Related papers: Improving Biomedical Entity Linking with Retrieval…

Automatic extraction of funding information from academic articles adds significant value to industry and research communities, such as tracking research outcomes by funding organizations, profiling researchers and universities based on the…

Biomedical event extraction is critical in understanding biomolecular interactions described in scientific corpus. One of the main challenges is to identify nested structured events that are associated with non-indicative trigger words. We…

In the field of language modeling, models augmented with retrieval components have emerged as a promising solution to address several challenges faced in the natural language processing (NLP) field, including knowledge grounding,…

Clinical trials (CTs) often fail due to inadequate patient recruitment. This paper tackles the challenges of CT retrieval by presenting an approach that addresses the patient-to-trials paradigm. Our approach involves two key components in a…

Learning relational tabular data has gained significant attention recently, but most studies focus on single tables, overlooking the potential of cross-table learning. Cross-table learning, especially in scenarios where tables lack shared…

Neural entity linking models are very powerful, but run the risk of overfitting to the domain they are trained in. For this problem, a domain is characterized not just by genre of text but even by factors as specific as the particular…

Automatic relationship extraction (RE) from biomedical literature is critical for managing the vast amount of scientific knowledge produced each year. In recent years, utilizing pre-trained language models (PLMs) has become the prevalent…

Cross-lingual named entity recognition (CrossNER) faces challenges stemming from uneven performance due to the scarcity of multilingual corpora, especially for non-English data. While prior efforts mainly focus on data-driven transfer…

Document-Level Biomedical Relation Extraction (Bio-RE) aims to identify relations between biomedical entities within extensive texts, serving as a crucial subfield of biomedical text mining. Existing Bio-RE methods struggle with…

The increasing amount of data on the Web, in particular of Linked Data, has led to a diverse landscape of datasets, which make entity retrieval a challenging task. Explicit cross-dataset links, for instance to indicate co-references or…

In this paper, we present our system for the BioNNE English track, which aims to extract 8 types of biomedical nested named entities from biomedical text. We use a large language model (Mixtral 8x7B instruct) and ScispaCy NER model to…

We consider the problem of Named Entity Recognition (NER) on biomedical scientific literature, and more specifically the genomic variants recognition in this work. Significant success has been achieved for NER on canonical tasks in recent…

Capturing sentence semantics plays a vital role in a range of text mining applications. Despite continuous efforts on the development of related datasets and models in the general domain, both datasets and models are limited in biomedical…

Biomedical named entities often play important roles in many biomedical text mining tools. However, due to the incompleteness of provided synonyms and numerous variations in their surface forms, normalization of biomedical entities is very…

Large Language Models (LLMs) have demonstrated impressive capabilities for generalizing in unseen tasks. In the Named Entity Recognition (NER) task, recent advancements have seen the remarkable improvement of LLMs in a broad range of entity…

Biomedical queries have become increasingly prevalent in web searches, reflecting the growing interest in accessing biomedical literature. Despite recent research on large-language models (LLMs) motivated by endeavours to attain generalized…

Motivation: Named Entity Recognition (NER) is a key task to support biomedical research. In Biomedical Named Entity Recognition (BioNER), obtaining high-quality expert annotated data is laborious and expensive, leading to the development of…

Natural language inference (NLI) is critical for complex decision-making in biomedical domain. One key question, for example, is whether a given biomedical mechanism is supported by experimental evidence. This can be seen as an NLI problem…

Retrieval-enhanced language models (LMs), which condition their predictions on text retrieved from large external datastores, have recently shown significant perplexity improvements compared to standard LMs. One such approach, the $k$NN-LM,…

Entity Linking (EL) is an essential task for semantic text understanding and information extraction. Popular methods separately address the Mention Detection (MD) and Entity Disambiguation (ED) stages of EL, without leveraging their mutual…