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Jonathan Pillow, Ph.D. - Publications

Affiliations: 
2009-2014 Psychology University of Texas at Austin, Austin, Texas, U.S.A. 
 2014- Princeton Neuroscience Institute Princeton University, Princeton, NJ 
Area:
Computational Neuroscience, Machine Learning
Website:
http://pillowlab.princeton.edu/
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88 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Jha A, Gupta D, Brody CD, Pillow JW. Disentangling the Roles of Distinct Cell Classes with Cell-Type Dynamical Systems. Biorxiv : the Preprint Server For Biology. PMID 39574751 DOI: 10.1101/2024.07.08.602520  0.623
2024 Pan-Vazquez A, Sanchez Araujo Y, McMannon B, Louka M, Bandi A, Haetzel L, Faulkner M, Pillow JW, Daw ND, Witten IB. Pre-existing visual responses in a projection-defined dopamine population explain individual learning trajectories. Current Biology : Cb. PMID 39413788 DOI: 10.1016/j.cub.2024.09.045  0.776
2024 Geadah V, Barello G, Greenidge D, Charles AS, Pillow JW. Sparse-Coding Variational Autoencoders. Neural Computation. 1-31. PMID 39383030 DOI: 10.1162/neco_a_01715  0.573
2024 Pospisil DA, Aragon MJ, Dorkenwald S, Matsliah A, Sterling AR, Schlegel P, Yu SC, McKellar CE, Costa M, Eichler K, Jefferis GSXE, Murthy M, Pillow JW. The fly connectome reveals a path to the effectome. Nature. 634: 201-209. PMID 39358526 DOI: 10.1038/s41586-024-07982-0  0.806
2024 DePasquale B, Brody CD, Pillow JW. Neural population dynamics underlying evidence accumulation in multiple rat brain regions. Elife. 13. PMID 39162374 DOI: 10.7554/eLife.84955  0.807
2024 Jha A, Ashwood ZC, Pillow JW. Active Learning for Discrete Latent Variable Models. Neural Computation. 36: 437-474. PMID 38363661 DOI: 10.1162/neco_a_01646  0.793
2023 Greenidge CD, Scholl B, Yates JL, Pillow JW. Efficient Decoding of Large-Scale Neural Population Responses With Gaussian-Process Multiclass Regression. Neural Computation. 1-35. PMID 38101329 DOI: 10.1162/neco_a_01630  0.522
2023 Cowley BR, Stan PL, Pillow JW, Smith MA. Compact deep neural network models of visual cortex. Biorxiv : the Preprint Server For Biology. PMID 38045255 DOI: 10.1101/2023.11.22.568315  0.323
2023 Kim TD, Luo TZ, Can T, Krishnamurthy K, Pillow JW, Brody CD. Flow-field inference from neural data using deep recurrent networks. Biorxiv : the Preprint Server For Biology. PMID 38014290 DOI: 10.1101/2023.11.14.567136  0.658
2023 Chen KS, Pillow JW, Leifer AM. Olfactory learning alters navigation strategies and behavioral variability in C. elegans. Arxiv. PMID 38013890  0.77
2023 Pospisil D, Aragon M, Pillow J. From connectome to effectome: learning the causal interaction map of the fly brain. Biorxiv : the Preprint Server For Biology. PMID 37961285 DOI: 10.1101/2023.10.31.564922  0.807
2023 Hyafil A, de la Rocha J, Pericas C, Katz LN, Huk AC, Pillow JW. Temporal integration is a robust feature of perceptual decisions. Elife. 12. PMID 37140191 DOI: 10.7554/eLife.84045  0.735
2023 Duncker L, Ruda KM, Field GD, Pillow JW. Scalable Variational Inference for Low-Rank Spatiotemporal Receptive Fields. Neural Computation. 1-33. PMID 37037043 DOI: 10.1162/neco_a_01584  0.798
