*: Equal First-Author Contributions; **: Corresponding/Supervising Author; IF=Impact Factor, h-index=GG Scholar Index
Disclaimer: In Computer Science and Bioinformatics, Conference Proceedings are considered esteemed research outputs. For more information on Conference Ranking, please visit: https://csrankings.org/
--- 2025 ---
Jungyoun Janice Min, Jiong Chen, Jingxuan Bao, Shu Yang, Yize Zhao, Li Shen, Duy Duong-Tran*. "Integrating Slow Neural Oscillations and Physiological Burden for Train Anxiety Prediction." accepted, in-press in 2025 NeurIPS Workshop Time-Series for Health (TS4H) [Thirty-Ninth Annual Conference on Neural Information Processing Systems, Rank A++].
Frederick Xu, Duy Duong-Tran, Heng Huang, Andrew Saykin, Paul Thompson, Christos Davatzikos, Yize Zhao, Li Shen. "Quantifying Amyloid Spread in Alzheimer’s Disease Through A Network Diffusion Model." accepted, in-press in 2025 Association for Computing Machinery on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB), Philadelphia, PA.
Sophie Kearney, Shu Yang, Zixuan Wen, Bojian Hou, Duy Duong-Tran, Tianlong Chen, Jason Moore, Marylyn Ritchie, Li Shen. "Few-Shot Alzheimer’s Disease Diagnosis on Tabular Biomarker Data with Large Language Models." accepted, in-press in 2025 Association for Computing Machinery on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB), Philadelphia, PA.
Chen H, Shukla R, Wu R, Yang S, Duong-Tran D, Nguyen DMH, Niepert M, Beeche C, Gee J, Duda J, Sharma R, Davaztikos C, Witschey W, Hou B, Shen L. (2025) "Adapting Vision-Language Models for 3D CT/MRI Understanding on PMBB via Slice Selection and Explanation Analysis." ICCV-VADH’25: ICCV Workshop on Vision-Based AI for Digital Health: From Pixels to Practice, Oct 19-20, 2025, in press
Duy Minh Ho Nguyen, Trung Quoc Nguyen, Ha Thi Hong Le, Mai Thanh Nhat Truong, TrungTin Nguyen, Nhat Ho, Khoa D Doan, Duy Duong-Tran, Li Shen, Daniel Sonntag, James Zou, Mathias Niepert, Hyojin Kim, Jonathan E Allen. "From Fragments to Geometry : A Unified Graph Transformer for Molecular Representation from Conformer Ensembles." accepted in the 2025 International Conference on Machine Learning (ICML) 2nd Workshop on Generative AI and Biology (GenBIO)
Bach Viet Nguyen, Tianlong Chen, Shu Yang, Bojian Hou, Li Shen, Duy Duong-Tran. "Evaluating topological fitness of human brain-inspired sub-circuits in Echo State Networks". (2025) in-press Proceedings of Machine Learning Research (PMLR) - 2025 Association for the Advancement of Artificial Intelligence (AAAI): Bridge Program's AI for Medical Health (AIMedHealth), Philadelphia, Pennsylvania, February, 2025. [Archived] [Honor: Runner-up paper Award!]
