prompting Framework for Conversational Search](https://mlsanity.com/paper/2303.06573/) (2023)
- [CONQRR: Conversational Query Rewriting for Retrieval with Reinforcement Learning](https://mlsanity.com/paper/2112.08558/) (2021)
- [Large Language Model based Long-tail Query Rewriting in Taobao Search](https://mlsanity.com/paper/2311.03758/) (2023)
- [Biomedical Entity Representations with Synonym Marginalization](https://mlsanity.com/paper/2005.00239/) (2020)
- [COMETA: A Corpus for Medical Entity Linking in the Social Media](https://mlsanity.com/paper/2010.03295/) (2020)
- [RaFe: Ranking Feedback Improves Query Rewriting for RAG](https://mlsanity.com/paper/2405.14431/) (2024)
- [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)
- [BERT might be Overkill: A Tiny but Effective Biomedical Entity Linker based on Residual Convolutional Neural Networks](https://mlsanity.com/paper/2109.02237/) (2021)
- [AutoPCR: Automated Phenotype Concept Recognition by Prompting](https://mlsanity.com/paper/2507.19315/) (2025)
- [Learning from Negative Samples in Biomedical Generative Entity Linking](https://mlsanity.com/paper/2408.16493/) (2024)

## Abstract (arXiv)

Biomedical entity linking grounds mentions in clinical and scientific text to entities in a curated knowledge base (KB) with ontological structure, which supports downstream applications such as literature-scale information extraction and patient-record normalization. The task has several challenges at once: the KB contains large numbers of entities, mentions are often ambiguous, and gold labels follow annotation conventions specific to each corpus. To address these challenges, we propose PILOT, a three-stage framework made up of neighborhood-aware retrieval, dual reranking, and score fusion. The retriever injects ontological structure from both the query and KB side, by reformulating mentions and pooling entity embeddings. The retrieved pool is then scored from two complementary views, one over surface forms and one over context, and fused together. PILOT achieves the state of the art on average across five widely-used benchmarks and remains efficient at inference.