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Demixed principal component analysis of neural population data

Dmitry Kobak, Wieland Brendel, Christos Constantinidis and 7 more

eLife · 2016 · CC BY

doi:10.7554/elife.10989

Abstract

Neurons in higher cortical areas, such as the prefrontal cortex, are often tuned to a variety of sensory and motor variables, and are therefore said to display mixed selectivity. This complexity of single neuron responses can obscure what information these areas represent and how it is represented. Here we demonstrate the advantages of a new dimensionality reduction technique, demixed principal component analysis (dPCA), that decomposes population activity into a few components. In addition to systematically capturing the majority of the variance of the data, dPCA also exposes the dependence of the neural representation on task parameters such as stimuli, decisions, or rewards. To illustrate our method we reanalyze population data from four datasets comprising different species, different cortical areas and different experimental tasks. In each case, dPCA provides a concise way of visualizing the data that summarizes the task-dependent features of the population response in a single figure.

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References 48

  1. 1.

    Barak O, Tsodyks M, Romo R. Neuronal population coding of parametric working memory. The Journal of Neuroscience. 2010;30:9424-9430.

    Not in our library10.1523/jneurosci.1875-10.2010

  2. 2.

    Brendel W, Romo R, Machens CK. Demixed principal component analysis. 2011;2654-2662.

    Not in our library

  3. 3.

    Brody CD, Hernández A, Zainos A, Romo R. Timing and neural encoding of somatosensory parametric working memory in macaque prefrontal cortex. Cerebral Cortex. 2003;13:1196-1207.

    Not in our library10.1093/cercor/bhg100

  4. 4.

    Buesing L, Macke JH, Sahani M. Learning stable, regularised latent models of neural population dynamics. Network. 2012a;23:24-47.

    Not in our library10.3109/0954898x.2012.677095

  5. 5.

    Buesing L, Sahani M, Macke JH. Spectral learning of linear dynamics from generalised-linear observations with application to neural population data. 2012b;1682-1690.

    Not in our library

  6. 6.

    Christensen R. Springer Science & Business Media. 2011.

    Not in our library10.1111/j.1751-5823.2011.00159_25.x

  7. 7.

    Churchland MM, Cunningham JP, Kaufman MT, Foster JD, Nuyujukian P, Ryu SI, Shenoy KV. Neural population dynamics during reaching. Nature. 2012;487:51-56.

    Not in our library10.1038/nature11129

  8. 8.

    Constantinidis, Qi XL, Meyer T. CRCNS.org. 2016.

    Not in our library10.6080/k0zw1hvd

  9. 9.

    Cunningham JP, Yu BM. Dimensionality reduction for large-scale neural recordings. Nature Neuroscience. 2014;17.

    Not in our library10.1038/nn.3776

  10. 10.

    De la Torre F. A least-squares framework for component analysis. Pattern Analysis and Machine Intelligence, IEEE Transactions. 2012;34:1041-1055.

    Not in our library10.1109/tpami.2011.184

  11. 11.

    Eldar E, Cohen JD, Niv Y. The effects of neural gain on attention and learning. Nature Neuroscience. 2013;16:1146-1153.

    Not in our library10.1038/nn.3428

  12. 12.

    Feierstein CE, Quirk MC, Uchida N, Sosulski DL, Mainen ZF. CRCNS.org. 2016.

    Not in our library10.6080/k0qc01d2

  13. 13.

    Feierstein CE, Quirk MC, Uchida N, Sosulski DL, Mainen ZF. Representation of spatial goals in rat orbitofrontal cortex. Neuron. 2006;51:495-507.

    Not in our library10.1016/j.neuron.2006.06.032

  14. 14.

    Gouvêa TS, Monteiro T, Soares S, Atallah BV, Paton JJ. Ongoing behavior predicts perceptual report of interval duration. Frontiers in Neurorobotics. 2014;8.

    Not in our library10.3389/fnbot.2014.00010

  15. 15.

    Hastie T, Tibshirani R, Friedman J, Hastie T, Friedman J, Tibshirani R. The Elements of Statistical Learning. 2009.

    Not in our library10.1007/b94608

  16. 16.

    Hernández A, Nácher V, , R, Zainos A, Lemus L, Alvarez M, Vázquez Y, Camarillo L, Romo R. Decoding a perceptual decision process across cortex. Neuron. 2010;66:300-314.

    Not in our library10.1016/j.neuron.2010.03.031

  17. 17.

    Huijbers W, Pennartz CM, Beldzik E, Domagalik A, Vinck M, Hofman WF, Cabeza R, Daselaar SM. Respiration phase-locks to fast stimulus presentations: Implications for the interpretation of posterior midline "deactivations". Human Brain Mapping. 2014;35:4932-4943.

    Not in our library10.1002/hbm.22523

  18. 18.

    Izenman AJ. Reduced-rank regression for the multivariate linear model. Journal of Multivariate Analysis. 1975;5:248-264.

    Not in our library10.1016/0047-259x(75)90042-1

  19. 19.