2022 Ashwood ZC, Roy NA, Bak JH, Pillow JW. Inferring learning rules from animal decision-making. Advances in Neural Information Processing Systems. 33: 3442-3453. PMID 36177341  0.774
2022 Creamer MS, Chen KS, Leifer AM, Pillow JW. Correcting motion induced fluorescence artifacts in two-channel neural imaging. Plos Computational Biology. 18: e1010421. PMID 36170268 DOI: 10.1371/journal.pcbi.1010421  0.777
2022 Christensen AJ, Pillow JW. Reduced neural activity but improved coding in rodent higher-order visual cortex during locomotion. Nature Communications. 13: 1676. PMID 35354804 DOI: 10.1038/s41467-022-29200-z  0.784
2022 Gauthier JL, Koay SA, Nieh EH, Tank DW, Pillow JW, Charles AS. Detecting and correcting false transients in calcium imaging. Nature Methods. 19: 470-478. PMID 35347320 DOI: 10.1038/s41592-022-01422-5  0.668
2022 Bolkan SS, Stone IR, Pinto L, Ashwood ZC, Iravedra Garcia JM, Herman AL, Singh P, Bandi A, Cox J, Zimmerman CA, Cho JR, Engelhard B, Pillow JW, Witten IB. Opponent control of behavior by dorsomedial striatal pathways depends on task demands and internal state. Nature Neuroscience. 25: 345-357. PMID 35260863 DOI: 10.1038/s41593-022-01021-9  0.755
2022 Ashwood ZC, Roy NA, Stone IR, Urai AE, Churchland AK, Pouget A, Pillow JW. Mice alternate between discrete strategies during perceptual decision-making. Nature Neuroscience. 25: 201-212. PMID 35132235 DOI: 10.1038/s41593-021-01007-z  0.773
2021 Wu A, Nastase SA, Baldassano CA, Turk-Browne NB, Norman KA, Engelhardt BE, Pillow JW. Brain kernel: a new spatial covariance function for fMRI data. Neuroimage. 118580. PMID 34740792 DOI: 10.1016/j.neuroimage.2021.118580  0.708
2021 Song A, Gauthier JL, Pillow JW, Tank DW, Charles AS. Neural Anatomy and Optical Microscopy (NAOMi) Simulation for evaluating calcium imaging methods. Journal of Neuroscience Methods. 109173. PMID 33839190 DOI: 10.1016/j.jneumeth.2021.109173  0.658
2021 Roy NA, Bak JH, Akrami A, Brody CD, Pillow JW. Extracting the dynamics of behavior in sensory decision-making experiments. Neuron. PMID 33412101 DOI: 10.1016/j.neuron.2020.12.004  0.799
2020 Keeley SL, Zoltowski DM, Aoi MC, Pillow JW. Modeling statistical dependencies in multi-region spike train data. Current Opinion in Neurobiology. PMID 33334641 DOI: 10.1016/j.conb.2020.11.005  0.793
2020 Aoi MC, Mante V, Pillow JW. Prefrontal cortex exhibits multidimensional dynamic encoding during decision-making. Nature Neuroscience. PMID 33020653 DOI: 10.1038/s41593-020-0696-5  0.692
2019 Yates JL, Katz LN, Levi AJ, Pillow JW, Huk A. A simple linear readout of MT supports motion direction-discrimination performance. Journal of Neurophysiology. PMID 31852399 DOI: 10.1152/jn.00117.2019  0.794
2019 Latimer KW, Rieke F, Pillow JW. Inferring synaptic inputs from spikes with a conductance-based neural encoding model. Elife. 8. PMID 31850846 DOI: 10.7554/Elife.47012  0.728
2019 Calhoun AJ, Pillow JW, Murthy M. Unsupervised identification of the internal states that shape natural behavior. Nature Neuroscience. 22: 2040-2049. PMID 31768056 DOI: 10.1038/S41593-019-0533-X  0.374
2019 Panichello MF, DePasquale B, Pillow JW, Buschman TJ. Error-correcting dynamics in visual working memory. Nature Communications. 10: 3366. PMID 31358740 DOI: 10.1038/S41467-019-11298-3  0.721
