Berens Lab @ University of Tübingen

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73 repositories

Learning-Disease-State
Public
Learning Disease State from Noisy Ordinal Disease Progression Labels
Jupyter Notebook
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MIT License
•1•1•0•0•Updated Mar 12, 2025Mar 12, 2025
AIMS2025-NeuroSimInf
Public
Course repository for Simulation and Inference for Neuroscience
Jupyter Notebook
•2•0•1•0•Updated Mar 10, 2025Mar 10, 2025
hh_sbi
Public
Jupyter Notebook
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GNU General Public License v3.0
•0•1•0•0•Updated Mar 7, 2025Mar 7, 2025
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 causality retinal-fundus-images disentanglement-learning
Python
•0•0•0•0•Updated Mar 7, 2025Mar 7, 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
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MIT License
•6•52•1•0•Updated Mar 6, 2025Mar 6, 2025
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•24•3•Updated Feb 26, 2025Feb 26, 2025
sBNN
Public
A sparse bottleneck neural network to predict electrophysiological properties of neurons from their gene expression.
visualization machine-learning lasso sparse neural-networks electrophysiology omics bottleneck
Jupyter Notebook
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GNU General Public License v3.0
•0•4•0•0•Updated Feb 25, 2025Feb 25, 2025
llm-excess-vocab
Public
Delving into LLM-assisted writing in biomedical publications through excess vocabulary
Jupyter Notebook
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MIT License
•5•34•1•0•Updated Feb 19, 2025Feb 19, 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
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GNU General Public License v3.0
•0•6•0•0•Updated Feb 13, 2025Feb 13, 2025
fundus_image_toolbox
Public
A Python package for fundus image processing.
Jupyter Notebook
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MIT License
•1•7•0•0•Updated Feb 11, 2025Feb 11, 2025
iclr-dataset
Public
ICLR dataset
Jupyter Notebook
•5•23•1•0•Updated Feb 7, 2025Feb 7, 2025
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 Jan 18, 2025Jan 18, 2025
t-simcne
Public
Unsupervised visualization of image datasets using contrastive learning
visualization dimensionality-reduction
Python
•12•116•1•1•Updated Jan 10, 2025Jan 10, 2025
patch-seq-rrr
Public
Sparse reduced-rank regression
Jupyter Notebook
•5•20•1•0•Updated Jan 8, 2025Jan 8, 2025
rna-seq-tsne
Public
The art of using t-SNE for single-cell transcriptomics
Jupyter Notebook
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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-representations shortcut-learning domain-shift
Python
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MIT License
•0•1•0•0•Updated Nov 4, 2024Nov 4, 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•3•0•0•Updated Oct 29, 2024Oct 29, 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•1•0•0•Updated Aug 12, 2024Aug 12, 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•37•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
ne_spectrum_scRNAseq
Public
Jupyter Notebook
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MIT License
•1•2•1•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
•3•3•0•0•Updated May 14, 2024May 14, 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
pubmed-landscape
Public
The landscape of biomedical research
Jupyter Notebook
•11•114•0•0•Updated Apr 18, 2024Apr 18, 2024