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181 Publications

Perpetual step-like restructuring of hippocampal circuit dynamics

S. Zheng, Roman Huszár, Thomas Hainmueller, Marlene Bartos, A. Williams, György Buzsáki

bioRxiv:2024.04.22.590576v1

Cell Reports, 43:114702

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September 24, 2024

Perpetual step-like restructuring of hippocampal circuit dynamics

@article{Zheng_WIlliams_CRS_2024.114702,
Archiveprefix = {CRS},
Author = {Zheng, Zheyang Sam and Huszár, Roman and Hainmueller, Thomas and Bartos, Marlene and \text{Williams, Alex H.} and Buzsáki, György},
Doi = {10.1016/j.celrep.2024.114702},
Eprint = {doi: 10.1016/j.celrep.2024.114702},
Journal = CRS,
Issue = {9},
month = {Sep},
Pages = {114702},
Publisher = {Elsevier},
Title = {{Perpetual step-like restructuring of hippocampal circuit dynamics}},
Url = {https://doi.org/10.1016/j.celrep.2024.114702},
OpenAccessURL = {https://doi.org/10.1016/j.celrep.2024.114702},
Volume = {43},
Year = {2024},
year_posted = {2024},
center = {CCN},
acrosscenters = {no},
external = {yes},
highlight = {no},
abstract = {Representation of the environment by hippocampal populations is known to drift even within a familiar environment, which could reflect gradual changes in single-cell activity or result from averaging across discrete switches of single neurons. Disambiguating these possibilities is crucial, as they each imply distinct mechanisms. Leveraging change point detection and model comparison, we find that CA1 population vectors decorrelate gradually within a session. In contrast, individual neurons exhibit predominantly step-like emergence and disappearance of place fields or sustained changes in within-field firing. The changes are not restricted to particular parts of the maze or trials and do not require apparent behavioral changes. The same place fields emerge, disappear, and reappear across days, suggesting that the hippocampus reuses pre-existing assemblies, rather than forming new fields de novo. Our results suggest an internally driven perpetual step-like reorganization of the neuronal assemblies.}
}

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Mapping models of V1 and V2 selectivity with local spectral reverse correlation

T. D. Oleskiw , Ramanujan Raghavan, Justin Lieber, E. P. Simoncelli, J. A. Movshon

Journal of Vision, 24: 1126-1126

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September 15, 2024

Mapping models of V1 and V2 selectivity with local spectral reverse correlation

@article{Simoncelli_JOV_2024,
title = {{Mapping models of V1 and V2 selectivity with local spectral reverse correlation}},
author = {Oleskiw, Timothy and Raghavan, Ramanujan and Lieber, Justin and Simoncelli, Eero and Movshon, J. Anthony},
abstract = {Neurons in macaque area V2 respond selectively to higher-order visual features, such as the quasi-periodic structure of natural texture, but it is unknown how selectivity for these features is built from V1 inputs tuned more simply for orientation and spatial frequency. We have recently developed an image-computable two-layer linear-nonlinear network that captures higher-order tuning from a sparse combination of subunits tuned in orientation and scale. This model can be independently trained to predict data from single-unit recordings of V1 and V2 neurons from the awake macaque, responding to a stimulus set comprised of multiple superimposed grating patches that localize oriented contrast energy. These optimized models accurately predict neural responses to other stimuli, including gratings and synthetic textures with higher-order features common to natural images. However, the high-dimensional parameter space of these models makes them difficult to interpret. A systematic comparison of V1 and V2 selectivity is therefore elusive. To address this limitation, we investigate neural tuning across our population of models in silico using local spectral reverse correlation (LSRC; Nishimoto et al., 2006). Here, we present thousands of ternary white noise stimuli to fitted models, computing a response-weighted windowed frequency spectrum across image coordinates. LSRC can effectively characterize the tuning properties of our model neurons, thereby estimating the linear and nonlinear components of model receptive fields. These estimates are qualitatively similar to our direct LSRC measurements made using identical methods from single-unit V1 and V2 recordings collected in separate experiments.},
acrosscenters = {no},
external = {yes},
highlight = {no},
center = {CCN},
OpenAccessURL = {https://jov.arvojournals.org/article.aspx?articleid=2801954},
Journal = JOV,
year = {2024},
ISSN = {1534-7362},
month = Sep,
pages = {1126},
publisher = {Association for Research in Vision and Ophthalmology (ARVO)},
volume = {24},
number = {10},
doi = {10.1167/jov.24.10.1126},
pages = {1126}
}

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Fixational eye movements enhance the precision of visual information transmitted by the primate retina

