Related papers: Improving Biomedical Entity Linking with Retrieval…

Recognition of biomedical entities from literature is a challenging research focus, which is the foundation for extracting a large amount of biomedical knowledge existing in unstructured texts into structured formats. Using the sequence…

Pre-trained language models (PLMs) have proven to be effective for document re-ranking task. However, they lack the ability to fully interpret the semantics of biomedical and health-care queries and often rely on simplistic patterns for…

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…

We present BEEP (Biomedical Evidence-Enhanced Predictions), a novel approach for clinical outcome prediction that retrieves patient-specific medical literature and incorporates it into predictive models. Based on each individual patient's…

Due to the exponential growth of biomedical literature, event and relation extraction are important tasks in biomedical text mining. Most work only focus on relation extraction, and detect a single entity pair mention on a short span of…

Recent progress in large language models (LLMs) has leveraged their in-context learning (ICL) abilities to enable quick adaptation to unseen biomedical NLP tasks. By incorporating only a few input-output examples into prompts, LLMs can…

With the large and increasing volume of textual data, automated methods for identifying significant topics to classify textual documents have received a growing interest. While many efforts have been made in this direction, it still remains…

Named entity recognition (NER) is a widely applicable natural language processing task and building block of question answering, topic modeling, information retrieval, etc. In the medical domain, NER plays a crucial role by extracting…

Biomedical entity linking, a main component in automatic information extraction from health-related texts, plays a pivotal role in connecting textual entities (such as diseases, drugs and body parts mentioned by patients) to their…

Automated entity relation extraction (RE) from literature provides an important source for constructing biomedical database, which is more efficient and extensible than manual curation. However, existing RE models usually ignore the…

In the legal domain it is important to differentiate between words in general, and afterwards to link the occurrences of the same entities. The topic to solve these challenges is called Named-Entity Linking (NEL). Current supervised neural…

State-of-the-art studies have demonstrated the superiority of joint modelling over pipeline implementation for medical named entity recognition and normalization due to the mutual benefits between the two processes. To exploit these…

Multimodal Entity Linking (MEL) is the task of mapping mentions with multimodal contexts to the referent entities from a knowledge base. Existing MEL methods mainly focus on designing complex multimodal interaction mechanisms and require…

Most existing methods for biomedical entity recognition task rely on explicit feature engineering where many features either are specific to a particular task or depends on output of other existing NLP tools. Neural architectures have been…

We propose Medical Entity Definition-based Sentence Embedding (MED-SE), a novel unsupervised contrastive learning framework designed for clinical texts, which exploits the definitions of medical entities. To this end, we conduct an…

We propose yet another entity linking model (YELM) which links words to entities instead of spans. This overcomes any difficulties associated with the selection of good candidate mention spans and makes the joint training of mention…

Entity Linking (EL) seeks to align entity mentions in text to entries in a knowledge-base and is usually comprised of two phases: candidate generation and candidate ranking. While most methods focus on the latter, it is the candidate…

Knowledge graphs (KGs) are an important tool for representing complex relationships between entities in the biomedical domain. Several methods have been proposed for learning embeddings that can be used to predict new links in such graphs.…

Named Entity Recognition (NER) in biomedical domains faces challenges due to data scarcity and imbalanced label distributions, especially with fine-grained entity types. We propose ReProCon, a novel few-shot NER framework that combines…

Compared to the general news domain, information extraction (IE) from biomedical text requires much broader domain knowledge. However, many previous IE methods do not utilize any external knowledge during inference. Due to the exponential…