Mazdak Abulnaga

Postdoc at MIT CSAIL and HMS
MIT Stata Center 32-G904
abulnaga AT mit DOT edu
Mazdak Abulnaga

I am a postdoctoral fellow at the MIT Computer Science and AI Lab and Harvard Medical School. I am broadly interested in problems in AI for science and health. I am interesting in developing machine learning systems that reason about the physical and geometric structure of scientific data. To this end, my work spans problems in geometry processing and computer vision and I have worked on applications in health, neuroscience, and structural biology.

Previously, I was a PhD student at MIT CSAIL, co-advised by Prof. Polina Golland and Prof. Justin Solomon. I was part of the Medical Vision Group and the Geometric Data Processing Group. My PhD research focused on developing volumetric shape analysis methods for applications in computer graphics and health care. Specifically, I worked on core mapping and parametrization problems for volumetric meshes. I also collaborated closely with physicians and researchers at the Boston Children's Hospital and Massachusetts General Hospital to deploy these methods for research in fetal-maternal health. My PhD research was supported by the NSF Graduate Research Fellowship, the NSERC PGS D, the MathWorks Fellowship, and the Siebel Fellowship.

News

  • April 2026: I gave talks at VirDX and at the Chung lab, MIT Department of Brain & Cognitive Sciences.
  • February 2026: Our work neural diffeomorphic flow led by Athena Taymourtash is accepted in the CVPR Findings track.
  • January 2026: Our work on unified volume-surface registration is accepted to ICLR.
  • December 2025: Our work on conditional atlas construction led by Marianne Rakic is accepted to Medical Image Analysis.
  • October 2025: I gave a talk at the MIT Physical Math Seminar.

Resources

I am passionate about improving technical communication in science and I am an advocate of improving mentorship of undergraduate students. Below are a few resources on these topics that I've written or co-written.

Mentorship
  • White paper: Best Practices for Undergraduate Mentorship in EECS
Technical Communication
  • Planning your Journal or Conference Paper
  • A Paper Writing Checklist
  • Paper Writing: Results
  • How to Communicate in Grad School
  • Why You Should Be a Professor and How to Become One (a summary from a panel of MIT EECS professors)
  • A Guide to the MIT EECS Qualifying Exam

Research

For a full list of my publications, see my Google Scholar page.

