Sheng Yu

57 papers Misc 4Journal 46Unranked 7
YearRankTypeTitle / Venue / Authors
2025 J jnl
DR.EHR: Dense Retrieval for Electronic Health Record with Knowledge Injection and Synthetic Data.
CoRR
Zhengyun Zhao, Huaiyuan Ying, Yue Zhong, Sheng Yu
2025 J jnl
Evaluating Entity Retrieval in Electronic Health Records: a Semantic Gap Perspective.
CoRR
Zhengyun Zhao, Hongyi Yuan, Jingjing Liu, Haichao Chen, Huaiyuan Ying, Songchi Zhou, Sheng Yu
2025 J jnl
GENIE: Generative Note Information Extraction model for structuring EHR data.
CoRR
Huaiyuan Ying, Hongyi Yuan, Jinsen Lu, Zitian Qu, Yang Zhao, Zhengyun Zhao, Isaac S. Kohane, Tianxi Cai, Sheng Yu
2025 J jnl
High-throughput biomedical relation extraction for semi-structured web articles empowered by large language models.
BMC Medical Informatics Decis. Mak.
Songchi Zhou, Sheng Yu
2024 J jnl
A Question Answering Based Pipeline for Comprehensive Chinese EHR Information Extraction.
CoRR
Huaiyuan Ying, Sheng Yu
2024 J jnl
Black-Box Segmentation of Electronic Medical Records.
CoRR
Hongyi Yuan, Sheng Yu
2024 J jnl
CoRTEx: contrastive learning for representing terms via explanations with applications on constructing biomedical knowledge graphs.
J. Am. Medical Informatics Assoc.
Huaiyuan Ying, Zhengyun Zhao, Yang Zhao, Sihang Zeng, Sheng Yu
2024 J jnl
EHRDiff : Exploring Realistic EHR Synthesis with Diffusion Models.
Trans. Mach. Learn. Res.
Hongyi Yuan, Songchi Zhou, Sheng Yu
2024 J jnl
Efficient symptom inquiring and diagnosis via adaptive alignment of reinforcement learning and classification.
Artif. Intell. Medicine
Hongyi Yuan, Sheng Yu
2023 J jnl
A machine learning method for improving liver cancer staging.
J. Biomed. Informatics
Zhengyun Zhao, Yichen Tian, Zheng Yuan, Peng Zhao, Feng Xia, Sheng Yu
2023 J jnl
Biomedical Question Answering: A Survey of Approaches and Challenges.
ACM Comput. Surv.
Qiao Jin, Zheng Yuan, Guangzhi Xiong, Qianlan Yu, Huaiyuan Ying, Chuanqi Tan, Mosha Chen, Songfang Huang, Xiaozhong Liu, Sheng Yu
2023 J jnl
Building a trustworthy AI differential diagnosis application for Crohn's disease and intestinal tuberculosis.
BMC Medical Informatics Decis. Mak.
Keming Lu, Yuanren Tong, Si Yu, Yucong Lin, Yingyun Yang, Hui Xu, Yue Li, Sheng Yu
2023 J jnl
CoRTEx: Contrastive Learning for Representing Terms via Explanations with Applications on Constructing Biomedical Knowledge Graphs.
CoRR
Huaiyuan Ying, Zhengyun Zhao, Yang Zhao, Sihang Zeng, Sheng Yu
2023 J jnl
EHRDiff: Exploring Realistic EHR Synthesis with Diffusion Models.
CoRR
Hongyi Yuan, Songchi Zhou, Sheng Yu
2023 J jnl
High-throughput Biomedical Relation Extraction for Semi-Structured Web Articles Empowered by Large Language Models.
CoRR
Songchi Zhou, Sheng Yu
2023 J jnl
Multimodal learning on graphs for disease relation extraction.
J. Biomed. Informatics
Yucong Lin, Keming Lu, Sheng Yu, Tianxi Cai, Marinka Zitnik
2022 — conf
An Accurate Unsupervised Method for Joint Entity Alignment and Dangling Entity Detection.
ACL (Findings)
Shengxuan Luo, Sheng Yu
2022 J jnl
An Accurate Unsupervised Method for Joint Entity Alignment and Dangling Entity Detection.
