NLP (Question Answering, Clinical NLP, Privacy-preserving NLP)

*: Equal Contributions

• CliniQG4QA: Generating Diverse Questions for Domain Adaptation of Clinical Question Answering
  Xiang Yue*, Frederick Zhang*, Ziyu Yao, Simon Lin, Huan Sun
  IEEE Internatinal Conference on Bioinformatics and Biomedicine 2021 (BIBM 2021)
  (Best Paper Award) [arXiv version] [Code]
  Poster Version in Machine Learning for Health Workshop at NeurIPS 2020
  

• COUGH: A Challenge Dataset and Models for COVID-19 FAQ Retrieval
  Frederick Zhang, Heming Sun, Xiang Yue, Simon Lin and Huan Sun
  The 2021 Conference on Empirical Methods in Natural Language Processing
  (EMNLP 2021, Short Paper)
  [Datasets]

• Differential Privacy for Text Analytics via Natural Text Sanitization
  Xiang Yue*, Minxin Du*, Tianhao Wang, Yaliang Li, Huan Sun and Sherman S. M. Chow
  The Joint Conference of the 59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing
  (ACL-IJCNLP 2021, Findings, Long Paper)
  

• Clinical Reading Comprehension: A Thorough Analysis of the emrQA Dataset
  Xiang Yue, Bernal Jimenez Gutierrez and Huan Sun
  The 58th Annual Meeting of the Association for Computational Linguistics (ACL 2020, long paper)
  [arXiv version] [Code] [Slides & Video]

• Clinical Phrase Mining with Language Models
  Kaushik Mani*, Xiang Yue*, Bernal Jimenez Gutierrez, Yungui Huang, Simon Lin, and Huan Sun
  IEEE Internatinal Conference on Bioinformatics and Biomedicine 2020 (BIBM 2020)
  [arXiv extended version] [Code]

• PHICON: Improving Generalization of Clinical Text De-identification Models via Data Augmentation
  Xiang Yue and Shuang Zhou
  The 3rd Clinical Natural Language Processing Workshop at EMNLP 2020
  [arXiv version] [Code]

• Practical Annotation Strategies for Question Answering Datasets
  Bernhard Kratzwald, Xiang Yue, Huan Sun and Stefan Feuerriegel
  arXiv Preprint
  

Data Mining (Graph Embedding, Graph Mining, Bioinformatics)

• Graph Embedding on Biomedical Networks: Methods, Applications, and Evaluations
  Xiang Yue, Zhen Wang, Jingong Huang, Srinivasan Parthasarathy, Soheil Moosavinasab, Yungui Huang, Simon M. Lin, Wen Zhang, Ping Zhang and Huan Sun
  Bioinformatics (Vol 36 Issue 4, 15 Feb 2020, Page 1241-1251) (Impact Factor: 4.531)
  (ESI Highly Cited Paper: top 1% cited paper of its academic field)
  [arXiv version] [Code & Datasets]

• Tensor decomposition with relational constraints for predicting multiple types of microRNA-disease associations
  Feng Huang*, Xiang Yue*, Zhankun Xiong, Zhouxin Yu, Shichao Liu, Wen Zhang
  Briefings in Bioinformatics (Impact Factor: 8.990)
  [arXiv version] [Code&Datasets]

• SurfCon: Synonym Discovery on Privacy-Aware Clinical Data
  Zhen Wang, Xiang Yue, Soheil Moosavinasab, Yungui Huang, Simon Lin and Huan Sun
  The 25th ACM SIGKDD Conference on Knowledge Discovery and Data Mining 2019 (KDD 2019, research track, acceptance rate: ~110/~1200=9.2%, oral)
  [Code] | [Slides]

• SFPEL-LPI: Sequence-based Feature Projection Ensemble Learning for Predicting LncRNA-Protein Interactions
  Wen Zhang, Xiang Yue, Guifeng Tang, Wenjian Wu, Feng Huang, Xining Zhang
  PLOS Computational Biology (14 (12): e1006616) (Impact Factor: 4.428)
  Web Server | Suppl Proof | Code&Dataset

• Predicting drug-disease associations by using similarity constrained matrix factorization
  Wen Zhang, Xiang Yue, Weiran Lin, Wenjian Wu, Ruoqi Liu, Feng Huang, Feng Liu
  BMC Bioinformatics (2018 Vol 19:233)
  Web Server | Code&Datasets

• Predicting drug-disease associations and their therapeutic function based on the drug-disease association bipartite network
  Wen Zhang, Xiang Yue, Feng Huang, Ruoqi Liu, Yanlin Chen, Feng Huang, Chunyang Ruan
  Methods (2018 Vol 145:51-59)

---