Related papers: BeLink: Biomedical Entity Linking Meets Generative…

SUMMARY: Recently, novel machine-learning algorithms have shown potential for predicting undiscovered links in biomedical knowledge networks. However, dedicated benchmarks for measuring algorithmic progress have not yet emerged. With…

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…

Linking biomedical entities is an essential aspect in biomedical natural language processing tasks, such as text mining and question answering. However, a difficulty of linking the biomedical entities using current large language models…

Generative models have become widely used in biomedical entity linking (BioEL) due to their excellent performance and efficient memory usage. However, these models are usually trained only with positive samples, i.e., entities that match…

Biomedical question-answering (QA) has gained increased attention for its capability to provide users with high-quality information from a vast scientific literature. Although an increasing number of biomedical QA datasets has been recently…

To enhance the performance of large language models (LLMs) in biomedical natural language processing (BioNLP) by introducing a domain-specific instruction dataset and examining its impact when combined with multi-task learning principles.…

Large Language Models (LLMs) have demonstrated impressive capabilities in creative tasks such as storytelling and E-mail generation. However, as LLMs are primarily trained on final text results rather than intermediate revisions, it might…

Large Language Models (LLMs) have demonstrated remarkable capabilities and have been extensively deployed across various domains, including recommender systems. Prior research has employed specialized \textit{prompts} to leverage the…

Large Language Models (LLMs) demonstrate remarkable versatility in various NLP tasks but encounter distinct challenges in biomedical due to the complexities of language and data scarcity. This paper investigates LLMs application in the…

Large Language Models (LLMs), particularly those similar to ChatGPT, have significantly influenced the field of Natural Language Processing (NLP). While these models excel in general language tasks, their performance in domain-specific…

Open-source large language models (LLMs) have gained significant strength across diverse fields. Nevertheless, the majority of studies primarily concentrate on English, with only limited exploration into the realm of multilingual abilities.…

Large Language Models (LLMs) can exhibit considerable variation in the quality of their sampled outputs. Reranking and selecting the best generation from the sampled set is a popular way of obtaining strong gains in generation quality. In…

Biomedical entity linking is the task of linking entity mentions in a biomedical document to referent entities in a knowledge base. Recently, many BERT-based models have been introduced for the task. While these models have achieved…

Reranking is fundamental to information retrieval and retrieval-augmented generation, with recent Large Language Models (LLMs) significantly advancing reranking quality. Most current works rely on large-scale LLMs (>7B parameters),…

Large language models (LLMs) have demonstrated impressive capabilities in natural language generation. However, their output quality can be inconsistent, posing challenges for generating natural language from logical forms (LFs). This task…

Reward Modeling is critical in evaluating and improving the generation of Large Language Models (LLMs). While numerous recent works have shown its feasibility in improving safety, helpfulness, reasoning, and instruction-following ability,…

Patient matching is the process of linking patients to appropriate clinical trials by accurately identifying and matching their medical records with trial eligibility criteria. We propose LLM-Match, a novel framework for patient matching…

Aligning terminological resources, including ontologies, controlled vocabularies, taxonomies, and value sets is a critical part of data integration in many domains such as healthcare, chemistry, and biomedical research. Entity mapping is…

Biomedical entity linking aims to map nonstandard entities to standard entities in a knowledge base. Traditional supervised methods perform well but require extensive annotated data to transfer, limiting their usage in low-resource…

Entity linking (EL) for biomedical text is typically benchmarked on English-only corpora with flat mentions, leaving the more realistic scenario of nested and multilingual mentions largely unexplored. We present our system for the BioNNE…