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  • Building Biological Intelligence Investigating how the ingredients of biological computation come together to produce a system vastly more powerful than its constituent parts

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Computational Neuroscience

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    Building Biological Intelligence Investigating how the ingredients of biological computation come together to produce a system vastly more powerful than its constituent parts

    Computational Vision Developing novel computational methods to study how the brain analyzes and represents visual information.

    High Dimensional Dynamics and Computation Developing theories linking synaptic connectivity, neuronal dynamics and computation.

    Information Processing in Neural Networks Investigating the dynamics, statistical properties and principles of information processing in biological neural circuits and artificial neural networks.

    Neural Circuits and Algorithms Studying how the brain processes complex sensory data to inform AI networks and mental health treatments.

    NeuroRSE Building open source software for computational and systems neuroscience.

    Statistical Analysis of Neural Data Developing statistical models and computational tools to extract insights from neural data.

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Flatiron Institute Computational Neuroscience

Computational Neuroscience: Publications

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  1. End-to-end Topographic Auditory Models Replicate Signatures of Human Auditory Cortex

    arXiv:2509.24039, September 28, 2025

    Haider Al-Tahan, Mayukh Deb, J. Feather, and N. Apurva Ratan Murty

  2. Spatial Frequency Maps in Human Visual Cortex: A Replication and Extension

    bioRxiv:2025.01.21.634150, September 17, 2025

    Jiyeong Ha, B. Broderick, Kendrick Kay, and J. Winawer

  3. Stochastic Process Inference Without Trajectories: A Probabilistic Approach

    ACM SIGMETRICS Performance Evaluation Review, August 27, 2025

    D. Hathcock, Mark S Squillante, and Y. Tu

  4. Statistical mechanics of support vector regression

    Physical Review E, arXiv:2412.05439v2, August 4, 2025

    A. Canatar and S. Chung

  5. Feature Learning beyond the Lazy-Rich Dichotomy: Insights from Representational Geometry

    Proceedings of the 42nd International Conference on Machine Learning, arXiv:2503.18114v2, July 23, 2025

    C. Chou, H. Le, Y. Wang, and S. Chung

  6. Representational drift and learning-induced stabilization in the piriform cortex

    Proceedings of the National Academy of Sciences, July 16, 2025

    Guillermo B. Morales, Miguel A. Muñoz, and Y. Tu

  7. Variations in neuronal selectivity create efficient representational codes

    bioRxiv: 2025.06.26.661754, June 28, 2025

    S. Saraf, J. Movshon, and S. Chung

  8. Variations in neuronal selectivity create efficient representational geometries for perception

    biorxiv:2025.06.26.661754v1, June 28, 2025

    S. Saraf, J. Movshon, and S. Chung

  9. Uncertainty Prioritized Experience Replay

    arXiv:2506.09270, June 10, 2025

    Rodrigo Carrasco-Davis, S. Lee, Claudia Clopath, and Will Dabney

  10. A common computational and neural anomaly across mouse models of autism

    Nature Neuroscience, June 3, 2025

    Jean-Paul Noel, E. Balzani, Luigi Acerbi, Julius Benson, The International Brain Laboratory, C. Savin, et al.

  11. Discriminating image representations with principal distortions

    International Conference on Learning Representations (ICLR), https://arxiv.org/abs/2410.15433, May 16, 2025

    J. Feather, D. Lipshutz, S. Harvey, A. Williams, and E. Simoncelli

  12. Detection of Moving Objects Using Self-motion Constraints on Optic Flow

    arXiv:2505.06686, May 13, 2025

    H. Lutwak, Bas Rokers, and E. Simoncelli

  13. Detecting Moving Objects During Self-motion

    New York University ProQuest Dissertations & Theses, arXiv:2505.06686v2, May 10, 2025

    H. Lutwak

  14. Generalized Compressed Sensing for Image Reconstruction with Diffusion Probabilistic Models

    Transactions on Machine Learning Research, arXiv:2405.17456v4, 2025

    Ling-Qi Zhang, Z. Kadkhodaie, E. Simoncelli, and D. Brainard

  15. The first complete 3D reconstruction and morphofunctional mapping of an insect eye

    eLife, bioRxiv:2024.09.30.615804v1, May 1, 2025

    Anastasia A Makarova, N. Chua, Anna V Diakova, Inna A Desyatirkina, P. Gunn, Song Pang, et al.

