Reza Abbasi-Asl, PhD

Title(s)Assistant Professor, Neurology
UCSF Weill Institute for Neurosciences
SchoolSchool of Medicine
Address675 Nelson Rising Lane, #612B
San Francisco CA 94158
Phone415-476-3199
ORCID ORCID Icon0000-0001-7824-4628 Additional info
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Collapse Biography 
Collapse education and training
UC BerkeleyPhD05/2018Electrical Engineering and Computer Sciences
UC BerkeleyMSc05/2018Electrical Engineering and Computer Sciences
Sharif University of TechnologyMSc01/2013Biomedical Engineering
Amirkabir University of TechnologyBSc09/2010Electrical Engineering
Collapse awards and honors
UCSF Innovation Ventures2023Catalyst Award
Sandler Program for Breakthrough Biomedical Research (PBBR)2021New Frontiers Research Award
Weill Neurohub2021Next Great Ideas Award
UC Berkeley, Department of Electrical Engineering and Computer Sciences2018Eli Jury Award
UC Berkeley Graduate Division2017May J. Koshland Fund in Memory of H.A. Jastro Award
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Collapse Overview 
Collapse overview
We are a research team at the University of California, San Francisco where we investigate the role of advanced computational tools in understanding brain functions and its related disorders. More specifically, our research program revolves around the development of interpretable machine learning tools to (1) integrate multi-modal data collected from the brain (and body) in both microscopic and macroscopic resolutions, (2) predict functions of biological systems in different resolutions, and (3) determine the functional differences across neurological disorders. We are a part of the Neuroscape Center and Cognitive Neuroscience division at UCSF and our team is supported through funding from NIH National Institute of Mental Health, NIH National Institute of Aging, Weill Neurohub, Sandler Program for Breakthrough in Biomedical Research, UCSF Innovation Ventures, and Google.

Collapse Research 
Collapse research activities and funding
Determining the circuits and signals of sleep dysfunction in Parkinson’s disease through chronic intracranial recordings and closed-loop Deep Brain Stimulation
NIH R01NS131405Jul 1, 2023 - Jun 30, 2028
Role: co-Investigator
Interpretable Machine Learning for Video-Assisted Diagnosis and Tracking of Parkinson’s Disease
UCSF Innovation Ventures Catalyst AwardFeb 1, 2023 - Feb 1, 2025
Role: PI
Integrated functional and structural analysis of an entire column in mouse primary visual cortex
NIH/NIMH RF1MH128672Aug 1, 2022 - Jul 31, 2025
Role: PI
Revealing regionalization in whole-organ spatial datasets via interpretable machine learning
Sandler Program for Breakthrough Biomedical Research Jan 1, 2022 - Jan 1, 2023
Role: PI
Synthetic and Augmented MRI for a shared neuroimaging infrastructure across the Weill Neurohub
Weill Neurohub Pillars Program AwardOct 1, 2021 - Sep 30, 2024
Role: PI
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Collapse Bibliographic 
Collapse selected publications
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Data-driven fine-grained region discovery in the mouse brain with transformers. bioRxiv. 2025 Feb 26. Lee AJ, Dubuc A, Kunst M, Yao S, Lusk N, Ng L, Zeng H, Tasic B, Abbasi-Asl R. PMID: 38766132; PMCID: PMC11100623.
    View in: PubMed   Mentions:
  2. Compression-enabled interpretability of voxelwise encoding models. PLoS Comput Biol. 2025 Feb; 21(2):e1012822. Kamali F, Suratgar AA, Menhaj M, Abbasi-Asl R. PMID: 39970189; PMCID: PMC11867343.
    View in: PubMed   Mentions:    Fields:    
  3. Deep brain stimulation-entrained gamma oscillations in chronic home recordings in Parkinson's disease. Brain Stimul. 2025 Feb 01; 18(2):132-141. Olaru M, Hahn A, Shcherbakova M, Little S, Neumann WJ, Abbasi-Asl R, Starr PA. PMID: 39894343.
    View in: PubMed   Mentions:    Fields:    
  4. Unsupervised pattern identification in spatial gene expression atlas reveals mouse brain regions beyond established ontology. Proc Natl Acad Sci U S A. 2024 Sep 10; 121(37):e2319804121. Cahill R, Wang Y, Xian RP, Lee AJ, Zeng H, Yu B, Tasic B, Abbasi-Asl R. PMID: 39226356; PMCID: PMC11406299.
