My Bibliography

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Orlenko A, Li B, Khanjani N, Venkatesan M, Shen L, Ritchie MD, Wang ZP, Obafemi-Ajayi T, Moore JH. A random-walk-based learning framework to uncover novel gene candidates for Alzheimer's disease therapy. Pac Symp Biocomput. 2026;31:815-829. doi: 10.1142/9789819824755_0059. PubMed PMID: 41758187; PubMed Central PMCID: PMC12952682.

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Venkatesh R, Cherlin T, BioBank PM, Ritchie MD, Guerraty MA, Verma SS. Integrating Imaging-Derived Clinical Endotypes with Plasma Proteomics and External Polygenic Risk Scores Enhances Coronary Microvascular Disease Risk Prediction. Pac Symp Biocomput. 2026;31:612-628. doi: 10.1142/9789819824755_0045. PubMed PMID: 41758173; PubMed Central PMCID: PMC12952676.

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Lopez-Garcia G, Xu D, Luu M, Zheng R, Daskivich TJ, Gonzalez-Hernandez G. Scoring Physician Risk Communication in Prostate Cancer Using Large Language Models. Pac Symp Biocomput. 2026;31:71-84. doi: 10.1142/9789819824755_0006. PubMed PMID: 41758134; NIHMSID:NIHMS2173315.

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Du L, Yan J, Kim S, Risacher SL, Huang H, Inlow M, Moore JH, Saykin AJ, Shen L. GN-SCCA: GraphNet based Sparse Canonical Correlation Analysis for Brain Imaging Genetics. Brain Informatics and Health, BIH 2015, LNAI 9250. Forthcoming.

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Li H, Fang S, Goni J, contreras JA, Liang Y, Cai C, West JD, Risacher SL, Wang Y, Sporns O, Saykin AJ, Shen L. Integrated Visualization of Human Brain Connectome Data. Brain Informatics and Health, BIH 2015, LNAI 9250. Forthcoming.

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Nair AA, Wen Z, Wang Z, Yan J, Saykin AJ, Huang H, Thompson PM, Davatzikos C, Shen L. Staging and Pseudotime Inference of Alzheimer's Disease Progression using Multimodal Imaging Data. Proc (IEEE Int Conf Healthc Inform). 2026;2026:331-340. doi: 10.1109/ichi69079.2026.00051. Epub 2026 Aug 12. PubMed PMID: 42609863; PubMed Central PMCID: PMC13480406.

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Zhuang F, Yang S, Aliyeva D, Wen Z, Duong-Tran D, Davatzikos C, Chen T, Wang S, Shen L. Interpretable Alzheimer's Diagnosis via Multimodal Fusion of Regional Brain Experts. Proc (IEEE Int Conf Healthc Inform). 2026;2026:311-320. doi: 10.1109/ichi69079.2026.00049. Epub 2026 Aug 12. PubMed PMID: 42609893; PubMed Central PMCID: PMC13480405.

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Zhao L, Zhai T, Shen L. UniPocket: Unified Ligand and Cryptic Pocket Prediction from Protein Language Model Embeddings. ACM BCB. 2026;2026. doi: 10.1145/3807503.3819482. Epub 2026 Jul 28. PubMed PMID: 42605276; PubMed Central PMCID: PMC13477581.

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Wang Z, Zhou Z, Zhan Q, Shen L. Faithful Supervised Dimensionality Reduction for Biomedical Data via Decision Geometry. ACM BCB. 2026;2026. doi: 10.1145/3807503.3819496. Epub 2026 Jul 28. PubMed PMID: 42605274; PubMed Central PMCID: PMC13477580.

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Tate Q, Markova DZ, Bao J, Shofer FS, Chen K, Kepler CK, Canseco JA, Baker JF, Dillingham T, Shen L, Zhang Y. Serum IL-19 and Biglycan as Candidate Biomarkers by Proteomic Approach in Patients with Severe Low Back Pain-a Pilot Study. Am J Phys Med Rehabil. 2026 Jul 17;. doi: 10.1097/PHM.0000000000003103. [Epub ahead of print] PubMed PMID: 42464048.

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Lee J, Shang T, Baik JY, Duong-Tran D, Yang S, Li L, Shen L. From Promising Capabilities to Pervasive Bias: Assessing Large Language Models for Emergency Department Triage. J Healthc Inform Res. 2026 Jun 22;. doi: 10.1007/s41666-026-00241-z. [Epub ahead of print] PubMed PMID: 42582984; PubMed Central PMCID: PMC13459022.

