Difference between revisions of "Publications"

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J. Sohl-Dickstein, S. Teng, C. Rodgers, M.R. DeWeese, and N. Harper. [https://redwood.berkeley.edu/w/images/b/bb/Sohl-Dickstein_Teng_Gaub_Rodgers_Li_DeWeese_Harper_sonic_eye_no_marquee_preprint.pdf  A device for human ultrasonic echolocation.] IEEE Transactions on Biomedical Engineering (in press) (2015)
 
J. Sohl-Dickstein, S. Teng, C. Rodgers, M.R. DeWeese, and N. Harper. [https://redwood.berkeley.edu/w/images/b/bb/Sohl-Dickstein_Teng_Gaub_Rodgers_Li_DeWeese_Harper_sonic_eye_no_marquee_preprint.pdf  A device for human ultrasonic echolocation.] IEEE Transactions on Biomedical Engineering (in press) (2015)
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Revision as of 22:26, 14 March 2015

Journal Papers and reviewed Bookchapters

2015

J. Sohl-Dickstein, S. Teng, C. Rodgers, M.R. DeWeese, and N. Harper. A device for human ultrasonic echolocation. IEEE Transactions on Biomedical Engineering (in press) (2015)


2014

J. Sohl-Dickstein, M. Mudigonda, M. Deweese (2014) Hamiltonian Monte Carlo Without Detailed Balance. ICML (2014) pdf

P. R. Zulkowski and M. R. DeWeese. (2014) Optimal finite-time erasure of a classical bit. Physical Review E. 89(5):052140. pdf

G. Agarwal, I. H. Stevenson, A. Berényi, K. Mizuseki, G. Buzsáki, F. T. Sommer: Spatially distributed local fields in the hippocampus encode rat position. Science 344 (2014): 626-630. pdf Supplement

J. A. Hirsch, X. Wang, V. Vaingankar, F. T. Sommer: Inhibitory circuits in the visual thalamus. Chapter in: The New Visual Neurosciences, Eds.: Leo M. Chalupa and John S. Werner, MIT Press (2014)

A. Knoblauch, E. Koerner, U. Koerner, F. T. Sommer: Structural synaptic plasticity has high memory capacity and can explain graded amnesia, catastrophic forgetting, and the spacing effect. PLOS ONE (2014) in the press

L. M. Martinez, M. Molano-Mazon, X. Wang, F. T. Sommer, J. A. Hirsch: Statistical wiring of thalamic receptive fields optimizes spatial sampling of the retinal image. Neuron 81 (2014) 943-956

C. Rodgers and M. R. DeWeese. Neural correlates of task switching in prefrontal cortex and primary auditory cortex in a novel stimulus selection task for rodents. Neuron. (in press) (2014). pdf

F. T. Sommer: Neural oscillatons and synchrony as mechanisms for coding, communication and computation in the visual system. Chapter in: The New Visual Neurosciences, Eds.: Leo M. Chalupa and John S. Werner, MIT Press (2014)


2013

T. Hromádka, A.M. Zador, and M. R. DeWeese. (2013) Up-states are rare in awake auditory cortex. Journal of Neurophysiology, 109(8):1989-95. pdf

P. King, J. Zylberberg, and M. R. DeWeese. (2013) Inhibitory interneurons decorrelate excitatory cells to drive sparse code formation in a spiking model of V1. Journal of Neuroscience, 33(13):5475–85. pdf

D. Y. Little, F. T. Sommer: Learning and exploration in action-perception loops. Frontiers in Neural Circuits, 22 March 2013 doi: 10.3389/fncir.2013.00037 online

D. Y. Little, F. T. Sommer: Maximal mutual information, not minimal entropy, for escaping the "Dark Room". Comment on "Whatever next? Predictive brains, situated agents, and the future of cognitive science." in Behavioral Brain Sciences 2013 Jun;36(3):220-221. doi: 10.1017/S0140525X12002415 [1]

P. R. Zulkowski, D. A. Sivak, and M. R. DeWeese. Optimal control of transitions between nonequilibrium steady states. Public Library of Science ONE. 8(12):e82754 (2013). pdf

J. Zylberberg and M. R. DeWeese. (2013) Sparse coding models can exhibit decreasing sparseness while learning sparse codes for natural images. PLoS Computational Biology. 9(8):e1003182. pdf


