Core Competencies & Strategic Capabilities
EXECUTIVE & TECHNICAL PILLARSAI, Representation Learning & Math
Multi-View Representation Learning (SiMLR), Non-Negative Stiefel Approximating Flow (NSA-Flow), Deep Computational Anatomy, Normalizing Flows, 3D Concurrent Super-Resolution, Disease Subtyping & Staging (subtyper, Aligned-UMAP), Multimodal Learning with Missing Modalities.
Biotech, Pharma & Clinical Trials
Quantitative Imaging Biomarkers (Structural MRI, Amyloid/Tau/TSPO PET, DTI, rs-fMRI, ASL, CT), Phase I–III Endpoint Strategy, Patient Stratification, Regulatory Analytics, Translational Neuroscience (Alzheimer's, Parkinson's, FTD, ALS, TBI / Blast Overpressure).
Software Architecture & Engineering
Creator and architect of globally deployed open-source medical imaging and data science platforms. High-performance C++ numerical optimization, Python/R statistical bindings, automated quality control, and cloud/HPC clinical pipelines.
Entrepreneurial, Executive & Industry Leadership
BIOTECH · CRO · VENTURE CONSULTINGFounder & Principal Consultant
2018 – Present
Cingulate LLC — Portsmouth, NH
- Founded and lead a specialized AI, computational anatomy, and quantitative biomarker consultancy delivering machine learning architecture and clinical trial analytics for biotechnology, pharmaceutical, defense (DoD/CDMRP), and academic clients.
- Created NSA-Flow (Non-Negative Stiefel Approximating Flow, PyTorch) and SiMLR (Similarity-driven Multi-view Linear Reconstruction, Nature Computational Science 2021) for interpretable, sparse multi-omics and multi-modal neuroimaging representation learning.
- Lead quantitative phenotyping and normative neuroimaging library development across major population and disease cohorts, including the UK Biobank (N > 40,000), Parkinson's Progression Markers Initiative (PPMI), and LIMBIC-CENC.
Senior Director of Machine Learning
2018 – 2024
Invicro (a Konica Minolta Company) — Boston, MA
- Directed enterprise Machine Learning strategy and clinical trial software engineering across neurodegenerative, neuro-oncology, pulmonary, and multi-species therapeutic pipelines for a leading global imaging CRO.
- Architected and deployed ANTsPyMM and automated deep learning quality control, tissue/lesion segmentation, and concurrent 3D super-resolution pipelines to accelerate biomarker readouts in multi-center clinical trials.
- Led multi-institutional AI collaborations (with Michael J. Fox Foundation, NIH/NIA, and pharma sponsors) on multimodal patient representation learning with missing modalities (ICLR 2023) and longitudinal Parkinson's disease subtyping (Patterns 2023, EJHG 2024).
Associate Director, Translational & Advanced Analytics (Biomarkers)
2016 – 2018
Biogen — Cambridge, MA
- Served as lead integrative imaging data scientist for the Aducanumab (Aduhelm) clinical trial program (Phase 1b PRIME and Phase 3 ENGAGE/EMERGE), driving quantitative biomarker evaluation and patient stratification in Alzheimer's disease.
- Conducted confirmatory amyloid PET SUVR reference/target region optimization and generated the primary visualization featured on the cover of Nature (Sevigny et al., 2016; Chiao et al., J. Nucl. Med. 2018).
- Pioneered longitudinal resting-state fMRI network biomarker analytics in amyloid-beta positive subjects (Neurobiology of Aging 2018) and launched ANTsPy to unify deep learning with diffeomorphic registration.
Algorithm Developer, Imaging Department
1999 – 2000
Siemens Corporate Research — Princeton, NJ
- Developed adaptive minimal-path vessel tracking and 3D segmentation algorithms for CTA and CE-MRA volumetric clinical imaging systems.
Academic & Research Appointments
UVA · BROWN ICERM · UPENN PICSLVisiting Associate Professor of Radiology and Medical Imaging
2018 – Present
University of Virginia School of Medicine — Charlottesville, VA
- Co-lead multi-view machine learning and neuroimaging biomarker studies investigating neuroinflammation (TSPO PET), brain volume change, and functional/structural connectivity in military Special Operations personnel and breachers exposed to repetitive blast overpressure (Journal of Neurotrauma 2020, 2022, 2024).