    Izenman A. Modern Multivariate Statistical Techniques. 2008.

    Not in our library10.1007/978-0-387-78189-1

  20. 20.

    Jun JK, Miller P, Hernández A, Zainos A, Lemus L, Brody CD, Romo R. Heterogenous population coding of a short-term memory and decision task. The Journal of Neuroscience. 2010;30:916-929.

    Not in our library10.1523/jneurosci.2062-09.2010

  21. 21.

    Kepecs A, Uchida N, Zariwala HA, Mainen ZF. Neural correlates, computation and behavioural impact of decision confidence. Nature. 2008;455:227-231.

    Not in our library10.1038/nature07200

  22. 22.

    Machens CK. Demixing population activity in higher cortical areas. Frontiers in Computational Neuroscience. 2010;4.

    Not in our library10.3389/fncom.2010.00126

  23. 23.

    Machens CK, Romo R, Brody CD. Flexible control of mutual inhibition: A neural model of two-interval discrimination. Science. 2005;307:1121-1124.

    Not in our library10.1126/science.1104171

  24. 24.

    Machens CK, Romo R, Brody CD. Functional, but not anatomical, separation of "what" and "when" in prefrontal cortex. The Journal of Neuroscience. 2010;30:350-360.

    Not in our library10.1523/jneurosci.3276-09.2010

  25. 25.

    Mante V, Sussillo D, Shenoy KV, Newsome WT. Context-dependent computation by recurrent dynamics in prefrontal cortex. Nature. 2013;503:78-84.

    Not in our library10.1038/nature12742

  26. 26.

    Meyers EM, Qi XL, Constantinidis C. Incorporation of new information into prefrontal cortical activity after learning working memory tasks. Proceedings of the National Academy of Sciences of the United States of America. 2012;109:4651-4656.

    Not in our library10.1073/pnas.1201022109

  27. 27.

    Meyer T, Qi XL, Stanford TR, Constantinidis C. Stimulus selectivity in dorsal and ventral prefrontal cortex after training in working memory tasks. The Journal of Neuroscience. 2011;31:6266-6276.

    Not in our library10.1523/jneurosci.6798-10.2011

  28. 28.

    Pagan M, Rust NC. Quantifying the signals contained in heterogeneous neural responses and determining their relationships with task performance. Journal of Neurophysiology. 2014;112:1584-1598.

    Not in our library10.1152/jn.00260.2014

  29. 29.

    Park IM, Meister ML, Huk AC, Pillow JW. Encoding and decoding in parietal cortex during sensorimotor decision-making. Nature Neuroscience. 2014;17:1395-1403.

    Not in our library10.1038/nn.3800

  30. 30.

    Pfau D, Pnevmatikakis EA, Paninski L. Robust learning of low-dimensional dynamics from large neural ensembles. 2013;2391-2399.

    Not in our library

  31. 31.

    Qi XL, Meyer T, Stanford TR, Constantinidis C. Changes in prefrontal neuronal activity after learning to perform a spatial working memory task. Cerebral Cortex. 2011;21.

    Not in our library10.1093/cercor/bhr058

  32. 32.

    Qi XL, Meyer T, Stanford TR, Constantinidis C. Neural correlates of a decision variable before learning to perform a match/non-match task. The Journal of Neuroscience. 2012;32:6161-6169.

    Not in our library10.1523/jneurosci.6365-11.2012

  33. 33.

    Raposo D, Kaufman MT, Churchland AK. A category-free neural population supports evolving demands during decision-making. Nature Neuroscience. 2014;17:1784-1792.

    Not in our library10.1038/nn.3865

  34. 34.

    Reinsel GC, Velu RP. Multivariate reduced-rank regression. 1998.

    Not in our library10.1007/978-1-4757-2853-8

  35. 35.

    Renart A, Machens CK. Variability in neural activity and behavior. Current Opinion in Neurobiology. 2014;25:211-220.

    Not in our library10.1016/j.conb.2014.02.013

  36. 36.

    Rigotti M, Barak O, Warden MR, Wang XJ, Daw ND, Miller EK, Fusi S. The importance of mixed selectivity in complex cognitive tasks. Nature. 2013;497:585-590.

    Not in our library10.1038/nature12160

  37. 37.

    Rishel CA, Huang G, Freedman DJ. Independent category and spatial encoding in parietal cortex. Neuron. 2013;77:969-979.

    Not in our library10.1016/j.neuron.2013.01.007

  38. 38.

    Rodriguez A, Laio A. Machine learning. clustering by fast search and find of density peaks. Science. 2014;344:1492-1496.

    Not in our library10.1126/science.1242072

  39. 39.

    Romo R, Brody CD, Hernández A, Lemus L. CRCNS.org. 2016.

    Not in our library10.6080/k0v40s4d

  40. 40.

    Romo R, Brody CD, Hernández A, Lemus L. Neuronal correlates of parametric working memory in the prefrontal cortex. Nature. 1999;399:470-473.

    Not in our library10.1038/20939

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