Degui Zhi

ORCID

Publication Activity (10 Years)

Years Active: 2006-2024
Publications (10 Years): 34

Top Venues

University of California, San Diego, USA (PHD)

Education History

University of California, San Diego, USA

PHD

Publications

Yaochen Xie, Ziqian Xie, Sheikh Muhammad Saiful Islam, Degui Zhi, Shuiwang Ji
Genetic InfoMax: Exploring Mutual Information Maximization in High-Dimensional Imaging Genetics Studies. Trans. Mach. Learn. Res. 2024 (2024)
Shenghan Zhang, Haoxuan Li, Ruixiang Tang, Sirui Ding, Laila Rasmy, Degui Zhi, Na Zou, Xia Hu
PheME: A deep ensemble framework for improving phenotype prediction from multi-modal data. ICHI (2023)
Laila Rasmy, Ziqian Xie, Degui Zhi
Training Recurrent Neural Network-Based Model to Predict COVID-19 Patient Risk for PASC using Pytorch_EHR - Hands-on Tutorial on N3C. ICHI (2023)
Bingyu Mao, Ziqian Xie, Laila Rasmy, Masayuki Nigo, Degui Zhi
A Deep-Learning-based Two-Compartment Predictive Model (PKRNN-2CM) for Vancomycin Therapeutic Drug Monitoring. ICHI (2023)
Victor Wang, Ardalan Naseri, Shaojie Zhang, Degui Zhi
Syllable-PBWT for space-efficient haplotype long-match query. Bioinform. 39 (1) (2023)
Shenghan Zhang, Haoxuan Li, Ruixiang Tang, Sirui Ding, Laila Rasmy, Degui Zhi, Na Zou, Xia Hu
PheME: A deep ensemble framework for improving phenotype prediction from multi-modal data. CoRR (2023)
Yaochen Xie, Ziqian Xie, Sheikh Muhammad Saiful Islam, Degui Zhi, Shuiwang Ji
Genetic InfoMax: Exploring Mutual Information Maximization in High-Dimensional Imaging Genetics Studies. CoRR (2023)
Laila Rasmy, Peter Beshara, Bijun S. Kannadath, Degui Zhi
Pancreatic cancer risk prediction using recurrent neural network models trained on electronic health records and claims data. AMIA (2022)
Masayuki Nigo, Hong Thoai Nga Tran, Ziqian Xie, Han Feng, Bingyu Mao, Laila Rasmy, Hongyu Miao, Degui Zhi
PK-RNN-V E: A deep learning model approach to vancomycin therapeutic drug monitoring using electronic health record data. J. Biomed. Informatics 133 (2022)
Evan Yu, Cui Tao, Jingcheng Du, Degui Zhi, Yang Xiang, Kayo Fujimoto, Xi Luo, John A. Schneider
Combining Transfer Learning with Graph Attention Models for HIV Risk Prediction. AMIA (2022)
Angela Ross, Laila Rasmy, Degui Zhi, Kathleen McGrow
Explainability versus Accuracy to Engender Trust. AMIA (2022)
Ahsan Sanaullah, Degui Zhi, Shaoije Zhang
Haplotype Threading Using the Positional Burrows-Wheeler Transform. WABI (2022)
Muhammad Tuan Amith, Licong Cui, Degui Zhi, Kirk Roberts, Xiaoqian Jiang, Fang Li, Evan Yu, Cui Tao
Toward a standard formal semantic representation of the model card report. BMC Bioinform. 23 (1) (2022)
Laila Rasmy, Bijun S. Kannadath, Masayuki Nigo, Ziqian Xie, Bingyu Mao, Khush A. Patel, Yujia Zhou, Xiao Dong, Hua Xu, Degui Zhi
Generalizable Gated Recurrent Neural Network based model to predict COVID-19 patient outcomes on admission. AMIA (2021)
Laila Rasmy, Yang Xiang, Ziqian Xie, Cui Tao, Degui Zhi
Med-BERT: pretrained contextualized embeddings on large-scale structured electronic health records for disease prediction. npj Digit. Medicine 4 (2021)
Ahsan Sanaullah, Degui Zhi, Shaojie Zhang
d-PBWT: dynamic positional Burrows-Wheeler transform. Bioinform. 37 (16) (2021)
Laila Rasmy, Jie Zhu, Zhiheng Li, Xin Hao, Hong Thoai Tran, Yujia Zhou, Firat Tiryaki, Yang Xiang, Hua Xu, Degui Zhi
Simple Recurrent Neural Networks is all we need for clinical events predictions using EHR data. CoRR (2021)
Laila Rasmy, Masayuki Nigo, Bijun S. Kannadath, Ziqian Xie, Bingyu Mao, Khush A. Patel, Wanheng Zhang, Yujia Zhou, Angela Ross, Hua Xu, Degui Zhi
CovRNN: predicting outcomes of COVID-19 patients on admission using their electronic health records with minimal data processing. AMIA (2021)
Pramesh Shakya, Ardalan Naseri, Degui Zhi, Shaojie Zhang
mcPBWT: Space-Efficient Multi-column PBWT Scanning Algorithm for Composite Haplotype Matching. ICCABS (2021)
Ardalan Naseri, William Yue, Shaojie Zhang, Degui Zhi
Efficient Haplotype Block Matching in Bi-Directional PBWT. WABI (2021)