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Ballard JL, Dai Z, Shen L, Long Q. A powerful representation learning method for enhanced analysis of incomplete multi-omics data. NPJ Syst Biol Appl. 2026 Jun 11;. doi: 10.1038/s41540-026-00759-3. [Epub ahead of print] PubMed PMID: 42277071.

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Qi X, Ruan JY, Zhong J, Wan Y, Wei DH, Ko E, Yang S, Shen L, Wu B. The landscape of knowledge graph and large language model-augmented knowledge graph applications in dementia caregiving support: a scoping review. Gerontologist. 2026 Jun 9;66(7). doi: 10.1093/geront/gnag125. PubMed PMID: 42286794; PubMed Central PMCID: PMC13318221.

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Garai S, Chen H, Xu F, Duong-Tran D, Chaudhari P, Davatzikos C, Brown BC, Shen L. Robust FDR Control for Neuroimaging-based Classification via Knockoffs. AMIA Jt Summits Transl Sci Proc. 2026;2026:137-146. eCollection 2026. PubMed PMID: 42317833; PubMed Central PMCID: PMC13274285.

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Shang T, He W, Zheng C, Li L, Shen L, Zhao B. DynamiCare: A Dynamic Multi-Agent Framework for Interactive and Open-Ended Medical Decision-Making. AMIA Jt Summits Transl Sci Proc. 2026;2026:408-417. eCollection 2026. PubMed PMID: 42317840; PubMed Central PMCID: PMC13274293.

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Ballard JL, Shen L, Long Q. Adaptive Integration of Incomplete Multimodal 3D Neuroimaging for Alzheimer's Prediction and Biomarker Discovery. AMIA Jt Summits Transl Sci Proc. 2026;2026:67-76. eCollection 2026. PubMed PMID: 42317807; PubMed Central PMCID: PMC13274276.

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Scholten C, McMaster EM, Saunders AM, Kim ME, Rudravaram G, Levy E, Geeraert B, Zuo L, Vandekar S, Lebel C, Landman BA. EVALUATION OF NEUROCOMBAT AND DEEP LEARNING HARMONIZATION FOR MULTI-SITE MAGNETIC RESONANCE NEUROIMAGING IN YOUTH WITH PRENATAL ALCOHOL EXPOSURE. Proc IEEE Int Symp Biomed Imaging. 2026;2026. doi: 10.1109/ISBI61048.2026.11515988. Epub 2026 May 20. PubMed PMID: 42583342; PubMed Central PMCID: PMC13460268.

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Xu FH, Duong-Tran D, Huang H, Saykin AJ, Thompson PM, Davatzikos C, Zhao Y, Shen L. Gene-Modulated Network Diffusion for Improved Modeling of Amyloid- β Spread in Alzheimer's Disease. bioRxiv. 2026 May 7;. doi: 10.64898/2026.05.04.722725. PubMed PMID: 42146687; PubMed Central PMCID: PMC13174398.

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Zhang Q, Chang C, Jin C, Shen L, Long Q. Simultaneous Representation Learning of Multi-Omics and Clinical Outcome Data via a Supervised Knowledge-Guided Bayesian Factor Model. Stat Med. 2026 May;45(10-12):e70570. doi: 10.1002/sim.70570. PubMed PMID: 42035335; PubMed Central PMCID: PMC13110451.

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Chandio BQ, Olivetti E, Romero-Bascones D, Thomopoulos SI, Villalon-Reina JE, Nir TM, Harezlak J, Thompson PM, Garyfallidis E. BundleWarp: Enhancing white matter tractometry and morphometry with precise neuronal mapping using streamline-based nonlinear registration. Med Image Anal. 2026 Jul;112:104114. doi: 10.1016/j.media.2026.104114. Epub 2026 Apr 28. PubMed PMID: 42091035; NIHMSID:NIHMS2172951.

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Goldstein D, Sahelijo N, Priyadarshi D, Panitch R, Nho K, Farrer LA, Stein TD, Jun GR. Blood-Brain Network-Based Polygenic Risk Scores Reveal Biomarker Signatures and the Progression of Alzheimer's Disease. J Clin Med. 2026 Apr 10;15(8). doi: 10.3390/jcm15082885. PubMed PMID: 42074686; PubMed Central PMCID: PMC13116307.

