Open gwaybio opened 8 years ago
Clearly written article predicting the location of enhancers using chromatin signatures. The method (CSI-ANN) does not have great performance predicting enhancers in HeLa cells or CD4+ T cells but it significantly outperformed the state of the art in 2010 (see table 2). It is possible (maybe even likely) that the gold standard for enhancer locations is diluting performance. Several of the computation steps I have not seen in this context before - but I think are clever manipulations of the data that actually seem to make sense.
Six chromatin marks from ENCODE to predict enhancers in HeLa cells and 39 histone marks to predict enhancers in CD4+ T cells.
Good discussion points about their feature engineering decisions - namely, a non-linear feature extractor may work better (an autoencoder maybe?). I also think lack of gold standards here harm performance reports - something that could be a major problem when applying to supervised learning problems and (although less so) unsupervised tasks
https://dx.doi.org/10.1093/bioinformatics/btq248