Research Output — Entire Period

Publications

Full list on Google Scholar  ·  DBLP  ·  OpenReview

100+
Peer-reviewed publications
~$12M
Total research funding
~$9M
As Principal Investigator
#20
MS AI program nationally (TechGuide)
See also
Research Funding — All Federal Grants & Awards →
→
Preprints Foundational AI / ML Use-Inspired AI Bioinformatics

Preprints (student as first author)

Under Review
Alignment of LRMs via Counter-Aligned Few-Shot Conversation Exposure
Zhou, X., Zade, S.Z. and Zhu, D. (2026)
arXiv
BiPVL-Seg: Bidirectional Progressive Vision-Language Fusion with Global-Local Alignment for Medical Image Segmentation
Sultan, R.I., Zhu, H., Li, C. and Zhu, D. — arXiv:2503.23534, 2025
arXiv
Learning to Poison Large Language Models During Instruction Tuning
Qiang, Y., Zhou, X., Zare Zade, S., Rosani, A., Zytko, D. and Zhu, D.
arXiv
Hijacking Large Language Models via Adversarial In-Context Learning
Qiang, Y., Zhou, X. and Zhu, D.
arXiv
FedDRO: Federated Compositional Optimization for Distributionally Robust Learning
Khanduri, P., Li, C., Sultan, R., Qiang, Y., Kliewer, J. and Zhu, D.

Foundational AI / Machine Learning Research (student as first author)