CoRR
Shengxuan Luo, Sheng Yu
2022 — conf
Automatic Biomedical Term Clustering by Learning Fine-grained Term Representations.
BioNLP@ACL
Sihang Zeng, Zheng Yuan, Sheng Yu
2022 J jnl
Automatic Biomedical Term Clustering by Learning Fine-grained Term Representations.
CoRR
Sihang Zeng, Zheng Yuan, Sheng Yu
2022 J jnl
BIOS: An Algorithmically Generated Biomedical Knowledge Graph.
CoRR
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
2022 — conf
BioBART: Pretraining and Evaluation of A Biomedical Generative Language Model.
BioNLP@ACL
Hongyi Yuan, Zheng Yuan, Ruyi Gan, Jiaxing Zhang, Yutao Xie, Sheng Yu
2022 J jnl
BioBART: Pretraining and Evaluation of A Biomedical Generative Language Model.
CoRR
Hongyi Yuan, Zheng Yuan, Ruyi Gan, Jiaxing Zhang, Yutao Xie, Sheng Yu
2022 J jnl
CODER: Knowledge-infused cross-lingual medical term embedding for term normalization.
J. Biomed. Informatics
Zheng Yuan, Zhengyun Zhao, Haixia Sun, Jiao Li, Fei Wang, Sheng Yu
2022 — conf
Generative Biomedical Entity Linking via Knowledge Base-Guided Pre-training and Synonyms-Aware Fine-tuning.
NAACL-HLT
Hongyi Yuan, Zheng Yuan, Sheng Yu
2022 J jnl
Generative Biomedical Entity Linking via Knowledge Base-Guided Pre-training and Synonyms-Aware Fine-tuning.
CoRR
Hongyi Yuan, Zheng Yuan, Sheng Yu
2022 — conf
Label Refinement via Contrastive Learning for Distantly-Supervised Named Entity Recognition.
NAACL-HLT (Findings)
Huaiyuan Ying, Shengxuan Luo, TianTian Dang, Sheng Yu
2022 J jnl
Multimodal Learning on Graphs for Disease Relation Extraction.
CoRR
Yucong Lin, Keming Lu, Sheng Yu, Tianxi Cai, Marinka Zitnik
2022 J jnl
PMC-Patients: A Large-scale Dataset of Patient Notes and Relations Extracted from Case Reports in PubMed Central.
CoRR
Zhengyun Zhao, Qiao Jin, Sheng Yu
2022 J jnl
Semi-constraint Optimal Transport for Entity Alignment with Dangling Cases.
CoRR
Shengxuan Luo, Pengyu Cheng, Sheng Yu
2021 J jnl
A Method for Generating Synthetic Electronic Medical Record Text.
IEEE ACM Trans. Comput. Biol. Bioinform.
Jiaqi Guan, Runzhe Li, Sheng Yu, Xuegong Zhang
2021 J jnl
Biomedical Question Answering: A Comprehensive Review.
CoRR
Qiao Jin, Zheng Yuan, Guangzhi Xiong, Qianlan Yu, Chuanqi Tan, Mosha Chen, Songfang Huang, Xiaozhong Liu, Sheng Yu
2021 J jnl
Efficient Symptom Inquiring and Diagnosis via Adaptive Alignment of Reinforcement Learning and Classification.
CoRR
Hongyi Yuan, Sheng Yu
2021 J jnl
Sentence Alignment with Parallel Documents Helps Biomedical Machine Translation.
CoRR
Shengxuan Luo, Huaiyuan Ying, Sheng Yu
2020 J jnl
Automated ICD coding via unsupervised knowledge integration (UNITE).
Int. J. Medical Informatics
Aaron Sonabend W., Winston Cai, Yuri Ahuja, Ashwin N. Ananthakrishnan, Zongqi Xia, Sheng Yu, Chuan Hong
2020 J jnl
CODER: Knowledge infused cross-lingual medical term embedding for term normalization.
CoRR
Zheng Yuan, Zhengyun Zhao, Sheng Yu
2020 J jnl
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.
Yuanren Tong, Keming Lu, Yingyun Yang, Ji Li, Yucong Lin, Dong Wu, Aiming Yang, Yue Li, Sheng Yu, Jiaming Qian
2020 J jnl
Developing an automated mechanism to identify medical articles from wikipedia for knowledge extraction.
