TaggerOne: joint named entity recognition and normalization with semi-Markov Models

R Leaman, Z Lu - Bioinformatics, 2016 - academic.oup.com
Motivation: Text mining is increasingly used to manage the accelerating pace of the
biomedical literature. Many text mining applications depend on accurate named entity …

D3NER: biomedical named entity recognition using CRF-biLSTM improved with fine-tuned embeddings of various linguistic information

TH Dang, HQ Le, TM Nguyen, ST Vu - Bioinformatics, 2018 - academic.oup.com
Motivation Recognition of biomedical named entities in the textual literature is a highly
challenging research topic with great interest, playing as the prerequisite for extracting huge …

[HTML][HTML] Improving biomedical named entity recognition with syntactic information

Y Tian, W Shen, Y Song, F Xia, M He, K Li - BMC bioinformatics, 2020 - Springer
Background Biomedical named entity recognition (BioNER) is an important task for
understanding biomedical texts, which can be challenging due to the lack of large-scale …

LPTK: a linguistic pattern-aware dependency tree kernel approach for the BioCreative VI CHEMPROT task

N Warikoo, YC Chang, WL Hsu - Database, 2018 - academic.oup.com
Identifying the interactions between chemical compounds and genes from biomedical
literatures is one of the frequently discussed topics of text mining in the life science field. In …

A knowledge-poor approach to chemical-disease relation extraction

F Alam, A Corazza, A Lavelli, R Zanoli - Database, 2016 - academic.oup.com
The article describes a knowledge-poor approach to the task of extracting Chemical-
Disease Relations from PubMed abstracts. A first version of the approach was applied …

Improving chemical-induced disease relation extraction with learned features based on convolutional neural network

HQ Le, DC Can, TH Dang, MV Tran… - … on Knowledge and …, 2017 - ieeexplore.ieee.org
There have been an increasing number of various machine learning-based models
successfully proposed and applied for automatic chemical-induced disease (CID) relation …

[HTML][HTML] RelSCAN–a system for extracting chemical-induced disease relation from biomedical literature

SC Onye, A Akkeleş, N Dimililer - Journal of Biomedical Informatics, 2018 - Elsevier
This paper proposes an effective and robust approach for Chemical-Induced Disease (CID)
relation extraction from PubMed articles. The study was performed on the Chemical Disease …

Distantly supervised end-to-end medical entity extraction from electronic health records with human-level quality

A Nesterov, D Umerenkov - arXiv preprint arXiv:2201.10463, 2022 - arxiv.org
Medical entity extraction (EE) is a standard procedure used as a first stage in medical texts
processing. Usually Medical EE is a two-step process: named entity recognition (NER) and …

Sieve-based coreference resolution enhances semi-supervised learning model for chemical-induced disease relation extraction

HQ Le, MV Tran, TH Dang, QT Ha, N Collier - Database, 2016 - academic.oup.com
The BioCreative V chemical-disease relation (CDR) track was proposed to accelerate the
progress of text mining in facilitating integrative understanding of chemicals, diseases and …

[PDF][PDF] Inferring implicit causal relationships in biomedical literature

H Kilicoglu - Proceedings of the 15th Workshop on Biomedical …, 2016 - aclanthology.org
Biomedical relations are often expressed between entities occurring within the same
sentence through syntactic means. However, a significant portion of such relations (in …