Reza Abbasi Asl, PhD

Assistant Professor
+1 415 476-3199

The Abbasi Lab develops interpretable models and algorithms based on machine learning principles to understand functions of the brain and related disorders. To discover and model the functions of neurons, the lab studies applications of machine learning in the analysis of large-scale multi-modal datasets including electrophysiology, calcium imaging, electron microscopy, and spatial gene expression profiles. In the next step and to reconcile our understanding of the brain with related disorders, the Abbasi Lab builds computational tools for scientific discovery in large-scale neurological clinical datasets. This involves interpretable analysis and visualization of medical images, multi-omics datasets, and electronic health records.


Robust Image Registration via Empirical Mode Decomposition


Reza Abbasi-Asl, Aboozar Ghaffari, Emad Fatemizadeh

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


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


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