Opportunities and obstacles for deep learning in biology and medicine

T Ching, DS Himmelstein… - Journal of the …, 2018 - royalsocietypublishing.org
Deep learning describes a class of machine learning algorithms that are capable of
combining raw inputs into layers of intermediate features. These algorithms have recently …

A neural joint model for entity and relation extraction from biomedical text

F Li, M Zhang, G Fu, D Ji - BMC bioinformatics, 2017 - Springer
Background Extracting biomedical entities and their relations from text has important
applications on biomedical research. Previous work primarily utilized feature-based pipeline …

A rule-based named-entity recognition method for knowledge extraction of evidence-based dietary recommendations

T Eftimov, B Koroušić Seljak, P Korošec - PloS one, 2017 - journals.plos.org
Evidence-based dietary information represented as unstructured text is a crucial information
that needs to be accessed in order to help dietitians follow the new knowledge arrives daily …

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 …

Neural relation extraction within and across sentence boundaries

P Gupta, S Rajaram, H Schütze… - Proceedings of the AAAI …, 2019 - ojs.aaai.org
Past work in relation extraction mostly focuses on binary relation between entity pairs within
single sentence. Recently, the NLP community has gained interest in relation extraction in …

STRING-ing together protein complexes: corpus and methods for extracting physical protein interactions from the biomedical literature

F Mehryary, K Nastou, T Ohta, LJ Jensen… - …, 2024 - academic.oup.com
Motivation Understanding biological processes relies heavily on curated knowledge of
physical interactions between proteins. Yet, a notable gap remains between the information …

RegulaTome: a corpus of typed, directed, and signed relations between biomedical entities in the scientific literature

K Nastou, F Mehryary, T Ohta, J Luoma, S Pyysalo… - Database, 2024 - academic.oup.com
In the field of biomedical text mining, the ability to extract relations from the literature is
crucial for advancing both theoretical research and practical applications. There is a notable …

Leveraging dependency forest for neural medical relation extraction

L Song, Y Zhang, D Gildea, M Yu, Z Wang… - arxiv preprint arxiv …, 2019 - arxiv.org
Medical relation extraction discovers relations between entity mentions in text, such as
research articles. For this task, dependency syntax has been recognized as a crucial source …

Novel event detection and classification for historical texts

R Sprugnoli, S Tonelli - Computational Linguistics, 2019 - direct.mit.edu
Event processing is an active area of research in the Natural Language Processing
community, but resources and automatic systems developed so far have mainly addressed …

Biomedical event extraction based on GRU integrating attention mechanism

L Li, J Wan, J Zheng, J Wang - Bmc Bioinformatics, 2018 - Springer
Background Biomedical event extraction is a crucial task in biomedical text mining. As the
primary forum for international evaluation of different biomedical event extraction …