    View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
  5. Structurally-constrained encoding framework using a multi-voxel reduced-rank latent model for human natural vision. J Neural Eng. 2024 Jul 26; 21(4). Ranjbar A, Suratgar AA, Menhaj MB, Abbasi-Asl R. PMID: 38986451.
    View in: PubMed   Mentions:    Fields:    Translation:HumansCells
  6. Interpretable video-based tracking and quantification of parkinsonism clinical motor states. NPJ Parkinsons Dis. 2024 Jun 25; 10(1):122. Deng D, Ostrem JL, Nguyen V, Cummins DD, Sun J, Pathak A, Little S, Abbasi-Asl R. PMID: 38918385; PMCID: PMC11199701.
    View in: PubMed   Mentions:
  7. Motor network gamma oscillations in chronic home recordings predict dyskinesia in Parkinson's disease. Brain. 2024 Jun 03; 147(6):2038-2052. Olaru M, Cernera S, Hahn A, Wozny TA, Anso J, de Hemptinne C, Little S, Neumann WJ, Abbasi-Asl R, Starr PA. PMID: 38195196; PMCID: PMC11146421.
    View in: PubMed   Mentions: 1     Fields:    Translation:Humans
  8. Interpretable prototype discovery in deep learning based time series classification. Integrated Systems: Innovations and Applications, Springer book chapter. 2023. Gaurav Ghosal, R. Abbasi-Asl. .
  9. Neurology. Diurnal Step Count Patterns in Progressive Multiple Sclerosis. 2023. D. Navani, V. Block, B. Cree, R. Abbasi-Asl. . View Publication.
  10. Journal of Vision. Reconstructing visual experience from a large-scale biologically realistic model of mouse primary visual cortex. 2023. R. Abbasi-Asl, Y. Chi, H. Yang, K. Dai, A. Arkhipov. View Publication.
  11. Interpretable Video-Based Tracking and Quantification of Parkinsonism Clinical Motor States. medRxiv preprint. 2023. D. Deng, J. L. Ostrem, V. Nguyen, D. D. Cummins, J. Sun, A. Pathak, S. Little*, R. Abbasi-Asl*. . View Publication.
  12. The entropic heart: Tracking the psychedelic state via heart rate dynamics. bioRxiv preprint. 2023. F. E. Rosas, P. A. M. Mediano, C. Timmermann, A. I Luppi, D. Candia-Rivera, R. Abbasi-Asl, A. Gazzaley, M. L. Kringelbach, S. D. Muthukumaraswamy, D. Bor, S. Garfinkel, R. Carhart-Harris. View Publication.
  13. Unsupervised pattern discovery in spatial gene expression atlas reveals mouse brain regions beyond established ontology. bioRxiv preprint. 2023. R. Cahill*, Y. Wang*, Patrick Xian, A. Lee, H. Zeng, B. Yu, B. Tasic, R. Abbasi-Asl. . View Publication.
  14. Machine Learning for Uncovering Biological Insights in Spatial Transcriptomics Data. ArXiv. 2023 Mar 29. Lee AJ, Cahill R, Abbasi-Asl R. PMID: 37033464; PMCID: PMC10081350.
    View in: PubMed   Mentions:
  15. Editorial: Functional microcircuits in the brain and in artificial intelligent systems. Front Comput Neurosci. 2023; 17:1135507. Lee JH, Choe Y, Ardid S, Abbasi-Asl R, McCarthy M, Hu B. PMID: 36761841; PMCID: PMC9904200.
    View in: PubMed   Mentions:
  16. Compression-enabled interpretability of voxel-wise encoding models. bioRxiv preprint. 2022. F Kamali, AA Suratgar, M Menhaj, R Abbasi-Asl. . View Publication.
  17. Robust Registration of Medical Images in the Presence of Spatially-Varying Noise. Algorithms. 2022; 15(2):58. Reza Abbasi-Asl, Aboozar Ghaffari, Emad Fatemizadeh. View Publication.
  18. Journal of Vision. A large-scale standardized survey of neural receptive fields in an entire column in mouse V1. 2021. R. Abbasi-Asl, A. Muslim, J. Larkin, K. Takasaki, D. Millman, D. Denman, J. Lecoq, A, Arkhipov, N. W Gouwens, J. Waters, R C. Reid, S. EJ de Vries. View Publication.
  19. Multi-Modal Prototype Learning for Interpretable Multivariable Time Series Classification. arxiv. 2021. Gaurav R Ghosal, Reza Abbasi-Asl. . View Publication.
