Gene coexpression network discovery with controlled statistical and biological significance. - Dongxiao Zhu; Alfred O. Hero III (ICASSP (5), 2005)

Network constrained clustering for gene microarray data. - Dongxiao Zhu; Alfred O. Hero III (ICASSP (5), 2005)

Network constrained clustering for gene microarray data. - Dongxiao Zhu; Alfred O. Hero III; Hong Cheng; Ritu Khanna; Anand Swaroop (Bioinform., 2005)

Structural comparison of metabolic networks in selected single cell organisms. - Dongxiao Zhu; Zhaohui S. Qin (BMC Bioinform., 2005)

High Throughput Screening of Co-Expressed Gene Pairs with Controlled False Discovery Rate (FDR) and Minimum Acceptable Strength (MAS). - Dongxiao Zhu; Alfred O. Hero III; Zhaohui S. Qin; Anand Swaroop (J. Comput. Biol., 2005)

Improvement of Bayesian Network Inference Using a Relaxed Gene Ordering. - Dongxiao Zhu; Hua Li (ICMLA, 2007)

Multivariate correlation estimator for inferring functional relationships from replicated genome-wide data. - Dongxiao Zhu; Youjuan Li; Hua Li (Bioinform., 2007)

Bayesian Hierarchical Model for Large-Scale Covariance Matrix Estimation. - Dongxiao Zhu; Alfred O. Hero III (J. Comput. Biol., 2007)

A Generalized Multivariate Approach for Correlation-Based Pattern Discovery from Replicated Molecular Profiling Data. - Dongxiao Zhu; Guorong Xu; Lipi R. Acharya (BIBM, 2009)

Estimating an Optimal Correlation Structure from Replicated Molecular Profiling Data Using Finite Mixture Models. - Lipi R. Acharya; Dongxiao Zhu (ICMLA, 2009)

Semi-supervised gene shaving method for predicting low variation biological pathways from genome-wide data. - Dongxiao Zhu (BMC Bioinform., 2009)

Breaking the computational barrier: a divide-conquer and aggregate based approach for Alu insertion site characterisation. - Kun Zhang 012; Wei Fan 001; Prescott Deininger; Andrea Edwards; Zujia Xu; Dongxiao Zhu (Int. J. Comput. Biol. Drug Des., 2009)

svdPPCS: an effective singular value decomposition-based method for conserved and divergent co-expression gene module identification. - Wensheng Zhang 005; Andrea Edwards; Wei Fan 001; Dongxiao Zhu; Kun Zhang 012 (BMC Bioinform., 2010)

Improved Bayesian Network inference using relaxed gene ordering. - Dongxiao Zhu; Hua Li (Int. J. Data Min. Bioinform., 2010)

iQuant: A fast yet accurate GUI tool for transcript quantification. - Tin Chi Nguyen; Nan Deng; Guorong Xu; Zhansheng Duan; Dongxiao Zhu (BIBM Workshops, 2011)

SPATA: A highly accurate GUI tool for de novo transcriptome assembly. - Tin Chi Nguyen; Zhiyu Zhao; Dongxiao Zhu (BIBM Workshops, 2011)

SPATA: A seeding and patching algorithm for de novo transcriptome assembly. - Zhiyu Zhao; Tin Chi Nguyen; Nan Deng; Kristen Marie Johnson; Dongxiao Zhu (BIBM Workshops, 2011)

SAMMate: a GUI tool for processing short read alignments in SAM/BAM format. - Guorong Xu; Nan Deng; Zhiyu Zhao; Thair Judeh; Erik K. Flemington; Dongxiao Zhu (Source Code Biol. Medicine, 2011)

A Generalized Multivariate Approach to Pattern Discovery from Replicated and Incomplete Genome-Wide Measurements. - Dongxiao Zhu; Lipi R. Acharya; Hui Zhang (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

QSEA for fuzzy subgraph querying of KEGG pathways. - Thair Judeh; Tin Chi Nguyen; Dongxiao Zhu (BCB, 2012)

Optimal structural inference of signaling pathways from unordered and overlapping gene sets. - Lipi R. Acharya; Thair Judeh; Guangdi Wang; Dongxiao Zhu (Bioinform., 2012)

SASeq: A Selective and Adaptive Shrinkage Approach to Detect and Quantify Active Transcripts using RNA-Seq - Tin Chi Nguyen; Nan Deng; Dongxiao Zhu (CoRR, 2012)

GSGS: A Computational Approach to Reconstruct Signaling Pathway Structures from Gene Sets. - Lipi R. Acharya; Thair Judeh; Zhansheng Duan; Michael G. Rabbat; Dongxiao Zhu (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Detecting various types of differential splicing events using RNA-Seq data. - Nan Deng; Dongxiao Zhu (BCB, 2013)

