psi-square

psi-square is a program for searching the space of gene vectors. The program starts with a gene vector, i.e., the set of measurements associated with a gene, and finds similar vectors, derives a probabilistic model of these vectors, then repeats search using this model as a query, and continues to update the model and search again, until convergence. When applied to three different pathway-discovery problems, psi-square was generally more sensitive and sometimes more specific than the ad hoc methods developed for solving each of these problems before. See the paper "Similarity searches in genome-wide numerical data sets" by Galina Glazko, Michael Coleman, and Arcady Mushegian for more details. Hua Li (Stowers Institute) also made contributions to this code.

psi-square-1.2
psi_square.py
psi_readme.txt
psi-square.cpp
Makefile
psi_op.py