Journal Papers
Brain-computer interface control with artificial intelligence copilots
Lee JY*, Lee S*, Mishra A*, Yan X*, McMahan B*, Gaisford B, Kobashigawa C, Qu M, Xie C, Kao JC
Nature Machine Intelligence (in press), 2025
Inter-brain neural dynamics in biological and artificial intelligence systems
Zhang X*, Phi N*, Li Q, Gorzek R, Zwingenberger N, Huang S, Zhou JL, Kingsbury L, Raam T, Wu YE, Wei D, Kao JC**, Hong W**
Nature, 2025 Article
Multiregional representations of intertemporal decision making in human single neurons
Gill JL*, Omidbeigi M*, Ryu J, Suthana N, Kao JC**, Bari A**
Scientific Reports, 2025 Article
(Preprint) Illusions of alignment between large language models and brains emerge from fragile methods and overlooked confounds
Hadidi N*, Feghhi E*, Song BH, Blank IA**, Kao JC**
bioRxiv, 2025 Article
Spontaneous pain dynamics characterized by stochasticity in neural recordings of awake humans with chronic pain
Ryu J, Kao JC, Bari A
Pain, 2025 Article
Volatile working memory representations crystallize with practice
Bellafard A, Namvar G, Kao JC, Vaziri A, Golshani P
Nature, 2024 Article
Control of feeding by a bottom up midbrain-subthalamic pathway
Reis FMCV, Maesta-Pereira S, Ollivier M, Schuette PJ, Sethi E, Miranda BA, Iniguez E, Chakerian M, Vaughn E, Sehgal M, Nguyen DCT, Yuan FTH, Torossian A, Ikebara JM, Kihara AH, Silva AJ, Kao JC, Khakh BS, Adhikari A
Nature Communications, 2024 Article
A cortical information bottleneck during decision-making
Kleinman M, Wang T, Xiao D, Feghhi E, Lee K, Carr N, Li Y, Hadidi N, Chandrasekaran C*, Kao JC*
eLife, 2023 Article
A pilot study of closed-loop neuromodulation for treatment-resistant post-traumatic stress disorder
Gill JL*, Schneiders JA*, Stangl M, Aghajan ZM, Vallejo M, Hiller S, Topalovic U, Inman CS, Villaroman D, Bari A, Adhikari A, Rao, VR, Fanselow MS, Craske MG, Krahl SE, Chen JWY, Vick M, Hasulak NR, Kao, JC, Koek RJ, Suthana N**, Langevin JP**
Nature Communications, 2023 Article
Dorsal premammillary projection to periaqueductal gray controls escape vigor from innate and conditioned threats
Wang W*, Schuette PJ*, La-Vu MQ, Torossian A, Tobias BC, Ceko M, Kragel P, Reis FMCV, Ji S, Sehgal M, Maesta-Pereira S, Chakerian M, Silva AJ, Canteras NS, Wager T, Kao JC, Adhikari A
An artificial intelligence that increases simulated brain-computer interface performance
Olsen S*, Zhang J*, Liang K, Lam M, Riaz U, Kao JC
Journal of Neural Engineering, 2021 Article | PDF | Supplement
Coordination of escape and spatial navigation circuits orchestrates versatile flight from threats
Wang W*, Schuette PJ*, Nagai J, Tobias BC, Reis FMCV, Ji S, de Lima MAX, La-Vu MQ, Maesta-Pereira S, Chakerian M, Leonard SJ, Lin L, Severino AL, Cahill CM, Canteras NS, Khakh BS, Kao JC, Adhikari A
Neuron, 2021 Article | PDF | Supplement
Structure in neural activity during observed and executed movements is shared at the neural population level, not in single neurons
Jiang X, Saggar H, Ryu SI, Shenoy KV, Kao JC
Cell Reports, 2020 Article | PDF | Supplement | Code
The code performs the various subspace optimizations in the article above. It is based on the manopt library.
