Code

Network Motif finding

This package contains a gzipped tar file, with C code and perl scripts that run it. Code developed by Adam Sadovsky and was tested on linux.

Download: the package (gzipped tar file) (14Kb). Browse the directory.

To install: tar -xvzf findmotifs.tgz; make clean all;

To run: findmotifs.pl --help

Reference: If you use this code, please refer to
Activity motifs reveal principles of timing in transcription control of the yeast metabolic network Nature Biotechnology, 26, 1251-1259 (26 Oct 2008) Gal Chechik, Eugene Oh, Oliver Rando, Jonathan Weissman, Aviv Regev, Daphne Koller
Co-Occurence Data Embedding (CODE)

This package contains a gzipped tar file, with multiple matlab files and one linux binary. Send me an email if you are intersted to run the code on another platform.

Download: the package (gzipped tar file) (14Kb).
Browse the main function.
or get C code for mexing on a different architecture.

To install: tar -xvzf code.tgz.

How to run: [phi_x,psi_y] = code(pxys,embed_dim,options)
use 'help code' for further instructions.

Reference:
Amir globerson, Gal Chechik, Fernando Pereira and Naftali Tishby
Euclidean Embedding of Co-occurrence Data.
Advances in Neural Information Processing Systems-18, (NIPS 2004).


Information Bottleneck with Side Information (IBSI)

An implementation of the sequential IB algorithm for IB with side information. The function also supports regular IB, and some specific form of multivairate-IB (see help for details).

Download: the matlab function(12Kb).

How to run: [Ptys,Ptx,trace]= ibsi_sequ(Pxys,parms)
use 'help ibsi_sequ' for further instructions.

Reference:
G. Chechik and N. Tishby
Extracting relevant structures with side information.
Advances in Neural Information Processing Systems-16, (NIPS 2002).


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