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Algorithm for applying a generative approach to network inference (RCweb) for the case when the network is sparse and the latent (not observed) variables affect the observed ones. From all possible factor analysis (FA) decompositions explaining the variance in the data, RCweb selects the FA decomposition that is consistent with a sparse underlyi…

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Inference of Sparse Networks with Unobserved Variables

This repository contains code the RCweb algorythm that allows inference of sparse networks with unobserved variables given a set of noisy measurements of the observed variables. The RCweb algorythm and its application to gene regulatory networks is described in Slavov, Proceedings of Machine Learning Research (2010). A brief overview of the algorythm was also presented at the Biological systems: In search of direct causal mechanisms.

Comparing the performance of different methods for network inference

Functions and scripts reproducing the analysis reported by Slavov, 2010

Man functions

  • SpAce.m
  • SpAce_Path.m

Supporting functions called by the main functions:

  • pm.m -- Computes the largest eigenvector and eigenvalue of a matrix from initial guess
  • inv_rank1_add.m -- Rank one (addition) update of an inverse
  • inv_rank1_red.m -- Rank one (subtraction) update of an inverse
  • inv_rank1.m -- Rank one update of an inverse addition or subtraction depending on the third argument
  • inv_up.m -- rank k update on an inverse

Supporting functions called by the scripts:

data_Gen.m -- Simulates data from a model of a sparse network c_corr.m -- Computes the the correlations between the most correlated columns of two matrices

Video presentaion of the RCweb algorythm applied to transcriptional networks

Inference of gene regulatroy networks

Correspondence

Questions can be directed to the Slavov Laboratory

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Algorithm for applying a generative approach to network inference (RCweb) for the case when the network is sparse and the latent (not observed) variables affect the observed ones. From all possible factor analysis (FA) decompositions explaining the variance in the data, RCweb selects the FA decomposition that is consistent with a sparse underlyi…

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