BELB: a biomedical entity linking benchmark

S Garda, L Weber-Genzel, R Martin, U Leser - Bioinformatics, 2023 - academic.oup.com
Motivation Biomedical entity linking (BEL) is the task of grounding entity mentions to a
knowledge base (KB). It plays a vital role in information extraction pipelines for the life …

Bring your own kg: Self-supervised program synthesis for zero-shot kgqa

D Agarwal, R Das, S Khosla… - arxiv preprint arxiv …, 2023 - arxiv.org
We present BYOKG, a universal question-answering (QA) system that can operate on any
knowledge graph (KG), requires no human-annotated training data, and can be ready to use …

[HTML][HTML] A comprehensive evaluation of biomedical entity linking models

D Kartchner, J Deng, S Lohiya, T Kopparthi… - Proceedings of the …, 2023 - ncbi.nlm.nih.gov
Biomedical entity linking (BioEL) is the process of connecting entities referenced in
documents to entries in biomedical databases such as the Unified Medical Language …

xMEN: a modular toolkit for cross-lingual medical entity normalization

F Borchert, I Llorca, R Roller, B Arnrich… - JAMIA …, 2025 - academic.oup.com
Objective To improve performance of medical entity normalization across many languages,
especially when fewer language resources are available compared to English. Materials …

Maverick: Efficient and accurate coreference resolution defying recent trends

G Martinelli, E Barba, R Navigli - arxiv preprint arxiv:2407.21489, 2024 - arxiv.org
Large autoregressive generative models have emerged as the cornerstone for achieving the
highest performance across several Natural Language Processing tasks. However, the urge …

CoRTEx: contrastive learning for representing terms via explanations with applications on constructing biomedical knowledge graphs

H Ying, Z Zhao, Y Zhao, S Zeng… - Journal of the American …, 2024 - academic.oup.com
Abstract Objectives Biomedical Knowledge Graphs play a pivotal role in various biomedical
research domains. Concurrently, term clustering emerges as a crucial step in constructing …

Multi-Source Soft Labeling and Hard Negative Sampling for Retrieval Distractor Ranking

J Wang, W Rong, J Bai, Z Sun… - IEEE Transactions on …, 2023 - ieeexplore.ieee.org
Multiple-choice questions (MCQs) are a kind of widely adopted approaches in learning
assessment. Recently, the automatic generation of MCQs has become a popular research …

Improving dual-encoder training through dynamic indexes for negative mining

N Monath, M Zaheer, K Allen… - … Conference on Artificial …, 2023 - proceedings.mlr.press
Dual encoder models are ubiquitous in modern classification and retrieval. Crucial for
training such dual encoders is an accurate estimation of gradients from the partition function …

BELHD: improving biomedical entity linking with homonym disambiguation

S Garda, U Leser - Bioinformatics, 2024 - academic.oup.com
Motivation Biomedical entity linking (BEL) is the task of grounding entity mentions to a given
knowledge base (KB). Recently, neural name-based methods, system identifying the most …

BioPRO: Context-Infused Prompt Learning for Biomedical Entity Linking

T Zhu, Y Qin, M Feng, Q Chen, B Hu… - IEEE/ACM Transactions …, 2023 - ieeexplore.ieee.org
Recent research tends to address the biomedical entity linking problem in a unified
framework solely based on surface form matching between mentions and entities …