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decoder.c
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/*
* Wapiti - A linear-chain CRF tool
*
* Copyright (c) 2009-2013 CNRS
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
* * Redistributions of source code must retain the above copyright
* notice, this list of conditions and the following disclaimer.
* * Redistributions in binary form must reproduce the above copyright
* notice, this list of conditions and the following disclaimer in the
* documentation and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGE.
*/
#include <inttypes.h>
#include <float.h>
#include <stdint.h>
#include <stddef.h>
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <math.h>
#include "wapiti.h"
#include "gradient.h"
#include "model.h"
#include "quark.h"
#include "reader.h"
#include "sequence.h"
#include "thread.h"
#include "tools.h"
#include "decoder.h"
#include "vmath.h"
/******************************************************************************
* Sequence tagging
*
* This module implement sequence tagging using a trained model and model
* evaluation on devlopment set.
*
* The viterbi can be quite intensive on the stack if you push in it long
* sequence and use large labels set. It's less a problem than in gradient
* computations but it can show up in particular cases. The fix is to call it
* through the mth_spawn function and request enough stack space, this will be
* fixed in next version.
******************************************************************************/
/* tag_expsc:
* Compute the score lattice for classical Viterbi decoding. This is the same
* as for the first step of the gradient computation with the exception that
* we don't need to take the exponential of the scores as the Viterbi decoding
* works in log-space.
*/
static int tag_expsc(mdl_t *mdl, const seq_t *seq, double *vpsi) {
const double *x = mdl->theta;
const uint32_t Y = mdl->nlbl;
const uint32_t T = seq->len;
double (*psi)[T][Y][Y] = (void *)vpsi;
// We first have to compute the Ψ_t(y',y,x_t) weights defined as
// Ψ_t(y',y,x_t) = \exp( ∑_k θ_k f_k(y',y,x_t) )
// So at position 't' in the sequence, for each couple (y',y) we have
// to sum weights of all features.
// This is the same than what we do for computing the gradient but, as
// the viterbi algorithm also work in the logarithmic space, we can
// remove the exponential.
//
// Only the observations present at this position will have a non-nul
// weight so we can sum only on thoses.
//
// As we use only two kind of features: unigram and bigram, we can
// rewrite this as
// ∑_k μ_k(y, x_t) f_k(y, x_t) + ∑_k λ_k(y', y, x_t) f_k(y', y, x_t)
// Where the first sum is over the unigrams features and the second is
// over bigrams ones.
//
// This allow us to compute Ψ efficiently in two steps
// 1/ we sum the unigrams features weights by looping over actives
// unigrams observations. (we compute this sum once and use it
// for each value of y')
// 2/ we add the bigrams features weights by looping over actives
// bigrams observations (we don't have to do this for t=0 since
// there is no bigrams here)
for (uint32_t t = 0; t < T; t++) {
const pos_t *pos = &(seq->pos[t]);
for (uint32_t y = 0; y < Y; y++) {
double sum = 0.0;
for (uint32_t n = 0; n < pos->ucnt; n++) {
const uint64_t o = pos->uobs[n];
sum += x[mdl->uoff[o] + y];
}
for (uint32_t yp = 0; yp < Y; yp++)
(*psi)[t][yp][y] = sum;
}
}
for (uint32_t t = 1; t < T; t++) {
const pos_t *pos = &(seq->pos[t]);
for (uint32_t yp = 0, d = 0; yp < Y; yp++) {
for (uint32_t y = 0; y < Y; y++, d++) {
double sum = 0.0;
for (uint32_t n = 0; n < pos->bcnt; n++) {
const uint64_t o = pos->bobs[n];
sum += x[mdl->boff[o] + d];
}
(*psi)[t][yp][y] += sum;
}
}
}
return 0;
}
/* tag_memmsc:
* Compute the score for viterbi decoding of MEMM models. This use the
* previous function to compute the classical score and then normalize them
* relative to the previous label. This normalization must be done in linear
* space, not in logarithm one.
*/
static int tag_memmsc(mdl_t *mdl, const seq_t *seq, double *vpsi) {
const uint32_t Y = mdl->nlbl;
const uint32_t T = seq->len;
tag_expsc(mdl, seq, vpsi);
xvm_expma(vpsi, vpsi, 0.0, T * Y * Y);
double (*psi)[T][Y][Y] = (void *)vpsi;
for (uint32_t t = 0; t < T; t++) {
for (uint32_t yp = 0; yp < Y; yp++) {
double sum = 0.0;
for (uint32_t y = 0; y < Y; y++)
sum += (*psi)[t][yp][y];
for (uint32_t y = 0; y < Y; y++)
(*psi)[t][yp][y] /= sum;
}
}
return 1;
}
/* tag_postsc:
* This function compute score lattice with posteriors. This generally result
* in a slightly best labelling and allow to output normalized score for the
* sequence and for each labels but this is more costly as we have to perform
* a full forward backward instead of just the forward pass.
