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A simplified minimodel of visual cortical neurons

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  • Fengtong Du

    (HHMI Janelia Research Campus)

  • Miguel Angel Núñez-Ochoa

    (HHMI Janelia Research Campus)

  • Marius Pachitariu

    (HHMI Janelia Research Campus)

  • Carsen Stringer

    (HHMI Janelia Research Campus)

Abstract

Artificial neural networks (ANNs) have been shown to predict neural responses in primary visual cortex (V1) better than classical models. However, this performance often comes at the expense of simplicity and interpretability. Here we introduce a new class of simplified ANN models that can predict over 70% of the response variance of V1 neurons. To achieve this high performance, we first recorded a new dataset of over 29,000 neurons responding to up to 65,000 natural image presentations in mouse V1. We found that ANN models required only two convolutional layers for good performance, with a relatively small first layer. We further found that we could make the second layer small without loss of performance, by fitting individual “minimodels” to each neuron. Similar simplifications applied for models of monkey V1 neurons. We show that the minimodels can be used to gain insight into how stimulus invariance arises in biological neurons.

Suggested Citation

  • Fengtong Du & Miguel Angel Núñez-Ochoa & Marius Pachitariu & Carsen Stringer, 2025. "A simplified minimodel of visual cortical neurons," Nature Communications, Nature, vol. 16(1), pages 1-13, December.
  • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-61171-9
    DOI: 10.1038/s41467-025-61171-9
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    References listed on IDEAS

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    1. Johannes Friedrich & Pengcheng Zhou & Liam Paninski, 2017. "Fast online deconvolution of calcium imaging data," PLOS Computational Biology, Public Library of Science, vol. 13(3), pages 1-26, March.
    2. Carsen Stringer & Marius Pachitariu & Nicholas Steinmetz & Matteo Carandini & Kenneth D. Harris, 2019. "High-dimensional geometry of population responses in visual cortex," Nature, Nature, vol. 571(7765), pages 361-365, July.
    3. Colin Conwell & Jacob S. Prince & Kendrick N. Kay & George A. Alvarez & Talia Konkle, 2024. "A large-scale examination of inductive biases shaping high-level visual representation in brains and machines," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    4. Yan Zhang & Márton Rózsa & Yajie Liang & Daniel Bushey & Ziqiang Wei & Jihong Zheng & Daniel Reep & Gerard Joey Broussard & Arthur Tsang & Getahun Tsegaye & Sujatha Narayan & Christopher J. Obara & Ji, 2023. "Fast and sensitive GCaMP calcium indicators for imaging neural populations," Nature, Nature, vol. 615(7954), pages 884-891, March.
    5. Maximilian Joesch & Markus Meister, 2016. "A neuronal circuit for colour vision based on rod–cone opponency," Nature, Nature, vol. 532(7598), pages 236-239, April.
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