[Papers] [Conference Abstracts]
Note: * and ** denote authorships with equal contributions.
Papers
Preprints
- Sedler AR, Pandarinath C. lfads-torch: A modular and extensible implementation of latent factor analysis via dynamical systems. In review. Preprint on arXiv: 2309.01230, posted Sep 6, 2023. [Code repository].
- Karpowicz BM, Ali YH, Wimalasena LN, Sedler AR, Keshtkaran MR, Bodkin K, Ma X, Miller LE, Pandarinath C. Stabilizing brain-computer interfaces through alignment of latent dynamics. In review. Preprint on BioRxiv: 10.1101/2021.11.21.469441, posted Apr 8, 2022.
- Zhu F, Kaufman MT, Pandarinath C. Temporally-precise inference of neural population dynamics from slow-sampling rate calcium imaging using deconvolution-free dynamics modeling. In review.
2024
- Ali YA, Bodkin K, Rigotti-Thompson M, Patel K, Card NS, Bhaduri B, Nason-Tomaszewski SR, Mifsud DM, Hou X, Nicolas C, Allcroft S, Hochberg LR, Au Yong N, Stavisky SD, Miller LE, Brandman DM*, Pandarinath C*. BRAND: A platform for closed-loop experiments with deep network models. Journal of Neural Engineering, 21:026046. doi: 10.1088/1741-2552/ad3b3a. Preprint on BioRxiv: 10.1101/2023.08.08.552473, posted Aug 12, 2023.
- Chung B*, Zia M*, Thomas K, Michaels JA, Jacob A, Pack A, Williams M, Nagapudi K, Teng LH, Arrambide E, Ouellette L, Oey N, Gibbs R, Anschutz P, Lu J, Wu Y, Kashefi M, Oya T, Kersten R, Mosberger M, O’Connell S, Wang R, Marques H, Mendes AR, Lenschow C, Kondakath G, Kim JJ, Olson W, Quinn K, Perkins P, Gatto G, Thanawalla A, Coltman S, Kim Y, Smith T, Binder-Markey B, Zaback M, Thompson CK, Giszter S, Person A, Goulding M, Azim E, Thakor N, O’Connor D, Trimmer B, Lima SQ, Carey M, Pandarinath C, Costa RM, Pruszynski JA, Bakir M, Sober SJ. Myomatrix arrays for high-definition muscle recording. eLife, 12:RP88551. doi: 10.7554/eLife.88551.
- Lee WH*, Karpowicz BM*, Pandarinath C**, Rouse AG**. Identifying distinct neural features between the initial and corrective phases of precise reaching using AutoLFADS. Journal of Neuroscience, Mar; e1224232024. doi: 10.1523/JNEUROSCI.1224-23.2024. Preprint on BioRxiv: 10.1101/2023.06.30.547252, posted July 2, 2023.
2023
- Versteeg C, Sedler AR, McCart JD, Pandarinath C. (2023) Expressive dynamics models with nonlinear injective readouts enable reliable recovery of latent features from neural activity. NeurIPS workshop on Symmetry and Geometry in Neural Representations (NeurReps). Preprint on arXiv: 2309.06402, posted Sep 15, 2023.
- Patel AN*, Sedler AR*, Huang J, Pandarinath C**, Gilja V**. (2023) High-performance neural population dynamics modeling enabled by scalable computational infrastructure. Journal of Open Source Software, 8(83), 5023. doi: 10.21105/joss.05023. [Code repository].
- Sedler AR, Versteeg C, Pandarinath C. (2023) Expressive architectures enhance interpretability of dynamics-based neural population models. Neurons, Behavior, Data analysis, and Theory, Mar. doi: 10.51628/001c.73987.
2022
- Zhu F, Grier HA, Tandon R, Cai C, Agarwal A, Giovannucci A, Kaufman MT*, Pandarinath C*. (2022) A deep learning framework for inference of single-trial neural population activity from calcium imaging with sub-frame temporal resolution. Nature Neuroscience, Dec; 25:1724-34. doi: 10.1038/s41593-022-01189-0. Preprint on BioRxiv: 10.1101/2021.11.21.469441, posted Nov 21, 2021.
- Keshtkaran MR*, Sedler AR*, Chowdhury RH**, Tandon R**, Basrai D, Nguyen SL, Sohn H, Jazayeri M, Miller LE, Pandarinath C. (2022) A large-scale neural network training framework for generalized estimation of single-trial population dynamics. Nature Methods, Dec; 19:1572-7. doi: 10.1038/s41592-022-01675-0. Expanded version on BioRxiv: 10.1101/2021.01.13.426570, posted Jun 07, 2022.
- Wimalasena LN, Braun JF, Keshtkaran MR, Alessandro C, Gallego JA, Tresch MC, Miller LE, Pandarinath C. (2022) Estimating muscle activation from EMG using deep learning-based dynamical systems models. Journal of Neural Engineering, May; 19:036013. doi: 10.1088/1741-2552/ac6369. Preprint on BioRxiv: 10.1101/2021.12.01.470827, posted Dec 03, 2021.
2021
- Zhu F*, Sedler AR*, Grier HA, Ahad N, Davenport MA, Kaufman MT, Giovannucci A, Pandarinath C. (2021) Deep inference of latent dynamics with spatio-temporal super resolution using selective backpropagation through time. Advances in Neural Information Processing Systems (NeurIPS) 34. arXiv version. Code demo on Github.
- Ye J, Pandarinath C. (2021) Representation learning for neural population activity with Neural Data Transformers. Neurons, Behavior, Data analysis, and Theory. August;5(3). doi: 10.51628/001c.27358.
