A Short Introduction to MiniNLP. - Sheng Yu 002; Tianxi Cai (CoRR, 2013)

Classification of CT pulmonary angiography reports by presence, chronicity, and location of pulmonary embolism with natural language processing. - Sheng Yu 002; Kanako K. Kumamaru; Elizabeth George; Ruth M. Dunne; Arash Bedayat; Matey Neykov; Andetta R. Hunsaker; Karin E. Dill; Tianxi Cai; Frank J. Rybicki (J. Biomed. Informatics, 2014)

Demonstrating the Advantages of Applying Data Mining Techniques on Time-Dependent Electronic Medical Records. - Uri Kartoun; Vishesh Kumar; Su-Chun Cheng; Sheng Yu 002; Katherine P. Liao; Elizabeth W. Karlson; Ashwin N. Ananthakrishnan; Zongqi Xia; Vivian S. Gainer; Andrew Cagan; Guergana Savova; Pei J. Chen; et al. (AMIA, 2015)

Computable Phenotypes enabled by the i2b2 Validation Platform. - Shawn N. Murphy; Vivian S. Gainer; Victor M. Castro; Alyssa P. Goodson; Lori C. Phillips; Sheng Yu 002; Tianxi Cai (AMIA, 2015)

Toward high-throughput phenotyping: unbiased automated feature extraction and selection from knowledge sources. - Sheng Yu 002; Katherine P. Liao; Stanley Y. Shaw; Vivian S. Gainer; Susanne E. Churchill; Peter Szolovits; Shawn N. Murphy; Isaac S. Kohane; Tianxi Cai (J. Am. Medical Informatics Assoc., 2015)

High-throughput Phenotyping via Denoised Normal Mixture Transformation. - Sheng Yu 002; Yumeng Ma; Jessica L. Gronsbell; Katherine P. Liao; Tianrun A. Cai; Ashwin N. Ananthakrishnan; Vivian S. Gainer; Susanne E. Churchill; Peter Szolovits; Shawn N. Murphy; Isaac S. Kohane; Tianxi Cai (AMIA, 2017)

Surrogate-assisted feature extraction for high-throughput phenotyping. - Sheng Yu 002; Abhishek Chakrabortty; Katherine P. Liao; Tianrun A. Cai; Ashwin N. Ananthakrishnan; Vivian S. Gainer; Susanne E. Churchill; Peter Szolovits; Shawn N. Murphy; Isaac S. Kohane; Tianxi Cai (J. Am. Medical Informatics Assoc., 2017)

High-Throughput Multimodal Automated Phenotyping (MAP) Incorporating Natural Language Processing with Application to PheWAS. - Katherine P. Liao; Jiehuan Sun; Tianrun A. Cai; Nicholas B. Link; Chuan Hong; Jie Huang 030; Jennifer E. Huffman; Jessica L. Gronsbell; Lauren Costa; Victor M. Castro; Vivian S. Gainer; Shawn N. Murphy; et al. (AMIA, 2018)

Generation of Synthetic Electronic Medical Record Text. - Jiaqi Guan; Runzhe Li; Sheng Yu 002; Xuegong Zhang (BIBM, 2018)

Word Segmentation as Graph Partition. - Yuanhao Liu; Sheng Yu 002 (CoRR, 2018)

PheProb: probabilistic phenotyping using diagnosis codes to improve power for genetic association studies. - Jennifer A. Sinnott; Fiona Cai; Sheng Yu 002; Boris P. Hejblum; Chuan Hong; Isaac S. Kohane; Katherine P. Liao (J. Am. Medical Informatics Assoc., 2018)

Enabling phenotypic big data with PheNorm. - Sheng Yu 002; Yumeng Ma; Jessica L. Gronsbell; Tianrun A. Cai; Ashwin N. Ananthakrishnan; Vivian S. Gainer; Susanne E. Churchill; Peter Szolovits; Shawn N. Murphy; Isaac S. Kohane; Katherine P. Liao; Tianxi Cai (J. Am. Medical Informatics Assoc., 2018)

Long distance entity relation extraction with article structure embedding and applied to mining medical knowledge. - Yucong Lin; Cheng Ma; Daiqi Gao; Zihao Fan; Zijie Cheng; Zheyu Wang; Sheng Yu 002 (ICHI, 2019)

