John P. Cunningham


Publications CV Google Scholar Code Teaching Other Contact

Research:

Many fields and industries are witnessing huge increases in the quantity and complexity of recorded data. This changing data paradigm will only lead to a similarly dramatic increase in theoretical understanding and useful technologies if we create the analytical methods to meaningfully interrogate this data. Creating these statistical and machine learning algorithms is the focus of our research.

Our primary area of focus is neural data: we use our brain in everything that we do, but we understand relatively little about how it works at a computational level. How do populations of neurons control complex, sophisticated movement?

The purpose of these algorithms is to advance scientific understanding of the neural basis of movement, and to advance computational learning methods in their own right. Our tools are drawn from statistics, computer science, and engineering, including: dynamical systems, dimensionality reduction, nonparametric statistics, approximate inference, optimization, and numerical linear algebra.


Affiliations:


Publications:

2014

Cunningham JP (2014) Analyzing neural data at huge scale. Nature Methods. In Press.
   - Download: URL ; PDF.

Cunningham JP and Yu BM (2014) Dimensionality reduction for large-scale neural recordings. Nature Neuroscience. In Press.
   - Download: URL ; PDF.
   - Press: CMU News ; Motherboard

Cunningham JP and Ghahramani Z (2014) Unifying linear dimensionality reduction. In Review.
   - Download: arXiv preprint.

Gilboa E, Cunningham JP, Nehorai A, and Gruev V (2014) Image interpolation and denoising for division of focal plane sensors using Gaussian Processes. Optics Express. 22:15277-15291.
   - Download: PDF.
   - Code: MLOSS Project URL

Gardner JR, Kusner MJ, Xu Z, Weinberger KQ, and Cunningham JP (2014) Bayesian optimization with inequality constraints. ICML 2014: JMLR W+CP.
   - Download: PDF.

Wilson AG*, Gilboa E* (contributing equally), Nehorai A, and Cunningham JP (2014) Fast kernel learning for multidimensional pattern extrapolation. In Review.
   - Download: arXiv preprint.

2013

Gilboa E, Saatci Y, and Cunningham JP (2013) Scaling multidimensional inference for sructured Gaussian Processes. IEEE TPAMI. Accepted, To appear.
   - Download: URL.
   - Code (1): MLOSS Project URL
   - Code (2): MLOSS Project URL

Leuthardt EC, Cunningham JP, and Barbour D (2013) Towards a Speech BCI Using ECoG. In Brain-computer Interface Research: Springer, pp93-100. ISBN: 978-3-642-36082-4.
   - Download: URL.

Gilboa E, Saatci Y, and Cunningham JP (2013) Scaling multidimensional Gaussian Processes using projected additive approximations. JMLR W+CP (ICML 2013). 28: 454-461.
   - Download: PDF.

2012

Churchland MM*, Cunningham JP* (contributing equally), Kaufman MT, Foster JD, Nuyujukian P, Ryu SI, Shenoy KV. (2012). Neural population dynamics during reaching. Nature, vol 487: 51-56.
   - Download: URL ; PDF (w supp mats) ; Lay Description
   - Press: The Atlantic ; Stanford News ; Wash U News
   - Code: ZIP
   - F1000Prime Recommended: URL

Gilja V, Nuyujukian P, Chestek CA, Cunningham JP, Fan JM, Yu BM, Ryu SI, Shenoy KV. (2012). A high-performance continuous cortically-controlled prosthesis enabled by feedback control design. Nature Neuroscience, vol 15: 1752-1758.
   - Download: URL ; PDF (w supp mats)
   - Press: Stanford News ; Many more

Cunningham JP, Rasmussen CE, Ghahramani Z (2012). Gaussian Processes for time-marked time-series data. JMLR W+CP (AISTATS 2012). 22: 255-263.
   - Download: PDF.