RNA-Seq analyses to reveal the human transcriptome landscape. - Nan Deng; Dongxiao Zhu (BCB, 2013)

Gene Set Cultural Algorithm: A Cultural Algorithm Approach to Reconstruct Networks from Gene Sets. - Thair Judeh; Thaer Jayyousi; Lipi R. Acharya; Robert G. Reynolds; Dongxiao Zhu (BCB, 2013)

MarkovBin: An Algorithm to Cluster Metagenomic Reads Using a Mixture Modeling of Hierarchical Distributions. - Tin Chi Nguyen; Dongxiao Zhu (BCB, 2013)

SPATA: A Seeding and Patching Algorithm for Hybrid Transcriptome Assembly. - Tin Chi Nguyen; Zhiyu Zhao; Dongxiao Zhu (CoRR, 2013)

A novel semi-supervised learning approach to analyzing metagenomic reads. - Yuliang Geng; Xue-wen Chen 001; Dongxiao Zhu (BCB, 2014)

GSCA: Reconstructing biological pathway topologies using a cultural algorithms approach. - Thair Judeh; Thaer Jayyousi; Lipi R. Acharya; Robert G. Reynolds; Dongxiao Zhu (IEEE Congress on Evolutionary Computation, 2014)

dSpliceType: A Multivariate Model for Detecting Various Types of Differential Splicing Events Using RNA-Seq. - Nan Deng; Dongxiao Zhu (ISBRA, 2014)

Network inference through synergistic subnetwork evolution. - Lipi R. Acharya; Robert G. Reynolds; Dongxiao Zhu (EURASIP J. Bioinform. Syst. Biol., 2015)

Knowledge Discovery Using Big Data in Biomedical Systems. - Sarath Chandra Janga; Dongxiao Zhu; Jake Y. Chen; Mohammed J. Zaki (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

Gene-set-based inference of biological network topologies from big molecular profiling data. - Lipi R. Acharya; Dongxiao Zhu (Big Data over Networks, 2016)

Text Classification with Topic-based Word Embedding and Convolutional Neural Networks. - Haotian Xu; Ming Dong 001; Dongxiao Zhu; Alexander Kotov 001; April Idalski Carcone; Sylvie Naar-King (BCB, 2016)

SAFS: A deep feature selection approach for precision medicine. - Milad Zafar Nezhad; Dongxiao Zhu; Xiangrui Li; Kai Yang 005; Phillip Levy (BIBM, 2016)

A Bayesian hierarchical appearance model for robust object tracking. - Raed Almomani; Ming Dong 001; Dongxiao Zhu (ICME, 2016)

Poisson-Markov Mixture Model and Parallel Algorithm for Binning Massive and Heterogenous DNA Sequencing Reads. - Lu Wang 004; Dongxiao Zhu; Yan Li 052; Ming Dong 001 (ISBRA, 2016)

Predictive deep network with leveraging clinical measure as auxiliary task. - Xiangrui Li; Dongxiao Zhu; Phillip Levy (BIBM, 2017)

SDT: A Tree Method for Detecting Patient Subgroups with Personalized Risk Factors. - Xiangrui Li; Dongxiao Zhu; Ming Dong 001; Milad Zafar Nezhad; Alexander T. Janke; Phillip Levy (CRI, 2017)

Multi-task Survival Analysis. - Lu Wang 004; Yan Li 052; Jiayu Zhou; Dongxiao Zhu; Jieping Ye (ICDM, 2017)

SUBIC: A Supervised Bi-Clustering Approach for Precision Medicine. - Milad Zafar Nezhad; Dongxiao Zhu; Najibesadat Sadati; Kai Yang 005; Phillip Levi (ICMLA, 2017)

Modeling Over-Dispersion for Network Data Clustering. - Lu Wang 004; Dongxiao Zhu; Ming Dong 001; Yan Li 052 (ICMLA, 2017)

Object tracking via Dirichlet process-based appearance models. - Raed Almomani; Ming Dong 001; Dongxiao Zhu (Neural Comput. Appl., 2017)

Cap-seq reveals complicated miRNA transcriptional mechanisms in C. elegans and mouse. - Jiao Chen 002; Dongxiao Zhu; Yanni Sun (Quant. Biol., 2017)

Transcriptome assembly strategies for precision medicine. - Lu Wang 004; Lipi R. Acharya; Changxin Bai; Dongxiao Zhu (Quant. Biol., 2017)