NeurAlign
Unified Brain Surface and Volume Registration
S. Mazdak Abulnaga, Andrew Hoopes, Malte Hoffmann, Robin Magnet, Maks Ovsjanikov, Lilla Zollei, John Guttag, Bruce Fischl*, Adrian V. Dalca*
International Conference on Learning Representations (ICLR), 2026 (To appear)
Paper | Project Page | BibTeX 
@article{abulnaga2025unified,
        title={Unified Brain Surface and Volume Registration},
        author={Abulnaga, S Mazdak and Hoopes, Andrew and Hoffmann, Malte and Magnet, Robin and Ovsjanikov, Maks and Z{\"o}llei, Lilla and Guttag, John and Fischl, Bruce and Dalca, Adrian V},
        booktitle={International Conference on Learning Representations {(ICLR)}},
        year={2026}
        }
MultiMorph
MultiMorph: On-demand Atlas Construction
S. Mazdak Abulnaga, Andrew Hoopes, Neel Dey, Malte Hoffmann, Bruce Fischl, John Guttag, Adrian V. Dalca
IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR), 2025
Paper | Project Page | Code | BibTeX 
@inproceedings{abulnaga2025multimorph,
        title={MultiMorph: On-demand Atlas Construction},
        author={Abulnaga, S. Mazdak and Hoopes, Andrew and Dey, Neel and Hoffmann, Malte and Fischl, Bruce and Guttag, John and Dalca, Adrian V},
        booktitle={Proceedings of the Computer Vision and Pattern Recognition Conference},
        pages={30906--30917},
        year={2025}
        }
CIRPIN
CIRPIN: Learning Circular Permutation-Invariant Representations to Uncover Putative Protein Homologs
Aiden R. Kolodziej, S. Mazdak Abulnaga, Sergey Ovchinnikov
bioRxiv, 2025
Paper | Code | CP Database | BibTeX 
@article{kolodziej2025cirpin,
  title={CIRPIN: Learning Circular Permutation-Invariant Representations to Uncover Putative Protein Homologs},
  author={Kolodziej, Aiden R and Abulnaga, S Mazdak and Ovchinnikov, Sergey},
  journal={bioRxiv},
  pages={2025--11},
  year={2025},
  publisher={Cold Spring Harbor Laboratory}
}
FaCE
Faraday Cage Estimation of Normals for Point Clouds and Ribbon Sketches
Daniel Scrivener, Daniel Cui, Ellis Coldren, S. Mazdak Abulnaga, Mikhail Bessmeltsev, Edward Chien
ACM Transactions on Graphics (SIGGRAPH), 2025
Honorable Mention for Best Paper Award
Paper | Paper (High Res) | Project Page | Code | BibTeX 
@inproceedings{scrivener2025faraday,
        author = {Scrivener, Daniel and Cui, Daniel and Coldren, Ellis and Abulnaga, S. Mazdak and Bessmeltsev, Mikhail and Chien, Edward},
        title = {Faraday Cage Estimation of Normals for Point Clouds and Ribbon Sketches},
        year = {2025},
        issue_date = {August 2025},
        publisher = {Association for Computing Machinery},
        journal={ACM Transactions on Graphics},
        address = {New York, NY, USA},
        volume = {44},
        number = {4},
        issn = {0730-0301},
        url = {https://doi.org/10.1145/3731212},
        doi = {10.1145/3731212}
        }
SchwarzSchur
Schwarz–Schur Involution: Lightspeed Differentiable Sparse Linear Solvers
Yu Wang, S. Mazdak Abulnaga, Yael Balbastre, Bruce Fischl
International Conference on Machine Learning (ICML), 2025
Paper | Code | BibTeX 
@inproceedings{wang2025schwarz},
        title={Schwarz-Schur Involution: Lightspeed Differentiable Sparse Linear Solvers},
        author={Wang, Y., Abulnaga, S. Mazdak, Balbastre, Y. and Fischl, B.},
        booktitle={International Conference on Machine Learning {(ICML)},
        year={2025}
        }
AnyStar
AnyStar: Domain Randomized Universal Star-convex 3D Instance Segmentation
Neel Dey, S. Mazdak Abulnaga, Benjamin Billot, Esra Abaci Turk, P. Ellen Grant, Adrian V. Dalca, Polina Golland
IEEE/CVF Winter Conference on Applications of Computer Vision (WACV), 2024
Paper | Code | Colab Demo | BibTeX 
@InProceedings{Dey_2024_WACV,
    author    = {Dey, Neel and Abulnaga, Mazdak and Billot, Benjamin and Turk, Esra Abaci and Grant, Ellen and Dalca, Adrian V. and Golland, Polina},
    title     = {AnyStar: Domain Randomized Universal Star-Convex 3D Instance Segmentation},
