Degui Zhi

60 papers A* 1B 3C 4Misc 8Journal 36Unranked 7
YearRankTypeTitle / Venue / Authors
2026 J jnl
An Efficient Dynamic Data Structure for Haplotype Matching and Compression on Biobank-Scale Data.
J. Comput. Biol.
Pramesh Shakya, Ahsan Sanaullah, Degui Zhi, Shaojie Zhang
2025 J jnl
Advancing Pancreatic Cancer Prediction with a Next Visit Token Prediction Head on top of Med-BERT.
CoRR
Jianping He, Laila Rasmy, Degui Zhi, Cui Tao
2025 C conf
An Efficient Data Structure and Algorithm for Long-Match Query in Run-Length Compressed BWT.
WABI
Ahsan Sanaullah, Degui Zhi, Shaojie Zhang
2025 J jnl
An Efficient Data Structure and Algorithm for Long-Match Query in Run-Length Compressed BWT.
CoRR
Ahsan Sanaullah, Degui Zhi, Shaojie Zhang
2025 B conf
Dynamic μ-PBWT: Dynamic Run-Length Compressed PBWT for Biobank Scale Data.
RECOMB
Pramesh Shakya, Ahsan Sanaullah, Degui Zhi, Shaojie Zhang
2025 — conf
Haplotype-Based Parallel PBWT for Biobank Scale Data.
ICCABS
Kecong Tang, Ahsan Sanaullah, Degui Zhi, Shaojie Zhang
2025 J jnl
Iterative Distillation for Reward-Guided Fine-Tuning of Diffusion Models in Biomolecular Design.
CoRR
Xingyu Su, Xiner Li, Masatoshi Uehara, Sunwoo Kim, Yulai Zhao, Gabriele Scalia, Ehsan Hajiramezanali, Tommaso Biancalani, Degui Zhi, Shuiwang Ji
2025 J jnl
Language Models for Controllable DNA Sequence Design.
CoRR
Xingyu Su, Xiner Li, Yuchao Lin, Ziqian Xie, Degui Zhi, Shuiwang Ji
2025 J jnl
Language Models for Controllable DNA Sequence Design.
Trans. Mach. Learn. Res.
Xingyu Su, Xiner Li, Yuchao Lin, Ziqian Xie, Degui Zhi, Shuiwang Ji
2025 A* conf
Learning to Discover Regulatory Elements for Gene Expression Prediction.
ICLR
Xingyu Su, Haiyang Yu, Degui Zhi, Shuiwang Ji
2025 J jnl
Learning to Discover Regulatory Elements for Gene Expression Prediction.
CoRR
Xingyu Su, Haiyang Yu, Degui Zhi, Shuiwang Ji
2025 — conf
Predicting Longitudinal Cognitive Decline via Multimodal Deep Learning Fusing Brain MRI and Clinical Data.
SIPAIM
Tamoghna Chattopadhyay, Pavithra Senthilkumar, Rahul H. Ankarath, Christopher Patterson, Emma J. Gleave, Sophia I. Thomopoulos, Heng Huang, Li Shen, Lei You, Degui Zhi, Paul M. Thompson
2025 J jnl
Recomb-Mix: fast and accurate local ancestry inference.
Bioinform.
Yuan Wei, Degui Zhi, Shaojie Zhang
2025 J jnl
Towards Precision Protein-Ligand Affinity Prediction Benchmark: A Complete and Modification-Aware DAVIS Dataset.
CoRR
Ming-Hsiu Wu, Ziqian Xie, Shuiwang Ji, Degui Zhi
2025 J jnl
iGTP: learning interpretable cellular embedding for inferring biological mechanisms underlying single-cell transcriptomics.
Briefings Bioinform.
Kanglin Hsieh, Kai Zhang, Yan Chu, Lishan Yu, Xiaoyang Li, Nuo Hu, Isha Kawosa, Patrick G. Pilié, Pratip K. Bhattacharya, Degui Zhi, Xiaoqian Jiang, Zhongming Zhao, Yulin Dai
2024 J jnl
Genetic InfoMax: Exploring Mutual Information Maximization in High-Dimensional Imaging Genetics Studies.
Trans. Mach. Learn. Res.
Yaochen Xie, Ziqian Xie, Sheikh Muhammad Saiful Islam, Degui Zhi, Shuiwang Ji
2024 J jnl
Prompting Large Language Models for Clinical Temporal Relation Extraction.
CoRR
Jianping He, Laila Rasmy, Haifang Li, Jianfu Li, Zenan Sun, Evan Yu, Degui Zhi, Cui Tao
2023 — conf
A Deep-Learning-based Two-Compartment Predictive Model (PKRNN-2CM) for Vancomycin Therapeutic Drug Monitoring.