  20. Structural Compression of Convolutional Neural Networks with Applications in Interpretability. Front Big Data. 2021; 4:704182. Abbasi-Asl R, Yu B. PMID: 34514381; PMCID: PMC8427695.
    View in: PubMed   Mentions: 3  
  21. Systematic Integration of Structural and Functional Data into Multi-scale Models of Mouse Primary Visual Cortex. Neuron. 2020 05 06; 106(3):388-403.e18. Billeh YN, Cai B, Gratiy SL, Dai K, Iyer R, Gouwens NW, Abbasi-Asl R, Jia X, Siegle JH, Olsen SR, Koch C, Mihalas S, Arkhipov A. PMID: 32142648.
    View in: PubMed   Mentions: 97     Fields:    Translation:AnimalsCells
  22. Superficial Bound of the Depth Limit of Two-Photon Imaging in Mouse Brain. eNeuro. 2020 Jan/Feb; 7(1). Takasaki K, Abbasi-Asl R, Waters J. PMID: 31907211; PMCID: PMC6984806.
    View in: PubMed   Mentions: 41     Fields:    Translation:Animals
  23. Definitions, methods, and applications in interpretable machine learning. Proc Natl Acad Sci U S A. 2019 10 29; 116(44):22071-22080. Murdoch WJ, Singh C, Kumbier K, Abbasi-Asl R, Yu B. PMID: 31619572; PMCID: PMC6825274.
    View in: PubMed   Mentions: 220     Fields:    
  24. 3-Photon Calcium Imaging of Deep Cortical Layers for Functional Connectomics. Optics and the Brain. 2019. Kevin Takasaki, Josh Larkin, Reza Abbasi-Asl, Dan Denman, Dan Millman, Saskia de Vries, Marc Takeno, Nuno M da Costa, R Clay Reid, Jack Waters. View Publication.
  25. Brain-Computer Interface in Virtual Reality. 9th International IEEE EMBS Conference on Neural Engineering (NER). 2019. R. Abbasi-Asl, M. Keshavarzi, D. Y. Chan. View Publication.
  26. Visual physiology of the layer 4 cortical circuit in silico. PLoS Comput Biol. 2018 11; 14(11):e1006535. Arkhipov A, Gouwens NW, Billeh YN, Gratiy S, Iyer R, Wei Z, Xu Z, Abbasi-Asl R, Berg J, Buice M, Cain N, da Costa N, de Vries S, Denman D, Durand S, Feng D, Jarsky T, Lecoq J, Lee B, Li L, Mihalas S, Ocker GK, Olsen SR, Reid RC, Soler-Llavina G, Sorensen SA, Wang Q, Waters J, Scanziani M, Koch C. PMID: 30419013; PMCID: PMC6258373.
    View in: PubMed   Mentions: 32     Fields:    Translation:AnimalsCells
  27. The DeepTune framework for modeling and characterizing neurons in visual cortex area V4. bioArxiv. 2018. Reza Abbasi-Asl, Yuansi Chen, Adam Bloniarz, Michael Oliver, Ben DB Willmore, Jack L Gallant, Bin Yu. View Publication.
  28. Interpreting Convolutional Neural Networks Through Compression. NIPS 2017 Symposium on Interpretable Machine Learning. 2017. Reza Abbasi-Asl, Bin Yu. View Publication.
  29. Do retinal ganglion cells project natural scenes to their principal subspace and whiten them?. IEEE Proceedings of 50th Asilomar Conference on Signals, Systems and Computers. 2016. R. Abbasi-Asl, C. Pehlevan, B. Yu and D. B. Chklovskii. View Publication.
  30. Automatic b-spline image registration using histogram-based landmark extraction. IEEE-EMBS Conference on Biomedical Engineering and Sciences. 2012. Abdollah Ghanbari, Reza Abbasi-Asl, Aboozar Ghaffari, Emad Fatemizadeh. View Publication.
  31. Estimation of muscle force with emg signals using hammerstein-wiener model. 5th Kuala Lumpur International Conference on Biomedical Engineering. 2011. Reza Abbasi-Asl, Rahman Khorsandi, Shahrokh Farzampour, Edmond Zahedi. View Publication.
  32. Hammerstein-Wiener model: A new approach to the estimation of formal neural information. Basic and Clinical Neuroscience. 4(3):45-51. Reza Abbasi-Asl, Rahman Khorsandi, Bijan Vosooghi-Vahdat. View Publication.
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