Related papers: Knowledge-Rich Self-Supervision for Biomedical Ent…

Entity linking (EL) is the process of linking entity mentions appearing in text with their corresponding entities in a knowledge base. EL features of entities (e.g., prior probability, relatedness score, and entity embedding) are usually…

Contextual word embedding models, such as BioBERT and Bio_ClinicalBERT, have achieved state-of-the-art results in biomedical natural language processing tasks by focusing their pre-training process on domain-specific corpora. However, such…

We introduce ReFinED, an efficient end-to-end entity linking model which uses fine-grained entity types and entity descriptions to perform linking. The model performs mention detection, fine-grained entity typing, and entity disambiguation…

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)…

Entity linking (EL) is the task of automatically identifying entity mentions in text and resolving them to a corresponding entity in a reference knowledge base like Wikipedia. Throughout the past decade, a plethora of EL systems and…

Supervised named entity recognition (NER) in the biomedical domain depends on large sets of annotated texts with the given named entities. The creation of such datasets can be time-consuming and expensive, while extraction of new entities…

Accurate entity linkers have been produced for domains and languages where annotated data (i.e., texts linked to a knowledge base) is available. However, little progress has been made for the settings where no or very limited amounts of…

Generative pre-trained transformer (GPT) models have shown promise in clinical entity and relation extraction tasks because of their precise extraction and contextual understanding capability. In this work, we further leverage the Unified…

A typical architecture for end-to-end entity linking systems consists of three steps: mention detection, candidate generation and entity disambiguation. In this study we investigate the following questions: (a) Can all those steps be…

Medical entity span extraction and linking are critical steps for many healthcare NLP tasks. Most existing entity extraction methods either have a fixed vocabulary of medical entities or require span annotations. In this paper, we propose a…

Detection and disambiguation of all entities in text is a crucial task for a wide range of applications. The typical formulation of the problem involves two stages: detect mention boundaries and link all mentions to a knowledge base. For a…

Zero-shot named entity recognition (NER) is the task of detecting named entities of specific types (such as 'Person' or 'Medicine') without any training examples. Current research increasingly relies on large synthetic datasets,…

Entity alignment, aiming to identify equivalent entities across different knowledge graphs (KGs), is a fundamental problem for constructing large-scale KGs. Over the course of its development, supervision has been considered necessary for…

When comparing entities extracted by a medical entity recognition system with gold standard annotations over a test set, two types of mismatches might occur, label mismatch or span mismatch. Here we focus on span mismatch and show that its…

Entity linking involves aligning textual mentions of named entities to their corresponding entries in a knowledge base. Entity linking systems often exploit relations between textual mentions in a document (e.g., coreference) to decide if…

Contextual word representations, typically trained on unstructured, unlabeled text, do not contain any explicit grounding to real world entities and are often unable to remember facts about those entities. We propose a general method to…

Entity alignment (EA) aims to discover the equivalent entities in different knowledge graphs (KGs). It is a pivotal step for integrating KGs to increase knowledge coverage and quality. Recent years have witnessed a rapid increase of EA…

We introduce the STEM (Science, Technology, Engineering, and Medicine) Dataset for Scientific Entity Extraction, Classification, and Resolution, version 1.0 (STEM-ECR v1.0). The STEM-ECR v1.0 dataset has been developed to provide a…

Cross-lingual biomedical entity linking (BEL) maps mentions in any language to unique identifiers in a biomedical knowledge base (KB), supporting clinical and biomedical NLP applications. However, expert-annotated training data for BEL are…

Zero-shot entity and relation classification models leverage available external information of unseen classes -- e.g., textual descriptions -- to annotate input text data. Thanks to the minimum data requirement, Zero-Shot Learning (ZSL)…