- Pandarinath C, Bensmaia SJ. (2021) The science and engineering behind sensitized, brain-controlled bionic hands. Physiological Reviews. Sep; 102:551-604. doi: 10.1152/physrev.00034.2020
- Pei F*, Ye J*, Zoltowski D, Wu A, Chowdhury RH, Sohn H, O'Doherty JE, Shenoy KV, Kaufman MT, Churchland MM, Jazayeri M, Miller LE, Pillow J, Park IM, Dyer EL, Pandarinath C. (2021) Neural Latents Benchmark '21: Evaluating latent variable models of neural population activity. Advances in Neural Information Processing Systems (NeurIPS) 34, Track on Datasets and Benchmarks. arXiv version. More info at neurallatents.github.io.
2020
- Wimalasena LN, Miller LE,Pandarinath C. (2020)From unstable input to robust output. Nature Biomedical Engineering (News & Views). July. doi: 10.1038/s41551-020-0587-9[Free access]
- Flint RD, Tate MC, Li K,Templer JW, Rosenow JM, Pandarinath C, Slutzky MW. (2020) The representation of finger movement and force in human motor and premotor cortices. eNeuro, July;7(4). doi: 10.1523/ENEURO.0063-20.2020
2019
- Keshtkaran MR, Pandarinath C. (2019) Enabling hyperparameter optimization in sequential autoencoders for spiking neural data. Advances in Neural Information Processing Systems (NeurIPS) 32. arXiv version.
- Pandarinath C, Ali YH. (2019) Brain implants that let you speak your mind. Nature (News & Views). Apr;568(7753):466-467. doi: 10.1038/d41586-019-01181-y
- Willett FR, Young D, Murphy BA, Memberg WD, Blabe CH, Pandarinath C, Saab J, Walter BL, Sweet JA, Miller JP, Henderson JM, Shenoy KV, Simeral JD, Jarosiewicz B, Hochberg LR, Kirsch RF, Ajiboye AB. Principled BCI decoder design and parameter selection using a feedback control model. Scientific Reports, Jun 20;9(1):8881. doi: 10.1038/s41598-019-44166-7.
- Milekovic T, Bacher D, Sarma A, Simeral JD, Saab J, Pandarinath C, Yvert B, Blabe CH, Eskandar EN, Cash SS, Shenoy KV*, Henderson JM*, Hochberg LR, Donoghue JP. Volitional control of single-electrode high gamma local field potentials (LFPs) by people with paralysis. Journal of Neurophysiology, Apr 1;121(4):1428-1450. doi: 10.1152/jn.00131.2018.
2018
- Pandarinath C, Ames KC, Russo AA, Farschian A, Miller LE, Dyer EL, Kao JC. (2018) Latent factors and dynamics in motor cortex and their application to brain-machine interfaces. Journal of Neuroscience. Oct;38(44) 9390-9401; doi: 10.1523/JNEUROSCI.1669-18.2018
- 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. (2018) Inferring single-trial neural population dynamics using sequential auto-encoders. Nature Methods. Sept;15(10). doi: 10.1038/s41592-018-0109-9
- Nuyujukian, P*, Albites Sanabria J*, Saab J*, Pandarinath C, Jarosiewicz B, Blabe CH, Franco B, Mernoff ST, Eskandar EN, Simeral JD, Hochberg LR, Shenoy KV**, Henderson JM**. Cortical control of a tablet computer by people with ALS. PLoS ONE. Nov;13(11): e0204566. doi: 10.1371/journal.pone.0204566
- Stavisky SD, Kao JC, Nuyujukian P, Pandarinath C, Blabe CH, Ryu SI, Hochberg LR, Henderson JM*, Shenoy KV*. Brain-machine interface cursor position only weakly affects monkey and human motor cortical activity in the absence of arm movements. Scientific Reports. Nov;8(1), 16357. doi: 10.1038/s41598-018-34711-1
- Milekovic T, Sarma A, Bacher D, Simeral JD, Saab J, Pandarinath C, Sorice BL, Blabe CH, Oakley E, Trinagle K, Eskandar EN, Cash SS, Henderson JM*, Shenoy KV*, Donoghue JP, Hochberg LR. (2018) Stable long-term BCI-enabled communication in ALS and locked-in syndrome using LFP signals. Journal of Neurophysiology. Jul 1;120(1):343-360. doi: 10.1152/jn.00493.2017
- Willett FR, Murphy BA, Memberg WD, Blabe CH, Young D, Jarosiewicz B, Pandarinath C, Franco B, Saab J, Walter BL, Sweet JA, Miller JP, Henderson JM, Shenoy KV, Simeral JD, Hochberg LR, Kirsch RF, Ajiboye AB. (2018) A comparison of intention estimation methods for decoder calibration in intracortical brain-computer interfaces. IEEE Transactions on Biomedical Engineering, Sep;65(9):2066-2078. doi: 10.1109/TBME.2017.2783358
- Even-Chen N, Stavisky SD, Pandarinath C, Nuyujukian P, Blabe CH, Hochberg LR, Henderson* JM, Shenoy* KV (2018) Feasibility of automatic error detect-and-undo system in human intracortical brain-computer interfaces. IEEE Transactions on Biomedical Engineering, Aug;65(8):1771-1784. doi: 10.1109/TBME.2017.2776204
- Brandman D, Hosman T, Saab J, Burkhart M, Shanahan B, Ciancibello J, Sarma A, Milstein D, Vargas-Irwin C, Franco B, Kelemen J, Blabe C, Murphy B, Young D, Willett FR, Pandarinath C, Stavisky SD, Kirsch R, Walter B, Ajiboye A, Cash S, Eskandar EN, Miller J, Sweet J, Shenoy KV, Henderson JM, Jarosiewicz B, Harrison M, Simeral JD, Hochberg LR. (2018) Rapid calibration of an intracortical brain computer interface for people with tetraplegia. Journal of Neural Engineering. Apr;15(2):026007. doi: 10.1088/1741-2552/aa9ee7
2017
- Pandarinath C*, Nuyujukian P*, Blabe CH, Sorice BL, Saab J, Willett F, Hochberg LR, Shenoy KV**, Henderson JM**. (2017) High performance communication by people with tetraplegia using an intracortical brain-machine interface. eLife. Feb 21; 6. doi: 10.7554/eLife.18554 [paper] [pubmed] [Video 1].