2012

J. Zylberberg, D. Pfau, and M. R. DeWeese. (2012) Dead leaves and the dirty ground: Low-level image statistics in transmissive and occlusive imaging environments. Physical Review E, 86:066112. pdf

P. R. Zulkowski, D. A. Sivak, G. E. Crooks, and M. R. DeWeese. (2012) The geometry of thermodynamic control. Physical Review E, 86(4 Pt 1):041148. pdf

N. Carlson, V. L. Ming, and M. R. DeWeese. (2012) Sparse codes for speech predict spectrotemporal receptive fields in the inferior colliculus. PLoS Computational Biology, 7(10):e1002250. pdf

2011

J. Sohl-Dickstein, P. Battaglino, and M. R. DeWeese (2011) New method for parameter estimation in probabilistic models: Minimum probability flow. Physical Review Letters, 107(22):220601. pdf

J. Zylberberg, J. T. Murphy, and M. R. DeWeese (2011) A sparse coding model with synaptically local plasticity and spiking neurons can account for the diverse shapes of V1 simple cell receptive fields. PLOS Computational Biology, 7(10):e1002250. pdf

J. Zylberberg, and M. R. DeWeese (2011) How should prey animals respond to uncertain threats? Frontiers in Computational Neuroscience, 5:20. doi: 10.3389/fncom.2011.00020. pdf

Tosic I., Olshausen B. A. and Culpepper B. J. (2011) Learning sparse representations of depth. IEEE Journal on Selected Topics in Signal Processing, Vol. 5, No 5, pp 941 - 952, 2011. pdf

Wang X, Sommer FT, Hirsch JA: Inhibitory circuits for visual processing in thalamus. Current Opinion in Neurobiology 21 (2011) 726-733

Wang X, Vaingankar V, Soto Sanchez C, Sommer FT, Hirsch JA (2011) Thalamic interneurons and relay cells use complementary synaptic mechanisms for visual processing. Nature Neuroscience 14: 224-231

2010

Cadieu CF, Koepsell K (2010) Phase Coupling Estimation from Multivariate Phase Statistics. Neural Computation 22(12), pp. 3107 - 3126. pdf

Canolty RT, Ganguly K, Kennerley SW, Cadieu CF, Koepsell K, Wallis JD, Carmena JM (2010) Oscillatory phase coupling coordinates anatomically-dispersed cell assemblies. PNAS 107(40) 17356 - 17361. journal pdfsupplement

Knoblauch A, Palm G, Sommer FT (2010) Memory capacities for synaptic and structural plasticity. Neural Computation, Volume 22 (2): 289-341 pdf

Koepsell K, Wang X, Hirsch JA, Sommer FT (2010) Exploring the function of neural oscillations in early sensory systems. Focused review in Frontiers in Neuroscience 4 (1): 53-61. Frontiers in Neuroscience

Lauritzen TZ, Ales JM, Wade AR (2010) The effects of visuospatial attention measured across visual cortex using source-imaged, steady-state EEG. J. of Vision 10(14)39: 1 - 17. pdfsupplement

Tsao DY, Cadieu C, and Livingstone M (2010) Object Recognition: Physiological and Computational Insights. In Primate Neuroethology. Edited by M. Platt and A. Ghazanfar. Oxford University Press. 2010 (in press)

Wang X, Hirsch JA, Sommer FT (2010) Recoding of sensory information across the retinothalamic synapse. Journal of Neuroscience 30: 13567-13577

2009

Kanerva P (2009). Hyperdimensional Computing: An introduction to computing in distributed representation with high-dimensional random vectors. Cognitive Computation 1(2): 139-159 link pdf

Koepsell K, Wang X, Vaingankar V, Wei Y, Wang Q, Rathbun DL, Usrey W, Hirsch J and Sommer FT (2009) Retinal oscillations carry visual information to cortex. Front Syst Neurosci 3:4 pdf

Lauritzen TZ, D’Esposito M, Heeger D and Silver MA. (2009) Top-down flow of visual spatial attention signals from parietal to occipital cortex. Journal of Vision, 9(13):18, 1-14. link

Ming, V. & Holt, L. (2009) Efficient coding in human auditory perception. J. Acoust. Soc. Am. 126.

