Related papers: EMBRE: Entity-aware Masking for Biomedical Relatio…

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…

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…

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…

The surging amount of biomedical literature & digital clinical records presents a growing need for text mining techniques that can not only identify but also semantically relate entities in unstructured data. In this paper we propose a text…

Document-level relation extraction is a challenging task which requires reasoning over multiple sentences in order to predict relations in a document. In this paper, we pro-pose a joint training frameworkE2GRE(Entity and Evidence Guided…

Automated relation extraction (RE) from biomedical literature is critical for many downstream text mining applications in both research and real-world settings. However, most existing benchmarking datasets for bio-medical RE only focus on…

Document-level relation extraction aims to extract relations among entities within a document. Compared with its sentence-level counterpart, Document-level relation extraction requires inference over multiple sentences to extract complex…

Large language models (LLMs) have demonstrated dominating performance in many NLP tasks, especially on generative tasks. However, they often fall short in some information extraction tasks, particularly those requiring domain-specific…

Multi-modal named entity recognition (NER) and relation extraction (RE) aim to leverage relevant image information to improve the performance of NER and RE. Most existing efforts largely focused on directly extracting potentially useful…

Named Entity Recognition (NER) and Relation Extraction (RE) are essential tools in distilling knowledge from biomedical literature. This paper presents our findings from participating in BioNLP Shared Tasks 2019. We addressed Named Entity…

In this study, a novel method for extracting named entities and relations from unstructured text based on the table representation is presented. By using contextualized word embeddings, the proposed method computes representations for…

Biological relation networks contain rich information for understanding the biological mechanisms behind the relationship of entities such as genes, proteins, diseases, and chemicals. The vast growth of biomedical literature poses…

Pre-trained language models induce dense entity representations that offer strong performance on entity-centric NLP tasks, but such representations are not immediately interpretable. This can be a barrier to model uptake in important…

We present a weakly-supervised data augmentation approach to improve Named Entity Recognition (NER) in a challenging domain: extracting biomedical entities (e.g., proteins) from the scientific literature. First, we train a neural NER (NNER)…

Multimodal named entity recognition (MNER) and multimodal relation extraction (MRE) are two fundamental subtasks in the multimodal knowledge graph construction task. However, the existing methods usually handle two tasks independently,…

Biomedical named entity recognition (BNER) serves as the foundation for numerous biomedical text mining tasks. Unlike general NER, BNER require a comprehensive grasp of the domain, and incorporating external knowledge beyond training data…

Entity and relation extraction is a key task in information extraction, where the output can be used for downstream NLP tasks. Existing approaches for entity and relation extraction tasks mainly focus on the English corpora and ignore other…

Biomedical entity linking and event extraction are two crucial tasks to support text understanding and retrieval in the biomedical domain. These two tasks intrinsically benefit each other: entity linking disambiguates the biomedical…

Named entity recognition (NER) stands as a fundamental and pivotal task within the realm of Natural Language Processing. Particularly within the domain of Biomedical Method NER, this task presents notable challenges, stemming from the…

Understanding the meaning of text often involves reasoning about entities and their relationships. This requires identifying textual mentions of entities, linking them to a canonical concept, and discerning their relationships. These tasks…