- Willett FR, Murphy BA, Memberg WD, Blabe CH, Pandarinath C, Walter BL, Sweet JA, Miller JP, Henderson JM, Shenoy KV, Simeral JD, Hochberg LR, Kirsch RF, Ajiboye AB. (2017) Signal-independent noise in intracortical brain-computer interfaces causes movement time properties inconsistent with Fitts’ law. Journal of Neural Engineering. Apr; 14(2):026010. doi: 10.1088/1741-2552/aa5990 [pubmed]
- Willett FR, Pandarinath C, Jarosiewicz B, Murphy BA, Memberg WD, Blabe CH, Saab J, Walter BL, Sweet JA, Miller JP, Henderson JM, Shenoy KV, Simeral JD, Hochberg LR, Kirsch RF, Ajiboye AB. (2017) Feedback control policies employed by people using intracortical brain-computer interfaces. Journal of Neural Engineering. Feb;14(1):016001. doi: 10.1088/1741-2560/14/1/016001[pubmed]
2016
- Sussillo D, Jozefowicz R, Abbott LF, Pandarinath C. (2016) LFADS - Latent Factor Analysis via Dynamical Systems. arXiv:1608.06315, 22 Aug. [arXiv] [PDF]
2015
- Gilja V*, Pandarinath C*, Blabe CH, Nuyujukian P, Simeral JD, Sarma AA, Sorice BL, Perge JA, Jarosiewicz B, Hochberg LR, Shenoy KV**, Henderson JM**. (2015) Clinical translation of a high performance neural prosthesis. Nature Medicine, Oct;21(10):1142-5. doi: dx.doi.org/10.1038/nm.3953 [PDF]
- Pandarinath C, Gilja V, Blabe CH, Nuyujukian P, Sarma AA, Sorice BL, Eskandar EN, Hochberg LR, Henderson JM*, Shenoy KV*. (2015) Neural population dynamics in human motor cortex during movements in people with ALS. eLife Jun 23;4:e07436. doi: dx.doi.org/10.7554/eLife.07436 [PDF]
- Jarosiewicz B, Bacher D, Sarma AA, Masse NY, Simeral JD, Sorice BL, Oakley EM, Blabe CH, Pandarinath C, Gilja V, Cash SS, Eskandar EN, Friehs G, Henderson JM, Shenoy KV, Donoghue JP, Hochberg LR. (2015) Virtual typing by people with tetraplegia using a stabilized, self-calibrating intracortical brain-computer interface. Science Translational Medicine. 7(313):179 doi: dx.doi.org/10.1126/scitranslmed.aac7328 [PDF]
2014
- Ukaegbu UE, Kishore SP, Kwiatkowski DP, Pandarinath C, Dahan-Pasternak N, Dzikowski R, Deitsch KW. (2014) Recruitment of PfSET2 by RNA polymerase II to variant antigen encoding loci contributes to antigenic variation in P. falciparum. PLOS Pathogens, Jan;10(1):e1003854. doi: dx.doi.org/10.1371/journal.ppat.1003854 [PDF]
2013
- Pandarinath C, Carlson ET, Nirenberg S (2013) A system for optically controlling neural circuits with very high spatial and temporal resolution. In Proceedings of the IEEE 13th International Conference on Bioinformatics and Bioengineering (BIBE), Nov 10-13, 2013, Chania, Greece. doi: dx.doi.org/10.1109/BIBE.2013.6701707 [PDF]
2012
- Nirenberg S, Pandarinath C (2012) A retinal prosthetic strategy with the capacity to restore normal vision. Proceedings of the National Academy of Sciences, Sept 11; 109(37):15012-7. doi: dx.doi.org/10.1073/pnas.1207035109 [PDF]
2010
- Pandarinath C, Victor JD, Nirenberg S (2010) Symmetry breakdown in the ON and OFF pathways of the retina at night: functional implications. Journal of Neuroscience, July 28; 30(30):10006-14. doi: dx.doi.org/10.1523/jneurosci.5616-09.2010 [PDF]
- Pandarinath C, Bomash I, Victor JD, Prusky GT, Tschetter WW, Nirenberg S (2010) A novel mechanism for switching a neural system from one state to another. Frontiers in Computational Neuroscience, Mar 4:2. doi: dx.doi.org/10.3389/fncom.2010.00002 [PDF]
2008
- Dedek K, Pandarinath C, Alam NM, Wellershaus K, Schubert T, Willecke K, Prusky GT, Weiler R, Nirenberg S (2008) Ganglion cell adaptability: Does the coupling of horizontal cells play a role? PLoS ONE, 3(3): e1714. doi: dx.doi.org/10.1371/journal.pone.0001714 [PDF]
2005
- Coppa BJ, Fulton CC, Kiesel SM, Davis RF, Pandarinath C, Burnette JE, Nemanich RJ, Smith DJ (2005) Structural, microstructural, and electrical properties of gold films and Schottky contacts on remote plasma cleaned, n-type ZNO{0001} surfaces. Journal of Applied Physics, 97:103571. doi: dx.doi.org/10.1063/1.1898436 [PDF]
2004
- Mecouch WJ, Wagner BP, Reitmeier ZJ, Davis RF, Pandarinath C, Rodriguez BJ, Nemanich RJ (2004) Preparation and characterization of atomically clean stoichiometric surfaces of AlN(0001). Journal of Vacuum Science & Technology A: Vacuum, Surfaces, and Films, 23:1. doi: dx.doi.org/10.1116/1.1830497 [PDF]
Conference Abstracts
Primary
2024
- Agarwal A, Zhu F, Yu Y, Grier HA, Zylbertal A, Bianco I, Smith SL, Kaufman MT, Pandarinath C (2024) Temporally-precise inference of neural dynamics from slow-sampling rate calcium imaging. Computational and Systems Neuroscience (COSYNE). Lisbon, Portugal. (poster) Ho N, Nason-Tomaszewski SR, Bechefsky P, Pritchard A, Hochberg LR, AuYong N*, Pandarinath C* (2024) Gamification of finger tasks to improve engagement for intra-cortical brain-computer interfaces. Shenoy Undergraduate Research Fellowship in Neuroscience Annual Meeting. New York, NY. (poster)