Obesity risk factors ranking using multi-task learning. - Lu Wang 004; Dongxiao Zhu; Elizabeth Towner; Ming Dong 001 (BHI, 2018)

Proteus: network-aware web browsing on heterogeneous mobile systems. - Jie Ren 007; Xiaoming Wang; Jianbin Fang; Yansong Feng 002; Dongxiao Zhu; Zhunchen Luo; Jie Zheng 005; Zheng Wang 001 (CoNEXT, 2018)

Joint Energy-Efficient Optimization of Downlink and Uplink with eICIC in HetNet. - Jie Zheng 005; Ling Gao; Dongxiao Zhu; Hai Wang 010; Qian Sun; Jinping Niu; Xiaoya Li 003; Jianfeng Yang (IoTaaS, 2018)

Joint Energy Management and Interference Coordination With Max-Min Fairness in Ultra-Dense HetNets. - Jie Zheng 005; Ling Gao; Haijun Zhang 001; Dongxiao Zhu; Hai Wang 010; Quanli Gao; Victor C. M. Leung (IEEE Access, 2018)

A Predictive Approach Using Deep Feature Learning for Electronic Medical Records: A Comparative Study. - Milad Zafar Nezhad; Dongxiao Zhu; Najibesadat Sadati; Kai Yang 005 (CoRR, 2018)

Learning and Interpreting Features to Rank: A Case Study on Age Estimation. - Shixing Chen; Ming Dong 001; Dongxiao Zhu (Int. J. Multim. Data Eng. Manag., 2018)

Leveraging auxiliary measures: a deep multi-task neural network for predictive modeling in clinical research. - Xiangrui Li; Dongxiao Zhu; Phillip Levy (BMC Medical Informatics Decis. Mak., 2018)

Robust feature selection via l2, 1-norm in finite mixture of regression. - Xiangrui Li; Dongxiao Zhu (Pattern Recognit. Lett., 2018)

Multinomial classification with class-conditional overlapping sparse feature groups. - Xiangrui Li; Dongxiao Zhu; Ming Dong 001 (Pattern Recognit. Lett., 2018)

Clustering over-dispersed data with mixed feature types. - Lu Wang 004; Dongxiao Zhu; Ming Dong 001 (Stat. Anal. Data Min., 2018)

Prioritization of Multi-Level Risk Factors for Obesity. - Lu Wang 004; Ming Dong 001; Elizabeth Towner; Dongxiao Zhu (BIBM, 2019)

Multi-task Prediction of Patient Workload. - Mohammad Hessam Olya; Dongxiao Zhu; Kai Yang 005 (CoRR, 2019)

CRCEN: A Generalized Cost-sensitive Neural Network Approach for Imbalanced Classification. - Xiangrui Li; Dongxiao Zhu (CoRR, 2019)

Vispi: Automatic Visual Perception and Interpretation of Chest X-rays. - Xin Li 081; Rui Cao; Dongxiao Zhu (CoRR, 2019)

Tackling Multiple Ordinal Regression Problems: Sparse and Deep Multi-Task Learning Approaches. - Lu Wang 004; Dongxiao Zhu (CoRR, 2019)

A Deep Active Survival Analysis approach for precision treatment recommendations: Application of prostate cancer. - Milad Zafar Nezhad; Najibesadat Sadati; Kai Yang 005; Dongxiao Zhu (Expert Syst. Appl., 2019)

On the Learning Property of Logistic and Softmax Losses for Deep Neural Networks. - Xiangrui Li; Xin Li 081; Deng Pan 001; Dongxiao Zhu (AAAI, 2020)

COVID-MobileXpert: On-Device COVID-19 Patient Triage and Follow-up using Chest X-rays. - Xin Li 081; Chengyin Li; Dongxiao Zhu (BIBM, 2020)

Explainable Recommendation via Interpretable Feature Mapping and Evaluation of Explainability. - Deng Pan 001; Xiangrui Li; Xin Li 081; Dongxiao Zhu (IJCAI, 2020)

Toward Tag-free Aspect Based Sentiment Analysis: A Multiple Attention Network Approach. - Yao Qiang; Xin Li 081; Dongxiao Zhu (IJCNN, 2020)

Interpreting Age Effects of Human Fetal Brain from Spontaneous fMRI Using Deep 3D Convolutional Neural Networks. - Xiangrui Li; Jasmine L. Hect; Moriah E. Thomason; Dongxiao Zhu (ISBI, 2020)

Robust Detection of Adversarial Attacks on Medical Images. - Xin Li 081; Dongxiao Zhu (ISBI, 2020)

Improve SGD Training via Aligning Mini-batches. - Xiangrui Li; Deng Pan 001; Xin Li 081; Dongxiao Zhu (CoRR, 2020)