Eric G. Wu, Nora Brackbill, Colleen Rhoades, Alexandra Kling, Alex R. Gogliettino, Nishal P. Shah, Alexander Sher, Alan M. Litke, E. P. Simoncelli, E. J. Chichilnisky

bioRxiv:2023.08.12.552902

Nature Communications, 15: 7964

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September 11, 2024

Fixational eye movements enhance the precision of visual information transmitted by the primate retina

@article{Wu_Simoncelli_biorxiv:08.12.552902_NATCOM_2024,
title = {{Fixational eye movements enhance the precision of visual information transmitted by the primate retina}},
author = {Wu, Eric G. and Brackbill, Nora and Rhoades, Colleen and Kling, Alexandra and Gogliettino, Alex R. and Shah, Nishal P. and Sher, Alexander and Litke, Alan M. and Simoncelli, Eero P. and Chichilnisky, E. J.},
abstract = {Fixational eye movements alter the number and timing of spikes transmitted from the retina to the brain, but whether these changes enhance or degrade the retinal signal is unclear. To quantify this, we developed a Bayesian method for reconstructing natural images from the recorded spikes of hundreds of retinal ganglion cells (RGCs) in the macaque retina (male), combining a likelihood model for RGC light responses with the natural image prior implicitly embedded in an artificial neural network optimized for denoising. The method matched or surpassed the performance of previous reconstruction algorithms, and provides an interpretable framework for characterizing the retinal signal. Reconstructions were improved with artificial stimulus jitter that emulated fixational eye movements, even when the eye movement trajectory was assumed to be unknown and had to be inferred from retinal spikes. Reconstructions were degraded by small artificial perturbations of spike times, revealing more precise temporal encoding than suggested by previous studies. Finally, reconstructions were substantially degraded when derived from a model that ignored cell-to-cell interactions, indicating the importance of stimulus-evoked correlations. Thus, fixational eye movements enhance the precision of the retinal representation.},
acrosscenters = {no},
external = {yes},
highlight = {no},
year_posted = {2024},
center = {CCN},
Archiveprefix = {bioRxiv},
doi = {10.1038/s41467-024-52304-7},
Eprint = {10.1101/2023.08.12.552902},
OpenAccessURL = {https://www.nature.com/articles/s41467-024-52304-7},
Journal = NATCOM,
Volume = {15},
pages = {7964},
year = {2024}
}

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Geometric changes in monkey V4 and IT neural responses during visual category learning

J. Feather, Long Sha, Gouki Okazawa, N. Yu Lo, S. Chung , R. Kiani

Journal of Vision, 24: 1430

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September 1, 2024

Geometric changes in monkey V4 and IT neural responses during visual category learning

@article{Feather_Chung_JOV_2024,
title = {{Geometric changes in monkey V4 and IT neural responses during visual category learning}},
author = {Feather,  Jenelle and Sha,  Long and Okazawa,  Gouki and Lo,  Nga Yu and Chung,  SueYeon and Kiani,  Roozbeh},
abstract = {Behavior changes over the course of learning a task. This behavioral change is due to shifts in neural responses that support improved performance. Here, we investigated how the underlying representational geometries in visual areas V4 and IT of the Macaque visual system change during a categorization learning task. Visual stimuli varied in two independent attributes, and monkeys learned to categorize them based on a category boundary in the stimulus space that was defined by a combination of the attributes. Chronic neural population recordings were obtained from V4 and IT over multiple days of training while a monkey learned the task through receiving correct/incorrect feedback. Additionally, we recorded from the same neural populations while a monkey performed a fixation task viewing the same sets of stimuli. In all eight analyzed tasks, the monkey’s performance on the categorization task improved with training. To link this behavioral improvement to the underlying population responses, we investigated how the geometry of neural population activity changed over the course of learning. We treated population responses to all stimuli in each of the two categories as manifold-like representations, and analyzed the geometric properties of these representations using mean-field theoretic manifold capacity analysis. As the monkey learned the task, we observed that the representations in both V4 and IT for the two classes became more separable as measured by an increase in manifold capacity. This increase in capacity was associated with a characteristic geometric change in the neural population response geometry. Our results suggest that both V4 and IT responses actively change during category learning in ways that directly lead to increased separability and improved readouts for downstream neural areas, and point towards future work linking these population-level geometric changes to local changes at the single-neuron level.},
acrosscenters = {no},
external = {yes},
highlight = {no},
center = {CCN},
OpenAccessURL = {https://jov.arvojournals.org/article.aspx?articleid=2801667},
Journal = JOV,
volume = {24},
ISSN = {1534-7362},
DOI = {10.1167/jov.24.10.1430},
number = {10},
publisher = {Association for Research in Vision and Ophthalmology (ARVO)},
month = sep,
pages = {1430},
year = {2024}
}

