Repositories list

• retinal-rl

  Public
  Testing theories about retinal coding in reinforcement learning environments

  Python

  •

  GNU Affero General Public License v3.0

  •1•0•22•1•Updated Dec 19, 2024Dec 19, 2024

• t-simcne

  Public
  Unsupervised visualization of image datasets using contrastive learning

  visualizationdimensionality-reduction

  Python

  •12•116•1•1•Updated Dec 17, 2024Dec 17, 2024

• retimgtools

  Public
  Web-based tools for retinal image annotation and evaluation.

  Python

  •0•1•0•0•Updated Dec 13, 2024Dec 13, 2024

• eff-ph

  Public
  Persistent homology for high-dimensional data based on spectral methods

  Jupyter Notebook

  •

  MIT License

  •1•2•0•0•Updated Dec 6, 2024Dec 6, 2024

• hh_sbi

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Dec 5, 2024Dec 5, 2024

• fundus_image_toolbox

  Public
  A Python package for fundus image processing.

  Jupyter Notebook

  •

  MIT License

  •1•6•0•1•Updated Dec 2, 2024Dec 2, 2024

• rna-seq-tsne

  Public
  The art of using t-SNE for single-cell transcriptomics

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •34•122•2•0•Updated Nov 29, 2024Nov 29, 2024

• 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 Nov 4, 2024Nov 4, 2024

• iclr-dataset

  Public
  ICLR dataset

  Jupyter Notebook

  •5•18•1•0•Updated Oct 31, 2024Oct 31, 2024

• interpretable-deep-survival-analysis

  Public
  An interpretable end-to-end CNN for disease progression modeling that predicts late AMD onset (MICCAI 2024)

  deep-learningcnnsurvival-analysis+ 4interpretabilitydisease-predictionimage-basedcoxph

  Python

  •0•1•0•0•Updated Oct 29, 2024Oct 29, 2024

• disentangling-retinal-images

  Public
  This repository contains the code for the paper "Disentangling representations of retinal images with generative models".

  deep-learninggenerative-modelspurious-correlations+ 3causalityretinal-fundus-imagesdisentanglement-learning

  Python

  •0•0•0•0•Updated Sep 19, 2024Sep 19, 2024

• RFEst

  Public
  A Python 3 toolbox for neural receptive field estimation using splines and Gaussian priors.

  matrix-factorizationsplinesjax+ 2receptive-fieldevidence-optimization

  Python

  •

  GNU General Public License v3.0

  •3•24•4•0•Updated Aug 20, 2024Aug 20, 2024

• medical-t-simcne

  Public
  This repository contains the codes to train a t-SimCNE model. This model has been shown to produce good representations on natural and medical images.

  visualisationmedical-imagingrepresentation-learning

  Python

  •1•2•0•0•Updated Aug 12, 2024Aug 12, 2024

• elephant-in-the-room

  Public
  Companion repository to our Lause, Berens & Kobak (2024) preprint "The art of seeing the elephant in the room: 2D embeddings of single-cell data do make sense" (bioRxiv)

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•6•0•0•Updated Jul 31, 2024Jul 31, 2024

• read-normalization

  Public
  Companion repository to our Lause et al. (2023) preprint "Compound models and Pearson residuals for normalization of single-cell RNA-seq data without UMIs" (bioRxiv))

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•3•0•0•Updated Jul 26, 2024Jul 26, 2024

• MorphoPy

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •11•37•1•4•Updated Jul 24, 2024Jul 24, 2024

• dLGN_movie_spline_model

  Public
  dLGN movie spline LNP model

  Jupyter Notebook

  •

  Creative Commons Zero v1.0 Universal

  •0•0•0•0•Updated Jul 22, 2024Jul 22, 2024

• chatgpt-excess-words

  Public
  Delving into ChatGPT usage in academic writing through excess vocabulary

  Jupyter Notebook

  •

  MIT License

  •5•33•1•0•Updated Jul 3, 2024Jul 3, 2024

• ne_spectrum_scRNAseq

  Public
  Jupyter Notebook

  •

  MIT License

  •1•2•0•0•Updated Jun 27, 2024Jun 27, 2024

• DiffusionTempering

  Public
  Jupyter Notebook

  •0•1•0•0•Updated May 29, 2024May 29, 2024

• retinal-rl-models

  Public
  Code for the pytorch models used in the retinal-rl project (and related non-rl usages)

  Python

  •0•0•5•0•Updated May 29, 2024May 29, 2024

• retinal-classification

  Public
  non-rl experiments for the retinal-rl project

  Python

  •

  GNU Affero General Public License v3.0

  •0•0•0•0•Updated May 21, 2024May 21, 2024

• Retinal-Vessel-Segmentation-Benchmark

  Public
  Jupyter Notebook

  •1•3•0•0•Updated May 14, 2024May 14, 2024

• neuroprobnum

  Public
  Probabilistic numerics for common neuroscience models.

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •1•5•0•0•Updated May 7, 2024May 7, 2024

• contrastive-ne

  Public
  Contrastive neighbor embeddings

  Jupyter Notebook

  •

  MIT License

  •7•52•1•0•Updated Apr 24, 2024Apr 24, 2024

• pubmed-landscape

  Public
  The landscape of biomedical research

  Jupyter Notebook

  •11•113•0•0•Updated Apr 18, 2024Apr 18, 2024

• poisson-gpfa

  Public
  Gaussian process factor analysis with Poisson observations

  Python

  •

  BSD 2-Clause "Simplified" License

  •15•0•0•0•Updated Apr 11, 2024Apr 11, 2024

• picasso

  Public
  Picasso: a methods for embedding points in 2D in a way that respects distances while fitting a user-specified shape.

  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •7•0•0•0•Updated Feb 22, 2024Feb 22, 2024

• MIDL24-segmentation_quality_control

  Public
  Experiments for MIDL 2024 Submission: Controlling Segmentation Quality per Image

  Jupyter Notebook

  •2•1•0•0•Updated Feb 11, 2024Feb 11, 2024

• fundus_circle_cropping

  Public
  Code for extracting a circular mask from fundus images and tightly cropping the images around the mask.

  Python

  •

  Other

  •1•3•0•0•Updated Feb 7, 2024Feb 7, 2024