2019 Williamson RS, Sahani M, Pillow JW. Correction: The equivalence of information-theoretic and likelihood-based methods for neural dimensionality reduction (Plos Comput Biol, (2015), 11, 4, 10.1371/journal.pcbi.1004141) Plos Computational Biology. 15. PMID 31199805 DOI: 10.1371/Journal.Pcbi.1007139  0.554
2019 Zoltowski DM, Latimer KW, Yates JL, Huk AC, Pillow JW. Discrete Stepping and Nonlinear Ramping Dynamics Underlie Spiking Responses of LIP Neurons during Decision-Making. Neuron. PMID 31130330 DOI: 10.1016/J.Neuron.2019.04.031  0.802
2019 Cai MB, Schuck NW, Pillow JW, Niv Y. Representational structure or task structure? Bias in neural representational similarity analysis and a Bayesian method for reducing bias. Plos Computational Biology. 15: e1006299. PMID 31125335 DOI: 10.1371/journal.pcbi.1006299  0.414
2019 Latimer KW, Rieke F, Pillow JW. Author response: Inferring synaptic inputs from spikes with a conductance-based neural encoding model Elife. DOI: 10.7554/Elife.47012.Sa2  0.704
2018 Aoi MC, Pillow JW. Model-based targeted dimensionality reduction for neuronal population data. Advances in Neural Information Processing Systems. 31: 6690-6699. PMID 31274967  0.711
2018 Roy NA, Bak JH, Akrami A, Brody CD, Pillow JW. Efficient inference for time-varying behavior during learning. Advances in Neural Information Processing Systems. 31: 5695-5705. PMID 31244514  0.796
2018 Zoltowski DM, Pillow JW. Scaling the Poisson GLM to massive neural datasets through polynomial approximations. Advances in Neural Information Processing Systems. 31: 3517-3527. PMID 31244513  0.818
2018 Bak JH, Pillow JW. Adaptive stimulus selection for multi-alternative psychometric functions with lapses. Journal of Vision. 18: 4. PMID 30458512 DOI: 10.1167/18.12.4  0.794
2018 Knöll J, Pillow JW, Huk AC. Lawful tracking of visual motion in humans, macaques, and marmosets in a naturalistic, continuous, and untrained behavioral context. Proceedings of the National Academy of Sciences of the United States of America. PMID 30322919 DOI: 10.1073/pnas.1807192115  0.754
2018 Charles AS, Park M, Weller JP, Horwitz GD, Pillow JW. Dethroning the Fano Factor: A Flexible, Model-Based Approach to Partitioning Neural Variability. Neural Computation. 1-34. PMID 29381442 DOI: 10.1162/Neco_A_01062  0.815
2018 Panichello M, DePasquale B, Pillow J, Buschman T. Memory load modulates the dynamics of visual working memory. Journal of Vision. 18: 189. DOI: 10.1167/18.10.189  0.704
2017 Wu A, Roy NA, Keeley S, Pillow JW. Gaussian process based nonlinear latent structure discovery in multivariate spike train data. Advances in Neural Information Processing Systems. 30: 3496-3505. PMID 31244512  0.793
2017 Murugan M, Jang HJ, Park M, Miller EM, Cox J, Taliaferro JP, Parker NF, Bhave V, Hur H, Liang Y, Nectow AR, Pillow JW, Witten IB. Combined Social and Spatial Coding in a Descending Projection from the Prefrontal Cortex. Cell. 171: 1663-1677.e16. PMID 29224779 DOI: 10.1016/J.Cell.2017.11.002  0.649
2017 Weber AI, Pillow JW. Capturing the Dynamical Repertoire of Single Neurons with Generalized Linear Models. Neural Computation. 1-30. PMID 28957020 DOI: 10.1162/neco_a_01021  0.444
