Pre-prints
R. Cahill, Y. Wang, A. Lee, H. Zeng, B. Yu, B. Tasic, R. Abbasi-Asl. Unsupervised pattern discovery in spatial gene expression atlas reveals mouse brain regions beyond established ontology, bioRxiv preprint, 2023. (WEB, Code)
A. Lee, R. Cahill, R. Abbasi-Asl.Machine Learning for Uncovering Biological Insights in Spatial Transcriptomics Data, arXiv preprint, 2023. (WEB)
F Kamali, AA Suratgar, M Menhaj, R Abbasi-Asl. Compression-enabled interpretability of voxel-wise encoding models, bioRxiv preprint, 2022. (WEB)
Gaurav Ghosal, R. Abbasi-Asl. Multi-Modal Prototype Learning for Interpretable Multivariable Time Series Classification, arXiv preprint, 2021. (WEB)
R. Abbasi-Asl∗, Y. Chen∗, A. Bloniarz, M. Oliver, Ben Willmore, J. L. Gallant and B. Yu. The DeepTune framework for modeling and characterizing neurons in visual cortex area V4, bioRxiv preprint, 2019. (WEB)
Peer-Reviewed Publications
J. H. Lee, Y. Choe, S. Ardid, R. Abbasi-Asl, M. McCarthy, B. Hu, Functional Microcircuits in the Brain and in Artificial Intelligent Systems, Frontiers in Comp. Neuro., 2023. (WEB)
R. Abbasi-Asl, A. Ghaffari and E. Fatemizadeh. Robust registration of medical images in the presence of spatially-varying noise, Algorithms, 2022. (WEB)
R. Abbasi-Asl and B. Yu. Structural Compression of Convolutional Neural Networks with Applications in Interpretability, Frontiers in Big Data, 2021. (WEB)
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. Systematic Integration of Structural and Functional Data into Multi-Scale Models of Mouse Primary Visual Cortex, Neuron, 2020. (Featured cover Image, WEB, bioRxiv version, DATA, Allen Institute Coverage)
K. Takasaki, R. Abbasi-Asl, J. Waters. Superficial bound of the depth limit of 2-photon imaging in mouse brain, eNeuro, 2020. (WEB, bioRxiv version , DATA)
J. Murdoch∗, C. Singh∗, K. Kumbier†, R. Abbasi-Asl†, and B. Yu. Interpretable machine learning: definitions, methods, and applications, PNAS, 2019. (WEB, NEWS)
R. Abbasi-Asl, M. Keshavarzi, D. Y. Chan. Brain-Computer Interface in Virtual Reality, 9th International IEEE EMBS Conference on Neural Engineering (NER), 2019.
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. 3-Photon Calcium Imaging of Deep Cortical Layers for Functional Connectomics, Optics and the Brain, 2019.
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. Visual physiology of the Layer 4 cortical circuit in silico. PLOS Comp. Bio., 2018. (WEB, DATA)
R. Abbasi-Asl and B. Yu. Interpreting Convolutional Neural Networks Through Compression, Neural Information Processing Conference 2017 Symposium on Interpretable Machine Learning (NIPS IML Symp.), Long Beach, CA, 2017. (WEB)
R. Abbasi-Asl, C. Pehlevan, B. Yu and D. B. Chklovskii. 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 (ACSSC), Pacific Grove, CA, 2016.
A. Ahadi, H. Hayati, J. Mitra, R. Abbasi-Asl, K. Awodele. A new method for estimating the longevity and degradation of photovoltaic systems considering weather states. Frontiers in Energy. 2016; 10 (3) :277 – 285.
R. Abbasi-Asl, R. Khorsandi, B. Vosooghi Vahdat. Hammerstein-Wiener Model: A New Ap- proach to the Estimation of Formal Neural Information. Basic and Clinical Neuroscience. 2012; 3 (4) :45-51. (WEB) (A conference paper version published in IEEE Proceedings of The 16th CSI Symposium on Artificial Intelligence and Signal Processing (AISP))
A. Ghanbari, R. Abbasi-Asl, A. Ghaffari, E. Fatemizadeh. Automatic B-spline Image Registra- tion Using Histogram-based Landmark Extraction. In: IEEE-EMBS Conference on Biomedical Engineering & Sciences (IECBES), 2012. (WEB)
R. Abbasi-Asl, R. Khorsandi, Sh. Farzampour, E. Zahedi. Estimation of Muscle Force with EMG Signals Using Hammerstein-Wiener Model. In: IFMBE Proceedings 5th Kuala lumpur International Conference on Biomedical Engineering (BIOMED), Malaysia, Vol. 35, pp. 157- 160, 2011. (WEB)
R. Abbasi-Asl, E. Fatemizadeh. MMRO: A Feature Selection Criterion for MR Images Based on Alpha Stable Filter Responses. In: IEEE Proceedings of 7th Iranian Conference on Machine Vision and Image Processing (MVIP), Iran, 2011.