A low-power band of neuronal spiking activity dominated by local single units improves the performance of brain–machine interfaces
Nason SR, Vaskov AK, Willsey MS, Welle EJ, An H, Vu PP, Bullard AJ, Nu CS, Kao JC, Shenoy KV, Jang T, Kim H-S, Blaauw D, Patil PG, Chestek CA
Nature Biomedical Engineering, 2020 Article | PDF | Supplement
Deep learning neural encoders for motor cortex
Liang K, Kao JC
IEEE Transactions on Biomedical Engineering, 2019 Article | PDF | Supplement
Conference Papers
(Preprint) Time-Masked Transformers with Lightweight Test-Time Adaptation for Neural Speech Decoding
Feghhi E, Kaasyap S, Hadidi N, Kao JC
arXiv, 2025 Article
(Preprint) SplashNet: Split-and-Share Encoders for Accurate and Efficient Typing with Surface Electromyography
Hadidi N, Chan J, Feghhi E, Kao JC
arXiv, 2025 Article
Using reinforcement learning to investigate neural dynamics during motor learning
Xiao D, Liang K, Ji K, Kao JC
IEEE EMBC, 2025
Shared autonomy with IDA: Interventional Diffusion Assistance
McMahan B, Peng Z, Zhou B, Kao JC
NeurIPS, 2024 Article
Reciprocal reward influence encourages cooperation from self-interested agents
Zhou JL, Hong W, Kao JC
NeurIPS, 2024 Article
Learning rule influences recurrent network representations but not attractor structure in decision-making tasks
McMahan B, Kleinman M, Kao JC
NeurIPS, 2021 Paper | PDF | Supplement | Code
A mechanistic multi-area recurrent network model of decision-making
Kleinman M, Chandrasekaran C*, Kao JC*
NeurIPS, 2021 Paper | PDF | Supplement
Usable information and evolution of optimal representations during training
Kleinman M, Achille A, Idnani D, Kao JC
International Conference on Learning Representations (ICLR), 2021 Paper
Redundant Information Neural Estimation
Kleinman M, Achille A, Soatto S, Kao JC
ICLR Workshop on Neural Compressions, 2021 Paper
Decoding and perturbing decision states in real time
Peixoto D*, Verhein JR*, Kiani R, Kao JC, Nuyujukian P, Chandrasekaran C, Brown J, Fong S, Ryu SI, Shenoy KV, Newsome WT
Nature, 2021. Article
Inferring single-trial neural population dynamics using sequential auto-encoders
Pandarinath C, O’Shea DJ, Collins J, Jozefowicz R, Stavisky SD, Kao JC, Trautmann EM, Kaufman MT, Ryu SI, Hochberg LR, Henderson JM, Shenoy KV, Abbott LF, Sussillo D
Nature Methods, 2018 Article
Augmenting intracortical brain-machine interface with neurally driven error detectors
Even-Chen N, Stavisky SD, Kao JC, Ryu SI, Shenoy KV
Journal of Neural Engineering, 2017 Article
Leveraging neural dynamics to extend functional lifetime of brain-machine interfaces
Kao JC, Ryu SI, Shenoy KV
Scientific Reports, 2017 Article
Motor cortical visuomotor feedback activity is initially isolated from downstream targets in output-null neural state space dimensions
Stavisky SD, Kao JC, Ryu SI, Shenoy KV
Neuron, 2017 Article
A high-performance neural prosthesis incorporating discrete state selection with hidden Markov models
Kao JC*, Nuyujukian P*, Ryu SI, Shenoy KV
IEEE Transactions on Biomedical Engineering, 2017 Article
Trial-by-trial motor cortical correlates of a rapidly adapting visuomotor internal model
Stavisky SD, Kao JC, Ryu SI, Shenoy KV
Journal of Neuroscience, 2017 Article
A non-human primate brain computer typing interface
Nuyujukian P, Kao JC, Ryu SI, Shenoy KV
Proceedings of the IEEE, 2017 Article