- Rigotti-Thompson M, Ali YH, Nason-Tomaszewski SR, Nicolas C, Hahn N, Avansino D, Mifsud DM, Tung K, Allcroft S, Henderson JM, Hochberg LR, Au Yong N, Pandarinath C (2024) Leveraging preparatory activity from the human motor cortex for high performance brain-computer interface control. Neural Control of Movement. Dubrovnik, Croatia. (selected talk)
- O'Connell S, Michaels JA, Wang R, Venkatesh M, Aresh N, Sober S, Pandarinath C (2024) EMUsort and LITMUS: the enhanced motor unit sorter and robust benchmarking of motor unit sorters. Neural Control of Movement. Dubrovnik, Croatia. (poster)
2023
- Karpowicz BM, Bhaduri BB, McCart JD, Ali YH, Flint RD, Slutzky MW, Pandarinath C (2023) Hybrid neural dynamics models enable high performing and stable iBCI decoding from local field potentials. Program No: 488.07. Neuroscience Meeting Planner. Washington, DC: Society for Neuroscience 2023. (poster)
- Agarwal A, Zhu F, Yu Y, Grier HA, Smith SL, Kaufman MT, Pandarinath C (2023) Temporally-precise inference of neural population dynamics from slow-sampling rate calcium imaging using deconvolution-free dynamics modeling. Program No: 244.19. Neuroscience Meeting Planner. Washington, DC: Society for Neuroscience 2023. (poster)
- Ali YH, Mifsud DM, Nason-Tomaszewski SR, Rigotti-Thompson M, Bhaduri B, Nicolas C, Allcroft S, Au Yong N, Hochberg LR, Pandarinath C (2023) Closed-loop latent dynamics modeling for iBCI control. Program No: 488.10. Neuroscience Meeting Planner. Washington, DC: Society for Neuroscience 2023. (poster)
- Nason-Tomaszewski SR, Ho N, Mifsud D, Rigotti-Thompson M, Ali YH, Nicolas C, Allcroft S, Hochberg LR, Willsey MS, Patil PG, Chestek CA, Au Yong N, Pandarinath C (2023) Modeling Neural Population Dynamics Improves Individuated Finger Movement Decoding. Program No: 488.08. Neuroscience Meeting Planner. Washington, DC: Society for Neuroscience 2023. (poster)
- Wimalasena LN, Pandarinath C*, Au Yong N* (2023) Dynamical mechanisms of flexible pattern generation in spinal neural populations. Program No: 377.08. Neuroscience Meeting Planner. Washington, DC: Society for Neuroscience 2023. (poster)
- Rigotti-Thompson M, Nason-Tomaszewski SR, Ali YH, Mifsud D, Nicolas C, Allcroft S, Hochberg LR, Au Yong N, Pandarinath C (2023) An intermittent movement intention decoding paradigm for BCI control. Program No: 488.06. Neuroscience Meeting Planner. Washington, DC: Society for Neuroscience 2023. (poster)
- Versteeg C, Sedler AR, McCart JD, Pandarinath C (2023) Interpreting Neural Computation via Sequential-Autoencoders with Injective, Nonlinear Readouts. Program No: 445.20. Neuroscience Meeting Planner. Washington, DC: Society for Neuroscience 2023. (poster)
- Chowdhury RH, Oby ER, Karpowicz BM, Dekleva BM, Sadeghi M, Sharif Razavian R, Bazzi S, Pandarinath C, Loughlin PJ*, Sternad D*, Batista AP* (2023) Neural activity in motor cortex evolves differently for continuously feedback-driven movements compared to discrete reaches. Program No: 349.13. Neuroscience Meeting Planner. Washington, DC: Society for Neuroscience 2023. (poster)
- Ali YH, Bodkin K, Rigotti-Thompson M, Patel K, Bhaduri B, Nason-Tomaszewski SR, Mifsud DM, Hou X, Nicolas C, Allcroft S, Hochberg LR, Au Yong N, Stavisky SD, Miller LE, Brandman DM*, Pandarinath C* (2023) BRAND: A platform for real-time deep network inference in closed-loop BCIs. Brussels, Belgium. 10th International BCI Meeting. (poster)
- Karpowicz BM, Ali YH, Wimalasena LN, Sedler AR, Keshtkaran M, Bodkin K, Ma X, Bhaduri B, Flint RD, Slutzky MW, Miller LE, Pandarinath C (2023) Stabilizing brain-computer interfaces through alignment of latent dynamics. Brussels, Belgium. 10th International BCI Meeting. (poster)
- Karpowicz BM, Ali YH, Wimalasena LN, Sedler AR, Keshtkaran M, Bodkin K, Ma X, Miller LE, Pandarinath C (2023) Stabilizing brain-computer interfaces through alignment of latent dynamics. As part of workshop, titled: “Transfer learning toward plug-and-play BCI,” organized by Rizzoglio F, Karpowicz BM, Oby ER. Brussels, Belgium. 10th International BCI Meeting. (workshop talk)
- Wimalasena LN, Pandarinath C*, Au Yong NA* (2023) Dynamical mechanisms of flexible pattern generation in spinal neural populations. Computational and Systems Neuroscience (Cosyne) 2023. (poster)
- Versteeg C, Sedler AR, Pandarinath C (2023) ODIN: Invertible readouts to improve the dynamical accuracy of neural population models. Computational and Systems Neuroscience (Cosyne) 2023. (poster)
2022
- Karpowicz BM, Ali YH, Wimalasena LN, Sedler AR, Keshtkaran MR, Bodkin K, Ma X, Miller LE, Pandarinath C (2022) Stabilizing brain-computer interfaces through alignment of latent dynamics. Program No: 475.04. Neuroscience Meeting Planner. San Diego, CA: Society for Neuroscience 2022. (poster)
