A cut-and-solve based feature selection algorithm for continous data.
Configure the Makefile with the locaion of the IBL ILOG CPLEX and open mpi libraries and binary
Compile with the Makefile by navigating to the root directory and entering: make
Update configuration file
Run the program. For an example enter: mpirun -np 4 ./csfs <cfg_file>
DATA_FILE - Tab seperated file where the first NUM_CASES columns are cases and the next NUM_CTRLS columns are controls. The row indicate features.
RISK - Boolean that indicates if risk patterns (true) or protective patterns (false) should be found.
NUM_CASES - The number of cases in DATA_FILE.
NUM_CTRLS - The number of controls in DATA_FILE.
NUM_EXPRS - The number of features in DATA_FILE.
NUM_HEAD_ROWS - The number of header rows in DATA_FILE.
NUM_HEAD_COLS - The number of header columns in DATA_FILE.
PATTERN_SIZE - The number of marker states in the pattern(s) to be found.
USE_LOWER_CUTOFF - A boolean indicates if the STARTING_LOWER_BOUND is used. This lower bound can be updated during the search. USE_LOWER_CUTOFF and USE_SOLUTION_POOL_THRESHOLD cannot both be set to true at the same time.
USE_SOLUTION_POOL_THRESHOLD - A boolean indicating of the SOLUTION_POOL_THRESHOLD is to be used. When using the SOLUTION_POOL_THRESHOLD, all patterns with a beter objective value will be retained. USE_LOWER_CUTOFF and USE_SOLUTION_POOL_THRESHOLD cannot both be set to true at the same time.
SOLUTION_POOL_THRESHOLD - Threshold used to retaine solutions in the pool. Used if USE_SOLUTION_POOL_THRESHOLD is true.
STARTING_LOWER_BOUND - Starting lower bound when 0 USE_LOWER_CUTOFF is true.
STARTING_UPPER_BOUND - Starting upper bound when 0 USE_LOWER_CUTOFF is true.
QUIET - Boolean that limits the output to only the most important items when true. QUIET and VERBOSE cannot both be set to true at the same time.
VERBOSE - Boolean that controls if all outputs are dispayed. QUIET and VERBOSE cannot both be set to true at the same time.
PRINT_CPLEX_OUTPUT - Boolean controlling if the CPLEX output is displayed.
TOL - Tolerance value for used for rounding decimals to integers in CPLEX.
ID_PREFIX - Prefix of ID column in DATA_FILE.
MISSING_SYMBOL - String used to indicate missing data in DATA_FILE.
CPLEX_SEED - Seed provide to CPLEX.
USE_SPARSE_CONTRAINTS - Boolean that indicates if additional contraints for the sparse problem are used.
NUM_BINS - The number of bins, from HIGH, NORM, LOW, NOT_HIGH, and NOT_LOW to be used.
USE_HIGH - Set to true if HIGH variable will be used in pattern.
USE_NORM - Set to true if NORM variable will be used in pattern.
USE_LOW - Set to true if LOW variable will be used in pattern.
USE_NOT_HIGH - Set to true if NOT_HIGH variable will be used in pattern.
USE_NOT_LOW - Set to true if NOT_LOW variable will be used in pattern.
HIGH_VALUE - Value in DATA_FILE that indicates high expression.
NORM_VALUE - Value in DATA_FILE that indicates normal expression.
LOW_VALUE - Value in DATA_FILE that indicates low expression.
NOT_LOW_VALUE - Value in DATA_FILE that indicates not low expression.
NOT_HIGH_VALUE - Value in DATA_FILE that indicates not high expression.
SET_NA_TRUE - Boolean used to indicate if missing data is treated as both high and low.
*.log - File containing the collection of patterns
Requires Open MPI and IBM ILOG CPLEX
DATA_FILE should be tab seperate, the columns represent individuals and the rows represent features