jmschrei
I am a post-doc at Stanford University (previously University of Washington), studying large scale machine learning and computational biology
Stanford University
Pinned Repositories
apricot
apricot implements submodular optimization for the purpose of selecting subsets of massive data sets to train machine learning models quickly. See the documentation page: https://apricot-select.readthedocs.io/en/latest/index.html
avocado
Avocado is a multi-scale deep tensor factorization model that learns a latent representation of the human epigenome and enables imputation of epigenomic experiments that have not yet been performed.
dragonnfruit
A method for analyzing scATAC-seq experiments.
ledidi
Ledidi turns any machine learning model into a biological sequence editor, allowing you to design sequences with desired properties.
notebooks
Various notebooks and tutorials on subjects of interest.
pomegranate
Fast, flexible and easy to use probabilistic modelling in Python.
tangermeme
Biological sequence analysis for the modern age.
tfmodisco-lite
A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.
torchegranate
A temporary repository hosting a pomegranate re-write using PyTorch as the backend.
yahmm
Yet Another Hidden Markov Model repository.
jmschrei's Repositories
jmschrei/pomegranate
Fast, flexible and easy to use probabilistic modelling in Python.
jmschrei/apricot
apricot implements submodular optimization for the purpose of selecting subsets of massive data sets to train machine learning models quickly. See the documentation page: https://apricot-select.readthedocs.io/en/latest/index.html
jmschrei/yahmm
Yet Another Hidden Markov Model repository.
jmschrei/tangermeme
Biological sequence analysis for the modern age.
jmschrei/avocado
Avocado is a multi-scale deep tensor factorization model that learns a latent representation of the human epigenome and enables imputation of epigenomic experiments that have not yet been performed.
jmschrei/torchegranate
A temporary repository hosting a pomegranate re-write using PyTorch as the backend.
jmschrei/ledidi
Ledidi turns any machine learning model into a biological sequence editor, allowing you to design sequences with desired properties.
jmschrei/tfmodisco-lite
A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.
jmschrei/notebooks
Various notebooks and tutorials on subjects of interest.
jmschrei/bpnet-lite
This repository hosts a minimal version of a Python API for BPNet.
jmschrei/rambutan
Prediction of the 3D structure of the genome through statistically significant Hi-C contacts.
jmschrei/dragonnfruit
A method for analyzing scATAC-seq experiments.
jmschrei/constraint_graphs
Repository for the data and associated notebook for the manuscript "Finding the optimal Bayesian network given a constraint graph."
jmschrei/deep-learning-notes
Experiments with Deep Learning
jmschrei/hmmlearn
Hidden Markov Models in Python, with scikit-learn like API
jmschrei/jmschrei.github.io
jmschrei/kiwano
Kiwano implements an approach for prioritizing epigenomic and transcriptomic characterization based on submodular selection and imputed experiments
jmschrei/lifelines
Survival analysis in Python
jmschrei/pystruct
Simple structured learning framework for python
jmschrei/blueberry
Inference of the 3D structure of genomes
jmschrei/COVID-19
Novel Coronavirus (COVID-19) Cases, provided by JHU CSSE
jmschrei/kantalope
because it can't alope
jmschrei/keras
Deep Learning library for Python. Convnets, recurrent neural networks, and more. Runs on Theano or TensorFlow.
jmschrei/mxnet
Lightweight, Portable, Flexible Distributed/Mobile Deep Learning with Dynamic, Mutation-aware Dataflow Dep Scheduler; for Python, R, Julia, Go, Javascript and more
jmschrei/pomegranate_archive
This is an archive of pomegranate 0.14.8 before the PyTorch remake for posterity.
jmschrei/pomegranate_wheel_builder
A temporary repository to play around with building wheels for the notoriously popular and industry revolutionizing package 'pomegranate'
jmschrei/readthedocs.org
source code to readthedocs.org
jmschrei/sail-blog
The SAIL blog
jmschrei/shap
A unified approach to explain the output of any machine learning model.
jmschrei/xgboost
Scalable, Portable and Distributed Gradient Boosting (GBDT, GBRT or GBM) Library, for Python, R, Java, Scala, C++ and more. Runs on single machine, Hadoop, Spark, Flink and DataFlow