Pre-Prints
CITS: Nonparametric Statistical Causal Modeling for High-Resolution Neural Time Series
R Biswas, S Sripada, S Mukherjee, R Abbasi-Asl
arXiv preprint, 2025
Enhancing the Safety of Medical Vision-Language Models by Synthetic Demonstrations
Z Xue, R Abbasi-Asl*, R Pedarsani*
arXiv preprint, 2025
Multi-Modal Prototype Learning for Interpretable Multivariable Time Series Classification
Gaurav Ghosal, R. 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
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
Peer-Reviewed Publications
Data-driven fine-grained region discovery in the mouse brain with transformers
A. J. Lee, Alma Dubuc, S. Yao, N. Lusk, H. Zeng, B. Tasic, R. Abbasi-Asl
Nature Communications, 2025 (in press)
Robustness tests for biomedical foundation models should tailor to specifications
P. Xian, N. R Baker, T. David, Q. Cui, A J. Holmgren, S. Bauer, M. Sushil, R. Abbasi-Asl
npj Digital Medicine, 2025 (in press)
Pre-trained Transformer-models using chronic invasive electrophysiology for symptom decoding without patient-individual training
T Merk, S Salehi, R M. Köhler, Q Cui, M Olaru, A Hahn, N R Provenza, S Little, R Abbasi-Asl, P A Starr, W Neumann
Proceedings of NER 2025 (in press)
Measuring temporal effects of agent knowledge by date-controlled tool use
RP Xian, Q Cui, S Bauer, R Abbasi-Asl
Proceedings of ACL 2025 Research on Agent Language Models Workshop, 2025
Imaging Joy with generalized Slice Dithered Enhanced Resolution (gSLIDER) and SWAT reconstruction: 3T high spatial-temporal resolution fMRI
JD Townsend, AM Muller, Z Naeem, A Beckett, B Kalisetti, R Abbasi-Asl, C Liao, AT Vu
Frontiers in Neuroimaging, 2025
Learning-related oscillatory dynamics in the human cortico-basal ganglia network during motor sequence initiation in Parkinson’s Disease
KN Presbrey, TA Wozny, KH Louie, S Little, PA Starr, R Abbasi-Asl*, D Wang*
Frontiers in Neuroscience, 2025
Structure-based synthetic data augmentation for protein language models
A. J. Lee, S. Alamdari, C. Wang, R. Abbasi-Asl, K. K. Yang, A. P. Amini
Proceedings of ICLR 2025 GEM Workshop, 2025.
Compression-enabled interpretability of voxel-wise encoding models
F Kamali, AA Suratgar, M Menhaj, R Abbasi-Asl
PLoS Computational Biology, 2025.
Deep brain stimulation-entrained gamma oscillations in chronic home recordings in Parkinson’s disease
M. Olaru, A. Hahn, M. Shcherbakova, S. Little, W. Neumann, R. Abbasi-Asl, P. A Starr
Brain Stimulation, 2025.
Assessing biomedical knowledge robustness in large language models by query-efficient sampling attacks
R. Patrick Xian, A. J. Lee, S. Lolla, V. Wang, R. Ro, Q. Cui, R. Abbasi-Asl
Transactions on Machine Learning Research (TMLR), 2024. (Code)
Unsupervised pattern identification 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
PNAS, 2024. (Code)
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, 2024. (Code)
7T MRI Synthesization from 3T Acquisitions
Q. Cui, D. Tosun, P. Mukherjee, R. Abbasi-Asl
MICCAI, 2024.
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, 2024.
Practical considerations for machine learning-enabled discoveries in spatial transcriptomics
A. Lee, R. Cahill, R. Abbasi-Asl
GEN Biotechnology, 2024.
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.
Interpretable Prototype Discovery in Deep Learning-Based Time Series Classification
G. Ghosal, R. Abbasi-Asl,
Integrated Systems: Innovations and Applications, Springer book chapter, 2024.
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.
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)
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)