2017 Pillow JW, Aoi MC. Is population activity more than the sum of its parts? Nature Neuroscience. 20: 1196-1198. PMID 28849790 DOI: 10.1038/Nn.4627  0.661
2017 Yates JL, Park IM, Katz LN, Pillow JW, Huk AC. Functional dissection of signal and noise in MT and LIP during decision-making. Nature Neuroscience. PMID 28758998 DOI: 10.1038/Nn.4611  0.795
2017 Song A, Charles AS, Koay SA, Gauthier JL, Thiberge SY, Pillow JW, Tank DW. Volumetric two-photon imaging of neurons using stereoscopy (vTwINS). Nature Methods. PMID 28319111 DOI: 10.1038/Nmeth.4226  0.689
2017 Cohen JD, Daw N, Engelhardt B, Hasson U, Li K, Niv Y, Norman KA, Pillow J, Ramadge PJ, Turk-Browne NB, Willke TL. Computational approaches to fMRI analysis. Nature Neuroscience. 20: 304-313. PMID 28230848 DOI: 10.1038/Nn.4499  0.627
2017 Yates JL, Pillow JW, Huk AC. Decoding from populations of MT neurons during motion-discrimination Journal of Vision. 17: 22. DOI: 10.1167/17.7.22  0.758
2017 Cai MB, Schuck N, Anderson M, Pillow J, Niv Y. Should you trust your RSA result? A Bayesian method for reducing bias in neural representational similarity analysis. Journal of Vision. 17: 571. DOI: 10.1167/17.10.571  0.346
2016 Sharpee TO, Destexhe A, Kawato M, Sekulić V, Skinner FK, Wójcik DK, Chintaluri C, Cserpán D, Somogyvári Z, Kim JK, Kilpatrick ZP, Bennett MR, Josić K, Elices I, Arroyo D, ... ... Pillow J, et al. 25th Annual Computational Neuroscience Meeting: CNS-2016 Bmc Neuroscience. 17: 54. PMID 27534393 DOI: 10.1186/S12868-016-0283-6  0.746
2016 Katz LN, Yates JL, Pillow JW, Huk AC. Dissociated functional significance of decision-related activity in the primate dorsal stream. Nature. PMID 27376476 DOI: 10.1038/nature18617  0.784
2016 Latimer KW, Yates JL, Meister ML, Huk AC, Pillow JW. Response to Comment on "Single-trial spike trains in parietal cortex reveal discrete steps during decision-making". Science (New York, N.Y.). 351: 1406. PMID 27013724 DOI: 10.1126/Science.Aad3596  0.817
2015 Latimer KW, Yates JL, Meister ML, Huk AC, Pillow JW. Single-trial spike trains in parietal cortex reveal discrete steps during decision-making. Science (New York, N.Y.). 349: 184-187. PMID 26160947 DOI: 10.1126/Science.Aaa4056  0.821
2015 Williamson RS, Sahani M, Pillow JW. The equivalence of information-theoretic and likelihood-based methods for neural dimensionality reduction. Plos Computational Biology. 11: e1004141. PMID 25831448 DOI: 10.1371/journal.pcbi.1004141  0.618
2015 Bonnen K, Burge J, Yates J, Pillow J, Cormack LK. Continuous psychophysics: Target-tracking to measure visual sensitivity. Journal of Vision. 15. PMID 25795437 DOI: 10.1167/15.3.14  0.536
2015 Latimer KW, Huk AC, Pillow JW. Bayesian inference for latent stepping and ramping models of spike train data Advanced State Space Methods For Neural and Clinical Data. 160-185. DOI: 10.1017/CBO9781139941433.008  0.801
2014 Knudson KC, Yates JL, Huk AC, Pillow J. Inferring sparse representations of continuous signals with continuous orthogonal matching pursuit. Advances in Neural Information Processing Systems. 27. PMID 25914512  0.76
2014 Park IM, Meister ML, Huk AC, Pillow JW. Encoding and decoding in parietal cortex during sensorimotor decision-making. Nature Neuroscience. 17: 1395-403. PMID 25174005 DOI: 10.1038/Nn.3800  0.818
