Enriching contextualized language model from knowledge graph for biomedical information extraction

H Fei, Y Ren, Y Zhang, D Ji, X Liang - Briefings in bioinformatics, 2021 - academic.oup.com
Biomedical information extraction (BioIE) is an important task. The aim is to analyze
biomedical texts and extract structured information such as named entities and semantic …

A deep-learning system bridging molecule structure and biomedical text with comprehension comparable to human professionals

Z Zeng, Y Yao, Z Liu, M Sun - Nature communications, 2022 - nature.com
To accelerate biomedical research process, deep-learning systems are developed to
automatically acquire knowledge about molecule entities by reading large-scale biomedical …

A survey of event extraction from text

W Xiang, B Wang - IEEE Access, 2019 - ieeexplore.ieee.org
Numerous important events happen everyday and everywhere but are reported in different
media sources with different narrative styles. How to detect whether real-world events have …

Text2mol: Cross-modal molecule retrieval with natural language queries

C Edwards, CX Zhai, H Ji - … of the 2021 Conference on Empirical …, 2021 - aclanthology.org
We propose a new task, Text2Mol, to retrieve molecules using natural language descriptions
as queries. Natural language and molecules encode information in very different ways …

COVID-19 literature knowledge graph construction and drug repurposing report generation

Q Wang, M Li, X Wang, N Parulian, G Han, J Ma… - arXiv preprint arXiv …, 2020 - arxiv.org
To combat COVID-19, both clinicians and scientists need to digest vast amounts of relevant
biomedical knowledge in scientific literature to understand the disease mechanism and …

A survey on deep learning event extraction: Approaches and applications

Q Li, J Li, J Sheng, S Cui, J Wu, Y Hei… - … on Neural Networks …, 2022 - ieeexplore.ieee.org
Event extraction (EE) is a crucial research task for promptly apprehending event information
from massive textual data. With the rapid development of deep learning, EE based on deep …

[PDF][PDF] Abstract meaning representation guided graph encoding and decoding for joint information extraction

Z Zhang, H Ji - Proc. The 2021 Conference of the North American …, 2021 - par.nsf.gov
Abstract The tasks of Rich Semantic Parsing, such as Abstract Meaning Representation
(AMR), share similar goals with Information Extraction (IE) to convert natural language texts …

Joint biomedical entity and relation extraction with knowledge-enhanced collective inference

T Lai, H Ji, CX Zhai, QH Tran - arXiv preprint arXiv:2105.13456, 2021 - arxiv.org
Compared to the general news domain, information extraction (IE) from biomedical text
requires much broader domain knowledge. However, many previous IE methods do not …

Named entity recognition in Spanish biomedical literature: Short review and BERT model

L Akhtyamova - 2020 26th Conference of Open Innovations …, 2020 - ieeexplore.ieee.org
Entity Recognition (NER) is the first step for knowledge acquisition when we deal with an
unknown corpus of texts. Having received these entities, we have an opportunity to form …

Biomedical event extraction with hierarchical knowledge graphs

KH Huang, M Yang, N Peng - arXiv preprint arXiv:2009.09335, 2020 - arxiv.org
Biomedical event extraction is critical in understanding biomolecular interactions described
in scientific corpus. One of the main challenges is to identify nested structured events that …