summaryrefslogtreecommitdiff
path: root/gi/pf/quasi_model2.h
diff options
context:
space:
mode:
Diffstat (limited to 'gi/pf/quasi_model2.h')
-rw-r--r--gi/pf/quasi_model2.h177
1 files changed, 0 insertions, 177 deletions
diff --git a/gi/pf/quasi_model2.h b/gi/pf/quasi_model2.h
deleted file mode 100644
index 4075affe..00000000
--- a/gi/pf/quasi_model2.h
+++ /dev/null
@@ -1,177 +0,0 @@
-#ifndef _QUASI_MODEL2_H_
-#define _QUASI_MODEL2_H_
-
-#include <vector>
-#include <cmath>
-#include <tr1/unordered_map>
-#include "boost/functional.hpp"
-#include "prob.h"
-#include "array2d.h"
-#include "slice_sampler.h"
-#include "m.h"
-#include "have_64_bits.h"
-
-struct AlignmentObservation {
- AlignmentObservation() : src_len(), trg_len(), j(), a_j() {}
- AlignmentObservation(unsigned sl, unsigned tl, unsigned tw, unsigned sw) :
- src_len(sl), trg_len(tl), j(tw), a_j(sw) {}
- unsigned short src_len;
- unsigned short trg_len;
- unsigned short j;
- unsigned short a_j;
-};
-
-#ifdef HAVE_64_BITS
-inline size_t hash_value(const AlignmentObservation& o) {
- return reinterpret_cast<const size_t&>(o);
-}
-inline bool operator==(const AlignmentObservation& a, const AlignmentObservation& b) {
- return hash_value(a) == hash_value(b);
-}
-#else
-inline size_t hash_value(const AlignmentObservation& o) {
- size_t h = 1;
- boost::hash_combine(h, o.src_len);
- boost::hash_combine(h, o.trg_len);
- boost::hash_combine(h, o.j);
- boost::hash_combine(h, o.a_j);
- return h;
-}
-#endif
-
-struct QuasiModel2 {
- explicit QuasiModel2(double alpha, double pnull = 0.1) :
- alpha_(alpha),
- pnull_(pnull),
- pnotnull_(1 - pnull) {}
-
- // a_j = 0 => NULL; src_len does *not* include null
- prob_t Prob(unsigned a_j, unsigned j, unsigned src_len, unsigned trg_len) const {
- if (!a_j) return pnull_;
- return pnotnull_ *
- prob_t(UnnormalizedProb(a_j, j, src_len, trg_len, alpha_) / GetOrComputeZ(j, src_len, trg_len));
- }
-
- void Increment(unsigned a_j, unsigned j, unsigned src_len, unsigned trg_len) {
- assert(a_j <= src_len);
- assert(j < trg_len);
- ++obs_[AlignmentObservation(src_len, trg_len, j, a_j)];
- }
-
- void Decrement(unsigned a_j, unsigned j, unsigned src_len, unsigned trg_len) {
- const AlignmentObservation ao(src_len, trg_len, j, a_j);
- int &cc = obs_[ao];
- assert(cc > 0);
- --cc;
- if (!cc) obs_.erase(ao);
- }
-
- struct PNullResampler {
- PNullResampler(const QuasiModel2& m) : m_(m) {}
- const QuasiModel2& m_;
- double operator()(const double& proposed_pnull) const {
- return log(m_.Likelihood(m_.alpha_, proposed_pnull));
- }
- };
-
- struct AlphaResampler {
- AlphaResampler(const QuasiModel2& m) : m_(m) {}
- const QuasiModel2& m_;
- double operator()(const double& proposed_alpha) const {
- return log(m_.Likelihood(proposed_alpha, m_.pnull_.as_float()));
- }
- };
-
- void ResampleHyperparameters(MT19937* rng, const unsigned nloop = 5, const unsigned niterations = 10) {
- const PNullResampler dr(*this);
- const AlphaResampler ar(*this);