*/
static int tag_postsc(mdl_t *mdl, const seq_t *seq, double *vpsi) {
const uint32_t Y = mdl->nlbl;
const uint32_t T = seq->len;
double (*psi)[T][Y][Y] = (void *)vpsi;
grd_st_t *grd_st = grd_stnew(mdl, NULL);
grd_st->first = 0;
grd_st->last = T - 1;
grd_stcheck(grd_st, seq->len);
if (mdl->opt->sparse) {
grd_spdopsi(grd_st, seq);
grd_spfwdbwd(grd_st, seq);
} else {
grd_fldopsi(grd_st, seq);
grd_flfwdbwd(grd_st, seq);
}
double (*alpha)[T][Y] = (void *)grd_st->alpha;
double (*beta )[T][Y] = (void *)grd_st->beta;
double *unorm = grd_st->unorm;
for (uint32_t t = 0; t < T; t++) {
for (uint32_t y = 0; y < Y; y++) {
double e = (*alpha)[t][y] * (*beta)[t][y] * unorm[t];
for (uint32_t yp = 0; yp < Y; yp++)
(*psi)[t][yp][y] = e;
}
}
grd_stfree(grd_st);
return 1;
}
/* tag_forced:
* This function apply correction to the psi table to take account of already
* known labels. If a label is known, all arcs leading or comming from other
* labels at this position are NULLified and will not be selected by the
* decoder.
*/
static void tag_forced(mdl_t *mdl, const seq_t *seq, double *vpsi, int op) {
const uint32_t Y = mdl->nlbl;
const uint32_t T = seq->len;
const double v = op ? 0.0 : -HUGE_VAL;
double (*psi)[T][Y][Y] = (void *)vpsi;
for (uint32_t t = 0; t < T; t++) {
const uint32_t yr = seq->pos[t].lbl;
if (yr == (uint32_t)-1)
continue;
if (t != 0)
for (uint32_t y = 0; y < Y; y++)
if (y != yr)
for (uint32_t yp = 0; yp < Y; yp++)
(*psi)[t][yp][y] = v;
if (t != T - 1)
for (uint32_t y = 0; y < Y; y++)
if (y != yr)
for (uint32_t yn = 0; yn < Y; yn++)
(*psi)[t + 1][y][yn] = v;
}
const uint32_t yr = seq->pos[0].lbl;
if (yr != (uint32_t)-1) {
for (uint32_t y = 0; y < Y; y++) {
if (yr == y)
continue;
for (uint32_t yp = 0; yp < Y; yp++)
(*psi)[0][yp][y] = v;
}
}
}
/* tag_viterbi:
* This function implement the Viterbi algorithm in order to decode the most
* probable sequence of labels according to the model. Some part of this code
* is very similar to the computation of the gradient as expected.
*
* And like for the gradient, the caller is responsible to ensure there is
* enough stack space.
*/
void tag_viterbi(mdl_t *mdl, const seq_t *seq,
uint32_t out[], double *sc, double psc[]) {
const uint32_t Y = mdl->nlbl;
const uint32_t T = seq->len;
double *vpsi = xvm_new(T * Y * Y);
uint32_t *vback = xmalloc(sizeof(uint32_t) * T * Y);
double (*psi) [T][Y][Y] = (void *)vpsi;
uint32_t (*back)[T][Y] = (void *)vback;
double *cur = xmalloc(sizeof(double) * Y);
double *old = xmalloc(sizeof(double) * Y);
// We first compute the scores for each transitions in the lattice of
// labels.
int op;
if (mdl->type == 1)
op = tag_memmsc(mdl, seq, vpsi);
else if (mdl->opt->lblpost)
op = tag_postsc(mdl, seq, vpsi);
else
op = tag_expsc(mdl, seq, vpsi);
if (mdl->opt->force)
tag_forced(mdl, seq, vpsi, op);
// Now we can do the Viterbi algorithm. This is very similar to the
// forward pass
// | α_1(y) = Ψ_1(y,x_1)
// | α_t(y) = max_{y'} α_{t-1}(y') + Ψ_t(y',y,x_t)
// We just replace the sum by a max and as we do the computation in the
// logarithmic space the product become a sum. (this also mean that we
// don't have to worry about numerical problems)
//
// Next we have to walk backward over the α in order to find the best
// path. In order to do this efficiently, we keep in the 'back' array
// the indice of the y value selected by the max. This also mean that
// we only need the current and previous value of the α vectors, not
// the full matrix.