ICHI
Bingyu Mao, Ziqian Xie, Laila Rasmy, Masayuki Nigo, Degui Zhi
2023 J jnl
Genetic InfoMax: Exploring Mutual Information Maximization in High-Dimensional Imaging Genetics Studies.
CoRR
Yaochen Xie, Ziqian Xie, Sheikh Muhammad Saiful Islam, Degui Zhi, Shuiwang Ji
2023 — conf
PheME: A deep ensemble framework for improving phenotype prediction from multi-modal data.
ICHI
Shenghan Zhang, Haoxuan Li, Ruixiang Tang, Sirui Ding, Laila Rasmy, Degui Zhi, Na Zou, Xia Hu
2023 J jnl
PheME: A deep ensemble framework for improving phenotype prediction from multi-modal data.
CoRR
Shenghan Zhang, Haoxuan Li, Ruixiang Tang, Sirui Ding, Laila Rasmy, Degui Zhi, Na Zou, Xia Hu
2023 J jnl
RaPID-Query for fast identity by descent search and genealogical analysis.
Bioinform.
Yuan Wei, Ardalan Naseri, Degui Zhi, Shaojie Zhang
2023 J jnl
Syllable-PBWT for space-efficient haplotype long-match query.
Bioinform.
Victor Wang, Ardalan Naseri, Shaojie Zhang, Degui Zhi
2023 — conf
Training Recurrent Neural Network-Based Model to Predict COVID-19 Patient Risk for PASC using Pytorch_EHR - Hands-on Tutorial on N3C.
ICHI
Laila Rasmy, Ziqian Xie, Degui Zhi
2022 Misc conf
Combining Transfer Learning with Graph Attention Models for HIV Risk Prediction.
AMIA
Evan Yu, Cui Tao, Jingcheng Du, Degui Zhi, Yang Xiang, Kayo Fujimoto, Xi Luo, John A. Schneider
2022 Misc conf
Explainability versus Accuracy to Engender Trust.
AMIA
Angela Ross, Laila Rasmy, Degui Zhi, Kathleen McGrow
2022 C conf
Haplotype Threading Using the Positional Burrows-Wheeler Transform.
WABI
Ahsan Sanaullah, Degui Zhi, Shaoije Zhang
2022 J jnl
PK-RNN-V E: A deep learning model approach to vancomycin therapeutic drug monitoring using electronic health record data.
J. Biomed. Informatics
Masayuki Nigo, Hong Thoai Nga Tran, Ziqian Xie, Han Feng, Bingyu Mao, Laila Rasmy, Hongyu Miao, Degui Zhi
2022 Misc conf
Pancreatic cancer risk prediction using recurrent neural network models trained on electronic health records and claims data.
AMIA
Laila Rasmy, Peter Beshara, Bijun S. Kannadath, Degui Zhi
2022 J jnl
Toward a standard formal semantic representation of the model card report.
BMC Bioinform.
Muhammad Tuan Amith, Licong Cui, Degui Zhi, Kirk Roberts, Xiaoqian Jiang, Fang Li, Evan Yu, Cui Tao
2021 Misc conf
CovRNN: predicting outcomes of COVID-19 patients on admission using their electronic health records with minimal data processing.
AMIA
Laila Rasmy, Masayuki Nigo, Bijun S. Kannadath, Ziqian Xie, Bingyu Mao, Khush A. Patel, Wanheng Zhang, Yujia Zhou, Angela Ross, Hua Xu, Degui Zhi
2021 C conf
Efficient Haplotype Block Matching in Bi-Directional PBWT.
WABI
Ardalan Naseri, William Yue, Shaojie Zhang, Degui Zhi
2021 Misc conf
Generalizable Gated Recurrent Neural Network based model to predict COVID-19 patient outcomes on admission.
AMIA
Laila Rasmy, Bijun S. Kannadath, Masayuki Nigo, Ziqian Xie, Bingyu Mao, Khush A. Patel, Yujia Zhou, Xiao Dong, Hua Xu, Degui Zhi
2021 J jnl
Med-BERT: pretrained contextualized embeddings on large-scale structured electronic health records for disease prediction.
npj Digit. Medicine
Laila Rasmy, Yang Xiang, Ziqian Xie, Cui Tao, Degui Zhi
2021 J jnl
Simple Recurrent Neural Networks is all we need for clinical events predictions using EHR data.
CoRR
Laila Rasmy, Jie Zhu, Zhiheng Li, Xin Hao, Hong Thoai Tran, Yujia Zhou, Firat Tiryaki, Yang Xiang, Hua Xu, Degui Zhi
2021 J jnl
d-PBWT: dynamic positional Burrows-Wheeler transform.
Bioinform.