Zhao M, Batista AP, Cunningham JP, Chestek CA, Rivera-Alvidrez Z, Kalmar R, Ryu SI, Shenoy KV, Iyengar S (2012). An L1-regularized logistic model for detecting short-term neuronal interactions. J Computational Neuroscience. 32(3):479-97. PMID: 22038503
   - Download: PDF.

Macke JH, Busing L, Cunningham JP, Yu BM, Shenoy KV, Sahani M (2012). Empirical models of spiking in neural populations. Advances in Neural Information Processing Systems (NIPS) 24, MIT Press, Cambridge, MA.
   - Download: PDF.

Petreska B, Yu BM, Cunningham JP, Santhanam G, Ryu SI, Shenoy KV, Sahani M (2012). Dynamical Segmentation of single trials from population neural data. Advances in Neural Information Processing Systems (NIPS) 24, MIT Press, Cambridge, MA.
   - Download: PDF.

2011

Cunningham JP, Hennig P, Lacoste-Julien S (2011) Gaussian probabilities and expectation propagation. arXiv.
   - Download: arXiv.

Chestek CA, Gilja V, Nuyujukian P, Foster JD, Fan JM, Kaufman MT, Churchland MM, Rivera-Alvidrez Z, Cunningham JP, Ryu SI, Shenoy KV (2011) Long-term stability of neural prosthetic control signals from silicon cortical arrays in rhesus macaque motor cortex. Journal of Neural Engineering. 8:045005. PMID: 21775782
   - Download: PDF.

Cunningham JP, Nuyujukian P, Gilja V, Chestek CA, Ryu SI, Shenoy KV (2011) A closed-loop human simulator for investigating the role of feedback-control in brain-machine interfaces. Journal of Neurophysiology. 105:1932-1949. PMID: 20943945
   - Download:PDF.

2010

Churchland MM, Cunningham JP, Kaufman MT, Ryu SI, Shenoy KV (2010) Cortical preparatory activity: Representation of movement or first cog in a dynamical machine? Neuron. 68:387-400. PMID: 21040842
   - Download:PDF (paper). PDF (supp mats).

Churchland MM*, Yu BM*, Cunningham JP, Sugrue LP, Cohen MR, Corrado GS, Newsome WT, Clark AM, Hosseini P, Scott BB, Bradley DC, Smith MA, Kohn A, Movshon JA, Armstrong KM, Moore T, Chang SW, Snyder LH, Lisberger SG, Priebe NJ, Finn IM, Ferster D, Ryu SI, Santhanam G, Sahani M, Shenoy KV (2010) Stimulus onset quenches neural variability: a widespread cortical phenomenon. Nature Neuroscience. 13:369-378. PMID: 20173745
   - Download:PDF.
   - Code: ZIP

2009

Chestek CA*, Cunningham JP*, Gilja V, Nuyujukian P, Ryu SI, Shenoy KV (2009) Neural prosthetic systems: Current problems and future directions. Proc. of the 31st Annual International Conf. of the IEEE EMBS, Minneapolis, MN: 3369-3375. PMID: 19963796
   - Download:PDF.

Cunningham JP, Gilja V, Ryu SI, Shenoy KV (2009) Methods for estimating neural firing rates and their application to brain-machine interfaces. Neural Networks, 22:1235-1246. PMID: 19349143
   - Download:PDF.

Chang C, Cunningham JP, Glover GH (2009) Influence of heart rate on the BOLD signal: The cardiac response function. Neuroimage, 44:857-869. PMID: 18951982
   - Download:PDF.