High-throughput multimodal automated phenotyping (MAP) with application to PheWAS. - Katherine P. Liao; Jiehuan Sun; Tianrun A. Cai; Nicholas B. Link; Chuan Hong; Jie Huang 030; Jennifer E. Huffman; Jessica L. Gronsbell; Yichi Zhang; Yuk-Lam Ho; Victor M. Castro; Vivian S. Gainer; et al. (J. Am. Medical Informatics Assoc., 2019)

Feature extraction for phenotyping from semantic and knowledge resources. - Wenxin Ning; Stephanie Chan 002; Andrew Beam; Ming Yu 003; Alon Geva; Katherine P. Liao; Mary Mullen; Kenneth D. Mandl; Isaac S. Kohane; Tianxi Cai; Sheng Yu 002 (J. Biomed. Informatics, 2019)

High-throughput relation extraction algorithm development associating knowledge articles and electronic health records. - Yucong Lin; Keming Lu; Yulin Chen; Chuan Hong; Sheng Yu 002 (CoRR, 2020)

CODER: Knowledge infused cross-lingual medical term embedding for term normalization. - Zheng Yuan 002; Zhengyun Zhao; Sheng Yu 002 (CoRR, 2020)

Automated ICD coding via unsupervised knowledge integration (UNITE). - Aaron Sonabend W.; Winston Cai; Yuri Ahuja; Ashwin N. Ananthakrishnan; Zongqi Xia; Sheng Yu 002; Chuan Hong (Int. J. Medical Informatics, 2020)

Developing an automated mechanism to identify medical articles from wikipedia for knowledge extraction. - Lishan Yu; Sheng Yu 002 (Int. J. Medical Informatics, 2020)

Long-distance disorder-disorder relation extraction with bootstrapped noisy data. - Yucong Lin; Yang Li; Keming Lu; Cheng Ma; Peng Zhao; Daiqi Gao; Zihao Fan; Zijie Cheng; Zheyu Wang; Sheng Yu 002 (J. Biomed. Informatics, 2020)

Unsupervised multi-granular Chinese word segmentation and term discovery via graph partition. - Zheng Yuan 002; Yuanhao Liu; Qiuyang Yin; Boyao Li; Xiaobin Feng; Guoming Zhang; Sheng Yu 002 (J. Biomed. Informatics, 2020)

Can natural language processing help differentiate inflammatory intestinal diseases in China? Models applying random forest and convolutional neural network approaches. - Yuanren Tong; Keming Lu; Yingyun Yang; Ji Li; Yucong Lin; Dong Wu; Aiming Yang; Yue Li; Sheng Yu 002; Jiaming Qian (BMC Medical Informatics Decis. Mak., 2020)

Biomedical Question Answering: A Comprehensive Review. - Qiao Jin 001; Zheng Yuan 002; Guangzhi Xiong; Qianlan Yu; Chuanqi Tan; Mosha Chen; Songfang Huang; Xiaozhong Liu; Sheng Yu 002 (CoRR, 2021)

Sentence Alignment with Parallel Documents Helps Biomedical Machine Translation. - Shengxuan Luo; Huaiyuan Ying; Sheng Yu 002 (CoRR, 2021)

A Method for Generating Synthetic Electronic Medical Record Text. - Jiaqi Guan; Runzhe Li; Sheng Yu 002; Xuegong Zhang (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

An Accurate Unsupervised Method for Joint Entity Alignment and Dangling Entity Detection. - Shengxuan Luo; Sheng Yu 002 (ACL (Findings), 2022)

BioBART: Pretraining and Evaluation of A Biomedical Generative Language Model. - Hongyi Yuan; Zheng Yuan 002; Ruyi Gan; Jiaxing Zhang 001; Yutao Xie; Sheng Yu 002 (BioNLP@ACL, 2022)

Automatic Biomedical Term Clustering by Learning Fine-grained Term Representations. - Sihang Zeng; Zheng Yuan 002; Sheng Yu 002 (BioNLP@ACL, 2022)

Label Refinement via Contrastive Learning for Distantly-Supervised Named Entity Recognition. - Huaiyuan Ying; Shengxuan Luo; Tiantian Dang; Sheng Yu 002 (NAACL-HLT (Findings), 2022)