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Schwartz TM, McMaster EM, Rudravaram G, Cho C, Krishnan A, Kim ME, Samir J, Bilgel M, Resnick S, Beason-Held L, Landman BA, Li Z. Modeling a Shared Reality of Tractography through Varied Structural Imaging. Proc SPIE Int Soc Opt Eng. 2026;13925. doi: 10.1117/12.3086475. Epub 2026 Apr 3. PubMed PMID: 42266433; PubMed Central PMCID: PMC13245530.

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Yoon J, McMaster EM, Kim ME, Rudravaram G, Schilling KG, Landman BA, Moyer D. Fully Differentiable dMRI Streamline Propagation in PyTorch. Proc SPIE Int Soc Opt Eng. 2026;13925. doi: 10.1117/12.3086590. Epub 2026 Apr 3. PubMed PMID: 42266435; PubMed Central PMCID: PMC13245533.

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Kim ME, Rudravaram G, Saunders A, Gao C, Ramadass K, Newlin NR, Kanakaraj P, Bogdanov S, Archer D, Hohman TJ, Jefferson AL, Morgan VL, Roche A, Englot DJ, Resnick SM, Held LLB, Bilgel M, Cutting LE, Barquero LA, D'Archangel MA, Nguyen TQ, Humphreys KL, Niu Y, Vinci-Booher S, Cascio CJ, Pechman KR, Shashikumar N, HABS-HD Study Team, Alzheimer’s Disease Neuroimaging Initiative, BIOCARD Study Team, Li Z, Vandekar SN, Zhang P, Gore JC, Liu Y, Zuo L, Schilling KG, Moyer DC, Landman BA. Analytic Bounds on GAMLSS Model Variability of Normative White Matter Brain Charts. Proc SPIE Int Soc Opt Eng. 2026;13930. doi: 10.1117/12.3085643. Epub 2026 Apr 2. PubMed PMID: 42267358; PubMed Central PMCID: PMC13245483.

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McMaster EM, Rudravaram G, Kim ME, Schwartz TM, Scholten C, Yoon J, Saunders AM, Hucke ATS, Ramadass K, Harriott EM, Meisler SL, Vandekar SN, Newton A, Smith SA, Sengupta S, Humphreys KL, Osmundson S, Moyer D, Cutting LE, Landman BA. HARMONIZATION MITIGATES DIFFUSION MRI SCANNER EFFECTS IN INFANCY: INSIGHTS FROM THE HEALTHY BRAIN AND CHILD DEVELOPMENT (HBCD) STUDY. Proc IEEE Int Symp Biomed Imaging. 2026 Apr;2026. doi: 10.1109/isbi61048.2026.11515503. Epub 2026 May 20. PubMed PMID: 42183016; PubMed Central PMCID: PMC13193239.

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Shao S, Ribeiro PH, Orlenko A, Cardone KM, Ramirez CM, Shen L, Ritchie MD, Moore JH. A biology-based quality-diversity algorithm for drug repurposing in Alzheimer's disease using automated machine learning. BioData Min. 2026 Mar 30;19(1). doi: 10.1186/s13040-026-00550-4. PubMed PMID: 41913218; PubMed Central PMCID: PMC13159293.

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Li B, Saini AK, Hernandez JG, Moore JH. Agentic AI and the rise of in silico team science in biomedical research. Nat Biotechnol. 2026 May;44(5):711-725. doi: 10.1038/s41587-026-03035-1. Epub 2026 Feb 24. Review. PubMed PMID: 41735549.

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Bice PJ, Nho K, Ertekin-Taner N, Saykin AJ. Systems biology of Alzheimer's Disease: a scoping review of key pathways and mechanisms. Mol Neurodegener. 2026 Feb 23;21(1). doi: 10.1186/s13024-026-00934-4. PubMed PMID: 41731612; PubMed Central PMCID: PMC13032323.

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Tong M, Mehfooz F, Zhang S, Wang Y, Fang S, Saykin AJ, Wang X, Yan J. Learning a Continuous Progression Trajectory of Amyloid in Alzheimer disease. bioRxiv. 2026 Feb 18;. doi: 10.64898/2026.02.03.703568. PubMed PMID: 41676727; PubMed Central PMCID: PMC12889634.

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Chattopadhyay T, Senthilkumar P, Ankarath RH, Patterson C, Gleave EJ, Thomopoulos SI, Huang H, Shen L, You L, Zhi D, Thompson PM. Deep learning to predict future cognitive decline: a multimodal approach using brain MRI and clinical data. Front Neuroimaging. 2026;5:1726037. doi: 10.3389/fnimg.2026.1726037. eCollection 2026. PubMed PMID: 41717278; PubMed Central PMCID: PMC12913073.

