Sheng Yu

Publication Activity (10 Years)

Years Active: 2013-2024
Publications (10 Years): 43

Top Topics

Natural Language Processing

Diffusion Models

Relation Extraction

Electronic Medical Record

Top Venues

J. Biomed. Informatics

J. Am. Medical Informatics Assoc.

Publications

Hongyi Yuan, Songchi Zhou, Sheng Yu
EHRDiff : Exploring Realistic EHR Synthesis with Diffusion Models. Trans. Mach. Learn. Res. 2024 (2024)
Huaiyuan Ying, Sheng Yu
A Question Answering Based Pipeline for Comprehensive Chinese EHR Information Extraction. CoRR (2024)
Hongyi Yuan, Sheng Yu
Efficient symptom inquiring and diagnosis via adaptive alignment of reinforcement learning and classification. Artif. Intell. Medicine 148 (2024)
Hongyi Yuan, Songchi Zhou, Sheng Yu
EHRDiff: Exploring Realistic EHR Synthesis with Diffusion Models. CoRR (2023)
Songchi Zhou, Sheng Yu
High-throughput Biomedical Relation Extraction for Semi-Structured Web Articles Empowered by Large Language Models. CoRR (2023)
Zhengyun Zhao, Yichen Tian, Zheng Yuan, Peng Zhao, Feng Xia, Sheng Yu
A machine learning method for improving liver cancer staging. J. Biomed. Informatics 137 (2023)
Huaiyuan Ying, Zhengyun Zhao, Yang Zhao, Sihang Zeng, Sheng Yu
CoRTEx: Contrastive Learning for Representing Terms via Explanations with Applications on Constructing Biomedical Knowledge Graphs. CoRR (2023)
Yucong Lin, Keming Lu, Sheng Yu, Tianxi Cai, Marinka Zitnik
Multimodal learning on graphs for disease relation extraction. J. Biomed. Informatics 143 (2023)
Qiao Jin, Zheng Yuan, Guangzhi Xiong, Qianlan Yu, Huaiyuan Ying, Chuanqi Tan, Mosha Chen, Songfang Huang, Xiaozhong Liu, Sheng Yu
Biomedical Question Answering: A Survey of Approaches and Challenges. ACM Comput. Surv. 55 (2) (2023)
Keming Lu, Yuanren Tong, Si Yu, Yucong Lin, Yingyun Yang, Hui Xu, Yue Li, Sheng Yu
Building a trustworthy AI differential diagnosis application for Crohn's disease and intestinal tuberculosis. BMC Medical Informatics Decis. Mak. 23 (1) (2023)
Shengxuan Luo, Pengyu Cheng, Sheng Yu
Semi-constraint Optimal Transport for Entity Alignment with Dangling Cases. CoRR (2022)
Huaiyuan Ying, Shengxuan Luo, Tiantian Dang, Sheng Yu
Label Refinement via Contrastive Learning for Distantly-Supervised Named Entity Recognition. NAACL-HLT (Findings) (2022)
Hongyi Yuan, Zheng Yuan, Sheng Yu
Generative Biomedical Entity Linking via Knowledge Base-Guided Pre-training and Synonyms-Aware Fine-tuning. CoRR (2022)
Yucong Lin, Keming Lu, Sheng Yu, Tianxi Cai, Marinka Zitnik
Multimodal Learning on Graphs for Disease Relation Extraction. CoRR (2022)
Shengxuan Luo, Sheng Yu
An Accurate Unsupervised Method for Joint Entity Alignment and Dangling Entity Detection. CoRR (2022)
Sihang Zeng, Zheng Yuan, Sheng Yu
Automatic Biomedical Term Clustering by Learning Fine-grained Term Representations. CoRR (2022)
Sheng Yu, Zheng Yuan, Jun Xia, Shengxuan Luo, Huaiyuan Ying, Sihang Zeng, Jingyi Ren, Hongyi Yuan, Zhengyun Zhao, Yucong Lin, Keming Lu, Jing Wang, Yutao Xie, Heung-Yeung Shum
BIOS: An Algorithmically Generated Biomedical Knowledge Graph. CoRR (2022)
Hongyi Yuan, Zheng Yuan, Ruyi Gan, Jiaxing Zhang, Yutao Xie, Sheng Yu