for (uint32_t y = 0; y < Y; y++)
cur[y] = (*psi)[0][0][y];
for (uint32_t t = 1; t < T; t++) {
for (uint32_t y = 0; y < Y; y++)
old[y] = cur[y];
for (uint32_t y = 0; y < Y; y++) {
double bst = -HUGE_VAL;
uint32_t idx = 0;
for (uint32_t yp = 0; yp < Y; yp++) {
double val = old[yp];
if (op)
val *= (*psi)[t][yp][y];
else
val += (*psi)[t][yp][y];
if (val > bst) {
bst = val;
idx = yp;
}
}
(*back)[t][y] = idx;
cur[y] = bst;
}
}
// We can now build the sequence of labels predicted by the model. For
// this we search in the last α vector the best value. Using this index
// as a starting point in the back-pointer array we finally can decode
// the best sequence.
uint32_t bst = 0;
for (uint32_t y = 1; y < Y; y++)
if (cur[y] > cur[bst])
bst = y;
if (sc != NULL)
*sc = cur[bst];
for (uint32_t t = T; t > 0; t--) {
const uint32_t yp = (t != 1) ? (*back)[t - 1][bst] : 0;
const uint32_t y = bst;
out[t - 1] = y;
if (psc != NULL)
psc[t - 1] = (*psi)[t - 1][yp][y];
bst = yp;
}
free(old);
free(cur);
free(vback);
xvm_free(vpsi);
}
/* tag_nbviterbi:
* This function implement the Viterbi algorithm in order to decode the N-most
* probable sequences of labels according to the model. It can be used to
* compute only the best one and will return the same sequence than the
* previous function but will be slower to do it.
*/
void tag_nbviterbi(mdl_t *mdl, const seq_t *seq, uint32_t N,
uint32_t out[][N], double sc[], double psc[][N]) {
const uint32_t Y = mdl->nlbl;
const uint32_t T = seq->len;
double *vpsi = xvm_new(T * Y * Y);
uint32_t *vback = xmalloc(sizeof(uint32_t) * T * Y * N);
double (*psi) [T][Y ][Y] = (void *)vpsi;
uint32_t (*back)[T][Y * N] = (void *)vback;
double *cur = xmalloc(sizeof(double) * Y * N);
double *old = xmalloc(sizeof(double) * Y * N);
// We first compute the scores for each transitions in the lattice of
// labels.
int op;
if (mdl->type == 1)
op = tag_memmsc(mdl, seq, vpsi);
else if (mdl->opt->lblpost)
op = tag_postsc(mdl, seq, (double *)psi);
else
op = tag_expsc(mdl, seq, (double *)psi);
if (mdl->opt->force)
tag_forced(mdl, seq, vpsi, op);
// Here also, it's classical but we have to keep the N best paths
// leading to each nodes of the lattice instead of only the best one.
// This mean that code is less trivial and the current implementation is
// not the most efficient way to do this but it works well and is good
// enough for the moment.
// We first build the list of all incoming arcs from all paths from all
// N-best nodes and next select the N-best one. There is a lot of room
// here for later optimisations if needed.
for (uint32_t y = 0, d = 0; y < Y; y++) {
cur[d++] = (*psi)[0][0][y];
for (uint32_t n = 1; n < N; n++)
cur[d++] = -DBL_MAX;
}
for (uint32_t t = 1; t < T; t++) {
for (uint32_t d = 0; d < Y * N; d++)
old[d] = cur[d];
for (uint32_t y = 0; y < Y; y++) {
// 1st, build the list of all incoming
double lst[Y * N];
for (uint32_t yp = 0, d = 0; yp < Y; yp++) {
for (uint32_t n = 0; n < N; n++, d++) {
lst[d] = old[d];
if (op)
lst[d] *= (*psi)[t][yp][y];
else
lst[d] += (*psi)[t][yp][y];
}
}
// 2nd, init the back with the N first
uint32_t *bk = &(*back)[t][y * N];
for (uint32_t n = 0; n < N; n++)
bk[n] = n;
// 3rd, search the N highest values
for (uint32_t i = N; i < N * Y; i++) {
// Search the smallest current value
uint32_t idx = 0;
for (uint32_t n = 1; n < N; n++)
if (lst[bk[n]] < lst[bk[idx]])
idx = n;
// And replace it if needed
if (lst[i] > lst[bk[idx]])
bk[idx] = i;
}
// 4th, get the new scores
for (uint32_t n = 0; n < N; n++)
cur[y * N + n] = lst[bk[n]];
}
}
// Retrieving the best paths is similar to classical Viterbi except that
// we have to search for the N bet ones and there is N time more
// possibles starts.
