Using ebic

Currently ebic can be used only as a command line tool.

In order to build a program simply run:

$ make

Check our 'input.txt' data file to see the required input file format. In order to run an example simply type:

$ ./ebic -i input.txt

The basic usage of ebic is:

$ ./ebic [OPTIONS]

To override any of default options extra arguments should be added:


  • -i,--input TEXT input file (required!)

  • -n,--iterations INT number of iterations [default: 5000]

  • -b,--biclusters INT number of biclusters [100]

  • -x,--overlap FLOAT overlap threshold [0.75]

  • -g,--gpus INT number of gpus [1]

  • -a,--approx FLOAT approximate trends acceptance ratio [0.85]

  • -t,--negative-trends INT negative trends [1]

  • -l,--log is logging enabled [false]


Input files are expected to have a row and a column headers, the values need to be separated by whitespace. The current release of ebic doesn't handle missing values. Check our toy file (input.txt) for the required file format.


ebic writes to its working directory two text files: [input_filename]-res and [input_filename]-blocks.

The first output file contains in its first line the number of detected biclusters and in consecutive lines each bicluster identifiers in the following format.

Bicluster([row0 row1 ... ],[column0, column1, ...])

The second file extracts the actual values of the bicluster from the dataset. Its format is as follows:

BC[bicluster_number] [number_of_rows x number_of columns]
Extracted part of the input dataset with rows and columns labels of the bicluster.