PK's repositories
learning_sequence_motifs
"Representation Learning of Genomic Sequence Motifs with Convolutional Neural Networks" by Peter K. Koo and Sean R. Eddy
tensorflow_tutorial_genomics
A collection of TensorFlow tutorials to analyze genomics datasets
theanomics
deep learning toolkit (written on top of Lasagne/Theano) to streamline computational biology analysis
awesome-deepbio
A curated list of awesome deep learning applications in the field of computational biology
cnn_exponential_activations
"Improving Convolutional Network Interpretability with Exponential Activations" by Peter K. Koo and Matt Ploenzke
deep_learning_notes
a collection of my notes on deep learning
mleBIC
maximum likelihood diffusion analysis for single particle trajectories undergoing (non-)normal diffusion with Bayesian model selection (http://arxiv.org/abs/1608.01419)
odie-tools
command line tools to process next generation sequencing data on Harvard's Odyssey cluster
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)
playground
fun projects to improve lifestyle
proteinnet
Standardized data set for machine learning of protein structure
tensorflow
Computation using data flow graphs for scalable machine learning
uncovering_regulatory_codes
"Robust Neural Networks are More Interpretable for Genomics" by Peter K. Koo, Sharon Qian, Gal Kaplun, Verena Volf, and Dimitris Kalimeris