tbepler

protein-sequence-embedding-iclr2019

Source code for "Learning protein sequence embeddings using information from structure" - ICLR 2019

topaz

Pipeline for particle picking in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Also featuring micrograph and tomogram denoising with DNNs.

prose

Multi-task and masked language model-based protein sequence embedding models.

spatial-VAE

Source code for "Explicitly disentangling image content from translation and rotation with spatial-VAE" - NeurIPS 2019

bayesian-regression

Matlab implementations of various regression methods

intro-DL-cryoEM-2019

maximum-longevity

Modelling of longevity data from the International Database on Longevity (http://www.supercentenarians.org/)

rnn

Recurrent neural network library

spearmint

antibody-2019

atomium

Python macromolecular parsing (with .pdb/.cif/.mmtf parsing and production)

c-patternsearch

C utilities and optimization algorithms

cell-circuit-framework

dream-tfbs-prediction-challenge-conference-round

dsprites-dataset

Dataset to assess the disentanglement properties of unsupervised learning methods

ets-analysis-scripts

harness

haskell-syntax.vim

Haskell syntax file for VIM

julia-regression

keras

Deep Learning library for Python. Convnets, recurrent neural networks, and more. Runs on Theano or TensorFlow.

makefile-base

MESS

MESS (Motif Enrichment in Sequence Sets) is a tool for finding enrichment of sequence motifs in sets of sequences using a GSEA based method.

ml-cpp

Machine learning package implemented in C++. Built on the Eigen linear algebra library.

programming-language

PWM-benchmarking

Benchmarking position weight matrix implementations in C

slurm-gcp

Slurm on Google Cloud Platform

telepath

Mid/low-level C++ template linear algebra library built on BLAS and LAPACK

transpose

Command line utility for transposing the rows and colums of files.

utils-cpp

yoyodyne.vim

A colorful, dark color scheme for Vim.