COVID-MobileXpert: On-Device COVID-19 Screening using Snapshots of Chest X-Ray. - Xin Li 081; Chengyin Li; Dongxiao Zhu (CoRR, 2020)

Improving Adversarial Robustness via Probabilistically Compact Loss with Logit Constraints. - Xin Li 081; Xiangrui Li; Deng Pan 001; Dongxiao Zhu (AAAI, 2021)

Explaining Deep Neural Network Models with Adversarial Gradient Integration. - Deng Pan 001; Xin Li 081; Dongxiao Zhu (IJCAI, 2021)

Defending Against Adversarial Attacks On Medical Imaging Ai System, Classification Or Detection? - Xin Li 081; Deng Pan 001; Dongxiao Zhu (ISBI, 2021)

Adversarially Robust and Explainable Model Compression with On-Device Personalization for Text Classification. - Yao Qiang; Supriya Tumkur Suresh Kumar; Marco Brocanelli; Dongxiao Zhu (CoRR, 2021)

Tackling ordinal regression problem for heterogeneous data: sparse and deep multi-task learning approaches. - Lu Wang 004; Dongxiao Zhu (Data Min. Knowl. Discov., 2021)

Counterfactual Interpolation Augmentation (CIA): A Unified Approach to Enhance Fairness and Explainability of DNN. - Yao Qiang; Chengyin Li; Marco Brocanelli; Dongxiao Zhu (IJCAI, 2022)

Tiny RNN Model with Certified Robustness for Text Classification. - Yao Qiang; Supriya Tumkur Suresh Kumar; Marco Brocanelli; Dongxiao Zhu (IJCNN, 2022)

AttCAT: Explaining Transformers via Attentive Class Activation Tokens. - Yao Qiang; Deng Pan 001; Chengyin Li; Xin Li 081; Rhongho Jang; Dongxiao Zhu (NeurIPS, 2022)

Coupling User Preference with External Rewards to Enable Driver-centered and Resource-aware EV Charging Recommendation. - Chengyin Li; Zheng Dong 002; Nathan Fisher; Dongxiao Zhu (ECML/PKDD (4), 2022)

Saliency Guided Adversarial Training for Learning Generalizable Features with Applications to Medical Imaging Classification System. - Xin Li 081; Yao Qiang; Chengyin Li; Sijia Liu; Dongxiao Zhu (CoRR, 2022)

FocalUNETR: A Focal Transformer for Boundary-aware Segmentation of CT Images. - Chengyin Li; Hassan Bagher-Ebadian; Vikram Goddla; Indrin J. Chetty; Dongxiao Zhu (CoRR, 2022)

Learning Compact Features via In-Training Representation Alignment. - Xin Li 081; Xiangrui Li; Deng Pan 001; Yao Qiang; Dongxiao Zhu (AAAI, 2023)

Negative Flux Aggregation to Estimate Feature Attributions. - Xin Li 081; Deng Pan 001; Chengyin Li; Yao Qiang; Dongxiao Zhu (IJCAI, 2023)

FocalUNETR: A Focal Transformer for Boundary-Aware Prostate Segmentation Using CT Images. - Chengyin Li; Yao Qiang; Rafi Ibn Sultan; Hassan Bagher-Ebadian; Prashant Khanduri; Indrin J. Chetty; Dongxiao Zhu (MICCAI (3), 2023)

Towards Trauma-Informed Data Donation of Sexual Experience in Online Dating to Improve Sexual Risk Detection AI. - Wenqi Zheng; Emma Walquist; Isha Datey; Xiangyu Zhou; Kelly Berishaj; Melissa Mcdonald; Michele Parkhill; Dongxiao Zhu; Douglas Zytko (UIST (Adjunct Volume), 2023)

Auto-Prompting SAM for Mobile Friendly 3D Medical Image Segmentation. - Chengyin Li; Prashant Khanduri; Yao Qiang; Rafi Ibn Sultan; Indrin J. Chetty; Dongxiao Zhu (CoRR, 2023)

Towards Trustworthy Artificial Intelligence for Equitable Global Health. - Hong Qin 003; Jude Kong; Wandi Ding; Ramneek Ahluwalia; Christo El-Morr; Zeynep Engin; Jake Okechukwu Effoduh; Rebecca Hwa; Serena Jingchuan Guo; Laleh Seyyed-Kalantari; Sylvia Kiwuwa Muyingo; Candace Makeda Moore; et al. (CoRR, 2023)

Interpretability-Aware Vision Transformer. - Yao Qiang; Chengyin Li; Prashant Khanduri; Dongxiao Zhu (CoRR, 2023)