for (uint32_t n = 0; n < N; n++) {
uint32_t bst = 0;
for (uint32_t d = 1; d < Y * N; d++)
if (cur[d] > cur[bst])
bst = d;
if (sc != NULL)
sc[n] = cur[bst];
cur[bst] = -DBL_MAX;
for (uint32_t t = T; t > 0; t--) {
const uint32_t yp = (t != 1) ? (*back)[t - 1][bst] / N: 0;
const uint32_t y = bst / N;
out[t - 1][n] = y;
if (psc != NULL)
psc[t - 1][n] = (*psi)[t - 1][yp][y];
bst = (*back)[t - 1][bst];
}
}
free(old);
free(cur);
free(vback);
xvm_free(vpsi);
}
/* tag_label:
* Label a data file using the current model. This output an almost exact copy
* of the input file with an additional column with the predicted label. If
* the check option is specified, the input file must be labelled and the
* predicted labels will be checked against the provided ones. This will
* output error rates during the labelling and detailed statistics per label
* at the end.
*/
void tag_label(mdl_t *mdl, FILE *fin, FILE *fout) {
qrk_t *lbls = mdl->reader->lbl;
const uint32_t Y = mdl->nlbl;
const uint32_t N = mdl->opt->nbest;
// We start by preparing the statistic collection to be ready if check
// option is used. The stat array hold the following for each label
// [0] # of reference with this label
// [1] # of token we have taged with this label
// [2] # of match of the two preceding
uint64_t tcnt = 0, terr = 0;
uint64_t scnt = 0, serr = 0;
uint64_t stat[3][Y];
for (uint32_t y = 0; y < Y; y++)
stat[0][y] = stat[1][y] = stat[2][y] = 0;
// Next read the input file sequence by sequence and label them, we have
// to take care of not discarding the raw input as we want to send it
// back to the output with the additional predicted labels.
while (!feof(fin)) {
// So, first read an input sequence keeping the raw_t object
// available, and label it with Viterbi.
raw_t *raw = rdr_readraw(mdl->reader, fin);
if (raw == NULL)
break;
seq_t *seq = rdr_raw2seq(mdl->reader, raw,
mdl->opt->check | mdl->opt->force);
const uint32_t T = seq->len;
uint32_t *out = xmalloc(sizeof(uint32_t) * T * N);
double *psc = xmalloc(sizeof(double ) * T * N);
double *scs = xmalloc(sizeof(double ) * N);
if (N == 1)
tag_viterbi(mdl, seq, (uint32_t*)out, scs, (double*)psc);
else
tag_nbviterbi(mdl, seq, N, (void*)out, scs, (void*)psc);
// Next we output the raw sequence with an aditional column for
// the predicted labels
for (uint32_t n = 0; n < N; n++) {
if (mdl->opt->outsc)
fprintf(fout, "# %d %f\n", (int)n, scs[n]);
for (uint32_t t = 0; t < T; t++) {
if (!mdl->opt->label)
fprintf(fout, "%s\t", raw->lines[t]);
uint32_t lbl = out[t * N + n];
const char *lblstr = qrk_id2str(lbls, lbl);
fprintf(fout, "%s", lblstr);
if (mdl->opt->outsc) {
fprintf(fout, "\t%s", lblstr);
fprintf(fout, "/%f", psc[t * N + n]);
}
fprintf(fout, "\n");
}
fprintf(fout, "\n");
}
fflush(fout);
// If user provided reference labels, use them to collect
// statistics about how well we have performed here. Labels
// unseen at training time are discarded.
if (mdl->opt->check) {
bool err = false;
for (uint32_t t = 0; t < T; t++) {
if (seq->pos[t].lbl == (uint32_t)-1)
continue;
stat[0][seq->pos[t].lbl]++;
stat[1][out[t * N]]++;
if (seq->pos[t].lbl != out[t * N])
terr++, err = true;
else
stat[2][out[t * N]]++;
}
tcnt += T;
serr += err;
}
// Cleanup memory used for this sequence
free(scs);
free(psc);
free(out);
rdr_freeseq(seq);
rdr_freeraw(raw);
// And report our progress, at regular interval we display how
// much sequence are labelled and if possible the current tokens
// and sequence error rates.