Int. J. Medical Informatics
Lishan Yu, Sheng Yu
2020 J jnl
High-throughput relation extraction algorithm development associating knowledge articles and electronic health records.
CoRR
Yucong Lin, Keming Lu, Yulin Chen, Chuan Hong, Sheng Yu
2020 J jnl
Long-distance disorder-disorder relation extraction with bootstrapped noisy data.
J. Biomed. Informatics
Yucong Lin, Yang Li, Keming Lu, Cheng Ma, Peng Zhao, Daiqi Gao, Zihao Fan, Zijie Cheng, Zheyu Wang, Sheng Yu
2020 J jnl
Unsupervised multi-granular Chinese word segmentation and term discovery via graph partition.
J. Biomed. Informatics
Zheng Yuan, Yuanhao Liu, Qiuyang Yin, Boyao Li, Xiaobin Feng, Guoming Zhang, Sheng Yu
2019 J jnl
Feature extraction for phenotyping from semantic and knowledge resources.
J. Biomed. Informatics
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
2019 J jnl
High-throughput multimodal automated phenotyping (MAP) with application to PheWAS.
J. Am. Medical Informatics Assoc.
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, John Michael Gaziano, Kelly Cho, Peter Szolovits, Isaac S. Kohane, Sheng Yu
2019 — conf
Long distance entity relation extraction with article structure embedding and applied to mining medical knowledge.
ICHI
Yucong Lin, Cheng Ma, Daiqi Gao, Zihao Fan, Zijie Cheng, Zheyu Wang, Sheng Yu
2018 J jnl
Enabling phenotypic big data with PheNorm.
J. Am. Medical Informatics Assoc.
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
2018 — conf
Generation of Synthetic Electronic Medical Record Text.
BIBM
Jiaqi Guan, Runzhe Li, Sheng Yu, Xuegong Zhang
2018 J jnl
Generation of Synthetic Electronic Medical Record Text.
CoRR
Jiaqi Guan, Runzhe Li, Sheng Yu, Xuegong Zhang
2018 Misc conf
High-Throughput Multimodal Automated Phenotyping (MAP) Incorporating Natural Language Processing with Application to PheWAS.
AMIA
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, John Michael Gaziano, Kelly Cho, Peter Szolovits, Isaac S. Kohane, Sheng Yu, Tianxi Cai
2018 J jnl
PheProb: probabilistic phenotyping using diagnosis codes to improve power for genetic association studies.
J. Am. Medical Informatics Assoc.
Jennifer A. Sinnott, Fiona Cai, Sheng Yu, Boris P. Hejblum, Chuan Hong, Isaac S. Kohane, Katherine P. Liao
2018 J jnl
Word Segmentation as Graph Partition.
CoRR
Yuanhao Liu, Sheng Yu
2017 Misc conf
High-throughput Phenotyping via Denoised Normal Mixture Transformation.
AMIA
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
2017 J jnl
Surrogate-assisted feature extraction for high-throughput phenotyping.
J. Am. Medical Informatics Assoc.
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
2015 Misc conf
Computable Phenotypes enabled by the i2b2 Validation Platform.
AMIA
Shawn N. Murphy, Vivian S. Gainer, Victor M. Castro, Alyssa P. Goodson, Lori C. Phillips, Sheng Yu, Tianxi Cai
2015 Misc conf
Demonstrating the Advantages of Applying Data Mining Techniques on Time-Dependent Electronic Medical Records.
AMIA
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
2015 J jnl
Toward high-throughput phenotyping: unbiased automated feature extraction and selection from knowledge sources.
J. Am. Medical Informatics Assoc.
Sheng Yu, Katherine P. Liao, Stanley Y. Shaw, Vivian S. Gainer, Susanne E. Churchill, Peter Szolovits, Shawn N. Murphy, Isaac S. Kohane, Tianxi Cai
2014 J jnl
Classification of CT pulmonary angiography reports by presence, chronicity, and location of pulmonary embolism with natural language processing.
J. Biomed. Informatics
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
2013 J jnl
A Short Introduction to MiniNLP.
CoRR
Sheng Yu, Tianxi Cai