////////////////////////////////////////////////////////////////////// // Config.hpp // // Global configuration file. ////////////////////////////////////////////////////////////////////// #ifndef CONFIG_HPP #define CONFIG_HPP #include #define COMMENT 0 ////////////////////////////////////////////////////////////////////// // Miscellaneous options ////////////////////////////////////////////////////////////////////// // upper bound on the number of logical parameters in the model; the // program will fail to operate properly if this value is set too low const int SHARED_PARAMETER_SIZE = 5000; ////////////////////////////////////////////////////////////////////// // Options related to general inference ////////////////////////////////////////////////////////////////////// // showing timings for inference routines #define SHOW_TIMINGS 0 // use straightforward calculation for FM2 matrix #define SIMPLE_FM2 0 // use candidate list optimization for Viterbi parsing #define CANDIDATE_LIST 1 // use unrolled computation for single branch loops #define FAST_SINGLE_BRANCH_LOOPS 1 // use caching algorithm for fast helix length scores #define FAST_HELIX_LENGTHS 1 ////////////////////////////////////////////////////////////////////// // Options related to training mode configuration ////////////////////////////////////////////////////////////////////// #define STOCHASTIC_GRADIENT 0 ////////////////////////////////////////////////////////////////////// // (A) Options related to max-margin training ////////////////////////////////////////////////////////////////////// // the maximum loss DELTA(y,y') allocated to each training example; if // this symbol is undefined, then the DELTA(y,y') loss function is not // included // -- for a straight CRF, this value should be undefined // -- for a max-margin model, this value should be set to 1 // #define HAMMING_LOSS 1 // multiplier used in the iterative convex-concave procedure (CCCP) for // improving the solution of a max-margin model // -- for a regular max-margin model, this value should be set to 0 // -- for a standard nonconvex model, this value should be set to 1 const double NONCONVEX_MULTIPLIER = 0.0; // number of steps of CCCP; there is no need to change this to 1 in the // case that NONCONVEX_MULTIPLIER == 0, as the code will detect this // and abort after the first CCCP iteration by default const int NUM_CCCP_STEPS = 5; // use smooth approximation of max-margin algorithm for inference // during training #define SMOOTH_MAX_MARGIN 0 ////////////////////////////////////////////////////////////////////// // (B) Regularization type ////////////////////////////////////////////////////////////////////// #define SINGLE_HYPERPARAMETER 0 #define MULTIPLE_HYPERPARAMETERS 1 #define ARD_HYPERPARAMETERS 0 ////////////////////////////////////////////////////////////////////// // (C) Options related to regularization hyperparameter estimation ////////////////////////////////////////////////////////////////////// // Three possible modes: // -- holdout cross-validation via grid search // -- holdout cross-validation via gradient-based optimization // -- majorization-minimization #define HYPERPARAMETER_GRID_SEARCH 0 #define HYPERPARAMETER_GRADIENT_OPTIMIZATION 1 #define HYPERPARAMETER_MAJORIZATION_MINIMIZATION 0 ////////////////////////////////////////////////////////////////////// // (C1) Grid-search options ////////////////////////////////////////////////////////////////////// // use logloss instead of regular holdout loss for holdout cross-validation #define CROSS_VALIDATE_USING_LOGLOSS 1 ////////////////////////////////////////////////////////////////////// // (C2) Gradient-based optimization options ////////////////////////////////////////////////////////////////////// // starting regularization parameter const double INITIAL_LOG_C = 5.0; ////////////////////////////////////////////////////////////////////// // (C3) majorization-minimization-options ////////////////////////////////////////////////////////////////////// // number of iterative relinearization steps if using // majorization-minmimization algorithm