BioBART: Pretraining and Evaluation of A Biomedical Generative Language Model. BioNLP@ACL (2022)
Sihang Zeng, Zheng Yuan, Sheng Yu
Automatic Biomedical Term Clustering by Learning Fine-grained Term Representations. BioNLP@ACL (2022)
Hongyi Yuan, Zheng Yuan, Ruyi Gan, Jiaxing Zhang, Yutao Xie, Sheng Yu
BioBART: Pretraining and Evaluation of A Biomedical Generative Language Model. CoRR (2022)
Shengxuan Luo, Sheng Yu
An Accurate Unsupervised Method for Joint Entity Alignment and Dangling Entity Detection. ACL (Findings) (2022)
Hongyi Yuan, Zheng Yuan, Sheng Yu
Generative Biomedical Entity Linking via Knowledge Base-Guided Pre-training and Synonyms-Aware Fine-tuning. NAACL-HLT (2022)
Zhengyun Zhao, Qiao Jin, Sheng Yu
PMC-Patients: A Large-scale Dataset of Patient Notes and Relations Extracted from Case Reports in PubMed Central. CoRR (2022)
Zheng Yuan, Zhengyun Zhao, Haixia Sun, Jiao Li, Fei Wang, Sheng Yu
CODER: Knowledge-infused cross-lingual medical term embedding for term normalization. J. Biomed. Informatics 126 (2022)
Jiaqi Guan, Runzhe Li, Sheng Yu, Xuegong Zhang
A Method for Generating Synthetic Electronic Medical Record Text. IEEE ACM Trans. Comput. Biol. Bioinform. 18 (1) (2021)
Qiao Jin, Zheng Yuan, Guangzhi Xiong, Qianlan Yu, Chuanqi Tan, Mosha Chen, Songfang Huang, Xiaozhong Liu, Sheng Yu
Biomedical Question Answering: A Comprehensive Review. CoRR (2021)
Zheng Yuan, Yuanhao Liu, Qiuyang Yin, Boyao Li, Xiaobin Feng, Guoming Zhang, Sheng Yu
Unsupervised multi-granular Chinese word segmentation and term discovery via graph partition. J. Biomed. Informatics 110 (2020)
Yucong Lin, Yang Li, Keming Lu, Cheng Ma, Peng Zhao, Daiqi Gao, Zihao Fan, Zijie Cheng, Zheyu Wang, Sheng Yu
Long-distance disorder-disorder relation extraction with bootstrapped noisy data. J. Biomed. Informatics 109 (2020)
Yuanren Tong, Keming Lu, Yingyun Yang, Ji Li, Yucong Lin, Dong Wu, Aiming Yang, Yue Li, Sheng Yu, Jiaming Qian
Can natural language processing help differentiate inflammatory intestinal diseases in China? Models applying random forest and convolutional neural network approaches. BMC Medical Informatics Decis. Mak. 20 (1) (2020)
Aaron Sonabend W., Winston Cai, Yuri Ahuja, Ashwin N. Ananthakrishnan, Zongqi Xia, Sheng Yu, Chuan Hong
Automated ICD coding via unsupervised knowledge integration (UNITE). Int. J. Medical Informatics 139 (2020)
Zheng Yuan, Zhengyun Zhao, Sheng Yu
CODER: Knowledge infused cross-lingual medical term embedding for term normalization. CoRR (2020)
Yucong Lin, Keming Lu, Yulin Chen, Chuan Hong, Sheng Yu
High-throughput relation extraction algorithm development associating knowledge articles and electronic health records. CoRR (2020)
Wenxin Ning, Stephanie Chan, Andrew Beam, Ming Yu, Alon Geva, Katherine P. Liao, Mary Mullen, Kenneth D. Mandl, Isaac S. Kohane, Tianxi Cai, Sheng Yu
Feature extraction for phenotyping from semantic and knowledge resources. J. Biomed. Informatics 91 (2019)
Katherine P. Liao, Jiehuan Sun, Tianrun A. Cai, Nicholas B. Link, Chuan Hong, Jie Huang, Jennifer E. Huffman, Jessica L. Gronsbell, Yichi Zhang, Yuk-Lam Ho, Victor M. Castro, Vivian S. Gainer, Shawn N. Murphy, Christopher J. O'Donnell, J. Michael Gaziano, Kelly Cho, Peter Szolovits, Isaac S. Kohane, Sheng Yu