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Visual Temporal Prediction: Representation, Estimation, and Modeling

P. Fiquet

New York University ProQuest Dissertations & Theses, 31489428

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September 1, 2024

Visual Temporal Prediction: Representation, Estimation, and Modeling

@PHDTHESIS{Fiquet-phd,
     TITLE= "Visual Temporal Prediction: {Representation}, Estimation, and Modeling",
     AUTHOR= "Pierre-Etienne Fiquet",
     ADVISOR= "Eero P. Simoncelli",
     SCHOOL= "Center for Neural Science, New York University",
     ADDRESS= "New York, NY",
     YEAR= 2024,
     MONTH= "Sep",
     PDF-URL= "https://www.cns.nyu.edu/pub/lcv/fiquet-phd.pdf",
}

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Natural Image Densities: Learning, Understanding and Utilizing

New York University ProQuest Dissertations & Theses

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September 1, 2024

Natural Image Densities: Learning, Understanding and Utilizing

@PHDTHESIS{Kadkhodaie-phd,
     TITLE= "Natural Image Densities: Learning, Understanding and Utilizing",
     AUTHOR= "Zahra Kadkhodaie",
     ADVISOR= "Eero P. Simoncelli",
     SCHOOL= "Center for Data Science, New York University",
     ADDRESS= "New York, NY",
     YEAR= 2024,
     MONTH= "Sep",
     PDF-URL= "https://www.cns.nyu.edu/pub/lcv/kadkhodaie-phd.pdf",
}

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Tensor Decomposition Meets RKHS: Efficient Algorithms for Smooth and Misaligned Data

B. Larsen, Tamara G. Kolda, Anru R. Zhang, A. Williams

arXiv:2408.05677

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August 11, 2024

Tensor Decomposition Meets RKHS: Efficient Algorithms for Smooth and Misaligned Data

@article{Larsen_Williams_arxiv:2408.05677,
title = {{Tensor Decomposition Meets RKHS: Efficient Algorithms for Smooth and Misaligned Data}},
author = {Brett W. Larsen and Tamara G. Kolda and Anru R. Zhang and Alex H. Williams},
abstract = {The canonical polyadic (CP) tensor decomposition decomposes a multidimensional data array into a sum of outer products of finite-dimensional vectors. Instead, we can replace some or all of the vectors with continuous functions (infinite-dimensional vectors) from a reproducing kernel Hilbert space (RKHS). We refer to tensors with some infinite-dimensional modes as quasitensors, and the approach of decomposing a tensor with some continuous RKHS modes is referred to as CP-HiFi (hybrid infinite and finite dimensional) tensor decomposition. An advantage of CP-HiFi is that it can enforce smoothness in the infinite dimensional modes. Further, CP-HiFi does not require the observed data to lie on a regular and finite rectangular grid and naturally incorporates misaligned data. We detail the methodology and illustrate it on a synthetic example.},
acrosscenters = {no},
external = {yes},
highlight = {no},
eprint = {2408.05677},
archivePrefix = {arXiv},
journal = {arXiv e-prints},
year_posted = {2024},
center = {CCN},
OpenAccessURL = {https://arxiv.org/abs/2408.05677},
year = {2024}
}

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Neuronal and behavioral responses to naturalistic texture images in macaque monkeys

C M Ziemba, R L T Goris, G M Stine, R K Perez, E. P. Simoncelli, J A Movshon

bioRxiv 2024.02.22.581645

The Journal of Neuroscience, 44: 42

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2024

Neuronal and behavioral responses to naturalistic texture images in macaque monkeys

@ARTICLE{Ziemba24,
  TITLE=        "Neuronal and behavioral responses to naturalistic texture images in macaque monkeys",
  AUTHOR=       "C M Ziemba and R L T Goris and G M Stine and R K Perez and E P
                 Simoncelli and J A Movshon",
  JOURNAL=      "The Journal of Neuroscience",
  VOLUME=       44,
  ISSUE=        42,
  MONTH=        "Aug",
  YEAR=         "2024",
%  PDF-URL=     "https://www.cns.nyu.edu/pub/lcv/ziemba24-preprint.pdf",
  PDF-URL=      "https://www.cns.nyu.edu/pub/lcv/ziemba24.pdf",
  URL=          "https://www.jneurosci.org/content/early/2024/08/26/JNEUROSCI.0349-24.2024.long",
  DOI=          "10.1523/JNEUROSCI.0349-24.2024",
  PMID=         "39197942",
}