- Ali YH, Bodkin K, Rigotti-Thompson M, Miller LE, Pandarinath C*, Brandman DM* (2022) Realtime asynchronous decoding for closed-loop neuroprosthetics. Program No: 475.05. Neuroscience Meeting Planner. San Diego, CA: Society for Neuroscience 2022. (poster)
- Lee W, Karpowicz BM, Pandarinath C, Rouse AG (2022) Different neural features between the initial and corrective phases of precise reaching identified with AutoLFADS. Neuroscience Meeting Planner. San Diego, CA: Society for Neuroscience 2022. (poster)
- Karpowicz BM, Ali YH, Wimalasena LN, Keshtkaran MR, Sedler AR, Bodkin K, Ma X, Miller LE, Pandarinath C (2022) Stabilizing brain-computer interfaces through nonlinear manifold alignment with dynamics. Computational and Systems Neuroscience (Cosyne) 2022. (poster)
2021
- Karpowicz BM, Ali YH, Wimalasena LN, Keshtkaran M, Sedler AR, Bodkin K, Ma X, Miller LE, Pandarinath C (2021) Stabilizing brain-computer interfaces through nonlinear manifold alignment with dynamics. Program No: 552.03. Neuroscience Meeting Planner. Chicago, IL: Society for Neuroscience 2021. Online. (poster)
- Wimalasena LN, Braun JF, Keshtkaran MR, Hofmann D, Alessandro C, Gallego JA, Miller LE, Tresch MC, Pandarinath C (2021) Estimating muscle activation using deep learning-based dynamical systems models. Program No:574.08. Neuroscience Meeting Planner. Chicago, IL: Society for Neuroscience 2021. Online. (poster)
- Ye J, Pandarinath C (2021). Representation learning for neural population activity with Neural Data Transformers. Program No: 964.02. Neuroscience Meeting Planner. Chicago, IL: Society for Neuroscience 2021. Online (poster)
- Pei F*, Ye J*, Zoltowski DM, Wu A, Chowdhury RH, Sohn H, O'Doherty JE, Shenoy KV, Kaufman MT, Churchland MM, Jazayeri M, Miller LE, Dyer EL, Park IM, Pillow JW, Pandarinath C (2021). Advancing the investigation of neural population structure with the Neural Latents Benchmark. Program No: 964.09. Neuroscience Meeting Planner. Chicago, IL: Society for Neuroscience 2021. Online (poster)
- Rigotti-Thompson M*, O'Connell S*, Corsten AN, Zhu F, Ali YH, Li K, Sober SJ, Pandarinath C (2021) A low-latency behavioral feedback system for training, analyzing, and perturbing skilled forelimb rotation in rats. Program No: 574.03. Neuroscience Meeting Planner. Chicago, IL: Society for Neuroscience 2021. Online. (poster)
- Zhu F, Grier H, Tandon R, Cai C, Giovannucci A, Kaufman M, Pandarinath C (2021) Inferring single-trial neural population dynamics from calcium imaging with sub-frame temporal resolution via deep learning. Program No: 928.04. Neuroscience Meeting Planner. Chicago, IL: Society for Neuroscience 2021. Online. (poster)
- Lee W, Karpowicz BM, Pandarinath C, Rouse AG (2021) Identifying distinct neural features between the initial and corrective phases of precise reaching using autoLFADS. Program No: 554.03. Neuroscience Meeting Planner. Chicago, IL: Society for Neuroscience 2021. Online. (poster)
- Karpowicz B, Ali Y, Wimalasena LN, Keshtkaran MR, Sedler A, Farschian A, Walner J, Ma X, Semel B, Bodkin K, Miller L, Pandarinath C (2021) Stabilizing brain-computer interfaces with nonlinear manifold alignment. Society for the Neural Control of Movement 2021. (poster)
- Wimalasena LN, Braun JF, Keshtkaran MR, Alessandro C, Gallego JA, Tresch MC, Miller LE, Pandarinath C (2021) Estimating motor commands from EMG using dynamical systems models of multi-muscle activity. Society for the Neural Control of Movement 2021 (talk)
- Zhu F, Grier H, Tandon R, Cai C, Giovannucci A, Kaufman MT, Pandarinath C (2021) Precise inference of single trial network dynamics from calcium imaging using LFADS. Computational and Systems Neuroscience (Cosyne) 2021. (poster)
2020
- Karpowicz B, Wimalasena L, Keshtkaran MR, Ali Y, Sedler A, Farschian A, Walner J, Ma X, Semel B, Bodkin K, Miller L, Pandarinath C (2020) Improving brain-machine interface robustness through deep learning-based manifold alignment. Neuromatch 3.0 Conference. (talk)
- Sedler AR, Keshtkaran MR, Chowdhury RH, Tandon R, Basrai D, Nguyen S, Sohn H, Jazayeri M, Miller LE, Pandarinath C (2020) AutoLFADS: A large-scale neural network training framework for generalized estimation of single-trial population dynamics. Neuromatch 3.0 Conference. (talk)
- Ye J, Pandarinath C (2020) Representation learning for neural population activity with Neural Data Transformers. Neuromatch 3.0 Conference. (talk)
- Wimalasena LN, Braun JF, Keshtkaran MR, Alessandro C, Gallego JA, Tresch MC, Miller LE, Pandarinath C (2020) De-noising EMG using dynamical systems models of muscle population activity. Neuromatch 3.0 Conference (talk)
- Wimalasena LN, Braun JF, Keshtkaran MR, Alessandro C, Gallego JA, Cherian A, Tresch MC, Miller LE, Pandarinath C (2020) De-noising EMG using deep learning models of muscle population dynamics. Society for the Neural Control of Movement 2020. (poster)
