The Grossman Center Publications

Automated customization of large-scale spiking network models to neuronal population activity
Shenghao Wu, Chengcheng Huang, Adam C. Snyder, Matthew A. Smith, Brent Doiron & Byron M. Yu
Nat Comput Sci (2024). https://doi.org/10.1038/s43588-024-00688-3

The mechanics of correlated variability in segregated cortical excitatory subnetworks
Alex Negrón, Matthew P. Getz, Gregory Handy & Brent Doiron
PNAS (2024). https://doi.org/10.1073/pnas.2306800121

Heavy-tailed neuronal connectivity arises from Hebbian self-organization
Christopher W. Lynn, Caroline M. Holmes & Stephanie E. Palmer
Nature Physics (2024). https://doi.org/10.1038/s41567-023-02332-9

The logic of recurrent circuits in the primary visual cortex
Ian Antón Oldenburg, William D. Hendricks, Gregory Handy, Kiarash Shamardani, Hayley A. Bounds, Brent Doiron & Hillel Adesnik 
Nat Neurosci (2024). https://doi.org/10.1038/s41593-023-01510-5

Sampling-based Bayesian inference in recurrent circuits of stochastic spiking neurons
Wen-Hao Zhang, Si Wu, Kresimir Josic, Brent Doiron
Nat Commun 14, 7074 (2023). https://doi.org/10.1038/s41467-023-41743-3

Cell-type-specific plasticity of inhibitory interneurons in the rehabilitation of auditory cortex after peripheral damage
Manoj Kumar, Gregory Handy, Stylianos Kouvaros, Yanjun Zhao, Lovisa Ljungqvist Brinson, Eric Wei, Brandon Bizup, Brent Doiron, Thanos Tzounopoulos
Nat Commun 14, 4170 (2023). https://doi.org/10.1038/s41467-023-39732-7

Cortical VIP neurons locally control the gain but globally control the coherence of gamma band rhythms
Julia Veit, Gregory Handy, Daniel P. Mossing, Brent Doiron, Hillel Adesnik
Neuron, 111, 405–417 (2023). DOI: https://doi.org/10.1016/j.neuron.2022.10.036

Automated customization of large-scale spiking network models to neuronal population activity
Shenghao Wu, Chengcheng Huang, Adam Snyder, Matthew Smith, Brent Doiron, Byron Yu
bioRxiv 2023.09.21.558920; doi: https://doi.org/10.1101/2023.09.21.558920

The mechanics of correlated variability in segregated cortical excitatory subnetworks
Alex Negrón, Matthew P. Getz, Gregory Handy, Brent Doiron
bioRxiv 2023.04.25.538323; doi: https://doi.org/10.1101/2023.04.25.538323

A dynamic scale-mixture model of motion in natural scenes
JM Salisbury, SE Palmer
bioRxiv, 2023.10. 19.563101; doi: https://doi.org/10.1101/2023.10.19.563101

Exactly solvable statistical physics models for large neuronal populations
CW Lynn, Q Yu, R Pang, W Bialek, SE Palmer
arXiv preprint arXiv:2310.10860. https://doi.org/10.48550/arXiv.2310.10860

The double-drift illusion biases the marmoset oculomotor system
NM Dotson, ZW Davis, JM Salisbury, SE Palmer, P Cavanagh, JH Reynolds
Journal of Vision 23 (10), 4-4. doi:https://doi.org/10.1167/jov.23.10.4

Stimulus invariant aspects of the retinal code drive discriminability of natural scenes
BD Hoshal, CM Holmes, K Bojanek, J Salisbury, MJ Berry, O Marre, SE Palmer
bioRxiv 2023.08.08.552526; doi: https://doi.org/10.1101/2023.08.08.552526

Understanding Energy-Based Modeling of Proteins via an Empirically Motivated Minimal Ground Truth Model
PW Fields, V Ngampruetikorn, R Ranganathan, DJ Schwab, S Palmer
1st Workshop on the Synergy of Scientific and Machine Learning Modeling@ ICML2023

Predictive saccades and decision making in the beetle-predating saffron robber fly
J Talley, S Pusdekar, A Feltenberger, N Ketner, J Evers, M Liu, A Gosh, SE Palmer, T Wardill, PT Gonzalez-Bellido
Current Biology 33 (14), 2912-2924. e5. https://doi.org/10.1016/j.cub.2023.06.019