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Rudravaram G, Zuo L, Saunders AM, Kim ME, Kanakaraj P, Newlin NR, Krishnan AR, McMaster EM, Cho C, Resnick SM, Beason Held LL, Archer D, Hohman TJ, Moyer DC, Landman BA. Characterizing Continuous and Discrete Hybrid Latent Spaces for Structural Connectomes. Proc SPIE Int Soc Opt Eng. 2026 Feb;13925. doi: 10.1117/12.3086529. Epub 2026 Apr 3. PubMed PMID: 42181986; PubMed Central PMCID: PMC13196825.

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McMaster EM, Kim ME, Newlin NR, Rudravaram G, Saunders AM, Krishnan AR, Yoon J, Kim JS, Geeraert BL, Perdue MV, Lebel C, Moyer D, Schilling KG, Cutting LE, Landman BA. Personalized White Matter Bundle Segmentation for Early Childhood. Proc SPIE Int Soc Opt Eng. 2026 Feb;13925. doi: 10.1117/12.3086478. Epub 2026 Apr 3. PubMed PMID: 42266436; PubMed Central PMCID: PMC13245480.

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Scollard P, Mukherjee S, Choi SE, Lee ML, Klinedinst B, Gibbons LE, Trittschuh EH, Mez J, Saykin AJ, James BD, Proust-Lima C, Crane PK. Heterogeneous patterns of cognitive decline in Alzheimer's disease across three domains of cognition. J Alzheimers Dis. 2026 Mar;110(1):383-396. doi: 10.1177/13872877251414975. Epub 2026 Jan 28. PubMed PMID: 41603331; PubMed Central PMCID: PMC12934236.

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Wang Z, Zhan Q, Yang S, Zhou Z, Kan M, Zhai T, Shen L. An interpretable Graph-Regularized Optimal Transport Framework for Diagonal Single-Cell Integrative Analysis. Gigascience. 2026 Jan 21;15. doi: 10.1093/gigascience/giag012. PubMed PMID: 41661124; PubMed Central PMCID: PMC12970605.

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Cody KA, Sokołowski A, Johns E, Guerra LM, Winer JR, Young CB, Younes K, Dumitrescu L, Archer DB, Durant A, Sathe A, Koran MEI, Mez J, Saykin AJ, Toga A, Cuccaro M, Tosun D, Insel PS, Johnson SC, Harrison TM, Hohman TJ, Mormino EC. Characterizing amyloid and tau positron emission tomography-based stages across the clinical continuum. Alzheimers Dement. 2026 Jan;22(1):e71017. doi: 10.1002/alz.71017. PubMed PMID: 41505234; PubMed Central PMCID: PMC12782155.

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Noshin K, Boland MR, Hou B, Lu V, Manning C, Shen L, Zhang A. Uncovering Important Diagnostic Features for Alzheimer's, Parkinson's and Other Dementias Using Interpretable Association Mining Methods. Pac Symp Biocomput. 2025;30:631-646. PubMed PMID: 39670401; PubMed Central PMCID: PMC11649014.

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Jones SC, Cardone KM, Bradford Y, Tishkoff SA, Ritchie MD. The Impact of Ancestry on Genome-Wide Association Studies. Pac Symp Biocomput. 2025;30:251-267. doi: 10.1142/9789819807024_0019. PubMed PMID: 39670375; PubMed Central PMCID: PMC11694900.

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Moore A, Venkatesh R, Levin MG, Damrauer SM, Reza N, Cappola TP, Ritchie MD. Connecting intermediate phenotypes to disease using multi-omics in heart failure. Pac Symp Biocomput. 2025;30:504-521. doi: 10.1142/9789819807024_0036. PubMed PMID: 39670392; PubMed Central PMCID: PMC11822568.

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He B, Zhang S, Risacher SL, Saykin AJ, Yan J. Multi-modal Imaging-based Pseudotime Analysis of Alzheimer progression. Pac Symp Biocomput. 2025;30:664-674. doi: 10.1142/9789819807024_0047. PubMed PMID: 39670403; PubMed Central PMCID: PMC12044618.

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Jin R, Tong B, Yang S, Hou B, Shen L, Alzheimer’s Disease Neuroimaging Initiative. ICAFS: Inter-Client-Aware Feature Selection for Vertical Federated Learning. IEEE Trans Artif Intell. 2025 Dec 23;. doi: 10.1109/tai.2025.3647596. [Epub ahead of print] PubMed PMID: 41684643; PubMed Central PMCID: PMC12893625.

