From e26434979adc33bd949566ba7bf02dff64e80a3e Mon Sep 17 00:00:00 2001 From: Chris Dyer Date: Tue, 2 Oct 2012 00:19:43 -0400 Subject: cdec cleanup, remove bayesian stuff, parsing stuff --- gi/pf/quasi_model2.h | 177 --------------------------------------------------- 1 file changed, 177 deletions(-) delete mode 100644 gi/pf/quasi_model2.h (limited to 'gi/pf/quasi_model2.h') 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 -#include -#include -#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(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::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& 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 > > zcache_; - typedef std::tr1::unordered_map > ObsCount; - ObsCount obs_; -}; - -#endif -- cgit v1.2.3