Related papers: Efficient and Reliable Estimation of Named Entity …

Entity linking (EL) for biomedical text is typically benchmarked on English-only corpora with flat mentions, leaving the more realistic scenario of nested and multilingual mentions largely unexplored. We present our system for the BioNNE…

Identifying named entities such as a person, location or organization, in documents can highlight key information to readers. Training Named Entity Recognition (NER) models requires an annotated data set, which can be a time-consuming…

Entity Alignment (EA) aims to match equivalent entities across different Knowledge Graphs (KGs) and is an essential step of KG fusion. Current mainstream methods -- neural EA models -- rely on training with seed alignment, i.e., a set of…

Deep neural network models have recently achieved state-of-the-art performance gains in a variety of natural language processing (NLP) tasks (Young, Hazarika, Poria, & Cambria, 2017). However, these gains rely on the availability of large…

Nested named entity recognition identifies entities contained within other entities, but requires expensive multi-level annotation. While flat NER corpora exist abundantly, nested resources remain scarce. We investigate whether models can…

Clinical Named Entity Recognition (CNER) aims to automatically identity clinical terminologies in Electronic Health Records (EHRs), which is a fundamental and crucial step for clinical research. To train a high-performance model for CNER,…

Our objective in this study is to investigate the behavior of Boolean operators on combining annotation output from multiple Natural Language Processing (NLP) systems across multiple corpora and to assess how filtering by aggregation of…

Automatic medical image segmentation plays a critical role in scientific research and medical care. Existing high-performance deep learning methods typically rely on large training datasets with high-quality manual annotations, which are…

High-resolution mapping of cells and tissue structures provides a foundation for developing interpretable machine-learning models for computational pathology. Deep learning algorithms can provide accurate mappings given large numbers of…

Entity Linking is the task of matching a mention to an entity in a given knowledge base (KB). It contributes to annotating a massive amount of documents existing on the Web to harness new facts about their matched entities. However,…

This work investigates multiple approaches to Named Entity Recognition (NER) for text in Electronic Health Record (EHR) data. In particular, we look into the application of (i) rule-based, (ii) deep learning and (iii) transfer learning…

Biomedical entity linking (EL) consists of named entity recognition (NER) and named entity disambiguation (NED). EL models are trained on corpora labeled by a predefined KB. However, it is a common scenario that only entities within a…

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…

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…

This paper presents a simple and computationally efficient approach for entity linking (EL), compared with recurrent neural networks (RNNs) or convolutional neural networks (CNNs), by making use of feedforward neural networks (FFNNs) and…

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…

The processing of entities in natural language is essential to many medical NLP systems. Unfortunately, existing datasets vastly under-represent the entities required to model public health relevant texts such as health advice often found…

In the field of Natural Language Processing (NLP), Named Entity Recognition (NER) is recognized as a critical technology, employed across a wide array of applications. Traditional methodologies for annotating datasets for NER models are…

Biomedical entity linking maps textual mentions to concepts in structured knowledge bases such as UMLS or SNOMED CT. Most existing systems link each mention independently, using only the mention or its surrounding sentence. This ignores…

Electronic Health Records (EHRs) are digital records of patient information, often containing unstructured clinical text. Named Entity Recognition (NER) is essential in EHRs for extracting key medical entities like problems, tests, and…