Joseph Lee, Shu Yang, Jae Young Baik, Xiaoxi Liu, Zhen Tan, Dawei Li, Zixuan Wen, Bojian Hou, Duy Duong-Tran, Tianlong Chen, and Li Shen. "Knowledge-Driven Feature Selection and Engineering for Genotype Data with Large Language Models." (2025) in-press 2025 American Medical Informatics Association Informatics Summit (AMIA-IS), Pittsburgh, PA. [Honor: Marco Ramoni Distinguished Paper Award for Translational Bioinformatics]
--- 2024 ---
Dawei Li, Shu Yang, Zhen Tan, Jae Young Baik, Sukwon Yun, Joseph Lee, Aaron Chacko, Bojian Hou, Duy Duong-Tran, Ying Ding, Huan Liu, Li Shen, Tianlong Chen "DALK: Dynamic Co-Augmentation of Large Language Models and Knowledge Graph to answer Alzheimer’s Disease Questions with Scientific Literature." (2024) published in the 62nd Annual Meeting - Empirical Methods on Natural Language Processing (EMNLP 2024, Rank A++ in CSRanking). [DOI Link] [Archived Link]
Duy Nguyen, An T. Le, Nghiem Diep, Trung Nguyen, Duy Duong-Tran, Binh T. Nguyen, Jan Peters, Li Shen, Mathias Niepert, Daniel Sonntag. "Dude: Dual Distribution-Aware Context Prompt Learning For Large Vision-Language Model." (2024) published in the 16th Asian Conference on Machine Learning (ACML; Rank: A) [Published Link] [Archived Link]
Nghi Nguyen, Tao Hou, Enrico Amico, Jinny Zheng, Huajun Huang, Alan D. Kaplan, Giovanni Petri, Joaquin Goni, Ralph Kaufmann, Yize Zhao, Li Shen, Duy Duong-Tran**. "Volume-optimal persistence homological scaffolds of hemodynamic networks covary with MEG theta-alpha aperiodic dynamics." (2024) Conference Paper published in the 2024 Medical Image Computing and Computer Assisted Intervention (MICCAI - Rank: A1). [Publication Link] [top 11% out of 2869 submissions]
Duy Duong-Tran*, Mark Magsino*, Joaquin Goni, and Li Shen. "PRESERVING HUMAN LARGE-SCALE BRAIN CONNECTIVITY FINGERPRINT IDENTIFIABILITY WITH RANDOM PROJECTIONS." (2024) published in the 21st IEEE International Symposium on Biomedical Imaging (ISBI), IEEE Xplore Index, 2024. [DOI Link]
Frederick H. Xu, Michael Gao, Jiong Chen, Sumita Garai, Duy Duong-Tran, Yize Zhao, Li Shen. (2024) "Topology-based Clustering of Functional Brain Networks in an Alzheimer’s Disease Cohort." (2024) Conference paper published in AMIA-IS’24: AMIA Informatics Summit. [Publication Link]
Duong-Tran, D., Siqing Wei, Li Shen. "Theorizing neuro-induced relationships between cognitive diversity, motivation, grit and academic performance in multidisciplinary engineering education context." (2024) Conference Paper published in 2024 American Society of Engineering Education Conference, Portland, Oregon. [Publication Link]
Frederick Xu, Duy Duong-Tran, Yize Zhao, Li Shen. "Caudal and Thalamic Segregation in White Matter Brain Network Communities in Alzheimer's Disease Population." (2024) published in IEEE-EMBS International Conference on Biomedical and Health Informatics (IEEE BHI). [Publication Link]
Dachuan Song, Li Shen, Duy Duong-Tran, Xuan Wang. "Subject and Task Fingerprint using Dynamics Reconstruction from fMRI Time-series Data." (2024) accepted with oral presentation category (top 38 out of 204 submissions) in the 15th Association for Computing Machinery Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB). [2024] ACM-BCB has h5-index=28 and h5-median=50. [DOI Link]
--- <=2023 ---
S Garai, F Xu, D Duong-Tran, Y Zhao, L Shen. "Mining Correlation between Fluid Intelligence and Whole-brain Large Scale Structural Connectivity". (2023) Published in AMIA Summits on Translational Science Proceedings, 225
F Xu, S Garai, D Duong-Tran, AJ Saykin, Y Zhao, L Shen. "Consistency of Graph Theoretical Measurements of Alzheimer’s Disease Fiber Density Connectomes Across Multiple Parcellation Scales". (2022) pg 1323-1328. published in 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). Acceptance Rate=19.65%.
[Under Review/Revisions]
Farica Zhuang, Shu Yang, Zixuan Wen, Duy Duong-Tran, ...., Li Shen. "Mixture of REGIONAL BRAIN EXPERTS in ALZHEIMERS DIAGNOSIS" under-review in 2026 IEEE Index Symposium.
Jiong Chen, ..., Jingxuan Bao, Shu Yang, Duy Duong-Tran, ..., Li Shen. "Multi-Modality Cell Segmentation in Spatial Transcriptomics: Integrating Imaging and Molecular Data." pending submission to AMIA 2026 Informatics Summit.
Farica Zhuang, Dinara Aliyeva, Shu Yang, Duy Duong-Tran, Tianlong Chen, Song Wang, Li Shen. A Fusion DL Framework Interface Between Multimodal Neuroimaging and Large Language Model [application in AD/ADRD prediction] pending submission to AMIA 2026 Informatics Summit.