High-throughput multimodal automated phenotyping (MAP) with application to PheWAS. J. Am. Medical Informatics Assoc. 26 (11) (2019)
Yucong Lin, Cheng Ma, Daiqi Gao, Zihao Fan, Zijie Cheng, Zheyu Wang, Sheng Yu
Long distance entity relation extraction with article structure embedding and applied to mining medical knowledge. ICHI (2019)
Jiaqi Guan, Runzhe Li, Sheng Yu, Xuegong Zhang
Generation of Synthetic Electronic Medical Record Text. CoRR (2018)
Yuanhao Liu, Sheng Yu
Word Segmentation as Graph Partition. CoRR (2018)
Katherine P. Liao, Jiehuan Sun, Tianrun A. Cai, Nicholas B. Link, Chuan Hong, Jie Huang, Jennifer E. Huffman, Jessica L. Gronsbell, Lauren Costa, Victor M. Castro, Vivian S. Gainer, Shawn N. Murphy, J. Michael Gaziano, Kelly Cho, Peter Szolovits, Isaac S. Kohane, Sheng Yu, Tianxi Cai
High-Throughput Multimodal Automated Phenotyping (MAP) Incorporating Natural Language Processing with Application to PheWAS. AMIA (2018)
Sheng Yu, 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
Enabling phenotypic big data with PheNorm. J. Am. Medical Informatics Assoc. 25 (1) (2018)
Jennifer A. Sinnott, Fiona Cai, Sheng Yu, Boris P. Hejblum, Chuan Hong, Isaac S. Kohane, Katherine P. Liao
PheProb: probabilistic phenotyping using diagnosis codes to improve power for genetic association studies. J. Am. Medical Informatics Assoc. 25 (10) (2018)
Jiaqi Guan, Runzhe Li, Sheng Yu, Xuegong Zhang
Generation of Synthetic Electronic Medical Record Text. BIBM (2018)
Sheng Yu, 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
Surrogate-assisted feature extraction for high-throughput phenotyping. J. Am. Medical Informatics Assoc. 24 (e1) (2017)
Sheng Yu, 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
High-throughput Phenotyping via Denoised Normal Mixture Transformation. AMIA (2017)
Shawn N. Murphy, Vivian S. Gainer, Victor M. Castro, Alyssa P. Goodson, Lori C. Phillips, Sheng Yu, Tianxi Cai
Computable Phenotypes enabled by the i2b2 Validation Platform. AMIA (2015)
Uri Kartoun, Vishesh Kumar, Su-Chun Cheng, Sheng Yu, Katherine P. Liao, Elizabeth W. Karlson, Ashwin N. Ananthakrishnan, Zongqi Xia, Vivian S. Gainer, Andrew Cagan, Guergana Savova, Pei J. Chen, Shawn N. Murphy, Susanne E. Churchill, Isaac S. Kohane, Peter Szolovits, Tianxi Cai, Stanley Y. Shaw
Demonstrating the Advantages of Applying Data Mining Techniques on Time-Dependent Electronic Medical Records. AMIA (2015)
Sheng Yu, Katherine P. Liao, Stanley Y. Shaw, Vivian S. Gainer, Susanne E. Churchill, Peter Szolovits, Shawn N. Murphy, Isaac S. Kohane, Tianxi Cai
Toward high-throughput phenotyping: unbiased automated feature extraction and selection from knowledge sources. J. Am. Medical Informatics Assoc. 22 (5) (2015)
Sheng Yu, Kanako K. Kumamaru, Elizabeth George, Ruth M. Dunne, Arash Bedayat, Matey Neykov, Andetta R. Hunsaker, Karin E. Dill, Tianxi Cai, Frank J. Rybicki
Classification of CT pulmonary angiography reports by presence, chronicity, and location of pulmonary embolism with natural language processing. J. Biomed. Informatics 52 (2014)
Sheng Yu, Tianxi Cai
A Short Introduction to MiniNLP. CoRR (2013)