- Co-architect of the Normative Neuroimaging Library (J. Neurotrauma 2024) and Deep Computational Anatomy via Latent-Aligned Multiview Normalizing Flows (2026).
Visiting Scholar, Institute for Computational and Experimental Research in Mathematics (ICERM)
Spring 2020
Brown University — Providence, RI
- Invited visiting scientist for the semester program "Model and Dimension Reduction in Uncertain and Dynamic Systems"; established the mathematical foundations for similarity-driven multi-view embeddings (
SiMLR).
Assistant Professor of Radiology (2012–2016) · Research Associate (2008–2012) · Postdoctoral Fellow (2006–2008)
2006 – 2016
University of Pennsylvania Perelman School of Medicine (PICSL) — Philadelphia, PA
- Invented Symmetric Diffeomorphic Image Registration (
SyN) (Med. Image Anal. 2008; 7,700+ citations) and co-developed N4ITK bias correction (IEEE TMI 2010; 8,400+ citations), Atropos multivariate segmentation, Eigenanatomy, and SCCAN. - Principal Investigator on NIH Big Data to Knowledge (BD2K) K01 Career Development Award (Imaging Genomics of Pediatric Executive Function); Image Analysis Lead on IARPA KRNS; Registration Architecture Lead for the NLM Insight ToolKit (ITKv4) redesign.
Flagship Software Products & Open-Source Ecosystem
GLOBAL BIOMEDICAL INFRASTRUCTURE
Creator & Lead Architect
Advanced Normalization Tools: Premier C++ library for diffeomorphic image registration (SyN), bias field correction (N4), multivariate tissue segmentation (Atropos), and cortical thickness (DiReCT).
Co-Creator & Architect
Python and deep learning toolkit providing pre-trained 2D/3D neural networks for brain extraction, Deep Atropos, HippMapp3r, brain age estimation, lesion segmentation, and 3D super-resolution.
Lead Architect
Production multi-modal neuroimaging pipeline processing T1w, FLAIR, rs-fMRI, DTI, and neuromelanin scans into standardized Image Derived Phenotypes (IDPs) with automated quality control.
Creator (2025)
PyTorch matrix estimation and manifold optimization framework implementing Non-Negative Stiefel Approximating Flow for sparse, orthogonalish, interpretable embeddings across imaging and genomics.
Creator & Lead Designer
R statistical imaging ecosystem featuring Similarity-driven Multi-view Linear Reconstruction (SiMLR), Sparse Canonical Correlation Analysis (SCCAN), and longitudinal disease staging (subtyper).
Registration Lead
Led the NLM-sponsored architectural refactoring of deformable image registration, similarity metrics, and composite transforms for ITKv4, alongside co-founding Neuroconductor.
Education & International Benchmark Honors
ACADEMIC & COMPETITION DISTINCTIONS2006 – 2008
Postdoctoral Fellowship in Radiology — University of Pennsylvania, Philadelphia, PA
2005
Ph.D. in Bioengineering — University of Pennsylvania, Philadelphia, PA · Dissertation: Diffeomorphometry for Computational Anatomy
2002 / 2003
M.S. in Computer Science — University of Pennsylvania, Philadelphia, PA
1998
B.A. in Physics and Literature — New College of Florida, Sarasota, FL · With High Honors · National Merit Scholar (1994) · Humana Scholar (1995)
2014
Best Paper Award (with Nicholas J. Tustison) at the STACOM 2014 Challenge, MICCAI.
2013
1st Place, BRATS 2013 Brain Tumor Segmentation Challenge (
ANTsR) & 1st Place, SATA Segmentation Challenge (ANTs), MICCAI, Nagoya, Japan.2012 – 2013
"Standard Setting" Registration Benchmark for MICCAI 2013 Multi-Atlas Challenge; all top finishers in MICCAI 2012 multi-atlas segmentation used
ANTs.2010
1st Overall, EMPIRE10 International Lung CT Registration Challenge (IEEE Transactions on Medical Imaging, 2011).
2009
1st Rank, Klein International Brain MRI Registration Evaluation across 14 nonlinear deformation algorithms (NeuroImage, 2009).
2003 & 2007
MICCAI Young Investigator Award (2007, General Medical Computing) & SPIE Medical Imaging Best Poster Award (2003).