if (++scnt % 1000 == 0) {
info("%10"PRIu64" sequences labeled", scnt);
if (mdl->opt->check) {
const double te = (double)terr / tcnt * 100.0;
const double se = (double)serr / scnt * 100.0;
info("\t%5.2f%%/%5.2f%%", te, se);
}
info("\n");
}
}
// If user have provided reference labels, we have collected a lot of
// statistics and we can repport global token and sequence error rate as
// well as precision recall and f-measure for each labels.
if (mdl->opt->check) {
const double te = (double)terr / tcnt * 100.0;
const double se = (double)serr / scnt * 100.0;
info(" Nb sequences : %"PRIu64"\n", scnt);
info(" Token error : %5.2f%%\n", te);
info(" Sequence error: %5.2f%%\n", se);
info("* Per label statistics\n");
for (uint32_t y = 0; y < Y; y++) {
const char *lbl = qrk_id2str(lbls, y);
const double Rc = (double)stat[2][y] / stat[0][y];
const double Pr = (double)stat[2][y] / stat[1][y];
const double F1 = 2.0 * (Pr * Rc) / (Pr + Rc);
info(" %-6s", lbl);
info(" Pr=%.2f", Pr);
info(" Rc=%.2f", Rc);
info(" F1=%.2f\n", F1);
}
}
}
/* eval_t:
* This a state tracker used to communicate between the main eval function and
* its workers threads, the <mdl> and <dat> fields are used to transmit to the
* workers informations needed to make the computation, the other fields are
* for returning the partial results.
*/
typedef struct eval_s eval_t;
struct eval_s {
mdl_t *mdl;
dat_t *dat;
uint64_t tcnt; // Processed tokens count
uint64_t terr; // Tokens error found
uint64_t scnt; // Processes sequences count
uint64_t serr; // Sequence error found
};
/* tag_evalsub:
* This is where the real evaluation is done by the workers, we process data
* by batch and for each batch do a simple Viterbi and scan the result to find
* errors.
*/
static void tag_evalsub(job_t *job, uint32_t id, uint32_t cnt, eval_t *eval) {
unused(id && cnt);
mdl_t *mdl = eval->mdl;
dat_t *dat = eval->dat;
eval->tcnt = 0;
eval->terr = 0;
eval->scnt = 0;
eval->serr = 0;
// We just get a job a process all the squence in it.
uint32_t count, pos;
while (mth_getjob(job, &count, &pos)) {
for (uint32_t s = pos; s < pos + count; s++) {
// Tag the sequence with the viterbi
const seq_t *seq = dat->seq[s];
const uint32_t T = seq->len;
uint32_t *out = xmalloc(sizeof(uint32_t) * T);
tag_viterbi(mdl, seq, out, NULL, NULL);
// And check for eventual (probable ?) errors
bool err = false;
for (uint32_t t = 0; t < T; t++)
if (seq->pos[t].lbl != out[t])
eval->terr++, err = true;
eval->tcnt += T;
eval->scnt += 1;
eval->serr += err;
free(out);
}
}
}
/* tag_eval:
* Compute the token error rate and sequence error rate over the devel set (or
* taining set if not available).
*/
void tag_eval(mdl_t *mdl, double *te, double *se) {
const uint32_t W = mdl->opt->nthread;
dat_t *dat = (mdl->devel == NULL) ? mdl->train : mdl->devel;
// First we prepare the eval state for all the workers threads, we just
// have to give them the model and dataset to use. This state will be
// used to retrieve partial result they computed.
eval_t *eval[W];
for (uint32_t w = 0; w < W; w++) {
eval[w] = xmalloc(sizeof(eval_t));
eval[w]->mdl = mdl;
eval[w]->dat = dat;
}
// And next, we call the workers to do the job and reduce the partial
// result by summing them and computing the final error rates.
mth_spawn((func_t *)tag_evalsub, W, (void *)eval, dat->nseq,
mdl->opt->jobsize);
uint64_t tcnt = 0, terr = 0;
uint64_t scnt = 0, serr = 0;
for (uint32_t w = 0; w < W; w++) {
tcnt += eval[w]->tcnt;
terr += eval[w]->terr;
scnt += eval[w]->scnt;
serr += eval[w]->serr;
free(eval[w]);
}
*te = (double)terr / tcnt * 100.0;
*se = (double)serr / scnt * 100.0;
}