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UF Health University of Florida
Department of Neurology College of Medicine
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iBRAIN Lab Overview

Babak Ahmadi

Research Interests

My research lies at the intersection of machine learning and neuroscience, where I build scalable and interpretable models for multimodal brain data (MRI, PET, and MEG). In the iBRAIN Lab, I develop end-to-end pipelines for large multi-site neuroimaging cohorts and train 3D deep learning models to unravel the complexities of neurodegenerative diseases such as Alzheimer’s disease, Lewy body dementia, and Parkinson’s disease, with an emphasis on explainable AI to interpret model behavior and relate imaging biomarkers to cognitive outcomes. I have worked extensively with large-scale datasets and implemented reproducible preprocessing workflows, leveraging high-performance computing (HPC) clusters and GPU resources to accelerate processing, model training, and large-scale experimentation. In addition to image processing, I am interested in non-invasive MEG-based speech decoding, combining sequence models with language models to reconstruct perceived speech.  

In addition to my involvement with Dr. Babajani’s lab, I am part of the Data Informatics of Systems Improvement and DEsign (DESIDE) lab within the Industrial and Systems Engineering department at the University of Florida. My work there focuses on advancing tensor decomposition-based methodologies to model and monitor dynamic multilayer network systems characterized by heterogeneous and high-dimensional data. I develop algorithms that capture temporal and cross-layer structure, enabling efficient characterization of evolving system states and improved detection of shifts or anomalies in complex networks. This work supports more reliable inference and prediction in settings where relationships change over time and data streams are large, sparse, and noisy.

Degree

  • M.Sc. Industrial and Systems Engineering, University of Florida, Gainesville, FL, 2024
  • B.S. Industrial Engineering, Amirkabir University of Technology (Tehran Polytechnic), Tehran, Iran, 2020

Honors and Awards

  • Cluff Award for Aging Research (Winner), University of Florida, 2025
  • AAIC Featured Research Selection, Alzheimer’s Association International Conference (AAIC), Toronto, Canada, 2025
  • Graduate Student Fellowship (Awardee), University of Florida, 2021

Publications

Journal articles (Peer-reviewed and under review/revision)

  1. B. Ahmadi, M. Armstrong, B. Askan, M. Reisi-Gahrooei, and A. Babajani-Feremi, “Deep Learning-Based MRI Analysis Reveals Lewy Body Co-Pathology Accelerates Brain Aging in Alzheimer’s Disease,” under review.
  2. B. Ahmadi, M. Amini, S. Mankad, M. Reisi-Gahrooei, “Anomaly Detection in Dynamic Multilayer Networks using Tensor Decomposition,” under review.
  3. B. Ahmadi*, M.R. Hosseini-Siyanaki*, H. S. Sagdic, A. Raviprasad, S. Munjerin, A. Roy, A. Dogan, A. Babajani-Feremi, and K. R. Peters, “Deep Learning in Vertebral Fracture Detection: A Systematic Review and Meta-Analysis of Subject- vs. Vertebra-Level Approaches,” Academic Radiology, 2025.
  4. H. Sadeqi, B. Ahmadi, Z. Morshedizad, R. Burke, B. Patel, N. R. McFarland, M. J. Armstrong, and A. Babajani-Feremi, “Dynamic, State-dependent Characteristics of Cognitive Fluctuations in Lewy Body Dementia: A MEG Study,” under revision.
  5. B. Ahmadi*, M. Amini*, Y. Zhang, X. Xiong, C. Huggins-Manley, J. Templin, A. Goodwin, J. E. Block, and B. J. Dorr, “Bridging the Gap Between Small and Large Language Models Through Prompt Engineering and Fine-Tuning for Educational Item Generation,” under review.

          *Co-first authors (equal contribution)

    Conference papers & abstracts

    1. B. Ahmadi, A. Velez, B. Askan, M. Armstrong, M. Reisi-Gahrooei, and A. Babajani-Feremi, “Hidden players in MCI: how Lewy body pathology hastens Alzheimer’s disease progression,” The Society for Neuroscience (SfN), San Diego, California, Nov. 15–19, 2025.
    2. A. Velez, L. Ru, B. Ahmadi, and A. Babajani-Feremi, “Reconstructing perceived speech using magnetoencephalography and deep learning,” The Society for Neuroscience (SfN), San Diego, California, Nov. 15–19, 2025.
    3. B. Ahmadi, M. Armstrong, B. Askan, M. Reisi-Gahrooei, and A. Babajani-Feremi, “Neurodegenerative Impact of Alzheimer’s with Lewy Body Co-Pathology Characterized through MRI-based Brain Age Modeling with Deep Learning,” 2025 INFORMS Annual Meeting, Atlanta, Georgia, Oct. 26–29, 2025.
    4. B. Ahmadi, “Synergistic Neurodegeneration in Alzheimer’s Disease with Lewy Body Co-Pathology: Interpretable Deep Learning Approach,” Alzheimer’s Association International Conference (AAIC) (Selected as Featured Research), Toronto, Canada, Jul. 27–31, 2025.
    5. H. Sadeqi, Z. Morshedizad, B. Ahmadi, R. Burke, M. Armstrong, and A. Babajani-Feremi, “MEG Highlights Abnormal Neural Transitions in Lewy Body Dementia,” Alzheimer’s Association International Conference (AAIC), Toronto, Canada, Jul. 27–31, 2025.
    6. B. Ahmadi, Z. Morshedizad, H. Sadeqi, M. Armstrong, M. Reisi-Gahrooei, and A. Babajani-Feremi, “APOEε4 Modulates Accelerated Brain Aging and Cognitive Decline in Alzheimer’s Disease with Lewy Body Co-Pathology,” AAIC Advancements: APOE & Lipid Biology, Miami, FL, Mar. 17–18, 2025.
    7. H. Sadeqi, Z. Morshedizad, B. Ahmadi, M. Armstrong, and A. Babajani-Feremi, “Disrupted Brain Network Dynamics Underlying Cognitive Fluctuations in Lewy Body Dementia: Insights from MEG,” 14th Annual UF College of Medicine Celebration of Research, Gainesville, FL, Feb. 12–13, 2025.
    8. B. Ahmadi, Z. Morshedizad, H. Sadeqi, M. Armstrong, M. Reisi-Gahrooei, and A. Babajani-Feremi, “Accelerated Brain Aging and Cognitive Decline in Alzheimer’s Disease with Lewy Body Co-Pathology: Insights from Deep Learning on brain MRI and α-Synuclein SAAs,” 14th Annual UF College of Medicine Celebration of Research, Gainesville, FL, Feb. 12–13, 2025.
    9. B. Ahmadi, Z. Morshedizad, M. Reisi-Gahrooei, and A. Babajani-Feremi, “Exploring Dementia with Lewy Bodies through Deep Learning: Insights from structural MRI Data,” The Society for Neuroscience (SfN), Chicago, Oct. 5–9, 2024.
    10. B. Ahmadi, Z. Morshedizad, M. Reisi-Gahrooei, and A. Babajani-Feremi, “Advanced brain age prediction using 3D convolutional neural networks on structural MRI,” Alzheimer’s Association International Conference (AAIC), Philadelphia, Jul. 28–Aug. 1, 2024.
    11. B. Ahmadi and M. Reisi-Gahrooei, “Change detection in Dynamic Multilayer Networks using Tensor Decomposition methods,” Institute for Operations Research and the Management Sciences (INFORMS) annual meeting, Phoenix, October 15–18, 2023.