Publications

Pre-Prints


Data-driven fine-grained region discovery in the mouse brain with transformers
A. J. Lee, S. Yao, N. Lusk, H. Zeng, B. Tasic, R. Abbasi-Asl
arXiv preprint, 2024.


7T MRI Synthesization from 3T Acquisitions
Q. Cui, D. Tosun, P. Mukherjee, R. Abbasi-Asl
arXiv preprint, 2024.


Zero-shot sampling of adversarial entities in biomedical question answering.
R. Patrick Xian, Alex J. Lee, Vincent Wang, Qiming Cui, Russell Ro, Reza Abbasi-Asl
arXiv preprint, 2024.


The entropic heart: Tracking the psychedelic state via heart rate dynamics
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
bioRxiv preprint, 2023. (WEB)


Unsupervised pattern discovery in spatial gene expression atlas reveals mouse brain regions beyond established ontology
R. Cahill*, Y. Wang*, Patrick Xian, A. Lee, H. Zeng, B. Yu, B. Tasic, R. Abbasi-Asl
bioRxiv preprint, 2023. (WEB, Code)


Compression-enabled interpretability of voxel-wise encoding models
F Kamali, AA Suratgar, M Menhaj, R Abbasi-Asl
bioRxiv preprint, 2022. (WEB)


Multi-Modal Prototype Learning for Interpretable Multivariable Time Series Classification
Gaurav Ghosal, R. Abbasi-Asl
arXiv preprint, 2021. (WEB)


The DeepTune framework for modeling and characterizing neurons in visual cortex area V4
R. Abbasi-Asl*, Y. Chen*, A. Bloniarz, M. Oliver, Ben Willmore, J. L. Gallant and B. Yu
bioRxiv preprint, 2019. (WEB)



Peer- Reviewed Publications


Interpretable Video-Based Tracking and Quantification of Parkinsonism Clinical Motor States
D. Deng, J. L. Ostrem, V. Nguyen, D. D. Cummins, J. Sun, A. Pathak, S. Little*, R. Abbasi-Asl*
npj Parkinson’s Disease (in press), 2024. (WEB, Code)


Structurally-Constrained Encoding Framework using a Multi-Voxel Reduced-Rank Latent Model for Human Natural Vision
A. Ranjbar, A. Suratgar, M. Menhaj, R. Abbasi-Asl
Journal of Neural Engineering (in press), 2024.


Practical considerations for machine learning-enabled discoveries in spatial transcriptomics
A. Lee, R. Cahill, R. Abbasi-Asl
GEN Beiotechnology (in press), 2024. (WEB)


Motor network gamma oscillations in chronic home recordings predict dyskinesia in Parkinson’s disease
M. Olaru,  S. Cernera,  A. Hahn,  T. A Wozny,  J. Anso, C. de Hemptinne,  S. Little,  W. Neumann,  R. Abbasi-Asl,  P. A Starr
Brain, 2024. (WEB)


Interpretable prototype discovery in deep learning based time series classification
G. Ghosal, R. Abbasi-Asl,
Integrated Systems: Innovations and Applications, Springer book chapter, 2023 (in press).


Functional Microcircuits in the Brain and in Artificial Intelligent Systems
J. H. Lee, Y. Choe, S. Ardid, R. Abbasi-Asl, M. McCarthy, B. Hu
Frontiers in Comp. Neuro., 2023. (WEB)


Robust registration of medical images in the presence of spatially-varying noise
R. Abbasi-Asl, A. Ghaffari and E. Fatemizade
Algorithms, 2022. (WEB)


Structural Compression of Convolutional Neural Networks with Applications in Interpretability
R. Abbasi-Asl and B. Yu
Frontiers in Big Data, 2021. (WEB)


Systematic Integration of Structural and Functional Data into Multi-Scale Models of Mouse Primary Visual Cortex
Y.N. Billeh, B. Cai, S.L. Gratiy, K. Dai, R. Iyer, N.W. Gouwens, R. Abbasi-Asl, X. Jia, J.H. Siegle, S.R. Olsen, C. Koch, S. Mihalas, and A. Arkhipov
Neuron, 2020. (Featured cover Image, WEB, bioRxiv version, DATA, Allen Institute Coverage)