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Hou B, Wang Z, Zhou Z, Tong B, Wang Z, Bao J, Duong-Tran D, Long Q, Shen L. Fair CCA for Fair Representation Learning: An ADNI Study. ACM BCB. 2025;2025. doi: 10.1145/3765612.3767215. Epub 2025 Dec 10. PubMed PMID: 41488125; PubMed Central PMCID: PMC12758915.

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Kearney S, Yang S, Wen Z, Hou B, Duong-Tran D, Chen T, Moore J, Ritchie M, Shen L. Enabling Few-Shot Alzheimer's Disease Diagnosis on Biomarker Data with Tabular LLMs. ACM BCB. 2025;2025. doi: 10.1145/3765612.3767229. Epub 2025 Dec 10. PubMed PMID: 41488128; PubMed Central PMCID: PMC12758912.

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Xu FH, Duong-Tran D, Huang H, Saykin AJ, Thompson P, Davatzikos C, Zhao Y, Shen L. Characterizing Amyloid Pathogenic Spread in Alzheimer's Disease Through A Network Diffusion Model. ACM BCB. 2025;2025. doi: 10.1145/3765612.3767223. Epub 2025 Dec 10. PubMed PMID: 41488126; PubMed Central PMCID: PMC12758910.

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Garai S, Vo S, Blank L, Xu F, Chen J, Duong-Tran D, Zhao Y, Brown BC, Shen L. H-VIP: quantifying regional topological contributions of the brain network to cognition. Front Radiol. 2025;5:1686780. doi: 10.3389/fradi.2025.1686780. eCollection 2025. PubMed PMID: 41427113; PubMed Central PMCID: PMC12711701.

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Noshin K, Hou B, Boland MR, Wen Z, Tong B, Shen L, Zhang A. IRIS: Interpretable Risk Clustering Intelligence for Survival Analysis. Proc IEEE Int Conf Big Data. 2025 Dec;2025:1143-1152. doi: 10.1109/bigdata66926.2025.11402028. Epub 2026 Mar 6. PubMed PMID: 41809690; PubMed Central PMCID: PMC12971063.

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Jo T, Lee EH, Alzheimer’s Disease Neuroimaging Initiative (ADNI) and the Alzheimer’s Disease Sequencing Project (ADSP). Uncertainty-aware genomic classification of Alzheimer's disease: a transformer-based ensemble approach with Monte Carlo dropout. Brief Bioinform. 2025 Nov 1;26(6). doi: 10.1093/bib/bbaf587. PubMed PMID: 41212591; PubMed Central PMCID: PMC12599309.

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Song D, Shen L, Duong-Tran D, Wang X. Reconstructing brain causal dynamics for subject and task fingerprints using fMRI time-series data. Health Inf Sci Syst. 2025 Dec;13(1):70. doi: 10.1007/s13755-025-00388-w. eCollection 2025 Dec. PubMed PMID: 41170153; PubMed Central PMCID: PMC12569264.

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Chen R, Ghosh A, Hu J, Chen Y, Moore JH, Li R. Beyond P-values: A Multi-Metric Framework for Robust Feature Selection and Predictive Modeling. bioRxiv. 2025 Oct 6;. doi: 10.1101/2025.10.05.680380. PubMed PMID: 41279448; PubMed Central PMCID: PMC12632522.

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Abughofah Y, Risacher SL, Unverzagt FW, Farlow MR, Apostolova LG, Brosch JR, Clark DG, Mathew S, Gao S, Wang S, Wang S, Saykin AJ. The Cognitive Change Index in the Alzheimer's Disease Research Center setting: Self- and informant-ratings for perceived cognitive decline. Alzheimers Dement. 2025 Oct;21(10):e70754. doi: 10.1002/alz.70754. PubMed PMID: 41027849; PubMed Central PMCID: PMC12483767.

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Shang T, Yang S, Zhai T, He W, Mamourian E, Zhang J, Hou B, Lee J, Duong-Tran D, Moore JH, Ritchie MD, Shen L. A novel computational analysis integrating social determinants information from EHR and literature with Alzheimer's disease biological knowledge through large language models and knowledge graphs. Innov Aging. 2025 Dec;9(Suppl 1):S2-S13. doi: 10.1093/geroni/igaf102. eCollection 2025 Dec. PubMed PMID: 41458885; PubMed Central PMCID: PMC12742847.