- Keshtkaran MR, Tandon R, Basrai D, Nguyen SL, Chowdhury RH, Sohn H, Jazayeri M, Miller LE, Pandarinath C (2020) AutoLFADS:A large-scale neural network training framework for generalized estimation of single-trial population dynamics. Computational and Systems Neuroscience (Cosyne) 2020. (poster)
2019
- Tandon R, Grier H, Kaufman MT, Pandarinath C (2019) Deep learning to extract single-trial trajectories from two-photon calcium imaging. Program No:707.22. Neuroscience Meeting Planner. Chicago, IL: Society for Neuroscience 2019. Online. (poster)
- Li K, Flint R, Slutzky MW, Pandarinath C (2019) Modeling neural population dynamics informs and improves decoding of electrocorticographic signals. Program No:312.18. Neuroscience Meeting Planner. Chicago, IL: Society for Neuroscience 2019. Online. (poster)
- Wimalasena LN, Braun JF, Keshtkaran MR, Alessandro C, Gallego JA, Miller LE, Tresch MC, Pandarinath C (2019) Uncovering de-noised EMG representations using deep learning models of muscle population dynamics. Program No:670.05. Neuroscience Meeting Planner. Chicago, IL: Society for Neuroscience 2019. Online. (poster)
- Braun JF, Wimalasena LN, Alessandro C, Miller LE, Tresch MC, Pandarinath C (2019) Uncovering muscle population dynamics of locomotion using deep learning. Bernstein Conference 2019. doi: 10.12751/nncn.bc2019.0281
- Zhu F, Ly R, Kastner S, Pandarinath C (2019) Using deep learning to characterize cognitive population activity in the pulvinar. Statistical Analysis of Neuronal Data 2019. (poster)
2018
- Zhu F, Ly R, Kastner S, Pandarinath C (2018) Using deep learning to characterize cognitive population activity in the pulvinar. Program No:238.5995. Neuroscience Meeting Planner. San Diego, CA: Society for Neuroscience 2018. Online. (poster)
- Keshtkaran M, Pandarinath C (2018) Large-scale automated deep neural network training framework for robust inference of neural ensemble dynamics. Program No:703.8553. Neuroscience Meeting Planner. San Diego, CA: Society for Neuroscience 2018. Online. (poster)
- Wimalasena LN, Cherian A, Miller LE, Pandarinath C (2018) Modeling neural ensemble dynamics in motor cortex leads to improved EMG decoding of multiple muscles in goal-directed reaching tasks. Program No:312.9154. Neuroscience Meeting Planner. San Diego, CA: Society for Neuroscience 2018. Online. (poster)
- Wimalasena L, Cherian A, Miller LE, Pandarinath C (2018) Modeling neural population dynamics in motor cortex leads to improved kinetic decoding in an unstructured motor task. Society for the Neural Control of Movement 2018. (poster)
- Pandarinath C, O'Shea, DJ, Collins J, Jozefowicz R, Stavisky SD, Kao JC, Trautmann E, Kaufman MT, Ryu SI, Hochberg LR, Henderson JM, Shenoy KV, Abbott LF, Sussillo DS (2018) Precisely estimating neural population dynamics in motor cortex using deep learning. Society for the Neural Control of Movement 2018. (poster)
- Pandarinath C (2018) LFADS: A deep learning method to infer latent states and dynamics from neural population activity. Workshop on Closed-loop control of neural systems and circuits for scientific discovery. Computational and Systems Neuroscience (Cosyne) 2018. (invited talk)
- Pandarinath C, O'Shea, DJ, Collins J, Jozefowicz R, Stavisky SD, Kao JC, Trautmann E, Kaufman MT, Ryu SI, Henderson JM, Shenoy KV, Abbott LF, Sussillo DS (2018) LFADS: a deep learning technique to precisely estimate neural population dynamics on single trials. Computational and Systems Neuroscience (Cosyne) 2018. (poster)
2017
- Pandarinath C, O'Shea DJ, Collins J, Jozefowicz R, Stavisky SD, Kao JC, Trautmann E, Churchland MM, Kaufman MT, Ryu SI, Henderson JM, Shenoy KV, Abbott LF, Sussillo DS (2017) LFADS: A deep learning technique to precisely estimate neural population dynamics on single trials. Program No:346.23. Neuroscience Meeting Planner. Washington, DC: Society for Neuroscience 2017. Online. (poster)
- O'Shea DJ, Pandarinath C, Collins J, Jozefowicz R, Trautmann E, Stavisky SD, Kao JC, Churchland MM, Kaufman MT, Henderson JM, Shenoy KV, Abbott LF, Sussillo DS (2017) Dynamic neural stitching: Learning consistent neural population dynamics from separately recorded neural populations across months using LFADS. Program No:346.19. Neuroscience Meeting Planner. Washington, DC: Society for Neuroscience 2017. Online. (poster)
- Pandarinath C, Collins J, Jozefowicz R, Stavisky SD, Kao JC, Churchland MM, Kaufman MT, Ryu SI, Henderson JM, Shenoy KV, Abbott LF, Sussillo DS (2017) Precise estimates of single-trial neural population state in motor cortex via deep learning methods. Computational and Systems Neuroscience (Cosyne) 2017. (poster)
2016
- Pandarinath C (2016) Using dynamical models of motor cortical activity to improve BCIs. Workshop on Pathways to effective BCI communication and computer interaction for people with disability. International BCI Society 2016 (invited talk).
