Degui Zhi

According to our database, Degui Zhi authored at least 38 papers between 2006 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2023

Syllable-PBWT for space-efficient haplotype long-match query.

Victor Wang, Ardalan Naseri, Shaojie Zhang, Degui Zhi

Bioinform., January, 2023

Genetic InfoMax: Exploring Mutual Information Maximization in High-Dimensional Imaging Genetics Studies.

Yaochen Xie, Ziqian Xie, Sheikh Muhammad Saiful Islam, Degui Zhi, Shuiwang Ji

CoRR, 2023

PheME: A deep ensemble framework for improving phenotype prediction from multi-modal data.

Shenghan Zhang, Haoxuan Li, Ruixiang Tang, Sirui Ding, Laila Rasmy, Degui Zhi, Na Zou, Xia Hu

Proceedings of the 11th IEEE International Conference on Healthcare Informatics, 2023

Training Recurrent Neural Network-Based Model to Predict COVID-19 Patient Risk for PASC using Pytorch_EHR - Hands-on Tutorial on N3C.

Laila Rasmy, Ziqian Xie, Degui Zhi

Proceedings of the 11th IEEE International Conference on Healthcare Informatics, 2023

A Deep-Learning-based Two-Compartment Predictive Model (PKRNN-2CM) for Vancomycin Therapeutic Drug Monitoring.

Bingyu Mao, Ziqian Xie, Laila Rasmy, Masayuki Nigo, Degui Zhi

Proceedings of the 11th IEEE International Conference on Healthcare Informatics, 2023

2022

PK-RNN-V E: A deep learning model approach to vancomycin therapeutic drug monitoring using electronic health record data.

Masayuki Nigo, Hong Thoai Nga Tran, Ziqian Xie, Han Feng, Bingyu Mao, Laila Rasmy, Hongyu Miao, Degui Zhi

J. Biomed. Informatics, 2022

Toward a standard formal semantic representation of the model card report.

Muhammad Tuan Amith, Licong Cui, Degui Zhi, Kirk Roberts, Xiaoqian Jiang, Fang Li, Evan Yu, Cui Tao

BMC Bioinform., 2022

Haplotype Threading Using the Positional Burrows-Wheeler Transform.

Ahsan Sanaullah, Degui Zhi, Shaoije Zhang

Proceedings of the 22nd International Workshop on Algorithms in Bioinformatics, 2022

Combining Transfer Learning with Graph Attention Models for HIV Risk Prediction.

Evan Yu, Cui Tao, Jingcheng Du, Degui Zhi, Yang Xiang, Kayo Fujimoto, Xi Luo, John A. Schneider

Proceedings of the AMIA 2022, 2022

Explainability versus Accuracy to Engender Trust.

Angela Ross, Laila Rasmy, Degui Zhi, Kathleen McGrow

Proceedings of the AMIA 2022, 2022

Pancreatic cancer risk prediction using recurrent neural network models trained on electronic health records and claims data.

Laila Rasmy, Peter Beshara, Bijun S. Kannadath, Degui Zhi

Proceedings of the AMIA 2022, 2022

2021

Med-BERT: pretrained contextualized embeddings on large-scale structured electronic health records for disease prediction.

Laila Rasmy, Yang Xiang, Ziqian Xie, Cui Tao, Degui Zhi

npj Digit. Medicine, 2021

Simple Recurrent Neural Networks is all we need for clinical events predictions using EHR data.

Laila Rasmy, Jie Zhu, Zhiheng Li, Xin Hao, Hong Thoai Tran, Yujia Zhou, Firat Tiryaki, Yang Xiang, Hua Xu, Degui Zhi

CoRR, 2021

d-PBWT: dynamic positional Burrows-Wheeler transform.

Ahsan Sanaullah, Degui Zhi, Shaojie Zhang

Bioinform., 2021

Efficient Haplotype Block Matching in Bi-Directional PBWT.

Ardalan Naseri, William Yue, Shaojie Zhang, Degui Zhi

Proceedings of the 21st International Workshop on Algorithms in Bioinformatics, 2021

mcPBWT: Space-Efficient Multi-column PBWT Scanning Algorithm for Composite Haplotype Matching.

Pramesh Shakya, Ardalan Naseri, Degui Zhi, Shaojie Zhang

Proceedings of the Computational Advances in Bio and Medical Sciences: 11th International Conference, 2021

CovRNN: predicting outcomes of COVID-19 patients on admission using their electronic health records with minimal data processing.