Generative Biomedical Entity Linking via Knowledge Base-Guided Pre-training and Synonyms-Aware Fine-tuning. - Hongyi Yuan; Zheng Yuan 002; Sheng Yu 002 (NAACL-HLT, 2022)

PMC-Patients: A Large-scale Dataset of Patient Notes and Relations Extracted from Case Reports in PubMed Central. - Zhengyun Zhao; Qiao Jin 001; Sheng Yu 002 (CoRR, 2022)

Semi-constraint Optimal Transport for Entity Alignment with Dangling Cases. - Shengxuan Luo; Pengyu Cheng; Sheng Yu 002 (CoRR, 2022)

BIOS: An Algorithmically Generated Biomedical Knowledge Graph. - Sheng Yu 002; Zheng Yuan 002; Jun Xia; Shengxuan Luo; Huaiyuan Ying; Sihang Zeng; Jingyi Ren; Hongyi Yuan; Zhengyun Zhao; Yucong Lin; Keming Lu; Jing Wang; et al. (CoRR, 2022)

CODER: Knowledge-infused cross-lingual medical term embedding for term normalization. - Zheng Yuan 002; Zhengyun Zhao; Haixia Sun; Jiao Li 001; Fei Wang 001; Sheng Yu 002 (J. Biomed. Informatics, 2022)

High-throughput Biomedical Relation Extraction for Semi-Structured Web Articles Empowered by Large Language Models. - Songchi Zhou; Sheng Yu 002 (CoRR, 2023)

Biomedical Question Answering: A Survey of Approaches and Challenges. - Qiao Jin 001; Zheng Yuan 002; Guangzhi Xiong; Qianlan Yu; Huaiyuan Ying; Chuanqi Tan; Mosha Chen; Songfang Huang; Xiaozhong Liu; Sheng Yu 002 (ACM Comput. Surv., 2023)

Multimodal learning on graphs for disease relation extraction. - Yucong Lin; Keming Lu; Sheng Yu 002; Tianxi Cai; Marinka Zitnik (J. Biomed. Informatics, 2023)

A machine learning method for improving liver cancer staging. - Zhengyun Zhao; Yichen Tian; Zheng Yuan 002; Peng Zhao; Feng Xia 010; Sheng Yu 002 (J. Biomed. Informatics, 2023)

Building a trustworthy AI differential diagnosis application for Crohn's disease and intestinal tuberculosis. - Keming Lu; Yuanren Tong; Si Yu; Yucong Lin; Yingyun Yang; Hui Xu; Yue Li; Sheng Yu 002 (BMC Medical Informatics Decis. Mak., 2023)

Efficient symptom inquiring and diagnosis via adaptive alignment of reinforcement learning and classification. - Hongyi Yuan; Sheng Yu 002 (Artif. Intell. Medicine, 2024)

A Question Answering Based Pipeline for Comprehensive Chinese EHR Information Extraction. - Huaiyuan Ying; Sheng Yu 002 (CoRR, 2024)

CoRTEx: contrastive learning for representing terms via explanations with applications on constructing biomedical knowledge graphs. - Huaiyuan Ying; Zhengyun Zhao; Yang Zhao; Sihang Zeng; Sheng Yu 002 (J. Am. Medical Informatics Assoc., 2024)

EHRDiff : Exploring Realistic EHR Synthesis with Diffusion Models. - Hongyi Yuan; Songchi Zhou; Sheng Yu 002 (Trans. Mach. Learn. Res., 2024)

GENIE: Generative Note Information Extraction model for structuring EHR data. - Huaiyuan Ying; Hongyi Yuan; Jinsen Lu; Zitian Qu; Yang Zhao; Zhengyun Zhao; Isaac S. Kohane; Tianxi Cai; Sheng Yu 002 (CoRR, 2025)

Evaluating Entity Retrieval in Electronic Health Records: a Semantic Gap Perspective. - Zhengyun Zhao; Hongyi Yuan; Jingjing Liu; Haichao Chen; Huaiyuan Ying; Songchi Zhou; Sheng Yu 002 (CoRR, 2025)

DR.EHR: Dense Retrieval for Electronic Health Record with Knowledge Injection and Synthetic Data. - Zhengyun Zhao; Huaiyuan Ying; Yue Zhong; Sheng Yu 002 (CoRR, 2025)