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README.md

gfunk

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Whole-Genome Functional Classification of Genes using robust PCA

Back in the early aughts, full-genome microarray assays really hit their stride, and there was a boom in literature for analyzing the results. Trees. Clusters. Dimensionality reduction. Or choose two and go again.

Let's revisit those heady times with a more recent numerical technique -- L+S decompostion. SVD decomposition as both dimension reduction and as a way to impose a hierarchic ordering on the genes and experiments in the observation matrix seemed pretty promising before, except that microarray data suffers from spotty noise and dropouts. Back in the day, the cool kids were "imputing" the missing values through local or global regression (or just dropping the loser genes from the matrix altogether), and then applying stock clustering or factorization to the filled observation matrix. But more modern L+S decomposition directly addresses this model of a corrupted observation matrix. Will it do a nice job without all the pre-processing?

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numpy

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