2026 3
CVPR-26
WalkGPT: Grounded Vision–Language Conversation with Depth-Aware Segmentation for Pedestrian Navigation
Sultan, R., Zhu, H., Li, C., Khanduri, P., Brocanelli, M. and Zhu, D.
ICLR-26
Attention Smoothing Is All You Need For Unlearning
Zade, S.Z., Zhou, X., Liu, S. and Zhu, D.
AAAI-26
Not All Tokens Are Meant to Be Forgotten Oral
Zhou, X., Qiang, Y., Zade, S.Z., Zytko, D., Khanduri, P. and Zhu, D.
2025 6
ECAI-25
Automatic Calibration for Membership Inference Attack on Large Language Models
Zade, S.Z., Qiang, Y., Zhou, X., Zhu, H., Roshani, M.A., Khanduri, P. and Zhu, D.
ECAI-25
CSCW-25
Collective Consent: Who Needs to Consent to the Donation of Data Representing Multiple People?
Walquist, E., Datey, I., Zheng, W., Zhou, X., Berishaj, K., McDonald, M., Parkhill, M., Zhu, D. and Zytko, D.
IJCNN-25
Interpretability-Aware Vision Transformer
Qiang, Y., Li, C., Khanduri, P. and Zhu, D.
WACV-25
MulModSeg: Enhancing Unpaired Multi-Modal Medical Image Segmentation with Modality-Conditioned Text Embedding and Alternating Training
Li, C., Zhu, H., Sultan, R., Khanduri, P., Qiang, Y., Chetty, I., Thind, K. and Zhu, D.
WACV-25
AutoProSAM: Automated Prompting SAM for 3D Multi-Organ Segmentation
Li, C., Khanduri, P., Qiang, Y., Sultan, R., Chetty, I. and Zhu, D.
2024 3
ECCV-24
Fairness-aware Vision Transformer via Debiased Self-Attention
Qiang, Y., Li, C., Khanduri, P. and Zhu, D. — Accept rate: 2,395/8,585 = 27.9%
TheWebConf-24
Benchmark and Neural Architecture for Conversational Entity Retrieval from a Knowledge Graph
Zamiri, M., Qiang, Y., Nikolaev, F., Zhu, D. and Kotov, A. — Accept rate: 806/4,028 = 20.2%
CHI-24
"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
Zheng, W., Walquist, E., Datey, I., Zhou, X., Berishaj, K., Mcdonald, M., Parkhill, M., Zhu, D. and Zytko, D. — Accept rate: 1,060/4,028 = 26.3%
2023 4
AAAI-24
MFABA: A More Faithful and Accelerated Boundary-based Attribution Method for Deep Neural Networks
Zhu, Z., Chen, H., Zhang, J., Wang, X., Jin, Z., Xue, M., Zhu, D. and Choo, K.K.R. — Accept rate: 2,342/12,100 = 23.75%
MICCAI-23
FocalUNETR: A Focal Transformer for Boundary-aware Segmentation of CT Images
Li, C., Qiang, Y., Sultan, R., Bagher-Ebadian, P., Khanduri, V., Chetty, I.J. and Zhu, D. — Accept rate: 740/2,250 = 32%
IJCAI-23
Negative Flux Aggregation to Estimate Feature Attributions
Li, X., Pan, D., Li, C., Qiang, Y. and Zhu, D. — Accept rate: 685/4,566 = 15%
AAAI-23
Learning Compact Features via In-Training Representation Alignment
Li, X., Li, X., Pan, D., Qiang, Y. and Zhu, D. — Accept rate: 1,721/8,777 = 19.6%
Workshop 2023 1
AdvML@ICML-23
Proximal Composite Optimization for Distributionally Robust Learning
Khanduri, P., Li, C., Sultan, R., Qiang, Y. and Zhu, D.
2022 5
NeurIPS-22
AttCAT: Explaining Transformers via Attentive Class Activation Tokens
Qiang, Y., Pan, D., Li, C., Li, X., Jang, R. and Zhu, D. — Accept rate: 2,665/10,411 = 25.6%
IJCAI-22
Counterfactual Interpolation Augmentation (CIA): A Unified Approach to Enhance Fairness and Explainability of DNN
Qiang, Y., Li, C., Brocanelli, M. and Zhu, D. — Accept rate: 681/4,535 = 15%
ECML-22
IJCNN-22
Tiny RNN Model with Certified Robustness for Text Classification Oral
Qiang, Y., Supriya, T.S., Kumar, Brocanelli, M. and Zhu, D.
AdvML@ICML-22
2021 3
IJCAI-21
Explaining Deep Neural Network Models with Adversarial Gradient Integration
Pan, D., Li, X. and Zhu, D. — Accept rate: 587/4,204 = 13.9%
AAAI-21
Improving Adversarial Robustness via Probabilistically Compact Loss with Logit Constraints
Li, X., Li, X., Pan, D. and Zhu, D. — Accept rate: 1,692/7,911 = 21.4%
DMKD
Tackling Multiple Ordinal Regression Problems: Sparse and Deep Multi-task Learning Approaches
Wang, L. and Zhu, D. — Data Mining and Knowledge Discovery, 2021
2020 3
IJCAI-20
Explainable Recommendation via Interpretable Feature Mapping and Evaluating Explainability
Pan, D., Li, X., Li, X. and Zhu, D. — Accept rate: 592/4,717 = 12.6%
AAAI-20
On the Learning Behavior of Logistic and Softmax Losses for Deep Neural Networks
Li, X., Li, X., Pan, D. and Zhu, D. — Accept rate: 1,591/7,737 = 20.6%
IJCNN-20
2017–2018 4
ICDM-17
Multi-task Survival Analysis
Wang, L., Li, Y., Zhou, J., Zhu, D. and Ye, J. — Accept rate: 72/778 = 9.25%
Patt. Recog. Lett.
Robust Feature Selection via l2,1-norm in Finite Mixture of Regression
Li, X. and Zhu, D. — Pattern Recognition Letters, 108, 2018, pp 15–22
Stat. Anal. Data Min.
Clustering Over-Dispersed Data with Mixed Feature Types
Wang, L., Zhu, D. and Dong, M. — Statistical Analysis and Data Mining, 2018;11:55–65
Patt. Recog. Lett.
Multinomial Classification with Class-Conditional Overlapping Sparse Feature Groups
Li, X., Zhu, D. and Dong, M. — Pattern Recognition Letters, 101, 2018, pp 37–43

Use-Inspired AI Research (student as first author)