Monaci G, Vandergheynst P, Sommer FT (2009) Learning bimodal structure in audio-visual data. IEEE Transactions on Neural Networks 20:1898-1910 pdf

Para LC, Beck JM, Bell AJ (2009) On the maximization of information flow between spiking neurons. Neural Computation, in press

2008

Koepsell K, Sommer FT (2008) Information transmission in oscillatory neural activity. Biological Cybernetics 99:403–416 abstract pdf

Rozell CJ, Johnson DH, Baraniuk RG, Olshausen BA (2008) Sparse Coding via Thresholding and Local Competition in Neural Circuits. Neural Computation, 20:2526-2563 pdf

Teeters JL, Harris KD, Millman KJ, Olshausen BA, Sommer FT (2008) Data sharing for computational neuroscience. Neuroinformatics 6:47-55 pdf

Y. Yang, M. R. DeWeese, G. Otazu, and A. M. Zador. Millisecond-scale differences in neural activity in auditory cortex can drive decisions. Nature Neuroscience 11, 1262-1263 (2008). pdf

T. Hromadka, M. R. DeWeese, and A. M. Zador. Sparse representation of sounds in the unanesthetized auditory cortex. PLoS Biol. 6, 124-137 (2008). pdf

2007

Rehn M, Sommer FT (2007) A network that uses few active neurones to code visual input predicts the diverse shapes of cortical receptive fields. J. Comp. Neurosci. 22 (2): 135-146. pdf

Sommer FT (2007) Bunte Theorien für graue Zellen. Gehirn und Geist, Juni 70-76

Wang X, Wei Y, Vaingankar V, Wang Q, Koepsell K, Sommer FT, Hirsch JA (2007) Feedforward excitation and inhibition evoke dual modes of firing in the cat’s visual thalamus during naturalistic viewing. Neuron 55 (2007) 465-478. pdf See also the preview about this paper: P. Reinagel: The inner life of bursts. Neuron 55: 339-341

2006

Bethge M (2006) Factorial coding of natural images: how effective are linear models in removing higher-order dependencies? J. Opt. Soc. Am. A, 23(6): 1253-1268.

Rehn M, Sommer FT (2006) Storing and restoring visual input with collaborative rank coding and associative memory. Neurocomputing 69 (10-12) 1219-1223 pdf

Sommer FT, Kanerva P (2006) Can neural models of cognition benefit from the advantages of connectionism? Behavoral and Brain Sciences 29 (1) 86-87 pdf

M. R. DeWeese and A. M. Zador. Non-Gaussian membrane potential dynamics imply sparse, synchronous activity in auditory cortex. J. Neuroscience 26(47), 12206-12218 (2006). pdf

2005

George D, Sommer FT (2005) Computing with inter-spike inverval codes in networks of integrate and fire neurons. Neurocomputing 65-66, 414 - 420. pdf

Johnson JS, Olshausen BA (2005) The recognition of partially visible natural objects in the presence and absence of their occluders. Vision Research, 45, 3262-3276. pdf

Johnson JS, Olshausen BA (2005) The earliest EEG signatures of object recognition in a cued-target task are postsensory. Journal of Vision, 5, 299-312. link

Martinez LM, Wang Q, Reid RC, Pillai C, Alonso J-M, Sommer FT, Hirsch JA (2005) Receptive field structure varies with layer in the primary visual cortex. Nature Neuroscience 8 , 372 - 379 pdf

Olshausen BA, Field DJ (2005) How close are we to understanding V1? Neural Computation, 17, 1665-1699. pdf

Sommer FT, Wennekers T (2005) Synfire chains with conductance-based neurons: internal timing and coordination with timed input. Neurocomputing 65-66, 449 - 454. pdf

Refereed Conference Proceedings

2015

2014

J. Sohl-Dickstein, M. Mudigonda, M.R. DeWeese. Hamiltonian Monte Carlo Without Detailed Balance. Proceedings of the 31st International Conference on Machine Learning (Beijing) (2014). pdf

2013

2012

2011

J. Sohl-Dickstein, P. Battaglino, and M.R. DeWeese (2011) Minimum Probability Flow Learning. Proceedings of the 28th International Conference on Machine Learning (Bellevue, WA). pdf