Ahsan Sanaullah, Degui Zhi, Shaojie Zhang
d-PBWT: Dynamic Positional Burrows-Wheeler Transform. RECOMB (2020)
Laila Rasmy, Yang Xiang, Ziqian Xie, Cui Tao, Degui Zhi
Med-BERT: pre-trained contextualized embeddings on large-scale structured electronic health records for disease prediction. CoRR (2020)
Laila Rasmy, Firat Tiryaki, Yujia Zhou, Yang Xiang, Cui Tao, Hua Xu, Degui Zhi
Representation of EHR data for predictive modeling: a comparison between UMLS and other terminologies. J. Am. Medical Informatics Assoc. 27 (10) (2020)
Yang Xiang, Kayo Fujimoto, John A. Schneider, Yuxi Jia, Degui Zhi, Cui Tao
Network context matters: graph convolutional network model over social networks improves the detection of unknown HIV infections among young men who have sex with men. J. Am. Medical Informatics Assoc. 26 (11) (2019)
Yang Xiang, Jun Xu, Yuqi Si, Zhiheng Li, Laila Rasmy, Yujia Zhou, Firat Tiryaki, Fang Li, Yaoyun Zhang, Yonghui Wu, Xiaoqian Jiang, W. Jim Zheng, Degui Zhi, Cui Tao, Hua Xu
Time-sensitive clinical concept embeddings learned from large electronic health records. BMC Medical Informatics Decis. Mak. (2) (2019)
Ardalan Naseri, Degui Zhi, Shaojie Zhang
Multi-allelic positional Burrows-Wheeler transform. BMC Bioinform. (11) (2019)
Ardalan Naseri, Erwin Holzhauser, Degui Zhi, Shaojie Zhang
Efficient haplotype matching between a query and a panel for genealogical search. Bioinform. 35 (14) (2019)
Yang Xiang, Jun Xu, Jingcheng Du, Degui Zhi, Cui Tao
Asthma Onset Prediction Using Structured EMR Data. AMIA (2018)
Jing An, Mandana Salimi, Anupama E. Gururaj, Cui Tao, Degui Zhi, Hua Xu
Development of HeartData, a Data Discovery Index Prototype for Cardiovascular data. AMIA (2018)
Laila Rasmy, Yonghui Wu, Ningtao Wang, Xin Geng, W. Jim Zheng, Fei Wang, Hulin Wu, Hua Xu, Degui Zhi
A study of generalizability of recurrent neural network-based predictive models for heart failure onset risk using a large and heterogeneous EHR data set. J. Biomed. Informatics 84 (2018)
Xiaoming Liu, Lei Xie, Zhijin Wu, Kai Wang, Zhongming Zhao, Jianhua Ruan, Degui Zhi
The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: bioinformatics towards translational applications. BMC Bioinform. (17) (2018)
Yonghui Wu, Min Jiang, Jun Xu, Degui Zhi, Hua Xu
Clinical Named Entity Recognition Using Deep Learning Models. AMIA (2017)
Ardalan Naseri, Degui Zhi, Shaojie Zhang
Multi-allelic positional burrows-wheeler transform. ICCABS (2017)
Ardalan Naseri, Xiaoming Liu, Shaojie Zhang, Degui Zhi
Ultra-Fast Identity by Descent Detection in Biobank-Scale Cohorts Using Positional Burrows-Wheeler Transform. RECOMB (2017)
Kui Zhang, Degui Zhi
Joint haplotype phasing and genotype calling of multiple individuals using haplotype informative reads. Bioinform. 29 (19) (2013)
Degui Zhi, Jihua Wu, Nianjun Liu, Kui Zhang
Genotype calling from next-generation sequencing data using haplotype information of reads. Bioinform. 28 (7) (2012)
Liyan Gao, Zhide Fang, Kui Zhang, Degui Zhi, Xiangqin Cui
Length bias correction for RNA-seq data in gene set analyses. Bioinform. 27 (5) (2011)
Degui Zhi, Maxim Shatsky, Steven E. Brenner
Alignment-free local structural search by writhe decomposition. Bioinform. 26 (9) (2010)
Degui Zhi, Uri Keich, Pavel A. Pevzner, Steffen Heber, Haixu Tang
Correcting Base-Assignment Errors in Repeat Regions of Shotgun Assembly. IEEE ACM Trans. Comput. Biol. Bioinform. 4 (1) (2007)
Degui Zhi, Maxim Shatsky, Steven E. Brenner
Alignment-Free Local Structural Search by Writhe Decomposition. WABI (2007)
Degui Zhi, S. Sri Krishna, Haibo Cao, Pavel A. Pevzner, Adam Godzik
Representing and comparing protein structures as paths in three-dimensional space. BMC Bioinform. 7 (2006)
Neil C. Jones, Degui Zhi, Benjamin J. Raphael
AliWABA: alignment on the web through an A-Bruijn approach. Nucleic Acids Res. 34 (Web-Server-Issue) (2006)

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Publication Activity (10 Years)

Top Topics

Top Venues

Degui Zhi