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    31 repositories

    • cleo

      Public
      Closed-Loop, Electrophysiology, and Optophysiology experiment simulation testbed for mesoscale neuroscience
      simulationcomputational-neuroscienceelectrophysiology
      simulationcomputational-neuroscienceelectrophysiologyclosed-loop-controloptogenetics
      Python
      •
      MIT License
      •3•23•9•5•Updated Oct 5, 2026Oct 5, 2026

    • NEXT

      Public
      NEXT is a machine learning system that runs in the cloud and makes it easy to develop, evaluate, and apply active learning in the real-world. Ask better questio…
      Python
      •
      Apache License 2.0
      •52•0•0•0•Updated Aug 23, 2026Aug 23, 2026

    • tklfp

      Public
      Lightweight package for computing the kernel LFP approximation from Teleńczuk et al., 2020
      computational-neuroscience
      computational-neuroscience
      Python
      •
      Apache License 2.0
      •1•1•0•0•Updated Jun 4, 2026Jun 4, 2026

    • probabilistic-decomposed-linear-dynamical-systems

      Public
      Probabilistic Decomposed Linear Dynamical Systems
      Python
      •
      MIT License
      •1•7•0•0•Updated May 13, 2026May 13, 2026

    • perceptGT

      Public
      Toolbox for analyzing BrainSense Survey data from Medtronic's Percept Device
      MATLAB
      •0•0•0•0•Updated Dec 16, 2025Dec 16, 2025

    • cleo-v1-plasticity-expt

      Public
      Code for the V1 plasticity disruption experiment in the Cleo publication
      Python
      •0•0•0•0•Updated Jun 30, 2025Jun 30, 2025

    • cleo-traveling-wave-rejection

      Public
      Python
      •1•0•0•1•Updated Jun 9, 2025Jun 9, 2025

    • cleo-hpc-experiments

      Public
      Python
      •1•0•0•0•Updated Jun 4, 2025Jun 4, 2025

    • wslfp

      Public
      Lightweight package for computing the Weighted Sum of synaptic currents LFP proxy from Mazzoni, Lindén et al., 2015
      computational-neuroscience
      computational-neuroscience
      Python
      •
      MIT License
      •0•1•1•0•Updated May 30, 2025May 30, 2025

    • lds-ctrl-est

      Public
      A C++ library for estimation and control of linear dynamical systems (LDS) with Gaussian or Poisson observations.
      C++
      •
      Apache License 2.0
      •0•0•0•0•Updated Jan 17, 2025Jan 17, 2025

    • uot-irst

      Public
      Implementation of unbalanced optimal transport algorithms for infrared search and track from Bertrand et al., 2020
      unbalanced-optimal-transportinfrared-search-and-track
      unbalanced-optimal-transportinfrared-search-and-track
      MATLAB
      •0•1•0•0•Updated Oct 31, 2023Oct 31, 2023

    • emd-df

      Public
      MATLAB implementation of the Earth Mover's Distance Dynamic Filtering (EMD-DF) algorithm from Bertrand et al., 2018
      optimal-transportdynamic-filtering
      optimal-transportdynamic-filtering
      MATLAB
      •0•0•0•0•Updated Oct 31, 2023Oct 31, 2023

    • Decomposed-Linear-Dynamical-Systems

      Public
      This is code for the paper "Decomposed Linear Dynamical Systems (dLDS) for learning the latent components of neural dynamics" (Mudrik, 2022)
      0•0•0•0•Updated Oct 30, 2023Oct 30, 2023

    • .github

      Public
      0•0•0•0•Updated Sep 20, 2023Sep 20, 2023

    • Sparse-Coding-Dictionary-Learning-Library

      Public
      Code to implement the sparse coding dictionary learning algorithm described in "Emergence of simple-cell receptive field properties by learning a sparse code fo…
      MATLAB
      •0•0•0•0•Updated Oct 24, 2022Oct 24, 2022

    • Convergence-speed-of-a-dynamical-system-performing-sparse-coding

      Public
      Code to produce the results in the paper "Convergence Speed of a Dynamical System for Sparse Recovery" in IEEE Trans. Signal Processing (2013) by Balavoine, Roz…
      MATLAB
      •0•1•0•0•Updated Oct 24, 2022Oct 24, 2022

    • Tracking-sparse-signals-via-L1-filtering

      Public
      Code to produce the results in the paper "Discrete and Continuous-time Soft-Thresholding with Dynamic Inputs" by Balavoine, Rozell and Romberg. Code by A. Balav…
      MATLAB
      •0•1•0•0•Updated Oct 18, 2022Oct 18, 2022

    • Dynamic-filtering-for-sparse-signals

      Public
      Code to implement the algorithm described in the paper "Dynamic filtering of time-varying sparse signals via L1 minimization"
      MATLAB
      •0•0•0•0•Updated Oct 18, 2022Oct 18, 2022

    • Spatial-Filtering-for-Sparse-Signals

      Public
      Code to implement the algorithm described in the paper "Spectral super-resolution of hyperspectral imagery using re-weighted L1 spatial filtering" in IEEE GRSL …
      MATLAB
      •0•3•0•0•Updated Oct 4, 2022Oct 4, 2022

    • Inhibitory-interneuron-models-via-convex-optimization

      Public
      Code to produce the results in the paper "Modeling biologically realistic inhibitory interneurons in sensory coding models" in PLoS Computational Biology (2015)…
      MATLAB
      •0•0•0•0•Updated Oct 4, 2022Oct 4, 2022

    • DIC-Cell-Simulator

      Public
      Code to implement the simulation framework described in the manuscript "Cell Membrane Tracking in Living Brain Tissue using Differential Interference Contrast M…
      MATLAB
      •2•2•0•0•Updated Sep 30, 2022Sep 30, 2022

    • UOT-regularization

      Public
      Code for "Unbalanced Optimal Transport Regularization for Imaging Problems" by Lee, Bertrand, and Rozell.
      MATLAB
      •1•1•0•0•Updated Oct 12, 2021Oct 12, 2021

    • manifold-autoencoder-extended

      Public
      Jupyter Notebook
      •3•3•0•0•Updated Oct 3, 2021Oct 3, 2021

    • pairsearch

      Public
      Project code for "Active Embedding Search via Noisy Paired Comparisons" (ICML 2019)
      Python
      •3•8•0•0•Updated Sep 30, 2021Sep 30, 2021

    • APM-LR

      Public
      Approximate Posterior Matching for Logistic Regression (APM-LR). Project code for "Feedback Coding for Active Learning" (AISTATS 2021).
      Python
      •0•2•0•0•Updated Sep 30, 2021Sep 30, 2021

    • VAELLS

      Public
      Code for "Variational Autoencoder with Learned Latent Structure"
      Python
      •2•34•0•0•Updated Mar 5, 2021Mar 5, 2021

    • generative-causal-explanations

      Public
      Code for "Generative causal explanations of black-box classifiers"
      Python
      •15•36•0•0•Updated Jan 15, 2021Jan 15, 2021

    • localized-sparse-coding

      Public
      Sparse dictionary learning with biologically plausible compression matrices
      Jupyter Notebook
      •1•1•0•0•Updated Oct 22, 2020Oct 22, 2020

    • Manifold_Autoencoder

      Public
      Code for "Representing Closed Transformation Paths in Encoded Network Latent Space"
      Python
      •2•3•0•0•Updated Jul 22, 2020Jul 22, 2020

    • infotuple

      Public
      Code supplement for "Active Ordinal Querying for Tuplewise Similarity Learning", appearing in AAAI 2020
      Python
      •1•6•0•0•Updated Feb 2, 2020Feb 2, 2020
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