Grants, Sponsored Research & Consortium Leadership
DOD/CDMRP · NIH BD2K · IARPA · MJFF2018 – Present
DoD / CDMRP / LIMBIC-CENC Neurotrauma & Blast Overpressure Research Programs (with James R. Stone, M.D., Ph.D. & Nicholas J. Tustison, D.Sc., UVA): Multi-view neuroimaging biomarkers (
SiMLR, NSA-Flow), TSPO PET neuroinflammation, and Normative Neuroimaging Library development in Special Operations personnel and combat breachers (Role: Co-Investigator / Lead ML Consultant).2018 – 2024
Parkinson's Progression Markers Initiative (PPMI) & Multimodal Neurodegeneration Consortia (Invicro / Michael J. Fox Foundation / NIH CARD): Automated multi-modal MRI/PET phenotyping (
ANTsPyMM), Aligned-UMAP longitudinal subtyping, and missing-modality representation learning (Role: Senior Director of ML / Co-Investigator).2014 – 2019
The Imaging Genomics of Pediatric Executive Function, NIH Big Data to Knowledge (BD2K) K01-ES025432-01 (Avants, Brian, PI), $275,000/annual direct costs, 80% effort.
2015 – 2018
Multimodal Brain Maturation Indices Modulating Psychopathology and Neurocognition, NIH R01-MH107235-01 (Gur, Ruben, PI), $275,000/annual direct costs (Role: Collaborator).
2013 – 2018
Neuroscience Neuroimaging Center, NIH P30-NS045839-07 (Detre, John, PI), $499,727/annual direct costs (Role: Collaborator / Technical Core Lead).
2014
Knowledge Representation in Neural Systems (KRNS), IARPA-BAA-12-05, 50% effort (Role: Image Analysis Lead).
2012 – 2013
Age, Hearing Loss, and Sentence Comprehension: Neural Correlates, NIA/NIH 5-R01-AG038490-05 (Grossman, Murray, PI), $291,978/annual direct costs (Role: Co-PI).
2011 – 2015
Continued Development and Maintenance of ITK-SNAP 3D Image Segmentation Software, NIH R01-EB014346-01 (Yushkevich, Paul A., PI), $350,824/annual direct costs (Role: Collaborator).
2010 – 2015
TDP-43 Proteinopathies in ALS-Dementia, NIH P01-AG032953-02 (Lee, Virginia / Grossman, Murray, PI), $729,272/annual direct costs (Role: Collaborator).
2010 – 2013
Fundamental Refactoring of Deformable Image Registration in ITK with Distributed Computing and GPU Acceleration, NLM/NIH HHSN276201000492P (Gee, James C., PI), $472,861/annual direct costs (Role: Co-PI & Architecture Lead).
2004 – 2012
Additional NIH R01/P50/Pilot Awards: Longitudinal Multi-Modal Neuroimaging of TBI Recovery (Avants, PI, 2011–2012); Pediatric Template of Brain Perfusion (NIMH R01, Co-PI); Advanced Neuroimage Registration Methods (NIH, Co-PI); Shape Optimizing Diffeomorphisms for Computational Biology (NIH R01-EB006266); Surface-Based Cortical Analysis in ITK (NLM, Co-PI).
Mentorship, Editorial Service, Tutorials & Media
LEADERSHIP & COMMUNITY IMPACTMentorship
Ph.D., Postdoc & Industry Advising: Mentored ML scientists and interns at Invicro, Biogen, and Cingulate LLC (including Nicholas Cullen, co-creator of
ANTsPy); Faculty Advisor to Dr. Dorian Pustina (CHDI Foundation); Ph.D. Advisor/Co-Advisor to Dr. Benjamin Kandel (UPenn Bioengineering), Dr. Paramveer Dhillon (UPenn CS → MIT/U. Michigan), and Dr. Efstathios Gennatas (UPenn Neuroscience → UCSF).Editorial & Panels
Topic Editor: NeuroImage (Brain Parcellation, 2017) & Frontiers in Neuroinformatics (ITK, 2015). Advisory Panels: Cohen Veterans Bioscience Brain Injury Biomarker Strategy Panel (2019); ACR Head Injury Institute IT Committee; INCF Registration & Atlasing Task Force; Alzheimer's Association Grant Reviewer.
