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Reza Abbasi-Asl, PhD

Assistant Professor
Neurology
+1 415 476-3199

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.

Publications: 

Data-driven fine-grained region discovery in the mouse brain with transformers.

bioRxiv : the preprint server for biology

Lee AJ, Yao S, Lusk N, Ng L, Kunst M, Zeng H, Tasic B, Abbasi-Asl R

Compression-enabled interpretability of voxelwise encoding models.

PLoS computational biology

Kamali F, Suratgar AA, Menhaj M, Abbasi-Asl R

Deep brain stimulation-entrained gamma oscillations in chronic home recordings in Parkinson's disease.

Brain stimulation

Olaru M, Hahn A, Shcherbakova M, Little S, Neumann WJ, Abbasi-Asl R, Starr PA

Unsupervised pattern identification in spatial gene expression atlas reveals mouse brain regions beyond established ontology.

Proceedings of the National Academy of Sciences of the United States of America

Cahill R, Wang Y, Xian RP, Lee AJ, Zeng H, Yu B, Tasic B, Abbasi-Asl R

Structurally-constrained encoding framework using a multi-voxel reduced-rank latent model for human natural vision.

Journal of neural engineering

Ranjbar A, Suratgar AA, Menhaj MB, Abbasi-Asl R

Interpretable video-based tracking and quantification of parkinsonism clinical motor states.

NPJ Parkinson's disease

Deng D, Ostrem JL, Nguyen V, Cummins DD, Sun J, Pathak A, Little S, Abbasi-Asl R

Motor network gamma oscillations in chronic home recordings predict dyskinesia in Parkinson's disease.

Brain : a journal of neurology

Olaru M, Cernera S, Hahn A, Wozny TA, Anso J, de Hemptinne C, Little S, Neumann WJ, Abbasi-Asl R, Starr PA

Interpretable Video-Based Tracking and Quantification of Parkinsonism Clinical Motor States

medRxiv preprint

D. Deng, J. L. Ostrem, V. Nguyen, D. D. Cummins, J. Sun, A. Pathak, S. Little*, R. Abbasi-Asl*

Interpretable prototype discovery in deep learning based time series classification

Integrated Systems: Innovations and Applications, Springer book chapter

Gaurav Ghosal, R. Abbasi-Asl

Journal of Vision

Reconstructing visual experience from a large-scale biologically realistic model of mouse primary visual cortex

R. Abbasi-Asl, Y. Chi, H. Yang, K. Dai, A. Arkhipov

Neurology

Diurnal Step Count Patterns in Progressive Multiple Sclerosis

D. Navani, V. Block, B. Cree, R. Abbasi-Asl

The entropic heart: Tracking the psychedelic state via heart rate dynamics

bioRxiv preprint

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

Unsupervised pattern discovery in spatial gene expression atlas reveals mouse brain regions beyond established ontology

bioRxiv preprint

R. Cahill*, Y. Wang*, Patrick Xian, A. Lee, H. Zeng, B. Yu, B. Tasic, R. Abbasi-Asl

Editorial: Functional microcircuits in the brain and in artificial intelligent systems.

Frontiers in computational neuroscience

Lee JH, Choe Y, Ardid S, Abbasi-Asl R, McCarthy M, Hu B

Compression-enabled interpretability of voxel-wise encoding models

bioRxiv preprint

F Kamali, AA Suratgar, M Menhaj, R Abbasi-Asl

Robust Image Registration via Empirical Mode Decomposition

arXiv:1711.04247

Reza Abbasi-Asl, Aboozar Ghaffari, Emad Fatemizadeh

Journal of Vision

A large-scale standardized survey of neural receptive fields in an entire column in mouse V1

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

Systematic Integration of Structural and Functional Data into Multi-scale Models of Mouse Primary Visual Cortex.

Neuron

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

Definitions, methods, and applications in interpretable machine learning.

Proceedings of the National Academy of Sciences of the United States of America

Murdoch WJ, Singh C, Kumbier K, Abbasi-Asl R, Yu B

3-Photon Calcium Imaging of Deep Cortical Layers for Functional Connectomics

Optics and the Brain

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

Brain-Computer Interface in Virtual Reality

9th International IEEE EMBS Conference on Neural Engineering (NER)

R. Abbasi-Asl, M. Keshavarzi, D. Y. Chan

Visual physiology of the layer 4 cortical circuit in silico.

PLoS computational biology

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

The DeepTune framework for modeling and characterizing neurons in visual cortex area V4

bioArxiv

Reza Abbasi-Asl, Yuansi Chen, Adam Bloniarz, Michael Oliver, Ben DB Willmore, Jack L Gallant, Bin Yu

Interpreting Convolutional Neural Networks Through Compression

NIPS 2017 Symposium on Interpretable Machine Learning

Reza Abbasi-Asl, Bin Yu

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

R. Abbasi-Asl, C. Pehlevan, B. Yu and D. B. Chklovskii

Automatic b-spline image registration using histogram-based landmark extraction

IEEE-EMBS Conference on Biomedical Engineering and Sciences

Abdollah Ghanbari, Reza Abbasi-Asl, Aboozar Ghaffari, Emad Fatemizadeh

Estimation of muscle force with emg signals using hammerstein-wiener model

5th Kuala Lumpur International Conference on Biomedical Engineering

Reza Abbasi-Asl, Rahman Khorsandi, Shahrokh Farzampour, Edmond Zahedi

Hammerstein-Wiener model: A new approach to the estimation of formal neural information

Basic and Clinical Neuroscience

Reza Abbasi-Asl, Rahman Khorsandi, Bijan Vosooghi-Vahdat

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