Training a neural network to learn other dimensionality reduction removes data size restrictions in bioinformatics and provides a new route to exploring data representations

Author:

Dexter AlexORCID,Thomas Spencer A.,Steven Rory T.,Robinson Kenneth N.,Taylor Adam J.,Elia Efstathios,Nikula Chelsea,Campbell Andrew D.,Panina Yulia,Najumudeen Arafath K.,Murta Teresa,Yan Bin,Grabowski Piotr,Hamm Gregory,Swales John,Gilmore Ian S.,Yuneva Mariia O.,Goodwin Richard J.A.,Barry Simon,Sansom Owen J.,Takats Zoltan,Bunch JosephineORCID

Abstract

AbstractHigh dimensionality omics and hyperspectral imaging datasets present difficult challenges for feature extraction and data mining due to huge numbers of features that cannot be simultaneously examined. The sample numbers and variables of these methods are constantly growing as new technologies are developed, and computational analysis needs to evolve to keep up with growing demand. Current state of the art algorithms can handle some routine datasets but struggle when datasets grow above a certain size. We present a training deep learning via neural networks on non-linear dimensionality reduction, in particular t-distributed stochastic neighbour embedding (t-SNE), to overcome prior limitations of these methods.One Sentence SummaryAnalysis of prohibitively large datasets by combining deep learning via neural networks with non-linear dimensionality reduction.

Publisher

Cold Spring Harbor Laboratory

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