Ahsan Sanaullah, Degui Zhi, Shaojie Zhang
2021 — conf
mcPBWT: Space-Efficient Multi-column PBWT Scanning Algorithm for Composite Haplotype Matching.
ICCABS
Pramesh Shakya, Ardalan Naseri, Degui Zhi, Shaojie Zhang
2020 J jnl
Med-BERT: pre-trained contextualized embeddings on large-scale structured electronic health records for disease prediction.
CoRR
Laila Rasmy, Yang Xiang, Ziqian Xie, Cui Tao, Degui Zhi
2020 J jnl
Representation of EHR data for predictive modeling: a comparison between UMLS and other terminologies.
J. Am. Medical Informatics Assoc.
Laila Rasmy, Firat Tiryaki, Yujia Zhou, Yang Xiang, Cui Tao, Hua Xu, Degui Zhi
2020 B conf
d-PBWT: Dynamic Positional Burrows-Wheeler Transform.
RECOMB
Ahsan Sanaullah, Degui Zhi, Shaojie Zhang
2019 J jnl
Efficient haplotype matching between a query and a panel for genealogical search.
Bioinform.
Ardalan Naseri, Erwin Holzhauser, Degui Zhi, Shaojie Zhang
2019 J jnl
Multi-allelic positional Burrows-Wheeler transform.
BMC Bioinform.
Ardalan Naseri, Degui Zhi, Shaojie Zhang
2019 J jnl
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.
Yang Xiang, Kayo Fujimoto, John A. Schneider, Yuxi Jia, Degui Zhi, Cui Tao
2019 J jnl
Time-sensitive clinical concept embeddings learned from large electronic health records.
BMC Medical Informatics Decis. Mak.
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
2018 J jnl
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
Laila Rasmy, Yonghui Wu, Ningtao Wang, Xin Geng, W. Jim Zheng, Fei Wang, Hulin Wu, Hua Xu, Degui Zhi
2018 Misc conf
Asthma Onset Prediction Using Structured EMR Data.
AMIA
Yang Xiang, Jun Xu, Jingcheng Du, Degui Zhi, Cui Tao
2018 Misc conf
Development of HeartData, a Data Discovery Index Prototype for Cardiovascular data.
AMIA
Jing An, Mandana Salimi, Anupama E. Gururaj, Cui Tao, Degui Zhi, Hua Xu
2018 J jnl
The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: bioinformatics towards translational applications.
BMC Bioinform.
Xiaoming Liu, Lei Xie, Zhijin Wu, Kai Wang, Zhongming Zhao, Jianhua Ruan, Degui Zhi
2017 Misc conf
Clinical Named Entity Recognition Using Deep Learning Models.
AMIA
Yonghui Wu, Min Jiang, Jun Xu, Degui Zhi, Hua Xu
2017 — conf
Multi-allelic positional burrows-wheeler transform.
ICCABS
Ardalan Naseri, Degui Zhi, Shaojie Zhang
2017 B conf
Ultra-Fast Identity by Descent Detection in Biobank-Scale Cohorts Using Positional Burrows-Wheeler Transform.
RECOMB
Ardalan Naseri, Xiaoming Liu, Shaojie Zhang, Degui Zhi
2013 J jnl
Joint haplotype phasing and genotype calling of multiple individuals using haplotype informative reads.
Bioinform.
Kui Zhang, Degui Zhi
2012 J jnl
Genotype calling from next-generation sequencing data using haplotype information of reads.
Bioinform.
Degui Zhi, Jihua Wu, Nianjun Liu, Kui Zhang
2011 J jnl
Length bias correction for RNA-seq data in gene set analyses.
Bioinform.
Liyan Gao, Zhide Fang, Kui Zhang, Degui Zhi, Xiangqin Cui
2010 J jnl
Alignment-free local structural search by writhe decomposition.
Bioinform.
Degui Zhi, Maxim Shatsky, Steven E. Brenner
2007 C conf
Alignment-Free Local Structural Search by Writhe Decomposition.
WABI
Degui Zhi, Maxim Shatsky, Steven E. Brenner
2007 J jnl
Correcting Base-Assignment Errors in Repeat Regions of Shotgun Assembly.
IEEE ACM Trans. Comput. Biol. Bioinform.
Degui Zhi, Uri Keich, Pavel A. Pevzner, Steffen Heber, Haixu Tang
2006 J jnl
AliWABA: alignment on the web through an A-Bruijn approach.
Nucleic Acids Res.
Neil Christopher Jones, Degui Zhi, Benjamin J. Raphael
2006 — —
Discovery and analysis of mosaic arrangements in biological sequences and structures.
Degui Zhi
2006 J jnl
Representing and comparing protein structures as paths in three-dimensional space.
BMC Bioinform.
Degui Zhi, S. Sri Krishna, Haibo Cao, Pavel A. Pevzner, Adam Godzik