Towards understanding neural collapse in supervised contrastive learning with the information bottleneck method
S Wang, SE Palmer
arXiv preprint arXiv:2305.11957. https://doi.org/10.48550/arXiv.2305.11957

Quantifying stimulus-relevant representational drift using cross-modality contrastive learning
S Wang, EA de Laittre, J MacLean, SE Palmer
arXiv preprint arXiv:2305.11953. https://doi.org/10.48550/arXiv.2305.11953

Multi-Relevance: Coexisting but Distinct Notions of Scale in Large Systems
AG Kline, SE Palmer
arXiv preprint arXiv:2305.11009. https://doi.org/10.48550/arXiv.2305.11009

Aposematic coloration of Pacific newts (Taricha) provides a qualitatively but not quantitatively honest signal to predators
HA Moniz, SM Kruleski, AD Risbud, SJH Louden, RT Hanlon, AN Stokes, SE Palmer, CR Feldman
Biological Journal of the Linnean Society 139 (1), 1-17. https://doi.org/10.1093/biolinnean/blad007

Coarse-graining facilitates generalization in populations of retinal ganglion cells
K Bojanek, O Marre, M Berry, S Palmer
Bulletin of the American Physical Society

Sparse, consistent correlation structure in the retinal population code across natural movies
C Holmes, B Hoshal, M Berry, O Marre, S Palmer
Bulletin of the American Physical Society

Finding the Function-Determining Subset of Amino Acids in Protein Sequence Data
P Fields, V Ngampruetikorn, R Ranganathan, D Schwab, S Palmer
Bulletin of the American Physical Society

Synchrotron-source micro-x-ray computed tomography for examining butterfly eyes
D Paukner, GA Wildenberg, GS Badalamente, PB Littlewood, Marcus R Kronforst, Stephanie E Palmer, Narayanan Kasthuri
bioRxiv, 2023.12. 08.570583

Fast or slow? Clock readout sets internal periods
SE Palmer, CM Holmes
bioRxiv, 2023.03. 17.533212. https://doi.org/10.1101/2023.03.17.533212

A Step Towards Uncovering The Structure of Multistable Neural Networks
M Tournoy, B Doiron
arXiv preprint arXiv:2210.03241, 2022. DOI: https://doi.org/10.48550/arXiv.2210.03241

A general decoding strategy explains the relationship between behavior and correlated variability
Amy M Ni, Chengcheng Huang, Brent Doiron, Marlene R Cohen
eLife 11:e67258 (2022). DOI:  https://doi.org/10.7554/eLife.67258

Internally generated population activity in cortical networks hinders information transmission
C Huang, A Pouget, B Doiron
Sci. Adv.8,eabg5244(2022). DOI:10.1126/sciadv.abg5244

Between-area communication through the lens of within-area neuronal dynamics
Olivia Gozel, Brent Doiron
bioRxiv 2022.04.11.487906; doi: https://doi.org/10.1101/2022.04.11.487906

Subpopulation Codes Permit Information Modulation Across Cortical States
Matthew P. Getz, Chengcheng Huang, Brent Doiron
bioRxiv 2022.09.28.509815; doi: https://doi.org/10.1101/2022.09.28.509815

The logic of recurrent circuits in the primary visual cortex
Ian Antón Oldenburg, William D. Hendricks, Gregory Handy, Kiarash Shamardani, Hayley A. Bounds, Brent Doiron, Hillel Adesnik
bioRxiv 2022.09.20.508739; doi: https://doi.org/10.1101/2022.09.20.508739

Cell-type-specific roles of inhibitory interneurons in the rehabilitation of auditory cortex after peripheral damage
Manoj Kumar, Gregory Handy, Stylianos Kouvaros, Lovisa Ljungqvist Brinson, Brandon Bizup, Brent Doiron, Thanos Tzounopoulos
bioRxiv 2022.09.15.508128; doi: https://doi.org/10.1101/2022.09.15.508128

Large-scale neural recordings call for new insights to link brain and behavior
Anne E. Urai, Brent Doiron, Andrew M. Leifer & Anne K. Churchland 
Nature Neuroscience volume 25, 11–19 (2022). https://doi.org/10.1038/s41593-021-00980-9

Learning low-dimensional generalizable natural features from retina using a U-net
S Wang, B Hoshal, E de Laittre, O Marre, M Berry, S Palmer
Advances in neural information processing systems 35, 11355-11368

Emergent scale-free networks
CW Lynn, CM Holmes, SE Palmer
arXiv preprint arXiv:2210.06453. 