G. Isely, C. Hillar, F. T. Sommer: Decyphering subsampled data: Adaptive compressive sampling as a principle of brain communication. Advances in Neural Information Processing Systems 23. Eds: J. Lafferty and C. K. I. Williams and J. Shawe-Taylor and R.S. Zemel and A. Culotta (2011) 910-918 pdf

2010

Canolty RT, Ganguly K, Kennerley SW, Cadieu CF, Koepsell K, Wallis JD, Carmena JM (2010) Single-neuron spike timing depends on global brain dynamics. Computational and Systems Neuroscience 2010. doi: 10.3389/conf.fnins.2010.03.00264 abstract

M.A. Silver, A.N Landau, T.Z. Lauritzen, W Prinzmetal, L.C. Robertson. Isolating human brain functional connectivity associated with a specific cognitive process. Proceedings of SPIE Volume 7527 – In press.

Culpepper B.J., Olshausen B.A. Learning transport operators for image manifolds. Advances in Neural Information Processing Systems (NIPS), 22. (2010) Y. Bengio, D. Schuurmans, J. Lafferty, C. K. I. Williams and A. Culotta. pdf supplementary materials

2009

Huth A, Cadieu CF, Dale CL, Weber D, Pantazis D, Darvas F, Leahy R, Simpson GV, Koepsell K (2009) Detecting functional connectivity in networks of phase-coupled neural oscillators, Poster presentation, Computational and Systems Neuroscience. doi: 10.3389/conf.neuro.06.2009.03.258 abstract

Charles CF, Koepsell K (2009) A multivariate phase distribution and its estimation, Poster presentation, Computational and Systems Neuroscience. doi: 10.3389/conf.neuro.06.2009.03.260 abstract

Cadieu C.F., Olshausen B.A., (2009) Learning Transformational Invariants from Natural Movies. Advances in Neural Information Processing Systems (NIPS), 21:209-216, 2009. D. Koller and D. Schuurmans and Y. Bengio and L. Bottou, MIT Press, Cambridge, MA. pdf [Movies: Figure 2 wmv / mov , 4a avi / mov , 4b avi / mov , 4c avi / mov , 4d avi / mov ]

Olshausen, B., C. Cadieu, and D.K. Warland. (2009) Learning Real and Complex Overcomplete Representations from the Statistics of Natural Images, Proc. SPIE 7446, 74460S, 2009. link

2008

Garrigues P.J., El Ghaoui L., An Homotopy Algorithm for the Lasso with Online Observations. Advances in Neural Information Processing Systems 21 (NIPS 2008). pdf

Monaci G., Sommer F. T. and Vandergheynst P., Learning Sparse Generative Models of Audiovisual Signals, Proc. of European Conf. on Signal Processing (EUSIPCO08), 2008 pdf

2007

Garrigues P.J. Olshausen B.A. (2007) Learning Horizontal Connections in a Sparse Coding Model of Natural Images. To appear in Advances in Neural Information Processing Systems 20 (NIPS 2007) pdf

Olshausen, B., C. Cadieu, J. Culpepper, and D.K. Warland. (2007) Bilinear Models of Natural Images, Proc. SPIE Int. Soc. Opt. Eng. 6492, 649206, February 2007. pdf

2005

Bell A.J., Parra L.C. (2005) Maximising Sensitivity in a Spiking Network, Advances in Neural Information Processing Systems 17, Saul L.K. and Weiss Y. and Bottou L., MIT Press, Cambridge, MA pdf

Technical Reports

Cadieu CF, Koepsell K (2010) Modeling Image Structure with Factorized Phase-Coupled Boltzmann Machines. November 2010. arXiv:1011.4058v1 [cs.CV]. pdf

Kanerva P (2010). What we mean when we say "What's the Dollar of Mexico?": Prototypes and mapping in concept space. Report FS-10-08-006, AAAI Fall Symposium on Quantum Informatics for Cognitive, Social, and Semantic Processes. link. pdf

Sohl-Dickstein J, Wang CM, Olshausen BA (2010) An Unsupervised Algorithm For Learning Lie Group Transformations. pdf

Cadieu CF, Koepsell K (2009) Phase Coupling Estimation from Multivariate Phase Statistics. June 2009. arXiv:0906.3844v1 [nlin.AO]. pdf

