forward_pass.c

C-package of "Long Short-Term Memory" for Protein classification

/*
 * $Id: forward_pass.c 1273 2007-05-09 16:28:04Z mhe $
 */
 
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>

#include "lstm.h"
#include "forward_pass.h"

static union {
    double d;
    struct {
       #ifdef LITTLE_ENDIAN
        int j, i;
       #else
        int i, j;
       #endif
    } n;
} _eco;

void forward_pass(int train, int element, int **inp_idx, double **inp) {
    static int i,j,u,v,k;
    static double sum; // , sumblock[100];
    static char actfilename[255]; 
        
    /* ### memory cells ### */

    i=in_mod_b+1;
    for (u=0;u<num_blocks;u++) {

        /* input gates */
        sum = 0;
        /* input */
        /*
        for (j=0;j<in_nn_mod;j++) {
            sum += W[i][inp_idx[element][j]] * inp[element][j];
        }
        */
        
        /* lstm */
        for (j=in_mod_b;j<cell_mod;j++) {
            sum += W[i][j] * Yk_old[j];
        }
                 
        Y_in[u] = 1/(1+EXP(-sum));
        Yk_new[i]= Y_in[u];
        
        /* output gate */
        i++;
        sum = 0;
        /* input */
        /*
        for (j=0;j<in_nn_mod;j++) {
            sum += W[i][inp_idx[element][j]] * inp[element][j];
        }
        */
        /* lstm */
        for (j=in_mod_b;j<cell_mod;j++) {
            sum += W[i][j] * Yk_old[j];
        }
        
        /* peep hole */
        //sum -= S[u][0];
        Y_out[u] = 1/(1+EXP(-sum));
        Yk_new[i]= Y_out[u];
        
        /* uth memory cell block */
        for (v=0;v<block_size[u];v++) {
            /* activation of function g of vth memory cell of block u  */
            i++;
            sum = W[i][in_mod_b]; // bias
                        
#ifdef FF
           
            for (j = 0; j < in_mod_b; j++) {
                sum += W[i][j] * inp[element][j];
            }
            
#else
            
            for (j=0;j<in_nn_mod;j++) {
                sum += W[i][inp_idx[element][j]] * inp[element][j];
            }
           
#endif
            
            /* peep hole */
            //sum -= S[u][v];
            //sumblock[u] = sum;
            
            G[u][v] = 2.0/(1+EXP(-sum));
            /* update internal state  */
            S[u][v] += Y_in[u]*G[u][v];
            /* activation function h */
            
            if (S[u][v] > 500.0) {
                fprintf(stderr, "S drifted\n");
                H[u][v] = 1.0;
            }
            else {
                H[u][v] = 2.0/(1+EXP(-S[u][v]))-1.0;
            }
            
            /* activation of vth memory cell of block u */
            Yc[u][v] = H[u][v]*Y_out[u];
            Yk_new[i] = Yc[u][v];
        }
        i++;
    }



    /* ### output units activation ### */

    if (targ) /* only if target for this input */ {

        for (k=cell_mod;k<ges_mod;k++) {        
            /* bias */
            sum = W[k][in_mod_b];
            /* memory cells input */
            i=in_mod_b+1;
            for (u=0;u<num_blocks;u++) {
                i++;
                for (v=0;v<block_size[u];v++) {
                    i++;
                    sum += W[k][i]*Yk_new[i];
                }
                i++;
            }
            /* activation */
            Yk_new[k] = 1/(1+EXP(-sum));
        }       
        
    }
        
    // output of memory activity
    if (0) {
      if (element == 0) {
          //sprintf(actfilename, "%d%s", prand_t[prot_current_idx], ".possibleprotea.memoryactivity.train.dat");
          sprintf(actfilename, "%d.pos.test.dat", prot_current_idx);
          fprintf(stderr, "%s\n", actfilename);
          ma = fopen(actfilename, "w");
      }
      
      //for (u=0;u<num_blocks;u++) {
        //fprintf(ma, "%f %f %f %f ", Y_in[u], Y_out[u], sumblock[u], S[u][0]);
        //fprintf(ma, "%f ", S[u][0]);
      //}
      //fprintf(ma, "\n");
      fprintf(ma, "%f\n", S[4][0]);
      //fprintf(ma, "%f\n", Yk_new[cell_mod]);
      
      fflush(ma);
      
      /*
       * 
       * See in execute_act_test() for closing the file
       * 
       */
      
    }
    
    
    
}