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Context-invariant beliefs are supported by dynamic reconfiguration of single unit functional connectivity in prefrontal cortex of male macaques

Jean-Paul Noel, E. Balzani, Cristina Savin, D. Angelaki

bioRxiv:2023.07.30.551169

Nature Communications, 15:12

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July 9, 2024

Context-invariant beliefs are supported by dynamic reconfiguration of single unit functional connectivity in prefrontal cortex of male macaques

@article{Balzani_bioxiv2023.07.30.551169_NATCOM_2024,
Archiveprefix = {bioXiv},
Author = {Noel, Jean-Paul and \text{Balzani, Edoardo} and Savin, Cristina and Angelaki, Dora E.},
Doi = {10.1038/s41467-024-50203-5},
Eprint = {2023/07/31/2023.07.30.551169},
Journal = NATCOM,
Issue = {1},
month = {Jul},
Pages = {12},
Publisher = {Nature Portfolio},
Title = {{Context-invariant beliefs are supported by dynamic reconfiguration of single unit functional connectivity in prefrontal cortex of male macaques}},
Url = {https://doi.org/10.1038/s41467-024-50203-5},
OpenAccessURL = {https://www.biorxiv.org/content/early/2023/07/31/2023.07.30.551169},
Volume = {15},
Year = {2024},
year_posted = {2023},
center = {CCN},
acrosscenters = {no},
external = {yes},
highlight = {no},
abstract = {Natural behaviors occur in closed action-perception loops and are supported by dynamic and flexible beliefs abstracted away from our immediate sensory milieu. How this real-world flexibility is instantiated in neural circuits remains unknown. Here, we have male macaques navigate in a virtual environment by primarily leveraging sensory (optic flow) signals, or by more heavily relying on acquired internal models. We record single-unit spiking activity simultaneously from the dorsomedial superior temporal area (MSTd), parietal area 7a, and the dorso-lateral prefrontal cortex (dlPFC). Results show that while animals were able to maintain adaptive task-relevant beliefs regardless of sensory context, the fine-grain statistical dependencies between neurons, particularly in 7a and dlPFC, dynamically remapped with the changing computational demands. In dlPFC, but not 7a, destroying these statistical dependencies abolished the area’s ability for cross-context decoding. Lastly, correlational analyses suggested that the more unit-to-unit couplings remapped in dlPFC, and the less they did so in MSTd, the less were population codes and behavior impacted by the loss of sensory evidence. We conclude that dynamic functional connectivity between neurons in prefrontal cortex maintain a stable population code and context-invariant beliefs during naturalistic behavior.}
}

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Open Data In Neurophysiology: Advancements, Solutions & Challenges

Colleen J Gillon, Cody Baker, Ryan Ly, E. Balzani, Bingni W Brunton, Manuel Schottdorf, Satrajit Ghosh, Noma Dehghani

PMCID: PMC11247910

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July 1, 2024

Open Data In Neurophysiology: Advancements, Solutions & Challenges

@article{Gillon_Balzani_arXiv:2407.00976v1,
Archiveprefix = {arXiv},
Author = {Colleen J. Gillon and Cody Baker and Ryan Ly and Edoardo Balzani and Bingni W. Brunton and Manuel Schottdorf and Satrajit Ghosh and Nima Dehghani},
Eprint = {2407.00976},
Journal = {arXiv e-prints},
Title = {{Open Data In Neurophysiology: Advancements, Solutions \& Challenges.}},
OpenAccessURL = {https://pmc.ncbi.nlm.nih.gov/articles/PMC11247910/},
year_posted = {2024},
center = {CCN},
acrosscenters = {no},
external = {yes},
highlight = {no},
year = {2024},
abstract = {Across the life sciences, an ongoing effort over the last 50 years has made data and methods more reproducible and transparent. This openness has led to transformative insights and vastly accelerated scientific progress(1,2). For example, structural biology(3) and genomics(4,5) have undertaken systematic collection and publication of protein sequences and structures over the past half-century, and these data have led to scientific breakthroughs that were unthinkable when data collection first began (e.g.(6)). We believe that neuroscience is poised to follow the same path, and that principles of open data and open science will transform our understanding of the nervous system in ways that are impossible to predict at the moment. To this end, new social structures along with active and open scientific communities are essential(7) to facilitate and expand the still limited adoption of open science practices in our field(8). Unified by shared values of openness, we set out to organize a symposium for Open Data in Neuroscience (ODIN) to strengthen our community and facilitate transformative neuroscience research at large. In this report, we share what we learned during this first ODIN event. We also lay out plans for how to grow this movement, document emerging conversations, and propose a path toward a better and more transparent science of tomorrow.}
}

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