Media & Covers
Nature Cover Visualization (2016): Confirmatory amyloid PET analysis & Figure 1 / cover image for the landmark Aducanumab PRIME study (Nature 537, 50–56). Featured in CNN Health (2013), The Washington Post (2012), Daily Mail UK (2012), and Penn Medicine News (2012).
Tutorials & Talks
Selected Workshops & Keynotes: ICERM Brown University (2019, 2020), Dartmouth Haxby Lab (2018), Seattle Children's/UW (2017), Yale (2017), Duke (2017), AD/PD Vienna (2017), MD Anderson (2016), Park City Mathematics Institute (2016), USC ENIGMA (2015), McGill/MNI (2015), ISMRM (2015), Princeton (2014), HRL Labs (2014), MICCAI (2006, 2011, 2013), NIH/NLM, Stanford, Columbia, UCLA, UCSF, and Chinese Academy of Sciences.
Publications Explorer (1999 – 2026)
SHOWING SELECTED & RECENT WORKS-
Tustison, N. J., Avants, B. B., Cook, P. A., Gee, J. C., & Stone, J. R. (2026). Deep Computational Anatomy via Latent-Aligned Multiview Normalizing Flows. bioRxiv / PubMed (PMID: 42146611).2026
-
Pustina, D., Bogale, H., Das, S., Avants, B., Sathe, S., Sampaio, C., & Wood, A. (2026). Geometric properties of caudate and putamen mark the progression of Huntington's disease. Imaging Neuroscience, 4, IMAG.a.1351.2026
-
Theodorou, B., Dadu, A., Avants, B., Nalls, M., Sun, J., & Faghri, F. (2026). Realistic PET image synthesis from MRI for automated inference of brain atrophy and Alzheimer's. iScience, 29(5), 115747.2026
-
Avants, B. B., et al. (2025). Non-Negative Stiefel Approximating Flow: Orthogonalish Matrix Optimization for Interpretable Embeddings. arXiv:2511.06425.2025
-
Avants, B. B., Tustison, N. J., & Stone, J. R. (2025). Joint representations from multi-view MRI-based learning support cognitive and functional performance domains. medRxiv.2025
-
Tustison, N. J., Yassa, M. A., Rizvi, B., Cook, P. A., Holbrook, A. J., Sathishkumar, M. T., Tustison, M. G., Gee, J. C., Stone, J. R., & Avants, B. B. (2024). ANTsX neuroimaging-derived structural phenotypes of UK Biobank. Scientific Reports, 14(1), 8848.2024
-
Stone, J. R., Avants, B. B., Tustison, N. J., Gill, J., Wilde, E. A., Neumann, K. D., Gladney, L. A., Kilgore, M. O., Bowling, F., & Wilson, C. M. (2024). Neurological effects of repeated blast exposure in Special Operations personnel. Journal of Neurotrauma, 41(7–8), 942–956.2024
-
Tustison, N., Avants, B., Whitlow, C. T., Lancashire, L., Bhatt, S. D., & Haas, M. (2024). Normative Neuroimaging Library: Designing a Comprehensive and Demographically Diverse Dataset of Healthy Controls to Support Traumatic Brain Injury Diagnostic and Therapeutic Development. Journal of Neurotrauma, 41(23–24), 2497–2512.2024
-
Yang, Z., Wen, J., Erus, G., Avants, B. B., et al. (2024). Brain aging patterns in a large and diverse cohort of 49,482 individuals. Nature Medicine, 30, 3015–3026.2024
-
Avants, B. B., Fonville, L., Hampton, O., Reardon, A., Stenger, A., Wang, X., Tustison, N. J., Stone, J. R., Cook, P. A., Marebwa, B., & Chahine, L. M. (2024). Magnetic Resonance Imaging Data Phenotypes for the Parkinson's Progression Markers Initiative. medRxiv.2024
-
Dennis, E. L., Rowland, J., Esopenko, C., Tustison, N., Newsome, M., Avants, B., Gill, J., Hinds, S., Kenney, K., & Lindsey, H. (2024). Brain volume changes following blast-related mild TBI in service members and veterans: a LIMBIC-CENC study. medRxiv, 2024.02.27.24303460.2024
-