const int NUM_ITERATIVE_RELINEARIZATION_STEPS = 5; // smoothing used for majorization-minimization algorithm const double MM_SMOOTHING = 1.0; ////////////////////////////////////////////////////////////////////// // (D) Input type ////////////////////////////////////////////////////////////////////// #define PROFILE 0 ////////////////////////////////////////////////////////////////////// // (E) Used parameter groups ////////////////////////////////////////////////////////////////////// /* #define PARAMS_BASE_PAIR 1 #define PARAMS_BASE_PAIR_DIST 1 #define PARAMS_TERMINAL_MISMATCH 1 #define PARAMS_HAIRPIN_LENGTH 1 #define PARAMS_HAIRPIN_3_NUCLEOTIDES 1 #define PARAMS_HAIRPIN_4_NUCLEOTIDES 1 #define PARAMS_HELIX_LENGTH 1 #define PARAMS_ISOLATED_BASE_PAIR 1 #define PARAMS_INTERNAL_EXPLICIT 1 #define PARAMS_BULGE_LENGTH 1 #define PARAMS_INTERNAL_LENGTH 1 #define PARAMS_INTERNAL_SYMMETRY 1 #define PARAMS_INTERNAL_ASYMMETRY 1 #define PARAMS_BULGE_0x1_NUCLEOTIDES 1 #define PARAMS_BULGE_0x2_NUCLEOTIDES 1 #define PARAMS_BULGE_0x3_NUCLEOTIDES 1 #define PARAMS_INTERNAL_1x1_NUCLEOTIDES 1 #define PARAMS_INTERNAL_1x2_NUCLEOTIDES 1 #define PARAMS_INTERNAL_2x2_NUCLEOTIDES 1 #define PARAMS_HELIX_STACKING 1 #define PARAMS_HELIX_CLOSING 1 #define PARAMS_MULTI_LENGTH 1 #define PARAMS_DANGLE 1 #define PARAMS_EXTERNAL_LENGTH 1 */ #define PARAMS_BASE_PAIR 1 #define PARAMS_BASE_PAIR_DIST 0 #define PARAMS_TERMINAL_MISMATCH 1 #define PARAMS_HAIRPIN_LENGTH 1 #define PARAMS_HAIRPIN_3_NUCLEOTIDES 0 #define PARAMS_HAIRPIN_4_NUCLEOTIDES 0 #define PARAMS_HELIX_LENGTH 0 #define PARAMS_ISOLATED_BASE_PAIR 0 #define PARAMS_INTERNAL_EXPLICIT 1 #define PARAMS_BULGE_LENGTH 1 #define PARAMS_INTERNAL_LENGTH 1 #define PARAMS_INTERNAL_SYMMETRY 1 #define PARAMS_INTERNAL_ASYMMETRY 1 #define PARAMS_BULGE_0x1_NUCLEOTIDES 1 #define PARAMS_BULGE_0x2_NUCLEOTIDES 0 #define PARAMS_BULGE_0x3_NUCLEOTIDES 0 #define PARAMS_INTERNAL_1x1_NUCLEOTIDES 1 #define PARAMS_INTERNAL_1x2_NUCLEOTIDES 0 #define PARAMS_INTERNAL_2x2_NUCLEOTIDES 0 #define PARAMS_HELIX_STACKING 1 #define PARAMS_HELIX_CLOSING 1 #define PARAMS_MULTI_LENGTH 1 #define PARAMS_DANGLE 1 #define PARAMS_EXTERNAL_LENGTH 1 /* #define PARAMS_BASE_PAIR 1 #define PARAMS_BASE_PAIR_DIST 0 #define PARAMS_TERMINAL_MISMATCH 0 #define PARAMS_HAIRPIN_LENGTH 0 #define PARAMS_HAIRPIN_3_NUCLEOTIDES 0 #define PARAMS_HAIRPIN_4_NUCLEOTIDES 0 #define PARAMS_HELIX_LENGTH 0 #define PARAMS_ISOLATED_BASE_PAIR 0 #define PARAMS_INTERNAL_EXPLICIT 0 #define PARAMS_BULGE_LENGTH 0 #define PARAMS_INTERNAL_LENGTH 0 #define PARAMS_INTERNAL_SYMMETRY 0 #define PARAMS_INTERNAL_ASYMMETRY 0 #define PARAMS_BULGE_0x1_NUCLEOTIDES 0 #define PARAMS_BULGE_0x2_NUCLEOTIDES 0 #define PARAMS_BULGE_0x3_NUCLEOTIDES 0 #define PARAMS_INTERNAL_1x1_NUCLEOTIDES 0 #define PARAMS_INTERNAL_1x2_NUCLEOTIDES 0 #define PARAMS_INTERNAL_2x2_NUCLEOTIDES 0 #define PARAMS_HELIX_STACKING 0 #define PARAMS_HELIX_CLOSING 0 #define PARAMS_MULTI_LENGTH 0 #define PARAMS_DANGLE 0 #define PARAMS_EXTERNAL_LENGTH 0 */ ////////////////////////////////////////////////////////////////////// // (F) Miscellaneous model constants ////////////////////////////////////////////////////////////////////// const int C_MIN_HAIRPIN_LENGTH = 0; const int C_MAX_SINGLE_LENGTH = 30; const int D_MAX_HAIRPIN_LENGTH = 30; const int D_MAX_BP_DIST_THRESHOLDS = 10; const int D_MAX_BULGE_LENGTH = 30; const int D_MAX_INTERNAL_LENGTH = 30; const int D_MAX_INTERNAL_SYMMETRIC_LENGTH = 15; const int D_MAX_INTERNAL_ASYMMETRY = 28; const int D_MAX_INTERNAL_EXPLICIT_LENGTH = 4; const int D_MAX_HELIX_LENGTH = 30; const int BP_DIST_LAST_THRESHOLD = 132; const int BP_DIST_THRESHOLDS[D_MAX_BP_DIST_THRESHOLDS] = { 3, 9, 12, 16, 21, 26, 34, 47, 71, BP_DIST_LAST_THRESHOLD }; const std::string alphabet = "ACGU"; // allowed symbols -- all other letters ignored const int M = 4; // number of alphabet symbols const int MAX_DIMENSIONS = 4; ///////////////////////////////////////////////////////////////////// // (G) BMRM stuff ////////////////////////////////////////////////////////////////////// #define BMRM_AVAILABLE 0 // #define DAIFLETCHER #endif