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Useful Toolboxes and Databases

This page contains a collection of toolboxes and datasets that are public available. Edited by Tianpei Xie.

Machine Learning and Data Science

Network analysis

Bioinformatic Databases

  • Gene Expression Search Engine This database stored and manually annotated experimental design and keywords of thousands of gene expression experiments collected from GEO, Array Express, Japanese Toxicogenomic Project, Connectivity Map, DrugMatrix etc. Researchers can find previously conducted experiments involving genes of interest by search for genes or keywords.

Multi-view Face Recognition

Gaussian Process

Deep Learning

  • Caffe (Deep Learning toolbox). Caffe is a well-known and widely used machine-vision library that ported Matlab’s implementation of fast convolutional nets to C and C++. Caffe is not intended for other deep-learning applications such as text, sound or time series data. Like other frameworks mentioned here, Caffe has chosen Python for its API.
  • Theano is the grand-daddy of deep-learning frameworks, which is written in Python. It is powerful tools widely used for research purposes and serving the large Python community. It is well suited to data exploration and explicitly state that they are intended for research.
  • Keras A python framework built upon the Theano.


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