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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. Lyapunov spectrum of random neural networks

    arxiv:2610.12426, October 8, 2026

    D. Clark

  2. ​From stuff to things: Responses of neurons in macaque V4 to textures and objects

    bioRxiv:2024.02.20.581273, July 9, 2026

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

  3. The Squealer: Sensification of model exploration and model misfit

    arXiv:2606.29842, June 29, 2026

    A. Gelman, Andrew H. Jaffe, Eliot Carlson, and P. Greengard

  4. Similarity of Neural Network Representations in Superposition

    arXiv:2604.00208, June 22, 2026

    Sunny Liu, Habon Issa, André Longon, Liv Gorton, Meenakshi Khosla, A. Williams, et al.

  5. GEOPHYS: The Geometry of Physical Plausibility

    arXiv:2606.20707, June 15, 2026

    Christian Internò, Alexander Pondaven, Habon Issa, Fabio Pizzati, Francesco Pinto, Markus Olhofer, et al.

  6. Learning a Maximum Entropy Model for Visual Textures using Diffusion

    arXiv:2606.17342, June 15, 2026

    X. Zhao and E. Simoncelli

  7. Stochastic Thermodynamics of Score Matching in Diffusion Models

    arXiv:2606.17252, June 15, 2026

    X. Ding, H. T. Quan, and Y. Tu

  8. Task-Induced Representational Invariances Depend on Learning Objective in Deep RL

    arXiv:2606.01868, June 1, 2026

    Manu Srinath Halvagal, S. Lee, and S. Chung

  9. Diffusion models learn underlying trends in actomyosin networks and predict behavior at unseen filament turnover

    bioRxiv:2026.05.26.727950, May 29, 2026

    Elisabeth Rennert, A. Behera, Yuqing Qiu, and Suriyanarayanan Vaikuntanathan

  10. Two Speeds of Learning: A Representation-Readout Decomposition of Grokking and Double Descent

    arXiv:2605.27078v2, May 28, 2026

    C. Chou, Oscar Uzdelewicz, Neng-Chun Chiu, Yao-Yuan Yang, and S. Chung

  11. Learning Normalized Energy Models for Linear Inverse Problems

    arXiv:2605.15487, May 15, 2026

    Nicolas Zilberstein, Santiago Segarra, E. Simoncelli, and F. Guth

  12. How Data Augmentation Shapes Neural Representations

    arXiv:2605.15306, May 14, 2026

    Tianxiao He, A. Williams, and S. Harvey

  13. Tracking the Fidelity of Internal Neural Representations with Error-In-Variables Regression

    bioRxiv:2026.04.22.720005, May 12, 2026

    Isabel Garon, Stephen Keeley, and A. Williams

  14. There Will Be a Scientific Theory of Deep Learning

    arXiv:2604.21691, April 23, 2026

    Jamie Simon, Daniel Kunin, Alexander Atanasov, Enric Boix-Adser`, Blake Bordelon, J. Cohen, et al.

  15. Modulating Cross-Modal Convergence with Single-Stimulus, Intra-Modal Dispersion

    arXiv:2604.21836, April 23, 2026

    Eghbal A. Hosseini, Brian Cheung, Evelina Fedorenko, and A. Williams

  16. Spectral Analysis of Representational Similarity with Limited Neurons

    The Thirty-ninth Annual Conference on Neural Information Processing Systems (NeurIPS 2025), arXiv: 2502.19648v1, April 23, 2026

    Hyunmo Kang, A. Canatar, and S. Chung

  17. Reproducibility and model-selection stability in connectome-constrained circuit modeling

    bioRxiv: 2026.04. 18.717873, April 20, 2026

    Christos Karaneen, E. Schomburg, and D. Chklovskii

  18. Partial Soft-Matching Distance for Neural Representational Comparison with Partial Unit Correspondence

    International Conference on Learning Representations (ICLR), arXiv:2602.19331, April 10, 2026

    Chaitanya Kapoor, A. Williams, and Meenakshi Khosla

  19. Quasi Monte Carlo methods enable extremely low-dimensional deep generative models

    International Conference on Learning Representations (ICLR), arXiv:2601.18676, April 10, 2026

    Miles Martinez and A. Williams

  20. Estimating Dimensionality of Neural Representations from Finite Samples

    International Conference on Learning Representations (ICLR), arXiv:2509.26560v2, April 10, 2026

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

  21. Approximate posterior recalibration

    arXiv:2603.20068, March 20, 2026

    Tiffany Cai, P. Greengard, Ben Goodrich, and A. Gelman

  22. A Network of Biologically Inspired Rectified Spectral Units (ReSUs) Learns Hierarchical Features Without Error Backpropagation

    Proceedings of the AAAI Conference on Artificial Intelligence, arXiv:2512.23146, March 14, 2026

    S. Qin, J. Pughe-Sanford, A. Genkin, Pembe Gizem Ozdil, P. Greengard, A. Sengupta, et al.

  23. Linear Readout of Neural Manifolds with Continuous Variables

    arXiv:2603.10956v1, March 11, 2026

    Will Slatton, C. Chou, and S. Chung

  24. Diagnosing Generalization Failures from Representational Geometry Markers

    International Conference on Learning Representations (ICLR), arXiv:2603.01879, March 2, 2026

