Related papers: Exploring Partial Knowledge Base Inference in Biom…

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…

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…

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…

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…

Biomedical named entity recognition (NER) and entity linking (EL) strongly depend on annotated corpora, but the utility of these resources for benchmarking is often assumed rather than characterized. We present a corpus-centric framework…

Knowledge Graphs have emerged as a compelling abstraction for capturing key relationship among the entities of interest to enterprises and for integrating data from heterogeneous sources. JPMorgan Chase (JPMC) is leading this trend by…

Here we present the training and evaluation of NanoNER, a Named Entity Recognition (NER) model for Nanobiology. NER consists in the identification of specific entities in spans of unstructured texts and is often a primary task in Natural…

Biomedical named entities often play important roles in many biomedical text mining tools. However, due to the incompleteness of provided synonyms and numerous variations in their surface forms, normalization of biomedical entities is very…

Biomedical named entity recognition (NER) is a critial task that aims to identify structured information in clinical text, which is often replete with complex, technical terms and a high degree of variability. Accurate and reliable NER can…

Pretrained language models have shown success in many natural language processing tasks. Many works explore incorporating knowledge into language models. In the biomedical domain, experts have taken decades of effort on building large-scale…

Current systems of fine-grained entity typing use distant supervision in conjunction with existing knowledge bases to assign categories (type labels) to entity mentions. However, the type labels so obtained from knowledge bases are often…

Developing high-performing systems for detecting biomedical named entities has major implications. State-of-the-art deep-learning based solutions for entity recognition often require large annotated datasets, which is not available in the…

In biomedical literature, it is common for entity boundaries to not align with word boundaries. Therefore, effective identification of entity spans requires approaches capable of considering tokens that are smaller than words. We introduce…

Entity linking (EL) is the task of disambiguating mentions in text by associating them with entries in a predefined database of mentions (persons, organizations, etc). Most previous EL research has focused mainly on one language, English,…

Accurate recognition of biomedical named entities is critical for medical information extraction and knowledge discovery. However, existing methods often struggle with nested entities, entity boundary ambiguity, and cross-lingual…

Entity disambiguation (ED) is the last step of entity linking (EL), when candidate entities are reranked according to the context they appear in. All datasets for training and evaluating models for EL consist of convenience samples, such as…

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…

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…

Biomedical entity linking is the task of linking entity mentions in a biomedical document to referent entities in a knowledge base. Recently, many BERT-based models have been introduced for the task. While these models have achieved…

Named Entity Recognition (NER) encounters the challenge of unbalanced labels, where certain entity types are overrepresented while others are underrepresented in real-world datasets. This imbalance can lead to biased models that perform…