Related papers: BIBERT-Pipe on Biomedical Nested Named Entity Link…

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…

Linking biomedical entities is an essential aspect in biomedical natural language processing tasks, such as text mining and question answering. However, a difficulty of linking the biomedical entities using current large language models…

Motivation: The proliferation of Biomedical research articles has made the task of information retrieval more important than ever. Scientists and Researchers are having difficulty in finding articles that contain information relevant to…

Pre-trained models such as BERT are widely used in NLP tasks and are fine-tuned to improve the performance of various NLP tasks consistently. Nevertheless, the fine-tuned BERT model trained on our protocol corpus still has a weak…

This paper describes the system proposed by Sabanc{\i} University Natural Language Processing Group in the SemEval-2022 MultiCoNER task. We developed an unsupervised entity linking pipeline that detects potential entity mentions with the…

Background: Finding biomedical named entities is one of the most essential tasks in biomedical text mining. Recently, deep learning-based approaches have been applied to biomedical named entity recognition (BioNER) and showed promising…

This technical report introduces a Named Clinical Entity Recognition Benchmark for evaluating language models in healthcare, addressing the crucial natural language processing (NLP) task of extracting structured information from clinical…

The delivery of appropriate targeted therapies to cancer patients requires the complete analysis of the molecular profiling of tumors and the patient's clinical characteristics in the context of existing knowledge and recent findings…

Biomedical named entity recognition (NER) presents unique challenges due to specialized vocabularies, the sheer volume of entities, and the continuous emergence of novel entities. Traditional NER models, constrained by fixed taxonomies and…

We explore the suitability of unsupervised representation learning methods on biomedical text -- BioBERT, SciBERT, and BioSentVec -- for biomedical question answering. To further improve unsupervised representations for biomedical QA, we…

Medical entity linking is the task of identifying and standardizing medical concepts referred to in an unstructured text. Most of the existing methods adopt a three-step approach of (1) detecting mentions, (2) generating a list of candidate…

Weak supervision has shown promising results in many natural language processing tasks, such as Named Entity Recognition (NER). Existing work mainly focuses on learning deep NER models only with weak supervision, i.e., without any human…

In this study, we investigate the potential of Large Language Models to complement biomedical knowledge graphs in the training of semantic models for the biomedical and clinical domains. Drawing on the wealth of the UMLS knowledge graph and…

Using language models (LMs) pre-trained in a self-supervised setting on large corpora and then fine-tuning for a downstream task has helped to deal with the problem of limited label data for supervised learning tasks such as Named Entity…

Named Entity Recognition (NER) and Entity Linking (EL) play an essential role in voice assistant interaction, but are challenging due to the special difficulties associated with spoken user queries. In this paper, we propose a novel…

Small and imbalanced datasets commonly seen in healthcare represent a challenge when training classifiers based on deep learning models. So motivated, we propose a novel framework based on BioBERT (Bidirectional Encoder Representations from…

Biomedical Named Entity Recognition (BioNER) is a crucial step for analyzing Biomedical texts, which aims at extracting biomedical named entities from a given text. Different supervised machine learning algorithms have been applied for…

Entity linking (EL) is the task of linking a textual mention to its corresponding entry in a knowledge base, and is critical for many knowledge-intensive NLP applications. When applied to tables in scientific papers, EL is a step toward…

Due to large number of entities in biomedical knowledge bases, only a small fraction of entities have corresponding labelled training data. This necessitates entity linking models which are able to link mentions of unseen entities using…

In this paper we tackle multilingual named entity recognition task. We use the BERT Language Model as embeddings with bidirectional recurrent network, attention, and NCRF on the top. We apply multilingual BERT only as embedder without any…