GitPlanet

Cheap and reliable Node.js hosting starts at $3/month, and $1/month static HTML hosting

Created with love in Canada, visit hostnodejs.com today

Feel like to post an Ad? Learn Details
All Projects → BIMSBbioinfo → maui

BIMSBbioinfo / maui

Licence: GPL-3.0 license
Multi-omics Autoencoder Integration: Deep learning-based heterogenous data analysis toolkit

Programming Languages

Jupyter Notebook
11667 projects
python
139335 projects - #7 most used programming language

Labels

bioinformaticsdeep-learningcancer-genomicsautoencodermulti-omicslatent-factor-model

Projects that are alternatives of or similar to maui

Tybalt
Training and evaluating a variational autoencoder for pan-cancer gene expression data
Stars: ✭ 126 (+200%)
Mutual labels:  cancer-genomics, autoencoder
imagenet-autoencoder
Autoencoder trained on ImageNet Using Torch 7
Stars: ✭ 18 (-57.14%)
Mutual labels:  autoencoder
SigProfilerSimulator
SigProfilerSimulator allows realistic simulations of mutational patterns and mutational signatures in cancer genomes. The tool can be used to simulate signatures of single point mutations, double point mutations, and insertion/deletions. Further, the tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
Stars: ✭ 18 (-57.14%)
Mutual labels:  cancer-genomics
Continuous-Image-Autoencoder
Deep learning image autoencoder that not depends on image resolution
Stars: ✭ 20 (-52.38%)
Mutual labels:  autoencoder
Face-Landmarking
Real time face landmarking using decision trees and NN autoencoders
Stars: ✭ 73 (+73.81%)
Mutual labels:  autoencoder
Video-Compression-Net
A new approach to video compression by refining the shortcomings of conventional approach and substituting each traditional component with their neural network counterpart. Our proposed work consists of motion estimation, compression and compensation and residue compression, learned end-to-end to minimize the rate-distortion trade off. The whole…
Stars: ✭ 20 (-52.38%)
Mutual labels:  autoencoder
dltf
Hands-on in-person workshop for Deep Learning with TensorFlow
Stars: ✭ 14 (-66.67%)
Mutual labels:  autoencoder
IMPACT-Pipeline
Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay
Stars: ✭ 52 (+23.81%)
Mutual labels:  cancer-genomics
2D-and-3D-Deep-Autoencoder
Convolutional AutoEncoder application on MRI images
Stars: ✭ 57 (+35.71%)
Mutual labels:  autoencoder
topological-autoencoders
Code for the paper "Topological Autoencoders" by Michael Moor, Max Horn, Bastian Rieck, and Karsten Borgwardt.
Stars: ✭ 82 (+95.24%)
Mutual labels:  autoencoder
Dual-CNN-Models-for-Unsupervised-Monocular-Depth-Estimation
Dual CNN Models for Unsupervised Monocular Depth Estimation
Stars: ✭ 36 (-14.29%)
Mutual labels:  autoencoder
Unsupervised Deep Learning
Unsupervised (Self-Supervised) Clustering of Seismic Signals Using Deep Convolutional Autoencoders
Stars: ✭ 36 (-14.29%)
Mutual labels:  autoencoder
SESF-Fuse
SESF-Fuse: An Unsupervised Deep Model for Multi-Focus Image Fusion
Stars: ✭ 47 (+11.9%)
Mutual labels:  autoencoder
orchid
A novel management, annotation, and machine learning framework for analyzing cancer mutations
Stars: ✭ 29 (-30.95%)
Mutual labels:  cancer-genomics
handson-ml
도서 "핸즈온 머신러닝"의 예제와 연습문제를 담은 주피터 노트북입니다.
Stars: ✭ 285 (+578.57%)
Mutual labels:  autoencoder
civic-server
Backend Server for CIViC Project
Stars: ✭ 39 (-7.14%)
Mutual labels:  cancer-genomics
GATE
The implementation of "Gated Attentive-Autoencoder for Content-Aware Recommendation"
Stars: ✭ 65 (+54.76%)
Mutual labels:  autoencoder
peax
Peax is a tool for interactive visual pattern search and exploration in epigenomic data based on unsupervised representation learning with autoencoders
Stars: ✭ 63 (+50%)
Mutual labels:  autoencoder
mae-scalable-vision-learners
A TensorFlow 2.x implementation of Masked Autoencoders Are Scalable Vision Learners
Stars: ✭ 54 (+28.57%)
Mutual labels:  autoencoder
seq3
Source code for the NAACL 2019 paper "SEQ^3: Differentiable Sequence-to-Sequence-to-Sequence Autoencoder for Unsupervised Abstractive Sentence Compression"
Stars: ✭ 121 (+188.1%)
Mutual labels:  autoencoder
View All Similar Projects ➔
maui

maui

Downloads codecov Codacy Badge PyPI version Documentation Status Code style: black

Multi-omics Autoencoder Integration (maui) is a python package for multi-omics data analysis. It is based on a bayesian latent factor model, with inference done using artificial neural networks. For details, check out our LSA paper: https://www.life-science-alliance.org/content/2/6/e201900517

Installation

maui works with Python 3.6 and TensorFlow 1.1 (does not yet support the yet unreleased TensorFlow 2.0). The easiest way to install is from pypi:

pip install -U maui-tools

This will install all necessary dependencies including keras an tensorflow. The default tensorflow (cpu) will be installed. If tensorflow GPU is needed, please install it prior to installation of maui.

The development version may be installed by cloning this repo and running python setup.py install, or, using pip directly from github:

pip install -e git+https://github.com/BIMSBbioinfo/maui.git#egg=maui

Optional dependencies

Survival analysis functionality supplied by lifelines 1. It may be installed directly from pip using pip install lifelines.

Usage

See the vignette, and check out the documentation.

Citation

Evaluation of colorectal cancer subtypes and cell lines using deep learning. Jonathan Ronen, Sikander Hayat, Altuna Akalin. Life Science Alliance Dec 2019, 2 (6) e201900517; DOI: 10.26508/lsa.201900517

Contributing

Open an issue, send us a pull request, or shoot us an e-mail.

License

maui is released under the GNU General Public License v3.0 or later.

@jonathanronen, BIMSBbioinfo, 2018

Note that the project description data, including the texts, logos, images, and/or trademarks, for each open source project belongs to its rightful owner. If you wish to add or remove any projects, please contact us at [email protected].