Related papers: Improving Biomedical Pretrained Language Models wi…

Pre-trained language representation models (PLMs) cannot well capture factual knowledge from text. In contrast, knowledge embedding (KE) methods can effectively represent the relational facts in knowledge graphs (KGs) with informative…

External knowledge,e.g., entities and entity descriptions, can help humans understand texts. Many works have been explored to include external knowledge in the pre-trained models. These methods, generally, design pre-training tasks and…

In this work, we consider the medical concept normalization problem, i.e., the problem of mapping a disease mention in free-form text to a concept in a controlled vocabulary, usually to the standard thesaurus in the Unified Medical Language…

Pretrained language models have been suggested as a possible alternative or complement to structured knowledge bases. However, this emerging LM-as-KB paradigm has so far only been considered in a very limited setting, which only allows…

In recent years, Large Language Models (LLMs) have demonstrated an impressive ability to encode knowledge during pre-training on large text corpora. They can leverage this knowledge for downstream tasks like question answering (QA), even in…

Concept bottleneck models (CBMs), which predict human-interpretable concepts (e.g., nucleus shapes in cell images) before predicting the final output (e.g., cell type), provide insights into the decision-making processes of the model.…

Entity Matching (EM) involves identifying different data representations referring to the same entity from multiple data sources and is typically formulated as a binary classification problem. It is a challenging problem in data integration…

Europe's healthcare systems require enhanced interoperability and digitalization, driving a demand for innovative solutions to process legacy clinical data. This paper presents the results of our project, which aims to leverage Large…

Pre-trained language models such as BERT have been a key ingredient to achieve state-of-the-art results on a variety of tasks in natural language processing and, more recently, also in information retrieval.Recent research even claims that…

Language models (LMs) are typically trained once on a large-scale corpus and used for years without being updated. However, in a dynamic world, new entities constantly arise. We propose a framework to analyze what LMs can infer about new…

Biomedical word sense disambiguation (WSD) is an important intermediate task in many natural language processing applications such as named entity recognition, syntactic parsing, and relation extraction. In this paper, we employ…

Recent advances in natural language processing (NLP) have been driven bypretrained language models like BERT, RoBERTa, T5, and GPT. Thesemodels excel at understanding complex texts, but biomedical literature, withits domain-specific…

As retrieval-augmented generation prevails in large language models, embedding models are becoming increasingly crucial. Despite the growing number of general embedding models, prior work often overlooks the critical role of training data…

Biomedical entity linking is the task of identifying mentions of biomedical concepts in text documents and mapping them to canonical entities in a target thesaurus. Recent advancements in entity linking using BERT-based models follow a…

Open Named Entity Recognition (NER), which involves identifying arbitrary types of entities from arbitrary domains, remains challenging for Large Language Models (LLMs). Recent studies suggest that fine-tuning LLMs on extensive NER data can…

The rapid advancement of large language models (LLMs) has opened new boundaries in the extraction and synthesis of medical knowledge, particularly within evidence synthesis. This paper reviews the state-of-the-art applications of LLMs in…

Large language models (LLMs) are increasingly recognized as valuable tools across the medical environment, supporting clinical, research, and administrative workflows. However, strict privacy and network security regulations in hospital…

Biomedical entity linking (EL) consists of named entity recognition (NER) and named entity disambiguation (NED). EL models are trained on corpora labeled by a predefined KB. However, it is a common scenario that only entities within a…

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…

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,…