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musitedeep

MusiteDeep provides a deep-learning method for general and kinase-specific phosphorylation site prediction. It is implemented by deep learning library Keras and Theano backend (the Keras2.0 and Tensorflow backend implementation were also provided under folder MusiteDeep_Keras2.0). At present, MusiteDeep only provides prediction of human phosphorylation sites; however, it also provides customized model training that enables users to train other PTM prediction models by using their own training data sets based on either CPU or GPU.

musitedeep_web

This repository contains the stand-alone tool for MusiteDeep server

ngl

WebGL protein viewer

parametric-t-sne

Running parametric t-SNE by Laurens Van Der Maaten with Octave and oct2py.

prottrans

ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.

pubmed-batch-download

Batch download articles based on PMID (Pubmed ID)

python_mcl

markov cluster algorithm - python

recurrentshop

Framework for building complex recurrent neural networks with Keras

redd

s-plm

S-PLM: Structure-aware Protein Language Model via Contrastive Learning between Sequence and Structure

seq2seq

Sequence to Sequence Learning with Keras

seq2seq-1

Minimal Seq2Seq model with Attention for Neural Machine Translation in PyTorch

shannon

A python package for computing the mutual information and entropy for continuous and discrete data.

spacy

💫 Industrial-strength Natural Language Processing (NLP) with Python and Cython

spearmint

Spearmint is a package to perform Bayesian optimization according to the algorithms outlined in the paper: Practical Bayesian Optimization of Machine Learning Algorithms. Jasper Snoek, Hugo Larochelle and Ryan P. Adams. Advances in Neural Information Processing Systems, 2012

spearmint-1

Spearmint Bayesian optimization codebase

speech_recognition_with_tensorflow

Implementation of a seq2seq model for Speech Recognition using the latest version of TensorFlow. Architecture similar to Listen, Attend and Spell.

taiyaki

Training models for basecalling Oxford Nanopore reads

tensor2tensor

A library for generalized sequence to sequence models

tensorflow-machine-learning-cookbook

Code repository for TensorFlow Machine Learning Cookbook by Packt

tensorflow-mil

TF Implementation of Multiple Instance Learning FCN.

test

theano

Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. It can use GPUs and perform efficient symbolic differentiation.

transformer

A TensorFlow Implementation of the Transformer: Attention Is All You Need

unirep

UniRep model, usage, and examples.

vicreg

VICReg official code base

word2vec-keras-in-gensim

word2vec uisng keras inside gensim

word_cloud

A little word cloud generator in Python

zhusuan

A Library for Generative Models