- Pandarinath C, Nuyujukian P, Henderson JM, Shenoy KV (2016, selected talk) Implanted integrated circuit requirements for brain-machine interfaces. International Solid State Circuits Conference (ISSCC), San Francisco, CA (KVS speaking).
2015
- Pandarinath C, Sussillo D, Sorice BL, Eskandar EN, Hochberg LR, Abbot LF, Henderson JM*, Shenoy KV* (2015) Dynamic dimensionality reduction of human motor cortical activity using recurrent neural networks. Program No: 748.02. Neuroscience Meeting Planner. Chicago, IL: Society for Neuroscience 2015. Online. (talk) [abstract]
- Nuyujukian P, Pandarinath C, Blabe CH, Hochberg LR, Shenoy KV*, Henderson JM* (2015) A bluetooth wireless brain-machine interface for general purpose computer use. Program No: 748.01. Neuroscience Meeting Planner. Chicago, IL: Society for Neuroscience 2015. Online. (talk) [abstract]
- Pandarinath C*, Nuyujukian P*, Gilja V, Blabe CH, Perge JA, Jarosiewicz B, Hochberg LR, Shenoy KV**, Henderson JM** (2015) Towards high performance communication using intracortical brain-computer interfaces. Front. Hum. Neurosci. Conference Abstract: 2015 International Workshop on Clinical Brain-Machine Interfaces (CBMI2015). doi:dx.doi.org/10.3389/conf.fnhum.2015.218.00003
2014
- Pandarinath C*, Nuyujukian P*, Gilja V, Blabe CH, Perge JA, Jarosiewicz B, Hochberg LR, Shenoy KV**, Henderson JM** (2014) Application of a high performance intracortical brain computer interface for communication in a person with amyotrophic lateral sclerosis. Program No. 252.08. Neuroscience Meeting Planner. Washington, DC: Society for Neuroscience, 2014. Online. [abstract]
- Nuyujukian P*, Pandarinath C*, Gilja V, Blabe C, Perge JA, Jarosiewicz B, Hochberg LR, Shenoy KV**, Henderson JM** (2014) Design of a high performance intracortical brain computer interface for a person with amyotrophic lateral sclerosis. Program No. 252.09. Neuroscience Meeting Planner. Washington, DC: Society for Neuroscience, 2014. Online. [abstract]
- Pandarinath C*, Gilja V*, Blabe C, Jarosiewicz B, Perge JA, Hochberg LR, Shenoy KV**, Henderson JM** (2014) Rapid typing by a person with ALS using an intracortical brain-computer interface and Dasher. IEEE Brain Grand Challenges. Washington, D.C. GC217.
- Pandarinath C*, Gilja V*, Blabe C, Jarosiewicz B, Perge JA, Hochberg LR, Shenoy KV**, Henderson JM** (2014) High-performance communication using neuronal ensemble recordings from the motor cortex of a person with ALS. American Society for Stereotactic and Functional Neurosurgery. Washington, D.C. 92 (suppl 1) 1-75, #130. [abstract]
- Pandarinath C, Gilja V, Blabe C, Hochberg LR, Shenoy KV**, Henderson JM** (2014) Corresponding neural signatures of movement and imagined movement in human motor cortex. Frontiers in Neuroscience. Conference Abstract: Computational and Systems Neuroscience (COSYNE), Salt Lake City, UT. III-87. [abstract]
2013
- Pandarinath C*, Gilja V*, Blabe CH, Hochberg LR, Shenoy KV**, Henderson JM** (2013) Overlapping neural representations of upper extremity movements in human primary motor cortex during volitional, imagined, observed, and passive movements. Program No. 80.03. 2013 Neuroscience Meeting Planner. Washington, DC: Society for Neuroscience. Online. San Diego, CA. [abstract]
- Gilja V*, Pandarinath C*, Blabe CH, Hochberg LR, Shenoy KV**, Henderson JM** (2013) Design and application of a high performance intracortical brain computer interface for a person with amyotrophic lateral sclerosis. Program No. 80.06. 2013 Neuroscience Meeting Planner. Washington, DC: Society for Neuroscience. Online. San Diego, CA. [abstract]
- Henderson JM, Gilja V, Pandarinath C, Blabe C, Hochberg LR, Shenoy KV (2013) High performance computer cursor control using neuronal ensemble recordings from the motor cortex of a person with ALS. Neurosurgery. 60 Suppl 1:184 [abstract]
2010
- Pandarinath C, Nirenberg S (2010) A retinal prosthetic strategy with the capacity to restore normal vision: Quantifying the effects of the encoder and transducer. Program No. 891.4. 2010 Neuroscience Meeting Planner. Washington, DC: Society for Neuroscience. Online. San Diego, CA. [abstract]
- Nirenberg S, Pandarinath C (2010, selected talk) A retinal prosthetic strategy with the capacity to restore normal vision. Program No. 20.1. 2010 Neuroscience Meeting Planner. Washington, DC: Society for Neuroscience. Online. San Diego, CA. [abstract]