Polfus, L., Shirazi, H. M., Reardon, A., Varga, M., Tchourbanov, A., Gosselin, T., Dadu, A., Avants, B., Faghri, F., Nalls, M., & Hesterman, J. (2024). Genetic and brain imaging phenotype joint prediction of longitudinal Parkinson's Disease subtypes. European Journal of Human Genetics, 32, 653.2024
-
Wu, Z., Dadu, A., Tustison, N., Avants, B., Nalls, M., Sun, J., & Faghri, F. (2023). Multimodal Patient Representation Learning with Missing Modalities and Labels. The Twelfth International Conference on Learning Representations (ICLR).2023
-
Dadu, A., Satone, V. K., Kaur, R., Koretsky, M. J., Iwaki, H., Qi, Y. A., Ramos, D. M., Avants, B., Hesterman, J., & Gunn, R. (2023). Application of Aligned-UMAP to longitudinal biomedical studies. Patterns (Cell Press), 4(6), 100741.2023
-
Avants, B., Tustison, N. J., McMillan, C. T., Gosselin, T., Gunn, R., & Hesterman, J. (2023). Concurrent 3D super resolution on intensity and segmentation maps improves detection of structural effects in neurodegenerative disease. medRxiv, 2023.02.02.23285376.2023
-
Elhamod, M., Diamond, K. M., Maga, A. M., Bakis, Y., Bart Jr, H. L., Mabee, P., Dahdul, W., Leipzig, J., Greenberg, J., & Avants, B. (2022). Hierarchy-guided neural network for species classification. Methods in Ecology and Evolution, 13(3), 642–652.2022
-
Avants, B. B., & Tustison, N. J. (2022). Mapping the Spatial Distribution of Lesions in Stroke: Effect of Diffeomorphic Registration Strategy in the ATLAS Dataset. In Lesion-to-Symptom Mapping: Principles and Tools (pp. 79–94). Springer.2022
-
Stone, J., Avants, B., Tustison, N., Gill, J., Wilde, E., Neumann, K., Gladney, L., Kilgore, M., Modica, L. T., & Bowling, F. (2022). Increased Neuroinflammation in special operators with a history of blast overpressure exposure. Journal of Neurotrauma, 39(11–12), A27–A28.2022
-
Avants, B. B., Tustison, N. J., & Stone, J. R. (2021). Similarity-driven multi-view embeddings from high-dimensional biomedical data. Nature Computational Science, 1(2), 143–152.2021
-
Tustison, N. J., Cook, P. A., Holbrook, A. J., Johnson, H. J., Muschelli, J., Devenyi, G. A., Duda, J. T., Das, S. R., Cullen, N. C., Gillen, D. L., Yassa, M. A., Stone, J. R., Gee, J. C., & Avants, B. B. (2021). The ANTsX ecosystem for quantitative biological and medical imaging. Scientific Reports, 11(1), 9068.2021
-
Tustison, N. J., Altes, T. A., Qing, K., He, M., Miller, G. W., Avants, B. B., Shim, Y. M., Gee, J. C., Mugler III, J. P., & Mata, J. F. (2021). Image-versus histogram-based considerations in semantic segmentation of pulmonary hyperpolarized gas images. Magnetic Resonance in Medicine, 86(5), 2822–2836.2021
-
Stone, J. R., Avants, B. B., Tustison, N. J., Wassermann, E. M., Gill, J., Polejaeva, E., Dell, K. C., Carr, W., Yarnell, A. M., & LoPresti, M. L. (2020). Functional and structural neuroimaging correlates of repetitive low-level blast exposure in career breachers. Journal of Neurotrauma, 37(23), 2468–2481.2020
-
Tustison, N. J., Holbrook, A. J., Avants, B. B., Roberts, J. M., Cook, P. A., Reagh, Z. M., Duda, J. T., Stone, J. R., Gillen, D. L., & Yassa, M. A. (2019). Longitudinal Mapping of Cortical Thickness Measurements: An ANTs Longitudinal Cortical Thickness Pipeline. NeuroImage, 199, 523–536.2019
-
Avants, B. B., Hutchison, R. M., Mikulskis, A., Salinas-Valenzuela, C., Hargreaves, R., Beaver, J., Chiao, P., & ADNI (2018). Amyloid beta–positive subjects exhibit longitudinal network-specific reductions in spontaneous brain activity. Neurobiology of Aging, 74, 191–201.2018