Health & Medical Imaging 12
MIDL-26
JMIR AI
Generative Large Language Model—Powered Conversational AI App for Personalized Risk Assessment: Case Study in COVID-19
Roshani, M., Zhou, X., Qiang, Y., Suresh, S., Hicks, S., Sethuraman, U. and Zhu, D. — JMIR AI 2025;4:e67363
Cancer
ChatGPT — A Promising Generative AI Tool and its Implications on Cancer Care
Uprety, D., Zhu, D. and West, H. — Cancer, doi:10.1002/cncr.34827
Small
Mechanical Evolution of Metastatic Cancer Cells in 3D Microenvironment
Hilai, K., Grubich, D., Akrawi, M., Zhu, H., Zaghloul, R., Shi, C., Do, M., Zhu, D. and Zhang, J. — Small, 21(18), 2025
Med. Physics
Enhancing CT Image Segmentation Accuracy through Ensemble Loss Function Optimization
Li, X., Sultan, R., Bagher, H.E., Kim, J., Zhu, D. and Chetty, I. — Medical Physics, 2025 Jul;52(7):e17848
Med. Physics
ISBI-21
BIBM-20
MIDL-20
AMIA-20
Predicting Clinical Outcomes with Patient Stratification via Deep Mixture Neural Networks Best Student Paper
Li, X., Zhu, D.* and Levy, P. — AMIA Summit on Clinical Research Informatics (*Corresponding)
ISBI-20
ISBI-20
Transportation & Mobility 1
Trans. Res. Part D
Time-Series Fuel Consumption Prediction Assessing Delay Impacts on Energy using Vehicular Trajectory
Kabir, R., Remias, S., Wadell, J. and Zhu, D. — Transportation Research Part D, 2023
Electronic Health Records & Precision Medicine 6
BIBM-19
Prioritization of Multi-Level Risk Factors for Obesity
Wang, L., Dong, M., Towner, E. and Zhu, D.
Exp. Syst. Appl.
A Deep Active Survival Analysis Approach for Precision Treatment Recommendations: Application in Prostate Cancer
Nezhad, M.Z., Sadati, N., Yang, K. and Zhu, D. — Expert Systems with Applications, 2019
IEEE-BHI-18
Obesity Risk Factors Ranking Using Multi-Task Learning
Wang, L., Zhu, D., Towner, E. and Dong, M.
BIBM-17
AMIA-17
SDT: A Tree Method for Detecting Patient Subgroups with Personalized Risk Factors
Li, X., Zhu, D., Dong, M., Nezhad, M.Z. and Levy, P.
IEEE BIBM-16
SAFS: A Deep Feature Selection Approach for Precision Medicine
Nezhad, M.Z., Zhu, D., Li, X., Yang, C. and Levy, P.

Bioinformatics & Computational Biology

Journals 10
IJMS
Saliva microRNA Profile in Children with and without Severe SARS-CoV-2 Infection
Hicks, S.D., Zhu, D., Sullivan, R., Kannikeswaran, N., Meert, K., Chen, W., Suresh, S. and Sethuraman, U. — IJMS, 24(9), 2023
Pediatric Res.
Putting the 'mi' in omics: Discovering miRNA Biomarkers for Pediatric Precision Care
Li, C., Sullivan, R., Zhu, D. and Hicks, S. — Pediatrics Research, 2022
Quant. Biology
Transcriptome Assembly Strategies for Precision Medicine
Wang, L., Acharya, L., Bai, C. and Zhu, D. — Quantitative Biology, 2017
Brief. Funct. Genomics
An Overview of Bioinformatics Methods for Modeling Biological Pathways in Yeast
Hou, J., Acharya, L., Zhu, D. and Chen, J. — Briefings in Functional Genomics, 15(2), 95–108, 2016
IEEE TNB
An Event-Based Computational Framework for Comparing Transcriptomes
Zhu, D., Deng, N. and Bai, C. — IEEE Transaction on NanoBioScience, 2014
PLoS ONE
Nucleic Acids Res.
TEAK: Topological Enrichment Analysis frameworK for Detecting Activated Biological Subpathways
Judeh, T., Johnson, C., Kumar, A. and Zhu, D. — Nucleic Acids Res., 2013
Bioinformatics
Optimal Structural Inference of Signaling Pathways from Overlapping and Unordered Gene Sets
Acharya, L., Judeh, T., Wang, G. and Zhu, D. — Bioinformatics, 28(4), 546–556, 2012
IEEE/ACM TCBB
GSGS: A Computational Framework for Reconstructing Signaling Pathways from Gene Sets
Acharya, L., Judeh, T., Duan, Z., Rabbat, M. and Zhu, D. — IEEE/ACM TCBB, 9(2), 438–450, 2011
Nucleic Acids Res.
Isoform-Level microRNA-155 Target Prediction using RNA-seq
Deng, N., Puetter, A., Zhang, K., Johnson, K., Zhao, Z., Taylor, C., Flemington, E. and Zhu, D. — Nucleic Acids Res., 2011
Conference & Technical Reports 3
ACM BCB-13
Detecting Various Types of Differential Splicing Events using RNA-Seq Data
Deng, N. and Zhu, D. — ACM Conference on Bioinformatics, 2013
IEEE/ACM TCBB
A Generalized Multivariate Approach to Pattern Discovery from Replicated and Incomplete Genome-Wide Measurements
Zhu, D., Acharya, L. and Zhang, H. — IEEE/ACM TCBB, 8(5), pp 1153–1169, 2011
Src Code Bio Med
SAMMate: A GUI Tool for Processing Short Read Alignment Information in SAM/BAM Format (7,000+ downloads)
Xu, G., Deng, N., Zhao, Z., Flemington, E.K. and Zhu, D. — Source Code for Biology and Medicine, 6:2, 2011