2014 Park M, Weller JP, Horwitz GD, Pillow JW. Bayesian active learning of neural firing rate maps with transformed gaussian process priors. Neural Computation. 26: 1519-41. PMID 24877730 DOI: 10.1162/Neco_A_00615  0.758
2014 Latimer KW, Chichilnisky EJ, Rieke F, Pillow JW. Inferring synaptic conductances from spike trains under a biophysically inspired point process model Advances in Neural Information Processing Systems. 2: 954-962.  0.756
2014 Archer E, Park IM, Pillow JW. Bayesian entropy estimation for countable discrete distributions Journal of Machine Learning Research. 15: 2833-2868.  0.508
2014 Archer E, Köster U, Pillow J, Macke JH. Low-dimensional models of neural population activity in sensory cortical circuits Advances in Neural Information Processing Systems. 1: 343-351.  0.639
2013 Pillow JW, Shlens J, Chichilnisky EJ, Simoncelli EP. A model-based spike sorting algorithm for removing correlation artifacts in multi-neuron recordings. Plos One. 8: e62123. PMID 23671583 DOI: 10.1371/Journal.Pone.0062123  0.804
2013 Archer E, Park IM, Pillow JW. Bayesian and quasi-Bayesian estimators for mutual information from discrete data Entropy. 15: 1738-1755. DOI: 10.3390/E15051738  0.574
2013 Park IM, Archer E, Pillow J. Bayesian entropy estimators for spike trains Bmc Neuroscience. 14. DOI: 10.1186/1471-2202-14-S1-P316  0.576
2013 Park IM, Archer E, Priebe N, Pillow JW. Spectral methods for neural characterization using generalized quadratic models Advances in Neural Information Processing Systems.  0.59
2013 Park IM, Archer E, Latimer K, Pillow JW. Universal models for binary spike patterns using centered Dirichlet processes Advances in Neural Information Processing Systems.  0.745
2013 Archer E, Park IM, Pillow JW. Bayesian entropy estimation for binary spike train data using parametric prior knowledge Advances in Neural Information Processing Systems.  0.568
2012 Vidne M, Ahmadian Y, Shlens J, Pillow JW, Kulkarni J, Litke AM, Chichilnisky EJ, Simoncelli E, Paninski L. Modeling the impact of common noise inputs on the network activity of retinal ganglion cells. Journal of Computational Neuroscience. 33: 97-121. PMID 22203465 DOI: 10.1007/S10827-011-0376-2  0.802
2012 Yates J, Huk A, Cormack L, Pillow J. Psychophysical reverse correlation of motion perception Journal of Vision. 12: 746-746. DOI: 10.1167/12.9.746  0.734
2012 Archer E, Park IM, Pillow JW. Bayesian estimation of discrete entropy with mixtures of stick-breaking priors Advances in Neural Information Processing Systems. 3: 2015-2023.  0.516
2011 Park M, Pillow JW. Receptive field inference with localized priors. Plos Computational Biology. 7: e1002219. PMID 22046110 DOI: 10.1371/Journal.Pcbi.1002219  0.609
2011 Ahmadian Y, Pillow JW, Paninski L. Efficient Markov chain Monte Carlo methods for decoding neural spike trains. Neural Computation. 23: 46-96. PMID 20964539 DOI: 10.1162/Neco_A_00059  0.645
2011 Pillow JW, Ahmadian Y, Paninski L. Model-based decoding, information estimation, and change-point detection techniques for multineuron spike trains. Neural Computation. 23: 1-45. PMID 20964538 DOI: 10.1162/Neco_A_00058  0.66
