From 400d60b20e9e480b0eff9843404a4cb9f8bd02cc Mon Sep 17 00:00:00 2001 From: Chris Dyer Date: Wed, 8 Feb 2012 16:22:55 -0500 Subject: move widely duplicated math functions into m.h header --- gi/pf/base_distributions.cc | 22 +++++++++++----------- gi/pf/base_distributions.h | 21 ++------------------- gi/pf/conditional_pseg.h | 3 ++- gi/pf/pfdist.cc | 6 +++--- gi/pf/pfnaive.cc | 4 ++-- 5 files changed, 20 insertions(+), 36 deletions(-) (limited to 'gi') diff --git a/gi/pf/base_distributions.cc b/gi/pf/base_distributions.cc index d362fd76..d9761005 100644 --- a/gi/pf/base_distributions.cc +++ b/gi/pf/base_distributions.cc @@ -59,7 +59,7 @@ prob_t PhraseConditionalUninformativeUnigramBase::p0(const vector& vsrc, const int flen = vsrc.size() - start_src; const int elen = vtrg.size() - start_trg; prob_t p; - p.logeq(log_poisson(elen, flen + 0.01)); // elen | flen ~Pois(flen + 0.01) + p.logeq(Md::log_poisson(elen, flen + 0.01)); // elen | flen ~Pois(flen + 0.01) //p.logeq(log_poisson(elen, 1)); // elen | flen ~Pois(flen + 0.01) for (int i = 0; i < elen; ++i) p *= u(vtrg[i + start_trg]); // draw e_i ~Uniform @@ -73,7 +73,7 @@ prob_t PhraseConditionalUninformativeBase::p0(const vector& vsrc, const int elen = vtrg.size() - start_trg; prob_t p; //p.logeq(log_poisson(elen, flen + 0.01)); // elen | flen ~Pois(flen + 0.01) - p.logeq(log_poisson(elen, 1)); // elen | flen ~Pois(flen + 0.01) + p.logeq(Md::log_poisson(elen, 1)); // elen | flen ~Pois(flen + 0.01) for (int i = 0; i < elen; ++i) p *= kUNIFORM_TARGET; // draw e_i ~Uniform return p; @@ -113,7 +113,7 @@ prob_t PhraseConditionalBase::p0(const vector& vsrc, const int elen = vtrg.size() - start_trg; prob_t uniform_src_alignment; uniform_src_alignment.logeq(-log(flen + 1)); prob_t p; - p.logeq(log_poisson(elen, flen + 0.01)); // elen | flen ~Pois(flen + 0.01) + p.logeq(Md::log_poisson(elen, flen + 0.01)); // elen | flen ~Pois(flen + 0.01) for (int i = 0; i < elen; ++i) { // for each position i in e-RHS const WordID trg = vtrg[i + start_trg]; prob_t tp = prob_t::Zero(); @@ -139,9 +139,9 @@ prob_t PhraseJointBase::p0(const vector& vsrc, const int elen = vtrg.size() - start_trg; prob_t uniform_src_alignment; uniform_src_alignment.logeq(-log(flen + 1)); prob_t p; - p.logeq(log_poisson(flen, 1.0)); // flen ~Pois(1) + p.logeq(Md::log_poisson(flen, 1.0)); // flen ~Pois(1) // elen | flen ~Pois(flen + 0.01) - prob_t ptrglen; ptrglen.logeq(log_poisson(elen, flen + 0.01)); + prob_t ptrglen; ptrglen.logeq(Md::log_poisson(elen, flen + 0.01)); p *= ptrglen; p *= kUNIFORM_SOURCE.pow(flen); // each f in F ~Uniform for (int i = 0; i < elen; ++i) { // for each position i in E @@ -171,9 +171,9 @@ prob_t PhraseJointBase_BiDir::p0(const vector& vsrc, prob_t uniform_trg_alignment; uniform_trg_alignment.logeq(-log(elen + 1)); prob_t p1; - p1.logeq(log_poisson(flen, 1.0)); // flen ~Pois(1) + p1.logeq(Md::log_poisson(flen, 1.0)); // flen ~Pois(1) // elen | flen ~Pois(flen + 0.01) - prob_t ptrglen; ptrglen.logeq(log_poisson(elen, flen + 0.01)); + prob_t ptrglen; ptrglen.logeq(Md::log_poisson(elen, flen + 0.01)); p1 *= ptrglen; p1 *= kUNIFORM_SOURCE.pow(flen); // each f in F ~Uniform for (int i = 0; i < elen; ++i) { // for each position i in E @@ -193,9 +193,9 @@ prob_t PhraseJointBase_BiDir::p0(const vector& vsrc, } prob_t p2; - p2.logeq(log_poisson(elen, 1.0)); // elen ~Pois(1) + p2.logeq(Md::log_poisson(elen, 1.0)); // elen ~Pois(1) // flen | elen ~Pois(flen + 0.01) - prob_t psrclen; psrclen.logeq(log_poisson(flen, elen + 0.01)); + prob_t psrclen; psrclen.logeq(Md::log_poisson(flen, elen + 0.01)); p2 *= psrclen; p2 *= kUNIFORM_TARGET.pow(elen); // each f in F ~Uniform for (int i = 0; i < flen; ++i) { // for each position i in E @@ -227,9 +227,9 @@ JumpBase::JumpBase() : p(200) { for (int j = min_jump; j <= max_jump; ++j) { prob_t& cp = cpd[j]; if (j < 0) - cp.logeq(log_poisson(1.5-j, 1)); + cp.logeq(Md::log_poisson(1.5-j, 1)); else if (j > 0) - cp.logeq(log_poisson(j, 1)); + cp.logeq(Md::log_poisson(j, 1)); cp.poweq(0.2); z += cp; } diff --git a/gi/pf/base_distributions.h b/gi/pf/base_distributions.h index a23ac32b..0d597c5c 