- Nirenberg S, Pandarinath C, Bomash I, Victor JD, Prusky GT, Tschetter WW (2010) A novel role for gap junction coupling: a mechanism for allowing neural networks to change states. Association for Research in Vision and Ophthalmology, Fort Lauderdale, FL
2009
- Pandarinath C, Victor JD, Nirenberg S (2009) Symmetry breakdown in the ON and OFF pathways of the retina at night: Functional implications. Program No. 848.6.4. 2009 Neuroscience Meeting Planner. Washington, DC: Society for Neuroscience. Online. Chicago, IL. [abstract]
- Nirenberg S, Pandarinath C, Bomash I, Victor JD, Prusky GT, Tscetter WW (2009) A novel role for gap junction coupling: A mechanism for allowing neural networks to change states. Program No. 165.10. 2009 Neuroscience Meeting Planner. Washington, DC: Society for Neuroscience. Online. Chicago, IL. [abstract]
- Nirenberg S, Pandarinath C, Bomash I, Victor J and Tschetter W (2009, selected talk). How neural systems adjust to different environments: an intriguing role for gap junction coupling. Computational and Systems Neuroscience (COSYNE), Salt Lake City, UT. doi: dx.doi.org/10.3389/conf.neuro.06.2009.03.036
2007
- Pandarinath C, Dedek K, Alam NM, Wellershaus K, Schubert T, Willecke K, Prusky GT, Weiler R, Nirenberg S (2007) Ganglion cell adaptability: Does the coupling of horizontal cells play a role? Program No. 391.7. 2007 Neuroscience Meeting Planner. Washington, DC: Society for Neuroscience. Online. San Diego, CA. [abstract]
Other
- Sarma AA, Brandman D, Milekovic T, Jarosiewicz B, Saab J, Bacher D, Gilja V, Pandarinath C, Schmansky NJ, Willett F, Young D, Barrese J, Blabe C, Franco B, Memberg WD, Sorice BL, Trinagle K, Cash SS, Edlow B, Mernoff S, Walter B, Eskandar E, Miller J, Henderson JM, Shenoy KV, Ajiboye A, Kirsch RF, Donoghue JP, Simeral JD, Hochberg LR (2015) Local field potentials in the motor cortex of people with tetraplegia: comparison using unsupervised methods. Program No. 522.02. Neuroscience Meeting Planner. Washington, DC: Society for Neuroscience, 2015. Online. [abstract]
- Sarma AA, Bacher D, Blabe C, Homer ML, Jarosiewicz B, Matteson E, Milekovic T, Pandarinath C, Saab J, Simeral JD, Sorice B, Shenoy KV, Henderson JM, Donoghue JP, Hochberg, LR (2014) Advancing stability and performance of point-and-click cursor control by people with tetraplegia using an intracortical brain-computer interface. Program No. 252.01. Neuroscience Meeting Planner. Washington, DC: Society for Neuroscience, 2014. Online. [abstract]
- Blabe CH, Sorice B, Bacher D, Gilja V, Homer ML, Jarosiewicz B, Milekovic T, Nuyujukian P, Pandarinath C, Perge JA, Saab J, Sarma AA, Shenoy KV, Simeral JD, Donoghue JP, Henderson JM, Hochberg, LR (2014) Collaborative, multi-institutional intracortical bci research and the key role of the clinical neurotechnology research assistant. Program No. 252.02. Neuroscience Meeting Planner. Washington, DC: Society for Neuroscience, 2014. Online. [abstract]
- Jarosiewicz B, Bacher D, Sarma AA, Masse NY, Berhanu ED, Sorice B, Oakley EM, Newell K, Blabe CH, Pandarinath C, Shenoy KV, Henderson JM, Simeral JD, Donoghue JP, Hochberg LR (2014) Progress toward a self-calibrating, practical intracortical BCI for people with tetraplegiaProgram No. 252.03. Neuroscience Meeting Planner. Washington, DC: Society for Neuroscience, 2014. Online. [abstract]
- Sarma AA, Jarosiewicz B, Bacher D, Pandarinath C, Nuyujukian P, Sorice BL, Blabe C, Simeral JD, Donoghue JP, Mernoff S, Cash SS, Eskandar EN, Shenoy KV, Henderson JM, Hochberg LR (2014) Progress toward Robust, High-Performance Intracortically Controlled Point-and-Click Communication for People with Locked-In Syndrome. Annals of Neurology. 76:S125
- Simeral JD, Bacher D, Sarma AA, Schmansky NJ, Stavisky SD, Jarosiewicz B, Milekovic T, Rosler DM, Gilja V, Pandarinath C, Cornwell AS, Henderson JM, Shenoy KV, Kirsch RF, Donoghue JP, Hochberg LR (2013) Evolution of the BrainGate real-time Brain-Computer Interface (BCI) platform for individuals with tetraplegia or limb loss. Program No. 80.02. 2013 Neuroscience Meeting Planner. Washington, DC: Society for Neuroscience. Online. San Diego, CA. [abstract]
- Blabe C, Anderson KD, Chestek CA, Gilja V, Sachs AJ, Pandarinath C, Shenoy KV, Henderson JM (2012) Assessing brain-machine interface priorities from the perspective of spinal cord injury participants. Program No. 584.14. 2012 Neuroscience Meeting Planner. Washington, DC: Society for Neuroscience. Online. New Orleans, LA. [abstract]