Dynamic Factor Graphs for Gene Regulation Networks This repository contains the Matlab code for our 2010 Genome Biology paper: "Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate" G Krouk, P Mirowski, Y LeCun, DE Shasha, G Coruzzi The structure of the folders is as following: * Arabidopsis/ contains the Matlab scripts that are called by the main, batch, function. For instance, it contains scripts: Script_Arabidopsis76_Leave1.m Script_Arabidopsis76_Leave1_LARS.m which are used for leave-out-last learning of the Arabidopsis GRN using mRNA measurements from time points 0, 3, 6, 9, 12 and 15min and uses the two last time points (15min and 20min) to evaluate the out-of-sample trend. * DFG4GRN/ contains all the code for our SSM, minus the LARS library, which needs to be installed from the bolasso.zip file. * ClusterFrontend/ contains functions used for running the cluster code. Please see Matlab file Tutorial.m for an example of how to run the code.
timedreamer/DFG4GRN
Code for our 2010 Genome Biology paper on "Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate", using Dynamic Factor Graphs for learning gene regulation networks.
MATLAB