Superficial bound of the depth limit of 2-photon imaging in mouse brain
K. Takasaki, R. Abbasi-Asl, J. Waters
eNeuro, 2020. (WEB, bioRxiv version , DATA)


Interpretable machine learning: definitions, methods, and applications
J. Murdoch*, C. Singh*, K. Kumbier†, R. Abbasi-Asl†, and B. Yu
PNAS, 2019. (WEB, NEWS)


Brain-Computer Interface in Virtual Reality
R. Abbasi-Asl, M. Keshavarzi, D. Y. Chan
Proceedings of International IEEE EMBS Conference on Neural Engineering (NER), 2019. (WEB, arXiv version)


3-Photon Calcium Imaging of Deep Cortical Layers for Functional Connectomics
K. Takasaki, J. Larkin, R. Abbasi-Asl, D. Denman, D. Millman, S. de Vries, M. Takeno, N. M da Costa, R C. Reid, J. Waters
Optics and the Brain, 2019. (WEB)


Visual physiology of the Layer 4 cortical circuit in silico
A. Arkhipov, N. W. Gouwens, Y. N. Billeh, S. Gratiy, R. Iyer, Z. Wei, Z. Xu, R. Abbasi-Asl, J. Berg, M. Buice, N. Cain, N. da Costa, S. de Vries, D. Denman, S. Durand, D. Feng, T. Jarsky, J. Lecoq, B. Lee, L. Li, S. Mihalas, G. K. Ocker, S. R. Olsen, R. C. Reid, G. Soler-Llavina, S. A. Sorensen, Q. Wang, J. Waters, M. Scanziani, C. Koch
PLOS Comp. Bio., 2018. (WEB, DATA)


Interpreting Convolutional Neural Networks Through Compression
R. Abbasi-Asl and B. Yu
Proceedings of NeurIPS IML Symposium, 2017. (WEB)


Do retinal ganglion cells project natural scenes to their principal subspace and whiten them?
R. Abbasi-Asl, C. Pehlevan, B. Yu and D. B. Chklovskii. Proceedings of Asilomar IEEE Conference on Signals, Systems and Computers (ACSSC), 2016. (WEB, arXiv version)


Hammerstein-Wiener Model: A New Approach to the Estimation of Formal Neural Information
R. Abbasi-Asl, R. Khorsandi, B. Vosooghi Vahdat.
Basic and Clinical Neuroscience. 2012, (WEB)


Automatic B-spline Image Registration Using Histogram-based Landmark Extraction
A. Ghanbari, R. Abbasi-Asl, A. Ghaffari, E. Fatemizadeh
Proceedings of IEEE-EMBS Conference on Biomedical Engineering & Sciences (IECBES), 2012. (WEB)


Estimation of Muscle Force with EMG Signals Using Hammerstein-Wiener Model
R. Abbasi-Asl, R. Khorsandi, Sh. Farzampour, E. Zahedi
IFMBE Proceedings of International Conference on Biomedical Engineering (BIOMED), 2011. (WEB)


Selected Published Abstracts

Diurnal Step Count Patterns in Progressive Multiple Sclerosis
D. Navani, V. Block, B. Cree, R. Abbasi-Asl
Neurology, 2023. (WEB)


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
Journal of Vision, 2023. (WEB)


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
Journal of Vision, 2021. (WEB)


Towards multipurpose bio-realistic models of cortical circuits
A. Arkhipov, Y. N Billeh, B. Cai, S. L Gratiy, K. Dai, R. Iyer, N. W Gouwens, R. Abbasi-Asl, X. Jia, J. H Siegle, S. R Olsen, S. Mihalas, C. Koch
BMC Neuroscience, 2020. (WEB)


Systematic integration of experimental data in biologically realistic models of the mouse primary visual cortex: Insights and predictions
Y. Billeh, B. Cai, S, Gratiy, K. Dai, R. Iyer, N. Gouwens, R. Abbasi-Asl, X. Jia, J. Siegle, S. Olsen, C. Koch, S. Mihalas, A. Arkhipov
BMC Neuroscience, 2019. (WEB)