Ipm is a program for calculating direct information based on the inverse Potts Model using the persistative contrastive divergence method.
Version 0.1.0 (2021/10/18)
(Required)
-i STR InputFileName
-o STR OutputFileName
(Optional)
-e DBL The learning rate in parameter updates. [default:0.01]
-l DBL The hyperparameter of l2-regularization. [default: 0]
-c INT The number of parameter updates in Gibbs sampling. [default: 3000]
-s INT The sample size in Gibbs sampling. [default: 200]
"n l q" is described in the first line. The second line specifies the number of the genome, the number of gene families, and the number of states. After the third line, the state of each gene family in each genome is described.
n l q
3 5 2
1 0 0 1 1
1 0 1 0 1
0 1 0 1 0
Tsukasa Fukunaga and Wataru Iwasaki. "Inverse Potts model improves accuracy of phylogenetic profiling." in press, Bioinformatics