Related papers: SynCABEL: Synthetic Contextualized Augmentation fo…

Biomedical entity linking maps textual mentions to concepts in structured knowledge bases such as UMLS or SNOMED CT. Most existing systems link each mention independently, using only the mention or its surrounding sentence. This ignores…

Large Language Models (LLMs) with extended context windows promise direct reasoning over long documents, reducing the need for chunking or retrieval. Constructing annotated resources for training and evaluation, however, remains costly.…

In Biomedical Natural Language Processing (BioNLP) tasks, such as Relation Extraction, Named Entity Recognition, and Text Classification, the scarcity of high-quality data remains a significant challenge. This limitation poisons large…

Cross-lingual biomedical entity linking (BEL) maps mentions in any language to unique identifiers in a biomedical knowledge base (KB), supporting clinical and biomedical NLP applications. However, expert-annotated training data for BEL are…

Label scarcity remains a major challenge in deep learning-based medical image segmentation. Recent studies use strong-weak pseudo supervision to leverage unlabeled data. However, performance is often hindered by inconsistencies between…

Supervised neural approaches are hindered by their dependence on large, meticulously annotated datasets, a requirement that is particularly cumbersome for sequential tasks. The quality of annotations tends to deteriorate with the transition…

We introduce and formalize the Synthetic Dataset Quality Estimation (SynQuE) problem: ranking synthetic datasets by their expected real-world task performance using only limited unannotated real data. This addresses a critical and open…

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…

The rise of In-Context Learning (ICL) for universal medical image segmentation has introduced an unprecedented demand for large-scale, diverse datasets for training, exacerbating the long-standing problem of data scarcity. While data…

Specialized entity linking (EL) models are well-trained at mapping mentions to unique knowledge base (KB) entities according to a given context. However, specialized EL models struggle to disambiguate long-tail entities due to their limited…

Sentence embedding tasks are important in natural language processing (NLP), but improving their performance while keeping them reliable is still hard. This paper presents a framework that combines pseudo-label generation and model ensemble…

Automated requirement-to-code traceability link recovery, essential for industrial system quality and safety, is critically hindered by the scarcity of labeled data. To address this bottleneck, this paper proposes and validates a…

Longitudinal health agents must reason across multi-source trajectories that combine continuous device streams, sparse clinical exams, and episodic life events - yet evaluating them is hard: real-world data cannot be released at scale, and…

Database research and the development of learned query optimisers rely heavily on realistic SQL workloads. Acquiring real-world queries is increasingly difficult, however, due to strict privacy regulations, and publicly released anonymised…

Biomedical entity linking (BEL) is the task of grounding entity mentions to a knowledge base. It plays a vital role in information extraction pipelines for the life sciences literature. We review recent work in the field and find that, as…

Biomedical named entity recognition is one of the core tasks in biomedical natural language processing (BioNLP). To tackle this task, numerous supervised/distantly supervised approaches have been proposed. Despite their remarkable success,…

We introduce GENomic Encoding REpresentation with Language Model (GENEREL), a framework designed to bridge genetic and biomedical knowledge bases. What sets GENEREL apart is its ability to fine-tune language models to infuse biological…

Injecting external domain-specific knowledge (e.g., UMLS) into pretrained language models (LMs) advances their capability to handle specialised in-domain tasks such as biomedical entity linking (BEL). However, such abundant expert knowledge…

Entity Linking is the task of matching a mention to an entity in a given knowledge base (KB). It contributes to annotating a massive amount of documents existing on the Web to harness new facts about their matched entities. However,…

Synthetic data, an appealing alternative to extensive expert-annotated data for medical image segmentation, consistently fails to improve segmentation performance despite its visual realism. The reason being that synthetic and real medical…