p-koo Goto Github PK

awesome-deepbio

A curated list of awesome deep learning applications in the field of computational biology

chromo

cnn_exponential_activations

"Improving Convolutional Network Interpretability with Exponential Activations" by Peter K. Koo and Matt Ploenzke

convolutionalattention

creme-nn

https://www.biorxiv.org/content/10.1101/2023.07.03.547592v1

creme_paper_reproducibility

deep_learning_notes

a collection of my notes on deep learning

deepomics

deep learning toolkit (written on top of tensorflow) to streamline computational biology analysis

degu

dream-2022-submission-high_schoolers_are_all_you_need

High Schoolers Are All You Need Team

evoaug

Evolution-inspired data augmentations for PyTorch-based models for regulatory genomics

evoaug-tf

Evolution-inspired data augmentations for TensorFlow-based models for regulatory genomics

evoaug-tf_analysis

evoaug_analysis

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)

gopher

Toolset for training quantitative sequence to function models.

gradient_correction

gradientcorrection

hominid

hybrid_genomics

learning_sequence_motifs

"Representation Learning of Genomic Sequence Motifs with Convolutional Neural Networks" by Peter K. Koo and Sean R. Eddy

libre

m6a_analysis

mlebic

maximum likelihood diffusion analysis for single particle trajectories undergoing (non-)normal diffusion with Bayesian model selection (http://arxiv.org/abs/1608.01419)

model_zoo

odie-tools

command line tools to process next generation sequencing data on Harvard's Odyssey cluster

p-koo.github.io

pem

systems-level diffusion analysis for single particle tracks undergoing normal diffusion with no transitions between diffusion states (http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004297)

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)

playground

fun projects to improve lifestyle