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    83 repositories

    • DREAMS-CNE

      Public
      Contrastive neighbor embeddings with added regularization for global structure preservation.
      Jupyter Notebook
      •
      Other
      •9•0•0•0•Updated Aug 13, 2025Aug 13, 2025

    • DREAMS

      Public
      Extensible, parallel implementations of t-SNE with additional regularization for better global structure preservation.
      Python
      •
      Other
      •173•0•0•0•Updated Aug 13, 2025Aug 13, 2025

    • dreams-experiments

      Public
      DREAMS - Dimensionality Reduction Enhanced Across Multiple Scales
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Aug 13, 2025Aug 13, 2025

    • retinal-rl

      Public
      Testing theories about retinal coding in reinforcement learning environments
      Python
      •
      GNU Affero General Public License v3.0
      •1•0•25•0•Updated Aug 7, 2025Aug 7, 2025

    • text-embed-augm

      Public
      Companion repository to our González-Márquez et al. (2025) preprint "Cropping outperforms dropout as an augmentation strategy for training self-supervised text embeddings" (arXiv)
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Aug 5, 2025Aug 5, 2025

    • dependence-measures-medical-imaging

      Public
      This repository contains the code for the paper "Benchmarking Dependence Measures to Prevent Shortcut Learning in Medical Imaging".
      disentangled-representationsshortcut-learningdomain-shift
      Python
      •
      MIT License
      •0•1•0•0•Updated Aug 1, 2025Aug 1, 2025

    • llm-excess-vocab

      Public
      Delving into LLM-assisted writing in biomedical publications through excess vocabulary
      Jupyter Notebook
      •
      MIT License
      •7•45•0•0•Updated Aug 1, 2025Aug 1, 2025

    • contrastive-graphs

      Public
      Python
      •0•0•0•0•Updated Jul 30, 2025Jul 30, 2025

    • skeliner

      Public
      A lightweight neuromorphological mesh skeletonizer.
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 21, 2025Jul 21, 2025

    • flatone

      Public
      A command-line tool to flatten one EyeWire II neuron automatically.
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jul 14, 2025Jul 14, 2025

    • FedAdapterProto

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

    • disentangling-retinal-images

      Public
      This repository contains the code for the paper "Disentangling representations of retinal images with generative models".
      deep-learninggenerative-modelspurious-correlationscausalityretinal-fundus-imagesdisentanglement-learning
      Python
      •0•2•0•0•Updated Jul 3, 2025Jul 3, 2025

    • iclr-dataset

      Public
      ICLR dataset
      Jupyter Notebook
      •
      MIT License
      •6•32•1•1•Updated Jun 23, 2025Jun 23, 2025

    • pubmed-landscape

      Public
      The landscape of biomedical research
      Jupyter Notebook
      •
      MIT License
      •11•120•0•0•Updated Jun 23, 2025Jun 23, 2025

    • pywarper

      Public
      Conformal mapping-based warping of retinal meshes and skeletons.
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jun 19, 2025Jun 19, 2025

    • pygridfit

      Public
      Python port of gridfit (John D'Errico, 2006)
      Python
      •
      Other
      •0•0•0•0•Updated Jun 6, 2025Jun 6, 2025

    • fundus_image_toolbox

      Public
      A Python package for fundus image processing.
      Jupyter Notebook
      •
      MIT License
      •1•14•0•0•Updated May 23, 2025May 23, 2025

    • sBNN

      Public
      A sparse bottleneck neural network to predict electrophysiological properties of neurons from their gene expression.
      visualizationmachine-learninglassosparseneural-networkselectrophysiologyomicsbottleneck
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•4•0•0•Updated May 20, 2025May 20, 2025

    • hh_sbi

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated May 20, 2025May 20, 2025

    • MorphoPy

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •11•42•2•3•Updated May 20, 2025May 20, 2025

    • t-simcne

      Public
      Unsupervised visualization of image datasets using contrastive learning
      visualizationdimensionality-reduction
      Python
      •14•116•1•1•Updated May 19, 2025May 19, 2025

    • ne_spectrum_scRNAseq

      Public
      Jupyter Notebook
      •
      MIT License
      •1•2•1•0•Updated May 5, 2025May 5, 2025

    • ephyspy

      Public
      A Python package for electrophysiological feature extraction for patch-clamp experiments.
      pythonfeature-extractionelectrophysiologyfeaturesephyspatch-clampallensdk
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•4•7•0•Updated Mar 19, 2025Mar 19, 2025

    • AIMS2025-NeuroSimInf

      Public
      Course repository for Simulation and Inference for Neuroscience
      Jupyter Notebook
      •5•1•1•0•Updated Mar 19, 2025Mar 19, 2025

    • Learning-Disease-State

      Public
      Learning Disease State from Noisy Ordinal Disease Progression Labels
      Jupyter Notebook
      •
      MIT License
      •1•4•0•0•Updated Mar 14, 2025Mar 14, 2025

    • retimgtools

      Public
      Web-based tools for retinal image annotation and evaluation.
      Python
      •0•1•0•0•Updated Mar 7, 2025Mar 7, 2025

    • contrastive-ne

      Public
      Contrastive neighbor embeddings
      Jupyter Notebook
      •
      MIT License
      •9•54•1•0•Updated Mar 6, 2025Mar 6, 2025

    • elephant-in-the-room

      Public
      Companion repository to our Lause, Berens & Kobak (2024) paper "The art of seeing the elephant in the room: 2D embeddings of single-cell data do make sense" (PLOS Computational Biology)
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•7•0•0•Updated Feb 13, 2025Feb 13, 2025

    • eff-ph

      Public
      Persistent homology for high-dimensional data based on spectral methods
      Jupyter Notebook
      •
      MIT License
      •1•3•0•0•Updated Jan 18, 2025Jan 18, 2025

    • patch-seq-rrr

      Public
      Sparse reduced-rank regression
      Jupyter Notebook
      •5•20•1•0•Updated Jan 8, 2025Jan 8, 2025