virgo_solver: Construct a virgo solver

In mwcsr: Solvers for Maximum Weight Connected Subgraph Problem and Its Variants

Construct a virgo solver

Description

This solver uses reformulation of MWCS problem in terms of mixed integer programming. The later problem can be efficiently solved with commercial optimization software. Exact version of solver uses CPLEX and requires it to be installed. CPLEX 12.7.1 or higher is required.

Usage

virgo_solver(
  cplex_dir,
  threads = parallel::detectCores(),
  timelimit = NULL,
  penalty = 0,
  memory = "2G",
  log = 0,
  cplex_bin = NULL,
  cplex_jar = NULL,
  mst = FALSE,
  dryrun = FALSE,
  jvmargs = NULL
)

Arguments

cplex_dir	a path to dir containing cplex_bin and cplex_jar, setting this to NULL sets ⁠mst`` param to ⁠TRUE'
threads	number of threads for simultaneous computation
timelimit	maximum number of seconds to solve the problem
penalty	additional edge penalty for graph edges
memory	maximum amount of memory(-Xmx flag)
log	verbosity level
cplex_bin	a path to cplex binary dir
cplex_jar	a path to cplex jar file
mst	whether to use approximate MST solver, no CPLEX files required with this parameter is set to TRUE
dryrun	if set to TRUE only prints the solver command, without actually running it
jvmargs	character vector with additional arguments for Java Virtual Machine

Details

The solver currently does not support repeated negative signals, i.e. every negative signal should be present only once among all edges and vertices.

You can access solver directly using run_main function. See example.

Value

An object of class mwcs_solver.

References

Loboda A., Artyomov M., and Sergushichev A. (2016) "Solving generalized maximum-weight connected subgraph problem for network enrichment analysis" \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1007/978-3-319-43681-4_17")}

Examples

data("sgmwcs_small_instance")
approx_vs <- virgo_solver(mst=TRUE, threads = 1)
approx_vs$run_main("-h")
sol <- solve_mwcsp(approx_vs, sgmwcs_small_instance)
## Not run: 
vs <- virgo_solver(cplex_dir='/path/to/cplex')
sol <- solve_mwcsp(approx_vs, sgmwcs_example)

## End(Not run)

mwcsr documentation built on May 31, 2023, 8:41 p.m.