Selected Publications

Bao J, Wen J, Chang C, Mu S, Chen J, Shivakumar M, Cui Y, Erus G, Yang Z, Yang S, Wen Z; Alzheimer’s Disease Neuroimaging Initiative; Zhao Y, Kim D, Duong-Tran D, Saykin AJ, Zhao B, Davatzikos C, Long Q, Shen L.: A genetically informed brain atlas for enhancing brain imaging genomics. Nat Commun 16: 3524, Apr 2025.

Chen J, Ionita M, Feng Y, Lu Y, Orzechowski P, Garai S, Hassinger K, Bao J, Wen J, Duong-Tran D, Wagenaar J, McKeague ML, Painter MM, Mathew D, Pattekar A, Meyer NJ, Wherry EJ, Greenplate AR, Shen L.: Automated cytometric gating with human-level performance using bivariate segmentation. Nat Commun 16: 1576, Feb 2025.

Xu J, Wei T, Hou B, Orzechowski P, Yang S, Jin R, Paulbeck R, Wagenaar J, Demiris G, Shen L.: MentalChat16K: A Benchmark Dataset for Conversational Mental Health Assistance. KDD'25: 31st ACM SIGKDD Conference on Knowledge Discovery and Data Mining 2025.

Jin R, Hou B, Xiao J, Su WJ, Shen L: Fine-Tuning Attention Modules Only: Enhancing Weight Disentanglement in Task Arithmetic. ICLR’25: The International Conference on Learning Representations 2025.

Xiao J, Hou B, Wang Z, Jin R, Long Q, Su WJ, Shen L: Restoring Calibration for Aligned Large Language Models: A Calibration-Aware Fine-Tuning Approach. ICML’25: Forty-second International Conference on Machine Learning 2025.

Hou B, Wen Z, Bao J, Zhang R, Tong B, Yang S, Wen J, Cui Y, Moore JH, Saykin AJ, Huang H, Thompson PM, Ritchie MD, Davatzikos C, Shen L; Alzheimer’s Disease Neuroimaging Initiative.: Interpretable deep clustering survival machines for Alzheimer's disease subtype discovery. Med Image Anal 2024.

Li D, Yang S, Tan Z, Baik JY, Yun S, Lee J, Chacko A, Hou B, Duong-Tran D, Ding Y, Liu H*, Shen L*, Chen T*: DALK: Dynamic co-augmentation of LLMs and KG to answer Alzheimer's disease questions with scientific literature. EMNLP’24: The 2024 Conference on Empirical Methods in Natural Language Processing 2024.

Zhou Z, Tarzanagh DA, Hou B, Long Q, Shen L.: Fairness-Aware Estimation of Graphical Models. NeurIPS’24: 38th Conference on Neural Information Processing Systems 2024.

Wang Z, Zhan Q, Yang S, Mu S, Chen J, Garai S, Orzechowski P, Wagenaar J, Shen L.: QOT: Quantized Optimal Transport for sample-level distance matrix in single-cell omics. Brief Bioinform 26: bbae713, Nov 2024.

Yan Jingwen, Du Lei, Kim Sungeun, Risacher Shannon L, Huang Heng, Moore Jason H, Saykin Andrew J, Shen Li: Transcriptome-guided amyloid imaging genetic analysis via a novel structured sparse learning algorithm. Bioinformatics (Oxford, England) 30(17): i564-71, Sep 2014.

Shen Li, Kim Sungeun, Risacher Shannon L, Nho Kwangsik, Swaminathan Shanker, West John D, Foroud Tatiana, Pankratz Nathan, Moore Jason H, Sloan Chantel D, Huentelman Matthew J, Craig David W, Dechairo Bryan M, Potkin Steven G, Jack Clifford R, Weiner Michael W, Saykin Andrew J: Whole genome association study of brain-wide imaging phenotypes for identifying quantitative trait loci in MCI and AD: A study of the ADNI cohort. NeuroImage 53(3): 1051-63, Nov 2010.

Yao Xiaohui, Risacher Shannon L, Nho Kwangsik, Saykin Andrew J, Wang Ze, Shen Li: Targeted genetic analysis of cerebral blood flow imaging phenotypes implicates the INPP5D gene. Neurobiology of aging 81: 213-221, Sep 2019 Notes: https://doi.org/10.1016/j.neurobiolaging.2019.06.003.

Shen L, Thompson PM: Brain imaging genomics: integrated analysis and machine learning. Proceedings of the IEEE 108(1): 125-162, 2020 Notes: https://doi.org/10.1109/JPROC.2019.2947272

Bao, J., Wen, J., Wen, Z., Yang, S., Cui, Y., Yang, Z., Erus, G., Saykin, A. J., Long, Q., Davatzikos, C., Shen, L.: Brain-wide genome-wide colocalization study for integrating genetics, transcriptomics and brain morphometry in Alzheimer''s disease. Neuroimage 280: 120346, 2023.

Zhuoping Zhou, Davoud Ataee Tarzanagh, Bojian Hou, Boning Tong, Jia Xu, Yanbo Feng, Qi Long, Li Shen: Fair Canonical Correlation Analysis. NeurIPS’23: 37th Conference on Neural Information Processing Systems Page: https://openreview.net/forum?id=W3cDd5xlKZ, 2023 Notes: Proceeding represents original peer-reviewed research.

Jin R, Hou B, Tong B, Yang S, Shen L: ICAFS: Inter-Client-Aware Feature Selection for Vertical Federated Learning. IEEE Transactions on Artificial Intelligence (in press) 2026.