    booktitle = {Proceedings of the IEEE/CVF Winter Conference on Applications of Computer Vision (WACV)},
    month     = {January},
    year      = {2024},
    pages     = {7593-7603}}
Shape-aware Segmentation of the Placenta in BOLD Fetal MRI Time Series
Shape-aware Segmentation of the Placenta in BOLD Fetal MRI Time Series
S. Mazdak Abulnaga, Neel Dey, Sean I. Young, Katherine Hobgood, Eileen Pan, Clinton J. Wang, P. Ellen Grant, Esra Abaci Turk, Polina Golland
Machine Learning for Biomedical Imaging (MELBA), 2023
Paper | Code | BibTeX 
@article{abulnaga2023placenta,
                title = "Shape-aware Segmentation of the Placenta in BOLD Fetal MRI Time Series",
                author = "Abulnaga, S. Mazdak and Dey, Neel and Young, Sean I. and Pan, Eileen and Hobgood, Katherine I. and Wang, Clinton J. and Grant, P. Ellen and Abaci Turk, Esra and Golland, Polina",
                journal = "Machine Learning for Biomedical Imaging",
                volume = "2",
                issue = "PIPPI 2022 special issue",
                year = "2023",
                pages = "527--546",
                issn = "2766-905X",
                doi = "https://doi.org/10.59275/j.melba.2023-g3f8"
                }
Symmetric Volume Maps
Symmetric Volume Maps: Order-Invariant Volumetric Mesh Correspondence with Free Boundary
S. Mazdak Abulnaga, Oded Stein, Polina Golland, Justin Solomon
ACM Transactions on Graphics, 42(3), 2023
Paper | Code | MIT News | BibTeX 
@article{abulnaga2022symmetric,
  title={Symmetric Volume Maps: Order-Invariant Volumetric Mesh Correspondence with Free Boundary},
  author={Abulnaga, S Mazdak and Stein, Oded and Golland, Polina and Solomon, Justin},
  journal={ACM Transactions on Graphics},
  volume={42},
  number={3},
  pages={1--20},
  year={2023},
  publisher={ACM New York, NY}}
Volumetric Parameterization of the Placenta to a Flattened Template
Volumetric Parameterization of the Placenta to a Flattened Template
S. Mazdak Abulnaga, Esra Abaci Turk, Mikhail Bessmeltsev, P. Ellen Grant, Justin Solomon, Polina Golland
IEEE Transactions on Medical Imaging, 41.4, 2022
Paper | Code | MIT News | BibTeX 
@article{abulnaga2022volumetric,
    title={Volumetric Parameterization of the Placenta to a Flattened Template},
    author={Abulnaga, S. Mazdak and Abaci Turk, Esra and Bessmeltsev, Mikhail and Grant, P. Ellen and Solomon, Justin and Golland, Polina},
    journal={IEEE Transactions on Medical Imaging}, 
    year={2022},
    volume={41},
    number={4},
    pages={925-936}}
Interactive All-Hex Meshing via Cuboid Decomposition
Interactive All-Hex Meshing via Cuboid Decomposition
Lingxiao Li, Paul Zhang, Dmitriy Smirnov, S. Mazdak Abulnaga, Justin Solomon
SIGGRAPH Asia, 2021, Tokyo
Paper | Code | BibTeX 
@article{li2021hex,
  title={Interactive All-Hex Meshing via Cuboid Decomposition},
  author={Li, Lingxiao and Zhang, Paul and Smirnov, Dmitriy and Abulnaga, Mazdak and and Solomon, Justin},
  month={December},
  year={2021},
  journal={ACM Transactions on Graphics (TOG)},
  publisher={ACM},
  volume={40},
  number={6},
  pages={256:1--256:17}
}
Placental Flattening via Volumetric Parameterization
Placental Flattening via Volumetric Parameterization
S. Mazdak Abulnaga, Esra Abaci Turk, Mikhail Bessmeltsev, P. Ellen Grant, Justin Solomon, Polina Golland
International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2019, Shenzhen
Paper | Code | Poster | BibTeX 
@inproceedings{abulnaga2019placental,    
    title={Placental Flattening via Volumetric Parameterization},
    author={Abulnaga, S. Mazdak and Abaci Turk, Esra and Bessmeltsev, Mikhail and Grant, P. Ellen and Solomon, Justin and Golland, Polina},
    booktitle={Medical Image Computing and Computer Assisted Intervention -- MICCAI 2019},
    year={2019},
    publisher={Springer International Publishing},
    address={Cham},
    pages={39--47}
}