The program takes as input a file containing a list of drug-drug interactions with the following format:

d1 d2 0

d1 d3 1

d1 d4 1

...

This corresponds to a situation in which drug 1 (d1) and drug 2 (d2) have an interaction of type 0, d1 and d3 have an interaction of type 1, and so on. Interaction types must be integer between 0 and K-1, where K is the number of interaction types.

The program outputs a file predictions.dat with the following format:

d2 d3 0.50 0.20 0.30

d2 d4 0.15 0.55 0.30

...

This corresponds to a situation with three types of interactions (K=3), and indicates that: drugs 2 and 3 have an interaction of type 0 with probability 0.50, of type 1 with probability 0.20, and of type 2 with probability 0.30; drugs 2 and 4 have an interaction of type 0 with probability 0.15, of type 1 with probability 0.55, and of type 2 with probability 0.30; and so on.

Command line parameters

To run the program, type the following in the command line:

drugraph K net_file niterations seed

where:

• K is the number of types of interactions (for example, if interactions can be antagonistic, additive or synergistic, then K=3).

• net_file is the file containing the known interactions, and has the format described above.

• niterations is the number of sampling iterations carried out by the Metropolis algorithm.

• seed is the seed for the random number generator, and can be any positive integer.

Running output

After starting the program, the algorithm proceeds by: (i) determining a convenient thinning step; (ii) thermalizing the sampler; (iii) sampling. Please, be aware that each of these processes can take a long time (even days) in networks larger than a few hundreds of drugs.