p-koo

Pinned Repositories

creme-nn
https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2
Language:Python22 1 22
deepomics
deep learning toolkit (written on top of tensorflow) to streamline computational biology analysis
Language:Python23 3 07
evoaug
Evolution-inspired data augmentations for PyTorch-based models for regulatory genomics
Language:Python19 2 04
exponential_activations
"Improving representations of genomic sequence motifs in convolutional networks with exponential activations" by Koo and Ploenzke (https://doi.org/10.1101/2020.06.14.150706)
Language:Jupyter Notebook4 2 06
GOPHER
Toolset for training quantitative sequence to function models.
Language:Jupyter Notebook2 0 00
learning_sequence_motifs
"Representation Learning of Genomic Sequence Motifs with Convolutional Neural Networks" by Peter K. Koo and Sean R. Eddy
Language:Python31 4 313
residualbind
"Global Importance Analysis: A Method to Quantify Importance of Genomic Features in Deep Neural Networks" by Koo et al.
Language:Jupyter Notebook11 2 23
squid-nn
surrogate quantitative interpretability for deepnets
Language:Python1 0 00
tensorflow_tutorial_genomics
A collection of TensorFlow tutorials to analyze genomics datasets
Language:Jupyter Notebook8 3 07
tfomics
Language:Python4 3 26

p-koo's Repositories

p-koo/deepomics
deep learning toolkit (written on top of tensorflow) to streamline computational biology analysis
Language:Python23 3 07
p-koo/creme-nn
https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2
Language:Python22 1 22
p-koo/evoaug
Evolution-inspired data augmentations for PyTorch-based models for regulatory genomics
Language:Python19 2 04
p-koo/residualbind
"Global Importance Analysis: A Method to Quantify Importance of Genomic Features in Deep Neural Networks" by Koo et al.
Language:Jupyter Notebook11 2 23
p-koo/tfomics
Language:Python4 3 26
p-koo/GradientCorrection
Language:Jupyter Notebook3 0 01
p-koo/evoaug-tf
Evolution-inspired data augmentations for TensorFlow-based models for regulatory genomics
Language:Python2 0 0
p-koo/evoaug_analysis
Language:Jupyter Notebook2 1 11
p-koo/GOPHER
Toolset for training quantitative sequence to function models.
Language:Jupyter Notebook2 0 00
p-koo/evoaug-tf_analysis
Language:Jupyter Notebook1 0 0
p-koo/gradient_correction
Language:Python1 2 0
p-koo/squid-nn
surrogate quantitative interpretability for deepnets
Language:Python1 0 00
p-koo/wrangler
Language:Python1 1 0
p-koo/libre
Language:Python0 4 126
p-koo/chromo
Language:Jupyter Notebook0 0
p-koo/ConvolutionalAttention
Language:HTML1 0
p-koo/CREME_paper_reproducibility
Language:Jupyter Notebook
p-koo/degu
Language:Python1 0
p-koo/DREAM-2022-Submission-High_Schoolers_Are_All_You_Need
High Schoolers Are All You Need Team
Language:Python0 01
p-koo/HIPPO
HIPPO 🦛 is an explainable AI toolkit for weakly-supervised models in computational pathology. It enables hypothesis testing on tissue and searching for high-effect and low-effect tissue regions.
Language:Python0 0
p-koo/hominid
Language:Python1 0
p-koo/hybrid_genomics
Language:Jupyter Notebook2 01
p-koo/model_zoo
Language:Python2 0
p-koo/p-koo.github.io
Language:CSS1 0
p-koo/pEMv2
sytems-level diffusion analysis for single particle tracks undergoing normal/non-normal diffusion that can transition between diffusion states (https://journals.aps.org/pre/abstract/10.1103/PhysRevE.94.052412)
Language:MATLAB3 22
p-koo/robustness
Language:Python2 0
p-koo/squid-manuscript
squid repository for manuscript analysis
Language:Python0 0
p-koo/squid-nn-old
surrogate quantitative interpretability for deepnets
Language:Python0 0
p-koo/test_gpu
Language:Python1 0
p-koo/tfmodisco-lite
A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.
Language:Python0 0