Berens Lab @ University of Tübingen

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71 repositories

retinal-rl
Public
Testing theories about retinal coding in reinforcement learning environments
Python
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GNU Affero General Public License v3.0
•1•0•0•0•Updated Oct 2, 2024Oct 2, 2024
dependence-measures-medical-imaging
Public
This repository contains the code for the paper "Benchmarking Dependence Measures to Prevent Shortcut Learning in Medical Imaging".
Python
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MIT License
•0•0•0•0•Updated Sep 23, 2024Sep 23, 2024
disentangling-retinal-images
Public
This repository contains the code for the paper "Disentangling representations of retinal images with generative models".
deep-learning generative-model spurious-correlations retinal-fundus-images casuality disentanglement-learning
Python
•0•0•0•0•Updated Sep 19, 2024Sep 19, 2024
retimgtools
Public
Web-based tools for retinal image annotation and evaluation.
Python
•0•1•0•0•Updated Aug 27, 2024Aug 27, 2024
RFEst
Public
A Python 3 toolbox for neural receptive field estimation using splines and Gaussian priors.
matrix-factorization splines jax receptive-field evidence-optimization
Python
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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.
visualisation medical-imaging representation-learning
Python
•1•2•0•0•Updated Aug 12, 2024Aug 12, 2024
hh_sbi
Public
Jupyter Notebook
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GNU General Public License v3.0
•0•1•0•0•Updated Aug 5, 2024Aug 5, 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
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GNU General Public License v3.0
•0•5•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
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GNU General Public License v3.0
•0•3•0•0•Updated Jul 26, 2024Jul 26, 2024
MorphoPy
Public
Jupyter Notebook
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GNU General Public License v3.0
•11•34•1•4•Updated Jul 24, 2024Jul 24, 2024
dLGN_movie_spline_model
Public
dLGN movie spline LNP model
Jupyter Notebook
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Creative Commons Zero v1.0 Universal
•0•0•0•0•Updated Jul 22, 2024Jul 22, 2024
fundus_image_toolbox
Public
A Python package for fundus image processing.
Jupyter Notebook
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MIT License
•1•3•0•0•Updated Jul 17, 2024Jul 17, 2024
interpretable-deep-survival-analysis
Public
An interpretable end-to-end CNN for disease progression modeling that predicts late AMD onset (MICCAI 2024)
deep-learning cnn survival-analysis interpretability disease-prediction image-based coxph
Python
•0•0•0•0•Updated Jul 17, 2024Jul 17, 2024
chatgpt-excess-words
Public
Delving into ChatGPT usage in academic writing through excess vocabulary
Jupyter Notebook
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MIT License
•5•28•0•0•Updated Jul 3, 2024Jul 3, 2024
ne_spectrum_scRNAseq
Public
Jupyter Notebook
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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
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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•0•0•0•Updated May 14, 2024May 14, 2024
eff-ph
Public
Persistent homology for high-dimensional data based on spectral methods
Jupyter Notebook
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MIT License
•1•2•0•0•Updated May 8, 2024May 8, 2024
neuroprobnum
Public
Probabilistic numerics for common neuroscience models.
Jupyter Notebook
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GNU General Public License v3.0
•1•5•0•0•Updated May 7, 2024May 7, 2024
iclr-dataset
Public
ICLR dataset
Jupyter Notebook
•0•8•1•0•Updated May 2, 2024May 2, 2024
contrastive-ne
Public
Contrastive neighbor embeddings
Jupyter Notebook
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MIT License
•6•51•1•0•Updated Apr 24, 2024Apr 24, 2024
pubmed-landscape
Public
The landscape of biomedical research
Jupyter Notebook
•10•113•0•0•Updated Apr 18, 2024Apr 18, 2024
poisson-gpfa
Public
Gaussian process factor analysis with Poisson observations
Python
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BSD 2-Clause "Simplified" License
•15•0•0•0•Updated Apr 11, 2024Apr 11, 2024
t-simcne
Public
Unsupervised visualization of image datasets using contrastive learning
visualization dimensionality-reduction
Python
•13•114•2•1•Updated Mar 27, 2024Mar 27, 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
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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
•0•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
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Other
•1•3•0•0•Updated Feb 7, 2024Feb 7, 2024
retinal_image_counterfactuals
Public
Realistic retinal fundus and OCT counterfactuals using diffusion models and classifiers.
Python
•0•3•1•0•Updated Dec 5, 2023Dec 5, 2023