Yu BM, Cunningham JP, Santhanam G, Ryu SI, Shenoy KV, Sahani M (2009) Gaussian-process factor analysis for low-dimensional single-trial analysis of neural population activity. Advances in Neural Information Processing Systems (NIPS) 21, MIT Press, Cambridge, MA.
   - Download:PDF.
   - Code: TGZ

Yu BM, Cunningham JP, Santhanam G, Ryu SI, Shenoy KV*, Sahani M* (2009) Gaussian-process factor analysis for low-dimensional single-trial analysis of neural population activity. Journal of Neurophysiology, 102:614-635. PMID: 19357332
   - Download:PDF.
   - Code: TGZ

Cunningham JP (2009) Algorithms for Understanding Motor Cortical Processing and Neural Prosthetic Systems. PhD Dissertation, Stanford University, Department of Electrical Engineering, (Stanford, California, USA).
   - Download: PDF.

2008

Cunningham JP, Yu BM, Gilja V, Ryu SI, Shenoy KV (2008) Toward optimal target placement for neural prosthetic devices. Journal of Neurophysiology. 100:3445-3457. PMID: 18829845
   - Download:PDF.

Cunningham JP, Sahani M, Shenoy KV (2008) Fast gaussian process methods for point process intensity estimation. Proceedings of the 25th Annual International Conference on Machine Learning (ICML 2008), Omni Press, Helsinki, Finland: 192-199.
   - Download:PDF.

Cunningham JP, Yu BM, Shenoy KV, Sahani M (2008) Inferring neural firing rates from spike trains using Gaussian Processes. Advances in Neural Information Processing Systems (NIPS) 20, Editors Platt J, Koller D, Singer Y, Roweis S. MIT Press, Cambridge, MA: 329-336.
   - Download:PDF.

Cunningham JP (2008) Derivation of Expectation Propagation for "Fast Gaussian process methods for point process intensity estimation". Technical Report.
   - Download:PDF.

2007

Chestek CA*, Batista AP*, Santhanam G, Yu BM, Afshar A, Cunningham JP, Gilja V, Ryu SI, Churchland MM, Shenoy KV (2007) Single-neuron stability during repeated reaching in macaque premotor cortex. Journal of Neuroscience. 27:10742–10750. PMID: 17913908
   - Download:PDF.

Yu BM, Cunningham JP, Shenoy KV, Sahani M (2008) Neural decoding of movements: From linear to nonlinear trajectory models. Neural Information Processing, M. Ishikawa et al. (Eds.): ICONIP 2007, Part I, LNCS. Springer-Verlag Berlin Heidelberg. ISBN 978-3-540-69154-9. 4984:586-595.
   - Download:PDF.

2006

Cunningham JP, Yu BM, Shenoy KV (2006) Optimal target placement for neural communication prostheses. Proc IEEE Eng Med Biol Soc. 1:2912-2915. PMID: 17945745
   - Download:PDF.

Shenoy KV, Santhanam G, Ryu SI, Afshar A, Yu BM, Gilja V, Linderman MD, Kalmar RS, Cunningham JP, Kemere CT, Batista AP, Churchland MM, Meng TH (2006) Increasing the performance of cortically-controlled prostheses. Conf Proc IEEE Eng Med Biol Soc. Suppl:6652-6656. PMID: 17959477
   - Download:PDF.


Code:

Gilboa E, Saatci Y, and Cunningham JP (2013). GPgrid: a toolkit for fast GP analysis on grid input (from Gilboa et al (2013), IEEE PAMI; see below).
   - Code: MLOSS Project URL

Gilboa E, Saatci Y, and Cunningham JP (2013). Additive GP: a toolkit for fast GP inference using projective additive approximations (from Gilboa et al (2013), IEEE PAMI; see below).
   - Code: MLOSS Project URL

Zhang WB and Cunningham JP (2013). Toeblitz: a toolkit for fast Toeplitz matrix operations.
   - Code: MLOSS Project URL

Churchland MM and Cunningham JP (2012). jPCA: the code from Churchland**, Cunningham**, et al (2012), Nature (see below).
   - Code: URL ; ZIP

Yu BM and Cunningham JP (2009). GPFA: the code from Yu, Cunningham, et al (2009), Journal of Neurophysiology (see below).
   - Code: URL ; TGZ


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Last updated: August 28, 2014