Searchfvs is a simple solver for the directed feedback vertex set (FVS) problem.

The program is written in C++. You must prepare a C++ compiler implemented C++14 features. Type

$ make searchfvs

Then the binary searchfvs will be generated. This binary does not depend on any external libraries.

If COIN-OR Cbc solver is installed on your computer, type

$ make searchfvs_withcbc

or simply

$ make

Then the binary searchfvs_withcbc will be generated. This version is a bit faster than the "without Cbc" version thanks to finding a solution of a set cover problem as ILP by Cbc solver.

$ ./searchfvs [options] <network data>
$ ./searchfvs_withcbc [options] <network data>

<network data> should be a text file containing the list of edges of a network (see the next section). Then the program finds all the minimal FVSs of the network. The program outputs first the number of nodes of minimal FVSs, and the names of the nodes in each minimal FVS with running number.

For example, the file ciona.txt is a gene regulatory network data of Ciona embryos.

$ ./searchfvs ciona.txt

will give the list of minimal FVSs of the network.

One can specify several options. --help outputs the list of options.

For example, the line

ABC DE

means that there is an edge from a node "ABC" to a node "DE" in the network. Since space characters are used as delimiters, the names of nodes should not include space characters. If there is a # character at the begin of a line, the program ignores the line.

• Kenji Kobayashi, Kazuki Maeda, Miki Tokuoka, Atsushi Mochizuki and Yutaka Satou, Controlling cell fate specification system by key genes determined from network structure, iScience 4 (2018) 281–293.
• Kenji Kobayashi, Kazuki Maeda, Miki Tokuoka, Atsushi Mochizuki and Yutaka Satou, Using linkage logic theory to control dynamics of a gene regulatory network of a chordate embryo, Scientific Reports 11 (2021) 4001.

Kazuki Maeda "kmaeda at kmaeda.net"