Inferring couplings in networks across order-disorder phase transitions
V Ngampruetikorn, V Sachdeva, J Torrence, J Humplik, DJ Schwab, SE Palmer
Physical Review Research 4 (2), 023240. :https://doi.org/10.1103/PhysRevResearch.4.023240

Genetic and peripheral visual system changes underlie evolving butterfly mate preference
NW VanKuren, NP Buerkle, EL Westerman, AK Im, D Massardo, Laura M. Southcott, Wei Lu, Stephanie E. Palmer,  Marcus R. Kronforst
bioRxiv, 2022.04. 25.489404. doi: https://doi.org/10.1101/2022.04.25.489404

Failure of Inhibition Provides Transition From Population-Scale Computation to Focal Seizure
G Smith, J Cowan, S Palmer, W Drongelen
https://doi.org/10.21203/rs.3.rs-1502929/v1

Gaussian information bottleneck and the non-perturbative renormalization group
AG Kline, SE Palmer
New journal of physics 24 (3), 033007. DOI 10.1088/1367-2630/ac395d

Heavy-tailed neuronal connectivity arises from Hebbian self-organization
CW Lynn, CM Holmes, SE Palmer
bioRxiv, 2022.05. 30.494086. https://doi.org/10.1101/2022.05.30.494086

Sex-limited diversification of the eye in Heliconius butterflies
NP Buerkle, NW VanKuren, EL Westerman, MR Kronforst, SE Palmer
bioRxiv, 2022.04. 25.489414. https://doi.org/10.1101/2022.04.25.489414

Modeling circadian clocks in real environments
C Holmes, S Palmer
APS March Meeting Abstracts 2022, K04. 010

Merging Kalman Filtering with the information bottleneck technique for optimal state inference
V Sachdeva, T Mora, A Murugan, S Palmer, A Walczak
APS March Meeting Abstracts 2022, A03. 005

Energy-Based Models Capture Pairwise and Higher-Order Interactions in Protein Sequence Data
Peter Fields, Vudtiwat Ngampruetikorn, Stephanie Palmer, David Schwab
APS March Meeting Abstracts 2022, A03. 010

Assembly formation is stabilized by Parvalbumin neurons and accelerated by Somatostatin neurons
Fereshteh Lagzi, Martha Canto Bustos, Anne-Marie Oswald, Brent Doiron
bioRxiv 2021.09.06.459211; doi: https://doi.org/10.1101/2021.09.06.459211

Cortical VIP neurons locally control the gain but globally control the coherence of gamma band rhythms
Julia Veit, Gregory Handy, Daniel P. Mossing, Brent Doiron, Hillel Adesnik
bioRxiv 2021.05.20.444979; doi: https://doi.org/10.1101/2021.05.20.444979

Recurrent network dynamics shape direction selectivity in primary auditory cortex
DA Aponte, G Handy, AM Kline, H Tsukano, B Doiron, Hiroyuki K. Kato
Nature communications, 12, 314 (2021). https://doi.org/10.1038/s41467-020-20590

Remembering the past to see the future
NC Rust, SE Palmer
Annual review of vision science 7, 349-365

Spatially displaced excitation contributes to the encoding of interrupted motion by a retinal direction-selective circuit
Jennifer Ding, Albert Chen, Janet Chung, Hector Acaron Ledesma, Mofei Wu, David M Berson, Stephanie E Palmer, Wei Wei
PLoS computational biology 17 (5), e1008965. https://doi.org/10.7554/eLife.68181

Maximally efficient prediction in the early fly visual system may support evasive flight maneuvers
S Wang, I Segev, A Borst, S Palmer
PLoS computational biology 17 (5), e1008965. https://doi.org/10.1371/journal.pcbi.1008965

Optimal prediction with resource constraints using the information bottleneck
V Sachdeva, T Mora, AM Walczak, SE Palmer
PLOS Computational Biology 17 (3), e1008743. https://doi.org/10.1371/journal.pcbi.1008743

Variable but not random: temporal pattern coding in a songbird brain area necessary for song modification
SE Palmer, BD Wright, AJ Doupe, MH Kao
Journal of Neurophysiology 125 (2), 540-555. https://doi.org/10.1152/jn.00034.2019