Artificial Intelligence (AI) in Action: Addressing the COVID-19 Pandemic with Natural Language Processing (NLP)

no code implementations • 9 Oct 2020 • Qingyu Chen, Robert Leaman, Alexis Allot, Ling Luo, Chih-Hsuan Wei, Shankai Yan, Zhiyong Lu

The COVID-19 pandemic has had a significant impact on society, both because of the serious health effects of COVID-19 and because of public health measures implemented to slow its spread.

Emotion Recognition Information Retrieval +7

PhenoTagger: A Hybrid Method for Phenotype Concept Recognition using Human Phenotype Ontology

no code implementations • 17 Sep 2020 • Ling Luo, Shankai Yan, Po-Ting Lai, Daniel Veltri, Andrew Oler, Sandhya Xirasagar, Rajarshi Ghosh, Morgan Similuk, Peter N. Robinson, Zhiyong Lu

In this paper, we propose PhenoTagger, a hybrid method that combines both dictionary and machine learning-based methods to recognize Human Phenotype Ontology (HPO) concepts in unstructured biomedical text.

BIG-bench Machine Learning Sentence

BioConceptVec: creating and evaluating literature-based biomedical concept embeddings on a large scale

1 code implementation • 23 Dec 2019 • Qingyu Chen, Kyubum Lee, Shankai Yan, Sun Kim, Chih-Hsuan Wei, Zhiyong Lu

Capturing the semantics of related biological concepts, such as genes and mutations, is of significant importance to many research tasks in computational biology such as protein-protein interaction detection, gene-drug association prediction, and biomedical literature-based discovery.

Transfer Learning in Biomedical Natural Language Processing: An Evaluation of BERT and ELMo on Ten Benchmarking Datasets

4 code implementations • WS 2019 • Yifan Peng, Shankai Yan, Zhiyong Lu

Benchmarking Document Classification +7

Context awareness and embedding for biomedical event extraction

1 code implementation • 2 May 2019 • Shankai Yan, Ka-Chun Wong

We built our models on the datasets from BioNLP Shared Task for evaluations.

Event Detection Event Extraction +1