W. K. Coulter, C. J. Hillar, F. T. Sommer (2009) Adaptive compressed sensing - a new class of self-organizing coding models for neuroscience. arXiv.org > q-bio > arXiv:0906.1202 pdf

Cadieu C, Koepsell K (2008) A Multivariate Phase Distribution and its Estimation. September 2008. arXiv:0809.4291v2 [q-bio.NC]. pdf

M. R. DeWeese. Whole-Cell Recording In Vivo. Chapter 6 in Current Protocols in Neuroscience. John Wiley & Sons, Inc., pp. 6.22.1-15 (2007). pdf

Talks and Posters

2010

Koepsell K (2010) Collective computation with neural assemblies -- from connectivity to network dynamics and back. Invited talk, Center for Mind and Brain, UC Davis, CA.

Koepsell K (2010) The role of oscillations for cortical communications. Invited talk, Theory Group, Los Alamos National Lab, Los Alamos, NM.

Rokem A, Trumpis M, Perez F, Ivanov P, Koepsell K, Blanche T, Fegen D, D’Esposito M (2010) Nitime: an open-source package for time-series analysis of neuroscience data. Poster presentation, Human Brain Mapping Annual Meeting, Barcelona, Spain.

Koepsell K (2010) Detecting functional connectivity in networks of phase-coupled neural oscillators. Invited talk, Workshop on Multi-Scale Complex Dynamics in the Brain at CSYNE 2010.

2009

Cadieu, C., L. Secundo, E. Chang, B.J. Culpepper, N.M. Barbaro, B.A. Olshausen, R.T. Knight. (2009) Sparse Space-Time Decompositions of ECoG signals. Program No. 894.9/HH7. Chicago, IL: Society for Neuroscience, 2009.

Koepsell K (2009) Phase coupling estimation from multivariate phase statistics. Invited talk, Smith-Kettlewell Eye Research Institute, San Francisco, California.

Koepsell K (2009) Phase coupling estimation in coupled oscillator systems. Invited talk, Mathematical Biology Seminar, UC Davis.

Cadieu CF, Koepsell K (2009) A multivariate phase distribution and its estimation. Computational and Systems Neuroscience, Salt Lake City, UT. Frontiers in Systems Neuroscience. Conference Abstract: Computational and systems neuroscience. doi: 10.3389/conf.neuro.06.2009.03.260

Huth A, Cadieu CF, Dale CL, Weber D, Pantazis D, Darvas F, Leahy R, Simpson GV, Koepsell K (2009) Detecting functional connectivity in networks of phase-coupled neural oscillators. Computational and Systems Neuroscience, Salt Lake City, UT. Frontiers in Systems Neuroscience. Conference Abstract: Computational and systems neuroscience. doi: 10.3389/conf.neuro.06.2009.03.258

T.Z. Lauritzen and A. Wade. (2009) Different cortical areas are modulated in different ways by spatial attention in human visual cortex. Optical Society of America, Fall vision meeting. September 24-26, 2009, Seattle, Washington, and Journal of Vision, 9(14):44, 44a. link

T.Z. Lauritzen and A. Wade. (2009) Spatial attention modulates steady state visually-evoked potentials in human visual cortex by a multiplicative gain function. Annual meeting of the Organization for Human Brain Mapping, San Francisco, CA, June 18-23, 2009.

T.Z. Lauritzen and A. Wade. (2009) Spatial attention modulates steady state VEPs in retinotopic human visual cortex. COSYNE Meeting, Salt Lake City and Snowbird, Utah, February 26 - March 3, 2009.

2008

Blanche TJ, Koepsell K, Swindale N, Olshausen BA (2008) Predicting response variability in the primary visual cortex. Computational and Systems Neuroscience, Salt Lake City, UT.

Canolty RT, Soltani M, Koepsell K, Cadieu C, Dalal SS, Edwards E, Nagarajan SS, Kirsch HE, Barbaro NM and Knight RT (2008). Auditory target detection activates frontal and parietal cortices: Evidence from high gamma power and low-frequency phase coherence in the subdural electrocorticogram. Frontiers in Human Neuroscience. Conference Abstract: 10th International Conference on Cognitive Neuroscience. doi: 10.3389/conf.neuro.09.2009.01.119

Cadieu, C., B. Olshausen. (2008) Learning Transformational Invariants from Time-Varying Natural Images. Computational and Systems Neuroscience (Cosyne), Salt Lake City, March 2008. abstract talk

Koepsell K (2008) Spike timing in the context of network dynamics from retina to cortex. Conference talk, Computational and Systems Neuroscience, Salt Lake City, UT.