Laila Rasmy, Masayuki Nigo, Bijun S. Kannadath, Ziqian Xie, Bingyu Mao, Khush A. Patel, Wanheng Zhang, Yujia Zhou, Angela Ross, Hua Xu, Degui Zhi

Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

Generalizable Gated Recurrent Neural Network based model to predict COVID-19 patient outcomes on admission.

Laila Rasmy, Bijun S. Kannadath, Masayuki Nigo, Ziqian Xie, Bingyu Mao, Khush A. Patel, Yujia Zhou, Xiao Dong, Hua Xu, Degui Zhi

Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

2020

Representation of EHR data for predictive modeling: a comparison between UMLS and other terminologies.

Laila Rasmy, Firat Tiryaki, Yujia Zhou, Yang Xiang, Cui Tao, Hua Xu, Degui Zhi

J. Am. Medical Informatics Assoc., 2020

Med-BERT: pre-trained contextualized embeddings on large-scale structured electronic health records for disease prediction.

Laila Rasmy, Yang Xiang, Ziqian Xie, Cui Tao, Degui Zhi

CoRR, 2020

2019

Time-sensitive clinical concept embeddings learned from large electronic health records.

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

BMC Medical Informatics Decis. Mak., 2019

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.

Yang Xiang, Kayo Fujimoto, John A. Schneider, Yuxi Jia, Degui Zhi, Cui Tao

J. Am. Medical Informatics Assoc., 2019

Multi-allelic positional Burrows-Wheeler transform.

Ardalan Naseri, Degui Zhi, Shaojie Zhang

BMC Bioinform., 2019

Efficient haplotype matching between a query and a panel for genealogical search.

Ardalan Naseri, Erwin Holzhauser, Degui Zhi, Shaojie Zhang

Bioinform., 2019

2018

A study of generalizability of recurrent neural network-based predictive models for heart failure onset risk using a large and heterogeneous EHR data set.

Laila Rasmy, Yonghui Wu, Ningtao Wang, Xin Geng, W. Jim Zheng, Fei Wang, Hulin Wu, Hua Xu, Degui Zhi

J. Biomed. Informatics, 2018

The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: bioinformatics towards translational applications.

Xiaoming Liu, Lei Xie, Zhijin Wu, Kai Wang, Zhongming Zhao, Jianhua Ruan, Degui Zhi

BMC Bioinform., 2018

Asthma Onset Prediction Using Structured EMR Data.

Yang Xiang, Jun Xu, Jingcheng Du, Degui Zhi, Cui Tao

Proceedings of the AMIA 2018, 2018

Development of HeartData, a Data Discovery Index Prototype for Cardiovascular data.

Jing An, Mandana Salimi, Anupama E. Gururaj, Cui Tao, Degui Zhi, Hua Xu

Proceedings of the AMIA 2018, 2018

2017

Ultra-Fast Identity by Descent Detection in Biobank-Scale Cohorts Using Positional Burrows-Wheeler Transform.

Ardalan Naseri, Xiaoming Liu, Shaojie Zhang, Degui Zhi

Proceedings of the Research in Computational Molecular Biology, 2017

Clinical Named Entity Recognition Using Deep Learning Models.

Yonghui Wu, Min Jiang, Jun Xu, Degui Zhi, Hua Xu

Proceedings of the AMIA 2017, 2017

2013

Joint haplotype phasing and genotype calling of multiple individuals using haplotype informative reads.

Kui Zhang, Degui Zhi

Bioinform., 2013

2012

Genotype calling from next-generation sequencing data using haplotype information of reads.

Degui Zhi, Jihua Wu, Nianjun Liu, Kui Zhang

Bioinform., 2012

2011

Length bias correction for RNA-seq data in gene set analyses.

Liyan Gao, Zhide Fang, Kui Zhang, Degui Zhi, Xiangqin Cui

Bioinform., 2011

2010

Alignment-free local structural search by writhe decomposition.

Degui Zhi, Maxim Shatsky, Steven E. Brenner

Bioinform., 2010

2007

Correcting Base-Assignment Errors in Repeat Regions of Shotgun Assembly.

Degui Zhi, Uri Keich, Pavel A. Pevzner, Steffen Heber, Haixu Tang

IEEE ACM Trans. Comput. Biol. Bioinform., 2007

2006

Discovery and analysis of mosaic arrangements in biological sequences and structures.

Degui Zhi

PhD thesis, 2006

AliWABA: alignment on the web through an A-Bruijn approach.

Neil C. Jones, Degui Zhi, Benjamin J. Raphael

Nucleic Acids Res., 2006

Representing and comparing protein structures as paths in three-dimensional space.

Degui Zhi, S. Sri Krishna, Haibo Cao, Pavel A. Pevzner, Adam Godzik

BMC Bioinform., 2006