The need for calcium-based imaging in nonhuman primates; new neuroscience and brain-machine interfaces
O'Shea DJ, Trautmann E, Stavisky SD, Kao JC, Sahani M, Ryu SI, Deisseroth K, Shenoy KV
Experimental Neurology, 2017 Article
Feasibility analysis of genetically-encoded calcium indicators as a neural signal source for all-optical brain-machine interfaces
Sun X, Kao JC, Marshel JH, Ryu SI, Shenoy KV
IEEE Neural Engineering (NER) (Shanghai, China), 2017 Paper
Making brain-machine interfaces robust to future neural variability
Sussillo D*, Stavisky SD*, Kao JC* (*co-first author), Ryu SI, Shenoy KV
Nature Communications, 2016 Article
Single-trial dynamics of motor cortex and their applications to brain-machine interfaces
Kao JC, Nuyujukian P, Ryu SI, Churchland MM, Cunningham JP, Shenoy KV
Nature Communications, 2015 Article
A high performing brain-machine interface driven by low-frequency local field potentials alone and together with spikes
Stavisky SD, Kao JC, Nuyujukian P, Ryu SI, Shenoy KV
Journal of Neural Engineering, 2015 Article
A high-performance keyboard neural prosthesis enabled by task optimization
Nuyujukian P, Fan JM, Kao JC, Ryu SI, Shenoy KV
IEEE Transactions on Biomedical Engineering, 2015 Article
Leveraging historical knowledge of neural dynamics to rescue decoder performance as neural channels are lost; decoder hysteresis
Kao JC, Ryu SI, Shenoy KV
IEEE Engineering in Medicine and Biology Conference (EMBC) (Milan, Italy), 2015 Paper
An auto-correcting brain machine interface; error detection using spiking neuronal activity in the motor cortex
Even-Chen N, Stavisky S, Kao JC, Ryu SI, Shenoy KV
IEEE Engineering in Medicine and Biology Conference (EMBC) (Milan, Italy), 2015 Paper
System identification of brain-machine interface control using a cursor jump perturbation
Stavisky SD*, Kao JC*, Sorokin J, Ryu SI, Shenoy KV
IEEE Neural Engineering (NER) (Montpellier, France), 2015 Paper
Performance sustaining intracortical neural prostheses
Nuyujukian P, Kao JC, Fan JM, Stavisky S, Ryu SI, Shenoy KV
Journal of Neural Engineering, 2014 Article
Information systems opportunities in brain-machine interface decoders
Kao JC, Stavisky SD, Sussillo D, Nuyujukian P, Shenoy KV
Proceedings of the IEEE, 2014 Article
Intention estimation in brain machine interfaces
Fan JM, Nuyujukian P, Kao JC, Chestek CA, Ryu SI, Shenoy KV
Journal of Neural Engineering, 2014 Article
Hybrid decoding of both spike and low-frequency local field potentials for brain-machine interfaces
Stavisky SD, Kao JC, Nuyujukian P, Ryu SI, Shenoy KV
IEEE Engineering in Medicine and Biology Conference (EMBC) (Chicago, Illinois), 2014 Paper
Investigating the role of firing-rate normalization and dimensionality reduction on brain-machine interface robustness
Kao JC, Nuyujukian P, Stavisky SD, Ryu SI, Ganguli S, Shenoy KV
IEEE Engineering in Medicine and Biology Conference (EMBC) (Osaka, Japan), 2013 Paper
A high-performance neural prosthesis enabled by control algorithm design
Gilja V*, Nuyujukian P*, Chestek CA, Cunningham JP, Yu BM, Fan JM, Churchland MM, Kaufman MT, Kao JC, Ryu SI, Shenoy KV
Nature Neuroscience, 2012 Article
A recurrent neural network for closed-loop intracortical brain-machine interface decoders
Sussillo D, Nuyujukian P, Fan JM, Kao JC, Stavisky SD, Ryu SI, Shenoy KV
Journal of Neural Engineering, 2012 Article