  16. The Geometry of Prompting: Unveiling Distinct Mechanisms of Task Adaptation in Language Models

    Findings of the Association for Computational Linguistics NAACL 2025, arXiv:2502.08009v1, April 29, 2025

    A. Kirsanov, C. Chou, Kyunghyun Cho, and S. Chung

  17. Perceptual learning improves discrimination but does not reduce distortions in appearance

    PLOS Computational Biology, April 15, 2025

    Sarit F.A. Szpiro, Charlie S. Burlingham, E. Simoncelli, and Marisa Carrasco

  18. Geometry Linked to Untangling Efficiency Reveals Structure and Computation in Neural Populations

    bioRxiv:2024.02.26.582157, March 31, 2025

    C. Chou, Royoung Kim, Luke A. Arend, Yao-Yuan Yang, Brett D. Mensh, Won Mok Shim, et al.

  19. Disentangling 3D Animal Pose Dynamics With Scrubbed Conditional Latent Variables

    The Thirteenth International Conference on Learning Representations, March 14, 2025

    Joshua H Wu, Hari Koneru, J Russell Ravenel, Anshuman Sabath, James M Roach, Shaun SX Lim, et al.

  20. Nonlinear classification of neural manifolds with contextual information

    Phys. Rev. E, arXiv:2405.06851, March 6, 2025

    F. Mignacco, C. Chou, and S. Chung

  21. Comparing noisy neural population dynamics using optimal transport distances

    The Thirteenth International Conference on Learning Representations, arXiv:2412.14421, March 1, 2025

    A. Nejatbakhsh, Victor Geadah, A. Williams, and D. Lipshutz

  22. Estimating Neural Representation Alignment from Sparsely Sampled Inputs and Features

    arXiv:2502.15104, February 24, 2025

    C. Chun, A. Canatar, S. Chung, and Daniel D. Lee

  23. Brain-Model Evaluations Need the NeuroAI Turing Test

    arXiv:2502.16238, February 22, 2025

    J. Feather, Meenakshi Khosla, N. Apurva Ratan Murty, and Aran Nayebi

  24. Sub-cellular population imaging tools reveal stable apical dendrites in hippocampal area CA3

    Nature Communications volume, January 28, 2025

    J. Moore, Shannon K. Rashid, Emmett Bicker, Cara D. Johnson, Naomi Codrington, D. Chklovskii, et al.

  25. Learning predictable and robust neural representations by straightening image sequences

    Advances in Neural Information Processing Systems (NeurIPS 2024), January 20, 2025

    X. Niu, Cristina Savin, and E. Simoncelli

  26. Foundations of visual form selectivity in macaque areas V1 and V2

    bioRxiv:2024.03.04.583307, January 18, 2025

    T. Oleskiw , Justin D. Lieber, E. Simoncelli, and J. Movshon

  27. Shaping the distribution of neural responses with interneurons in a recurrent circuit model

    Advances in Neural Information Processing Systems (NeurIPS), arXiv:2405.17745, January 17, 2025

    D. Lipshutz and E. Simoncelli

  28. Contrastive-equivariant self-supervised learning improves alignment with primate visual area IT

    Advances on Neural Information Processing (NeurIPS), January 15, 2025

    T. Yerxa, J. Feather, E. Simoncelli, and S. Chung

  29. Quantifying Differences in Neural Population Activity With Shape Metrics

    bioRxiv:2025.01.10.632411v1, January 11, 2025

    Joao Barbosa, A. Nejatbakhsh, L. Duong, S. Harvey, Scott L. Brincat, Markus Siegel, et al.

  30. Hippocampal neuronal activity is aligned with action plans

    Nature, January 8, 2025

    Ipshita Zutshi, Athina Apostolelli, Wannan Yang, S. Zheng, Tora Dohi, E. Balzani, et al.

  31. How to optimize neuroscience data utilization and experiment design for advancing brain models of visual and linguistic cognition?

    arXiv:2401.03376v2, 2024

    Greta Tuckute, Dawn Finzi, Eshed Margalit, Joel Zylberberg, S. Chung, Alona Fyshe, et al.