Hijacking Large Language Models via Adversarial In-Context Learning. - Yao Qiang; Xiangyu Zhou; Dongxiao Zhu (CoRR, 2023)

GeoSAM: Fine-tuning SAM with Sparse and Dense Visual Prompting for Automated Segmentation of Mobility Infrastructure. - Rafi Ibn Sultan; Chengyin Li; Hui Zhu 016; Prashant Khanduri; Marco Brocanelli; Dongxiao Zhu (CoRR, 2023)

FedDRO: Federated Compositional Optimization for Distributionally Robust Learning. - Prashant Khanduri; Chengyin Li; Rafi Ibn Sultan; Yao Qiang; Jörg Kliewer; Dongxiao Zhu (CoRR, 2023)

MFABA: A More Faithful and Accelerated Boundary-Based Attribution Method for Deep Neural Networks. - Zhiyu Zhu; Huaming Chen; Jiayu Zhang 001; Xinyi Wang 005; Zhibo Jin; Minhui Xue 001; Dongxiao Zhu; Kim-Kwang Raymond Choo (AAAI, 2024)

"It's Not What We Were Trying to Get At, but I Think Maybe It Should Be": Learning How to Do Trauma-Informed Design with a Data Donation Platform for Online Dating Sexual Violence. - Wenqi Zheng; Emma Walquist; Isha Datey; Xiangyu Zhou; Kelly Berishaj; Melissa Mcdonald; Michele Parkhill; Dongxiao Zhu; Douglas Zytko (CHI, 2024)

Fairness-Aware Vision Transformer via Debiased Self-Attention. - Yao Qiang; Chengyin Li; Prashant Khanduri; Dongxiao Zhu (ECCV (37), 2024)

Evaluation of the Segment Anything Model (SAM) for Brain Tumor Segmentation. - Mohammad Peivandi; Jason Zhang; Michael Lu; Chengyin Li; Dongxiao Zhu; Zhifeng Kou (ISBI, 2024)

Benchmark and Neural Architecture for Conversational Entity Retrieval from a Knowledge Graph. - Mona Zamiri; Yao Qiang; Fedor Nikolaev; Dongxiao Zhu; Alexander Kotov 001 (WWW, 2024)

Learning to Poison Large Language Models During Instruction Tuning. - Yao Qiang; Xiangyu Zhou; Saleh Zare Zade; Mohammad Amin Roshani; Douglas Zytko; Dongxiao Zhu (CoRR, 2024)

Generative LLM Powered Conversational AI Application for Personalized Risk Assessment: A Case Study in COVID-19. - Mohammad Amin Roshani; Xiangyu Zhou; Yao Qiang; Srinivasan Suresh 001; Steve Hicks; Usha Sethuraman; Dongxiao Zhu (CoRR, 2024)

MulModSeg: Enhancing Unpaired Multi-Modal Medical Image Segmentation with Modality-Conditioned Text Embedding and Alternating Training. - Chengyin Li; Hui Zhu 016; Rafi Ibn Sultan; Hassan Bagher-Ebadian; Prashant Khanduri; Indrin J. Chetty; Kundan Thind; Dongxiao Zhu (CoRR, 2024)

AutoProSAM: Automated Prompting SAM for 3D Multi-Organ Segmentation. - Chengyin Li; Rafi Ibn Sultan; Prashant Khanduri; Yao Qiang; Chetty J. Indrin; Dongxiao Zhu (WACV, 2025)

MulModSeg: Enhancing Unpaired Multi-Modal Medical Image Segmentation with Modality-Conditioned Text Embedding and Alternating Training. - Chengyin Li; Hui Zhu 016; Rafi Ibn Sultan; Hassan Bagher-Ebadian; Prashant Khanduri; Chetty J. Indrin; Kundan Thind; Dongxiao Zhu (WACV, 2025)

BiPVL-Seg: Bidirectional Progressive Vision-Language Fusion with Global-Local Alignment for Medical Image Segmentation. - Rafi Ibn Sultan; Hui Zhu 016; Chengyin Li; Dongxiao Zhu (CoRR, 2025)

Automatic Calibration for Membership Inference Attack on Large Language Models. - Saleh Zare Zade; Yao Qiang; Xiangyu Zhou; Hui Zhu 016; Mohammad Amin Roshani; Prashant Khanduri; Dongxiao Zhu (CoRR, 2025)

Not All Tokens Are Meant to Be Forgotten. - Xiangyu Zhou; Yao Qiang; Saleh Zare Zade; Douglas Zytko; Prashant Khanduri; Dongxiao Zhu (CoRR, 2025)