2011 Park M, Horwitz G, Pillow JW. Active learning of neural response functions with Gaussian processes Advances in Neural Information Processing Systems 24: 25th Annual Conference On Neural Information Processing Systems 2011, Nips 2011.  0.626
2011 Park IM, Pillow JW. Bayesian spike-triggered covariance analysis Advances in Neural Information Processing Systems 24: 25th Annual Conference On Neural Information Processing Systems 2011, Nips 2011.  0.567
2010 Nirenberg S, Bomash I, Pillow JW, Victor JD. Heterogeneous response dynamics in retinal ganglion cells: the interplay of predictive coding and adaptation. Journal of Neurophysiology. 103: 3184-94. PMID 20357061 DOI: 10.1152/jn.00878.2009  0.324
2009 Pillow JW, Latham P. Neural characterization in partially observed populations of spiking neurons Advances in Neural Information Processing Systems 20 - Proceedings of the 2007 Conference.  0.516
2008 Pillow JW, Shlens J, Paninski L, Sher A, Litke AM, Chichilnisky EJ, Simoncelli EP. Spatio-temporal correlations and visual signalling in a complete neuronal population. Nature. 454: 995-9. PMID 18650810 DOI: 10.1038/Nature07140  0.806
2008 Goodhill G, Baker C, Balasubramanian V, Bazhenov M, Beck J, Becker S, Bethge M, Boahen K, Boden M, Bonin V, Bouret S, Fairhall A, Flash T, French R, Gillies A, ... ... Pillow J, et al. Network: Computation in Neural Systems: Editorial Network: Computation in Neural Systems. 19: 1-2. DOI: 10.1080/09548980801915409  0.685
2007 Paninski L, Pillow J, Lewi J. Statistical models for neural encoding, decoding, and optimal stimulus design. Progress in Brain Research. 165: 493-507. PMID 17925266 DOI: 10.1016/S0079-6123(06)65031-0  0.666
2006 Schwartz O, Pillow JW, Rust NC, Simoncelli EP. Spike-triggered neural characterization. Journal of Vision. 6: 484-507. PMID 16889482 DOI: 10.1167/6.4.13  0.804
2006 Pillow JW, Simoncelli EP. Dimensionality reduction in neural models: an information-theoretic generalization of spike-triggered average and covariance analysis. Journal of Vision. 6: 414-28. PMID 16889478 DOI: 10.1167/6.4.9  0.621
2005 Pillow JW, Paninski L, Uzzell VJ, Simoncelli EP, Chichilnisky EJ. Prediction and decoding of retinal ganglion cell responses with a probabilistic spiking model. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 25: 11003-13. PMID 16306413 DOI: 10.1523/Jneurosci.3305-05.2005  0.805
2005 Paninski L, Pillow J, Simoncelli E. Comparing integrate-and-fire models estimated using intracellular and extracellular data Neurocomputing. 65: 379-385. DOI: 10.1016/j.neucom.2004.10.032  0.742
2004 Paninski L, Pillow JW, Simoncelli EP. Maximum likelihood estimation of a stochastic integrate-and-fire neural encoding model. Neural Computation. 16: 2533-61. PMID 15516273 DOI: 10.1162/0899766042321797  0.745
2004 Pillow JW, Paninski L, Simoncelli EP. Maximum likelihood estimation of a stochastic integrate-and-fire neural model Advances in Neural Information Processing Systems.  0.686
2003 Pillow JW, Simoncelli EP. Biases in white noise analysis due to non-Poisson spike generation Neurocomputing. 52: 109-115. DOI: 10.1016/S0925-2312(02)00822-6  0.614
2000 Zemel RS, Pillow J. Encoding multiple orientations in a recurrent network Neurocomputing. 32: 609-616. DOI: 10.1016/S0925-2312(00)00222-8  0.659
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