  32. Soft Matching Distance: A metric on neural representations that captures single-neuron tuning

    Proceedings of UniReps: the First Workshop on Unifying Representations in Neural Models, arXiv:2311.09466, 2024

    A. Williams and Meenakshi Khosla

  33. Corrections to: Mapping Spatial Frequency Preferences Across Human Primary Visual Cortex

    Journal of Vision, December 1, 2024

    B. Broderick, E. Simoncelli, and J. Winawer

  34. Representational learning by optimization of neural manifolds in an olfactory memory network

    bioRxiv:2024.11.17.623906, November 18, 2024

    Bo Hu, Nesibe Z. Temiz, C. Chou, Peter Rupprecht, Claire Meissner-Bernard, Benjamin Titze, et al.

  35. Task-Relevant Covariance from Manifold Capacity Theory Improves Robustness in Deep Networks

    UniReps: 2nd Edition of the Workshop on Unifying Representations in Neural Models, November 3, 2024

    William Yang, C. Chou, and S. Chung

  36. WASPSYN: A Challenge for Domain Adaptive Synapse Detection in Microwasp Brain Connectomes

    IEEE Transactions on Medical Imaging, November 1, 2024

    Yicong Li, Wanhua Li, Qi Chen, Wei Huang, Yuda Zou, Xin Xiao, et al.

  37. Video prediction using score-based conditional density estimation

    arXiv:2411.00842, October 30, 2024

    P. Fiquet and E. Simoncelli

  38. Unsupervised discovery of family specific vocal usage in the Mongolian gerbil

    eLife, bioRxiv:2023.03.11.532197, October 28, 2024

    R. Peterson, A. Choudhri, Catalin Mitelut, A. Tanelus, Athena Capo-Battaglia, A. Williams, et al.

  39. Estimating the Spectral Moments of the Kernel Integral Operator from Finite Sample Matrices

    arXiv:2410.17998, October 23, 2024

    C. Chun, S. Chung, and D. Lee

  40. High-fidelity Image Restoration of Large 3D Electron Microscopy Volume

    Microscopy and Microanalysis, bioRxiv:2023.09.14.557785, October 18, 2024

    Yuri Kreinin, P. Gunn, D. Chklovskii, and J. Wu

  41. Neuronal and Behavioral Responses to Naturalistic Texture Images in Macaque Monkeys

    The Journal of Neuroscience, bioXriv:2024.02.22.581645, October 16, 2024

    Corey M. Ziemba, Robbe L.T. Goris, Gabriel M. Stine, Richard K. Perez, E. Simoncelli, and J. Movshon

  42. Feature-guided score diffusion for sampling conditional densities

    arXiv:2410.11646, October 15, 2024

    Z. Kadkhodaie, S. Mallat, and E. Simoncelli

  43. What Representational Similarity Measures Imply about Decodable Information

    UniReps: 2nd Edition of the Workshop on Unifying Representations in Neural Models, arXiv:2411.08197, October 10, 2024

    S. Harvey, D. Lipshutz, and A. Williams

  44. Equivalence between representational similarity analysis, centered kernel alignment, and canonical correlations analysis

    UniReps: 2nd Edition of the Workshop on Unifying Representations in Neural Models, bioXriv:2024.10.23.619871, October 10, 2024

    A. Williams

  45. Comparing the local information geometry across several image representations

    UniReps: 2nd Edition of the Workshop on Unifying Representations in Neural Models, October 10, 2024

    D. Lipshutz, J. Feather, S. Harvey, A. Williams, and E. Simoncelli

  46. Classification-Denoising Networks

    arXiv:2410.03505, October 4, 2024

    Louis Thiry and F. Guth

  47. A Rainbow in Deep Network Black Boxes

    Journal of Machine Learning Research, arXiv:2305.18512, 2024

    F. Guth, Brice Ménard, MD, Gaspar Rochette, and S. Mallat

  48. Vocal Call Locator Benchmark (VCL) for localizing rodent vocalizations from multi-channel audio

    The Thirty-eight Conference on Neural Information Processing Systems Datasets and Benchmarks Track, bioRxiv:2024.09.20.613758, 2024

    R. Peterson, A. Tanelus, Christopher Ick, Bartul Mimica, Niegil Francis, Violet J Ivan, et al.

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