S. Abadpour, R. Abbasi-Asl, Gh. Moradi. Analysis of Push-Push Oscillators and Designing a Push-Push Oscillator in S Band. In: IEEE Proceedings of 10th Mediterranean Microwave Symposium (MMS), Turkey, 2010.
Selected Conference Abstracts
R. Abbasi-Asl, R. Farhoodi, J. Larkin, K. Takasaki, D. Millman, D. Denman, J. Lecoq, A.Arkhipov, N. W. Gouwens, J. Waters, R. C. Reid, S. E. J. DE Vries. A large-scale survey of spatial and motion selectivity in an entire column in mouse V1. CNS, 2022
R. Abbasi-Asl, Arbaaz Muslim, J. Larkin, K. Takasaki, D. Millman, D. Denman, J. Lecoq, A.Arkhipov, N. W. Gouwens, J. Waters, R. C. Reid, S. E. J. DE Vries. A large-scale standardized survey of neural receptive fields in an entire column in mouse V1. VSS, 2021
R. Abbasi-Asl and B. Yu. Interpretable modeling of neurons in cortical area V4 via compressed convolutional neural networks. CNS, 2020.
R. Abbasi-Asl and B. Yu. Compressed interpretable models of neurons in cortical area V4, Cosyne, 2020.
R. Abbasi-Asl, J. Larkin, K. Takasaki, D. Millman, D. Denman, J. Lecoq, A. Arkhipov, N. W. Gouwens, J. Waters, R. C. Reid, S. E. J. DE Vries. Functional imaging of excitatory neurons in an entire column in mouse visual cortex, SfN, 2019.
G. K. Ocker, D. Millman, P. Ledochowitsch, M. D. Oliver, R. Abbasi-Asl, M. A. Buice, S. E. J. DE Vries. Measuring the effects of locomotion on visual activity in the mouse cortex in the Allen Brain Observatory, SfN, 2019.
Y.N. Billeh, B. Cai, S.L. Gratiy, K. Dai, R. Iyer, R. Abbasi-Asl, X. Jia, J.H. Siegle, S.R. Olsen, C. Koch, S. Mihalas, and A. Arkhipov. Systematic integration of structural and functional data into a multi-scale model of mouse primary visual cortex, SfN, 2019.
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. Systematic Integration of Experimental Data in Biologically Realistic Models of Mouse Primary Visual Cortex: Insights and Predictions, CNS, 2019.
R. Abbasi-Asl, M. Keeshavarzi, D. Y. Chan. Brain-Computer Interface in Virtual Reality, 7th International BCI Meeting, Pacific Grove, CA, 2018. (Accepted abstract and poster presentation)
R. Abbasi-Asl, Y. Chen, A. Bloniarz, M. Oliver, J. L. Gallant and B. Yu. Deep Nets Meet Real Neurons: Pattern Selectivity in V4, 8th International Workshop on Statistical Analysis of Neuronal Data (SAND8), Pittsburgh, PA, 2017. (Accepted abstract and poster presentation)
R. Abbasi-Asl, Y. Chen, A. Bloniarz, J. L. Gallant and B. Yu. Artificial Neurons Meet Real Neurons: Pattern Selectivity In V4, INFORMS Annual Meeting, Nashville, TN, 2016. (Invited oral presentation)
R. Abbasi-Asl, Y. Chen, A. Bloniarz, J. Mairal, J. L. Gallant and B. Yu. Explaining V4 Neurons Pattern Selectivity via Convolutional Neural Network, 7th International Workshop on Statistical Analysis of Neuronal Data (SAND7), Pittsburgh, PA, 2015. (Accepted abstract and poster presentation)
R. Abbasi-Asl, R. Khorsandi, N. Mozaffari, Sh. Farzampour. A Novel Model for Estimation of the Forearm Motor Forces Using EMG Signals. In: Proceedings of The 1st International Congress of Neuromuscular and Electrodiagnostic Medicine, Iran, 2011. (Accepted abstract and poster presentation)