-
Chiao, P., Bedell, B. J., Avants, B. B., Zijdenbos, A. P., Grand'Maison, M., O'Neill, P., O'Gorman, J., Chen, T., & Koeppe, R. (2018). Impact of Reference/Target Region Selection on Amyloid PET Standard Uptake Value Ratios in the Phase 1b PRIME Study of Aducanumab. Journal of Nuclear Medicine, 60(1), 100–106.2018
-
Muschelli, J., Fortin, J. P., Gherman, A., Avants, B. B., Whitcher, B., Caffo, B., & Crainiceanu, C. (2018). Neuroconductor: An R platform for medical imaging analysis. Biostatistics, 20(2), 218–239.2018
-
Gennatas, E. D., Avants, B. B., Wolf, D. H., Satterthwaite, T. D., Ruparel, K., Ciric, R., Hakonarson, H., Gur, R. E., & Gur, R. C. (2017). Age-related effects and sex differences in gray matter density, volume, mass, and cortical thickness from childhood to young adulthood. Journal of Neuroscience, 37(20), 5065–5073.2017
-
Legant, W. R., Shao, L., Grimm, J. B., Brown, T. A., Milkie, D. E., Avants, B. B., Lavis, L. D., & Betzig, E. (2016). High-density three-dimensional localization microscopy across large volumes. Nature Methods, 13(4), 359–365.2016
-
Kandel, B. M., Wang, D. J. J., Gee, J. C., & Avants, B. B. (2015). Eigenanatomy: sparse dimensionality reduction for multi-modal medical image analysis. Methods, 73, 43–53.2015
-
Tustison, N. J., Cook, P. A., Klein, A., Song, G., Das, S. R., Duda, J. T., Kandel, B. M., van Strien, N., Stone, J. R., Gee, J. C., & Avants, B. B. (2014). Large-scale evaluation of ANTs and FreeSurfer cortical thickness measurements. NeuroImage, 99, 166–179.2014
-
Avants, B. B., Tustison, N. J., Stauffer, M., Song, G., Wu, B., & Gee, J. C. (2014). The Insight ToolKit image registration framework. Frontiers in Neuroinformatics, 8, 44.2014
-
Avants, B. B., Libon, D. J., Rascovsky, K., Boller, A., McMillan, C. T., Massimo, L., Coslett, H. B., Chatterjee, A., Gross, R. G., & Grossman, M. (2014). Sparse canonical correlation analysis relates network-level atrophy to multivariate cognitive measures in a neurodegenerative population. NeuroImage, 84, 698–711.2014
-
Avants, B. B., Tustison, N. J., Song, G., Cook, P. A., Klein, A., & Gee, J. C. (2011). A reproducible evaluation of ANTs similarity metric performance in brain image registration. NeuroImage, 54(3), 2033–2044.2011
-
Avants, B. B., Tustison, N. J., Wu, J., Cook, P. A., & Gee, J. C. (2011). An Open Source Multivariate Framework for n-Tissue Segmentation with Evaluation on Public Data. Neuroinformatics, 9(4), 381–400.2011
-
Tustison, N. J., Avants, B. B., Cook, P. A., Zheng, Y., Egan, A., Yushkevich, P. A., & Gee, J. C. (2010). N4ITK: Improved N3 bias correction. IEEE Transactions on Medical Imaging, 29(6), 1310–1320.2010
-
Klein, A., Andersson, J., Ardekani, B. A., Ashburner, J., Avants, B., et al. (2009). Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration. NeuroImage, 46(3), 786–802.2009
-
Das, S. R., Avants, B. B., Grossman, M., & Gee, J. C. (2009). Registration based cortical thickness measurement. NeuroImage, 45(3), 867–879.2009
-
Avants, B. B., Epstein, C. L., Grossman, M., & Gee, J. C. (2008). Symmetric diffeomorphic image registration with cross-correlation: Evaluating automated labeling of elderly and neurodegenerative brain. Medical Image Analysis, 12(1), 26–41.2008
Full numbered bibliography of 180+ peer-reviewed articles, conference proceedings, and book chapters is included in the Comprehensive CV PDF and Google Scholar.