100644 --- a/gi/pf/base_distributions.h +++ b/gi/pf/base_distributions.h @@ -13,24 +13,7 @@ #include "prob.h" #include "tdict.h" #include "sampler.h" - -inline double log_poisson(unsigned x, const double& lambda) { - assert(lambda > 0.0); - return log(lambda) * x - lgamma(x + 1) - lambda; -} - -inline double log_binom_coeff(unsigned n, unsigned k) { - assert(n >= k); - if (n == k) return 0.0; - return lgamma(n + 1) - lgamma(k + 1) - lgamma(n - k + 1); -} - -// http://en.wikipedia.org/wiki/Negative_binomial_distribution -inline double log_negative_binom(unsigned x, unsigned r, double p) { - assert(p > 0.0); - assert(p < 1.0); - return log_binom_coeff(x + r - 1, x) + r * log(1 - p) + x * log(p); -} +#include "m.h" inline std::ostream& operator<<(std::ostream& os, const std::vector& p) { os << '['; @@ -68,7 +51,7 @@ struct Model1 { struct PoissonUniformUninformativeBase { explicit PoissonUniformUninformativeBase(const unsigned ves) : kUNIFORM(1.0 / ves) {} prob_t operator()(const TRule& r) const { - prob_t p; p.logeq(log_poisson(r.e_.size(), 1.0)); + prob_t p; p.logeq(Md::log_poisson(r.e_.size(), 1.0)); prob_t q = kUNIFORM; q.poweq(r.e_.size()); p *= q; return p; diff --git a/gi/pf/conditional_pseg.h b/gi/pf/conditional_pseg.h index 0aa5e8e0..2e9e38fc 100644 --- a/gi/pf/conditional_pseg.h +++ b/gi/pf/conditional_pseg.h @@ -6,6 +6,7 @@ #include #include +#include "m.h" #include "prob.h" #include "ccrp_nt.h" #include "mfcr.h" @@ -210,7 +211,7 @@ struct ConditionalParallelSegementationModel { prob_t AlignProbability(unsigned span) const { prob_t p; - p.logeq(aligns.logprob(span, log_poisson(span, 1.0))); + p.logeq(aligns.logprob(span, Md::log_poisson(span, 1.0))); return p; } diff --git a/gi/pf/pfdist.cc b/gi/pf/pfdist.cc index ef08a165..3d578db2 100644 --- a/gi/pf/pfdist.cc +++ b/gi/pf/pfdist.cc @@ -315,7 +315,7 @@ struct BackwardEstimate { for (int i = 0; i < src_cov.size(); ++i) if (!src_cov[i]) r.push_back(src_[i]); const prob_t uniform_alignment(1.0 / r.size()); - e.logeq(log_poisson(trg_.size() - trg_cov, r.size() - 1)); // p(trg len remaining | src len remaining) + e.logeq(Md::log_poisson(trg_.size() - trg_cov, r.size() - 1)); // p(trg len remaining | src len remaining) for (unsigned j = trg_cov; j < trg_.size(); ++j) { prob_t p; for (unsigned i = 0; i < r.size(); ++i) @@ -352,7 +352,7 @@ struct BackwardEstimateSym { if (!src_cov[i]) r.push_back(src_[i]); r.push_back(0); // NULL word const prob_t uniform_alignment(1.0 / r.size()); - e.logeq(log_poisson(trg_.size() - trg_cov, r.size() - 1)); // p(trg len remaining | src len remaining) + e.logeq(Md::log_poisson(trg_.size() - trg_cov, r.size() - 1)); // p(trg len remaining | src len remaining) for (unsigned j = trg_cov; j < trg_.size(); ++j) { prob_t p; for (unsigned i = 0; i < r.size(); ++i) @@ -367,7 +367,7 @@ struct BackwardEstimateSym { r.pop_back(); const prob_t inv_uniform(1.0 / (trg_.size() - trg_cov + 1.0)); prob_t inv; - inv.logeq(log_poisson(r.size(), trg_.size() - trg_cov)); + inv.logeq(Md::log_poisson(r.size(), trg_.size() - trg_cov)); for (unsigned i = 0; i < r.size(); ++i) { prob_t p; for (unsigned j = trg_cov - 1; j < trg_.size(); ++j) diff --git a/gi/pf/pfnaive.cc b/gi/pf/pfnaive.cc index acba9d22..e1a53f5c 100644 --- a/gi/pf/pfnaive.cc +++ b/gi/pf/pfnaive.cc @@ -77,7 +77,7 @@ struct BackwardEstimateSym { r.push_back(src_[i]); r.push_back(0); // NULL word const prob_t uniform_alignment(1.0 / r.size()); - e.logeq(log_poisson(trg_.size() - trg_cov, r.size() - 1)); // p(trg len remaining | src len remaining) + e.logeq(Md::log_poisson(trg_.size() - trg_cov, r.size() - 1)); // p(trg len remaining | src len remaining) for (unsigned j = trg_cov; j < trg_.size(); ++j) { prob_t p; for (unsigned i = 0; i < r.size(); ++i) @@ -92,7 +92,7 @@ struct BackwardEstimateSym { r.pop_back(); const prob_t inv_uniform(1.0 / (trg_.size() - trg_cov + 1.0)); prob_t inv; - inv.logeq(log_poisson(r.size(), trg_.size() - trg_cov)); + inv.logeq(Md::log_poisson(r.size(), trg_.size() - trg_cov)); for (unsigned i = 0; i < r.size(); ++i) { prob_t p; for (unsigned j = trg_cov - 1; j < trg_.size(); ++j) -- cgit v1.2.3