Related papers: Improving Biomedical Pretrained Language Models wi…

Knowledge enhanced pre-trained language models (K-PLMs) are shown to be effective for many public tasks in the literature but few of them have been successfully applied in practice. To address this problem, we propose K-AID, a systematic…

Named entity recognition is a key component of Information Extraction (IE), particularly in scientific domains such as biomedicine and chemistry, where large language models (LLMs), e.g., ChatGPT, fall short. We investigate the…

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…

The increasing depth of parametric domain knowledge in large language models (LLMs) is fueling their rapid deployment in real-world applications. Understanding model vulnerabilities in high-stakes and knowledge-intensive tasks is essential…

Knowledge-enhanced language representation learning has shown promising results across various knowledge-intensive NLP tasks. However, prior methods are limited in efficient utilization of multilingual knowledge graph (KG) data for language…

Biomedical Named Entity Recognition (NER) is a fundamental task of Biomedical Natural Language Processing for extracting relevant information from biomedical texts, such as clinical records, scientific publications, and electronic health…

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

Knowledge-enhanced pre-trained models for language representation have been shown to be more effective in knowledge base construction tasks (i.e.,~relation extraction) than language models such as BERT. These knowledge-enhanced language…

Drug repurposing is often framed as a candidate identification task, but existing approaches provide limited guidance for distinguishing biologically plausible candidates from historically well-connected ones. Here we introduce DrugKLM, a…

Language models (LMs) increasingly drive real-world applications that require world knowledge. However, the internal processes through which models turn data into representations of knowledge and beliefs about the world, are poorly…

Pre-trained language models (LMs) have become ubiquitous in solving various natural language processing (NLP) tasks. There has been increasing interest in what knowledge these LMs contain and how we can extract that knowledge, treating LMs…

How much knowledge do pretrained language models hold? Recent research observed that pretrained transformers are adept at modeling semantics but it is unclear to what degree they grasp human knowledge, or how to ensure they do so. In this…

As two important textual modalities in electronic health records (EHR), both structured data (clinical codes) and unstructured data (clinical narratives) have recently been increasingly applied to the healthcare domain. Most existing…

Motivation: State-of-the-art biomedical named entity recognition (BioNER) systems often require handcrafted features specific to each entity type, such as genes, chemicals and diseases. Although recent studies explored using neural network…

Using a language model (LM) pretrained on two languages with large monolingual data in order to initialize an unsupervised neural machine translation (UNMT) system yields state-of-the-art results. When limited data is available for one…

State of the art Named Entity Recognition (NER) models have achieved an impressive ability to extract common phrases from text that belong to labels such as location, organization, time, and person. However, typical NER systems that rely on…

Our work addresses the challenges of understanding tables. Existing methods often struggle with the unpredictable nature of table content, leading to a reliance on preprocessing and keyword matching. They also face limitations due to the…

The overwhelming amount of biomedical scientific texts calls for the development of effective language models able to tackle a wide range of biomedical natural language processing (NLP) tasks. The most recent dominant approaches are…

Progress in biomedical Named Entity Recognition (NER) and Entity Linking (EL) is currently hindered by a fragmented data landscape, a lack of resources for building explainable models, and the limitations of semantically-blind evaluation…

Named entity recognition (NER) and relation extraction (RE) are two important tasks in information extraction and retrieval (IE \& IR). Recent work has demonstrated that it is beneficial to learn these tasks jointly, which avoids the…