    C. Chou, A. Kirsanov, Yao-Yuan Yang, and S. Chung

  25. Natural Image Statistics, Visual Representation, and Denoising

    Proceedings of the Analytical Connectionism Schools 2023--2024, March 1, 2026

    Imran Thobani, Alisa Leshchenko, and E. Simoncelli

  26. The head-direction signal is generated by multiple attractor-like networks

    BioRxiv:2025.09.10.675474, February 27, 2026

    G. Viejo, Sofia Skromne Carrasco, and Adrien Peyrache

  27. Emergent Manifold Separability during Reasoning in Large Language Models

    arXiv:2602.20338, February 26, 2026

    Alexandre Polo, C. Chun, and S. Chung

  28. Learning a distance measure from the information-estimation geometry of data

    International Conference on Learning Representations (ICLR), arXiv:2510.02514, February 26, 2026

    G. Ohayon, P. Fiquet, F. Guth, Jona Ballé, and E. Simoncelli

  29. Months-long stability of the head-direction system

    Nature, bioRxiv:2024.06.13.598909, February 11, 2026

    Sofia Skromne Carrasco, G. Viejo, and Adrien Peyrache

  30. Blind denoising diffusion models and the blessings of dimensionality

    arXiv:2602.09639, February 10, 2026

    Z. Kadkhodaie, Aram-Alexandre Pooladian, Sinho Chewi, and E. Simoncelli

  31. On the Superlinear Relationship between SGD Noise Covariance and Loss Landscape Curvature

    arXiv:2602.05600, February 5, 2026

    Yikuan Zhang, Ning Yang, and Y. Tu

  32. Neural population geometry and optimal coding of tasks with shared latent structure

    Nature Neuroscience, arXiv:2402.16770, February 4, 2026

    Albert J. Wakhloo, Will Slatton, and S. Chung

  33. Sparse input representations explain odor discrimination in complex, concentration-varying mixtures

    bioRxiv: 2026.01. 27.702074, January 28, 2026

    Hannah McCalmon, George Cai, Constantine Tsibouris, Farhad Pashakhanloo, S. Chung, Vikrant Kapoor, et al.

  34. Nonequilibrium Thermodynamics of Biochemical Networks: Energetics of Cellular Functions

    ANNUAL REVIEW OF BIOPHYSICS, January 28, 2026

    Y. Tu

  35. Neurons as Detectors of Coherent Sets in Sensory Dynamics

    The Thirty-ninth Annual Conference on Neural Information Processing Systems (NeurIPS 2025), arXiv:2510.26955, January 21, 2026

    J. Pughe-Sanford, X. Ding, J. Moore, A. Sengupta, C. Epstein, P. Greengard, et al.

  36. Transient learning dynamics drive escape from sharp valleys in Stochastic Gradient Descent

    arXiv:2601.10962, January 16, 2026

    Ning Yang, Yikuan Zhang, Qi Ouyang, Chao Tang, and Y. Tu

  37. Learning normalized image densities via dual score matching

    Adv. Neural Information Processing (NeurIPS), arXiv:2506.05310, January 15, 2026

    F. Guth, Z. Kadkhodaie, and E. Simoncelli

  38. Mechanical origin for non-equilibrium ultrasensitivity in the bacterial flagellar motor

    Nature Physics, January 7, 2026

    H. Mattingly and Y. Tu

  39. Scalable inference of functional neural connectivity at submillisecond timescales

    The Thirty-ninth Annual Conference on Neural Information Processing Systems (NeurIPS 2025), arXiv:2510.20966, January 4, 2026

    A. Medvedeva, E. Balzani, A. Williams, and Stephen L Keeley

  40. Disentangled representations via score-based variational autoencoders

    arXiv:2512.17127, December 18, 2025

    Benjamin S. H. Lyo, C. Savin, and E. Simoncelli

  41. From labels to latents: revealing state-dependent hippocampal computations with Jump Latent Variable Model

    biorxiv:10.64898/2025.12.14.694183, December 16, 2025

    S. Zheng, Ipshita Zutshi, Roman Huszár, Yiyao Zhang, Mursel Karadas, György Buzsáki, et al.

  42. Comprehensive characterization of human color discrimination thresholds

    eLife, bioRxiv: 2025.07. 16.665219, November 25, 2025

    Fangfang Hong, Ruby Bouhassira, Jason Chow, Craig Sanders, Michael Shvartsman, Phillip Guan, et al.

  43. Open Data In Neurophysiology: Advancements, Solutions & Challenges

    eNeuro, PMCID: PMC11247910, November 20, 2025

    Colleen J Gillon, Cody Baker, Ryan Ly, E. Balzani, Bingni W Brunton, Manuel Schottdorf, et al.

  44. A theory of initialisation’s impact on specialisation

    Journal of Statistical Mechanics: Theory and Experiment, November 17, 2025

    Devon Jarvis, S. Lee, Clementine Carla Juliette Domine, Andrew M Saxe, and Stefano Sarao Mannelli

  45. Modeling Neural Activity with Conditionally Linear Dynamical Systems

    The Thirty-ninth Annual Conference on Neural Information Processing Systems, arXiv:2502.18347, 2025

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

  46. Unconditional CNN denoisers contain sparse semantic representation of images

    arXiv:2506.01912v2, October 14, 2025

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

  47. Effective computations for hippocampal place cell phenomena in sparse untrained random networks

    bioRxiv: 2025.10.04.680487, October 6, 2025

    José R. Hurtado Jr, S. Chung, and André A. Fenton

  48. Correcting Non-Uniform Milling in FIB-SEM Images with Unsupervised Cross-Plane Image-to-Image Translation

    bioRxiv:2025.09. 29.679411, October 1, 2025

    Yicong Li, Yuri Kreinin, Siyu Huang, E. Schomburg, D. Chklovskii, Hanspeter Pfister, et al.

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