Koepsell K, Blanche TJ, Swindale N, Olshausen BA (2008) Modeling the influence of local network activity on neuron spiking responses in primary visual cortex. Computational and Systems Neuroscience, Salt Lake City, UT.

T.Z. Lauritzen, M. D’Esposito, D. Heeger and M.A. Silver. (2008) Functional networks underlying human top-down visual spatial attention. Annual Cognitive Neuroscience Society Meeting. April 12-15, 2008, San Francisco, California.

T.Z. Lauritzen, M. D’Esposito, D. Heeger and M.A. Silver. (2008) Human visual attention networks revealed by fMRI coherency analysis. COSYNE Meeting, Salt Lake City and Snowbird, Utah, February 28 - March 4, 2008.

2007

Blanche TJ (2007) The influence of cortical dynamics on spike timing precision in cat V1. Smith-Kettlewell Eye Research Institute, San Francisco, California.

Cadieu, C., B. Olshausen. (2007) Learning Invariant and Variant Components of Time Varying Natural Images Using a Sparse, Multiplicative Model. Computational and Systems Neuroscience (Cosyne) Salt Lake City, March 2007, & Vision Sciences Society, Sarasota May 2007. abstract

Koepsell K (2007) The hidden clock in LGN -- is phase coding employed in early vision?. Göttingen Neurobiology Conference, Göttingen, Germany

Garrigues PJ, Olshausen BA (2007) Learning Horizontal Connections from the Statistics of Natural Images. Computational and Systems Neuroscience, Salt Lake City, Utah.

Blanche TJ (2007) How active is the cortex? COSYNE workshop, The Canyons, Utah.

Blanche TJ, Koepsell K (2007) Spike timing precision and the influence of cortical dynamics. Grand Challenges in Neural Computation, Santa Fe, New Mexico.

T.Z. Lauritzen, M. D’Esposito, D. Heeger and M.A. Silver. (2007) Functional networks underlying top-down visual spatial attention in the human brain. Society for neuroscience annual meeting, 2007, abstract 423.9.

Lauritzen TZ, Shenhav, Silver MA (2007) fMRI coherency analysis reveals feedforward progression of visual responses in human early visual cortex OSA fall vision meeting, Berkeley, CA.

Lauritzen TZ (2007) Functional networks underlying top-down visual spatial attention in the human brain IMM, Danish Technical University, Lyngby, Denmark.

Lauritzen TZ (2007) Neural mechanisms of sustained visual spatial attention ENS, Paris, France.

2006

Blanche TJ, Freiwald WA, Swindale NV (2006) Neural sparseness in cat and monkey visual cortex studied with silicon polytrode arrays. Society for Neuroscience.

Koepsell K, Wang X, Wei Y, Wang Q, Vaingankar V, Hirsch JA, Sommer FT (2006) Retinal oscillations carry visual information to cortex. Computational and Systems Neuroscience, Salt Lake City, Utah.

Koepsell K, Wang X, Wei Y, Wang Q, Vaingankar V, Hirsch JA, Sommer FT (2006) Two channels for visual information to travel from thalamus to cortex. Society for Neuroscience.

Lauritzen TZ (2006) Attention modulation mediated through correlations in the local field potential Annual cognitive neuroscience soc meeting, San Francisco, CA.

2005

Koepsell K, Wang X, Wei Y, Wang Q, Vaingankar V, Hirsch JA, Sommer FT (2005) Ongoing retinal activity explains variability of thalamic responses. Society for Neuroscience.

Lauritzen TZ (2005) Correlations in the local field potential yield non-linear neural response changes Society for Neuroscience, Abstract 274.25.

Lauritzen TZ (2005) Contribution of physiological noise to dendritic non-linearities COSYNE, Salt Lake City, Utah.


Redwood Neuroscience Institute

An incomplete list of publications from the Redwood Neuroscience Institute (2002-2005) is available here (will be updated soon).