- for (unsigned i = 0; i < nloop; ++i) {
- double pnull = slice_sampler1d(dr, pnull_.as_float(), *rng, 0.00000001,
- 1.0, 0.0, niterations, 100*niterations);
- pnull_ = prob_t(pnull);
- alpha_ = slice_sampler1d(ar, alpha_, *rng, 0.00000001,
- std::numeric_limits<double>::infinity(), 0.0, niterations, 100*niterations);
- }
- std::cerr << "QuasiModel2(alpha=" << alpha_ << ",p_null="
- << pnull_.as_float() << ") = " << Likelihood() << std::endl;
- zcache_.clear();
- }
-
- prob_t Likelihood() const {
- return Likelihood(alpha_, pnull_.as_float());
- }
-
- prob_t Likelihood(double alpha, double ppnull) const {
- const prob_t pnull(ppnull);
- const prob_t pnotnull(1 - ppnull);
-
- prob_t p;
- p.logeq(Md::log_gamma_density(alpha, 0.1, 25)); // TODO configure
- assert(!p.is_0());
- prob_t prob_of_ppnull; prob_of_ppnull.logeq(Md::log_beta_density(ppnull, 2, 10));
- assert(!prob_of_ppnull.is_0());
- p *= prob_of_ppnull;
- for (ObsCount::const_iterator it = obs_.begin(); it != obs_.end(); ++it) {
- const AlignmentObservation& ao = it->first;
- if (ao.a_j) {
- prob_t u = XUnnormalizedProb(ao.a_j, ao.j, ao.src_len, ao.trg_len, alpha);
- prob_t z = XComputeZ(ao.j, ao.src_len, ao.trg_len, alpha);
- prob_t pa(u / z);
- pa *= pnotnull;
- pa.poweq(it->second);
- p *= pa;
- } else {
- p *= pnull.pow(it->second);
- }
- }
- return p;
- }
-
- private:
- static prob_t XUnnormalizedProb(unsigned a_j, unsigned j, unsigned src_len, unsigned trg_len, double alpha) {
- prob_t p;
- p.logeq(-fabs(double(a_j - 1) / src_len - double(j) / trg_len) * alpha);
- return p;
- }
-
- static prob_t XComputeZ(unsigned j, unsigned src_len, unsigned trg_len, double alpha) {
- prob_t z = prob_t::Zero();
- for (int a_j = 1; a_j <= src_len; ++a_j)
- z += XUnnormalizedProb(a_j, j, src_len, trg_len, alpha);
- return z;
- }
-
- static double UnnormalizedProb(unsigned a_j, unsigned j, unsigned src_len, unsigned trg_len, double alpha) {
- return exp(-fabs(double(a_j - 1) / src_len - double(j) / trg_len) * alpha);
- }
-
- static double ComputeZ(unsigned j, unsigned src_len, unsigned trg_len, double alpha) {
- double z = 0;
- for (int a_j = 1; a_j <= src_len; ++a_j)
- z += UnnormalizedProb(a_j, j, src_len, trg_len, alpha);
- return z;
- }
-
- const double& GetOrComputeZ(unsigned j, unsigned src_len, unsigned trg_len) const {
- if (src_len >= zcache_.size())
- zcache_.resize(src_len + 1);
- if (trg_len >= zcache_[src_len].size())
- zcache_[src_len].resize(trg_len + 1);
- std::vector<double>& zv = zcache_[src_len][trg_len];
- if (zv.size() == 0)
- zv.resize(trg_len);
- double& z = zv[j];
- if (!z)
- z = ComputeZ(j, src_len, trg_len, alpha_);
- return z;
- }
-
- double alpha_;
- prob_t pnull_;
- prob_t pnotnull_;
- mutable std::vector<std::vector<std::vector<double> > > zcache_;
- typedef std::tr1::unordered_map<AlignmentObservation, int, boost::hash<AlignmentObservation> > ObsCount;
- ObsCount obs_;
-};
-
-#endif
generated by cgit v1.2.3 (git 2.39.1) at 2024-11-11 01:22:22 +0000