cdec cleanup, remove bayesian stuff, parsing stuff

1 files changed, 0 insertions, 291 deletions

diff --git a/gi/clda/src/ccrp.h b/gi/clda/src/ccrp.h
deleted file mode 100644
index a7c2825c..00000000
--- a/gi/clda/src/ccrp.h
+++ /dev/null
@@ -1,291 +0,0 @@
-#ifndef _CCRP_H_
-#define _CCRP_H_
-
-#include <numeric>
-#include <cassert>
-#include <cmath>
-#include <list>
-#include <iostream>
-#include <vector>
-#include <tr1/unordered_map>
-#include <boost/functional/hash.hpp>
-#include "sampler.h"
-#include "slice_sampler.h"
-
-// Chinese restaurant process (Pitman-Yor parameters) with table tracking.
-
-template <typename Dish, typename DishHash = boost::hash<Dish> >
-class CCRP {
- public:
-  CCRP(double disc, double conc) :
-    num_tables_(),
-    num_customers_(),
-    discount_(disc),
-    concentration_(conc),
-    discount_prior_alpha_(std::numeric_limits<double>::quiet_NaN()),
-    discount_prior_beta_(std::numeric_limits<double>::quiet_NaN()),
-    concentration_prior_shape_(std::numeric_limits<double>::quiet_NaN()),
-    concentration_prior_rate_(std::numeric_limits<double>::quiet_NaN()) {}
-
-  CCRP(double d_alpha, double d_beta, double c_shape, double c_rate, double d = 0.1, double c = 10.0) :
-    num_tables_(),
-    num_customers_(),
-    discount_(d),
-    concentration_(c),
-    discount_prior_alpha_(d_alpha),
-    discount_prior_beta_(d_beta),
-    concentration_prior_shape_(c_shape),
-    concentration_prior_rate_(c_rate) {}
-
-  double discount() const { return discount_; }
-  double concentration() const { return concentration_; }
-
-  bool has_discount_prior() const {
-    return !std::isnan(discount_prior_alpha_);
-  }
-
-  bool has_concentration_prior() const {
-    return !std::isnan(concentration_prior_shape_);
-  }
-
-  void clear() {
-    num_tables_ = 0;
-    num_customers_ = 0;
-    dish_locs_.clear();
-  }
-
-  unsigned num_tables(const Dish& dish) const {
-    const typename std::tr1::unordered_map<Dish, DishLocations, DishHash>::const_iterator it = dish_locs_.find(dish);
-    if (it == dish_locs_.end()) return 0;
-    return it->second.table_counts_.size();
-  }
-
-  unsigned num_customers() const {
-    return num_customers_;
-  }
-
-  unsigned num_customers(const Dish& dish) const {
-    const typename std::tr1::unordered_map<Dish, DishLocations, DishHash>::const_iterator it = dish_locs_.find(dish);
-    if (it == dish_locs_.end()) return 0;
-    return it->total_dish_count_;
-  }
-
-  // returns +1 or 0 indicating whether a new table was opened
-  int increment(const Dish& dish, const double& p0, MT19937* rng) {
-    DishLocations& loc = dish_locs_[dish];
-    bool share_table = false;
-    if (loc.total_dish_count_) {
-      const double p_empty = (concentration_ + num_tables_ * discount_) * p0;
-      const double p_share = (loc.total_dish_count_ - loc.table_counts_.size() * discount_);
-      share_table = rng->SelectSample(p_empty, p_share);
-    }
-    if (share_table) {
-      double r = rng->next() * (loc.total_dish_count_ - loc.table_counts_.size() * discount_);
-      for (typename std::list<unsigned>::iterator ti = loc.table_counts_.begin();
-           ti != loc.table_counts_.end(); ++ti) {
-        r -= (*ti - discount_);
-        if (r <= 0.0) {
-          ++(*ti);
-          break;
-        }
-      }
-      if (r > 0.0) {
-        std::cerr << "Serious error: r=" << r << std::endl;
-        Print(&std::cerr);
-        assert(r <= 0.0);
-      }
-    } else {
-      loc.table_counts_.push_back(1u);
-      ++num_tables_;
-    }
-    ++loc.total_dish_count_;
-    ++num_customers_;
-    return (share_table ? 0 : 1);
-  }
-
-  // returns -1 or 0, indicating whether a table was closed
-  int decrement(const Dish& dish, MT19937* rng) {
-    DishLocations& loc = dish_locs_[dish];
-    assert(loc.total_dish_count_);
-    if (loc.total_dish_count_ == 1) {
-      dish_locs_.erase(dish);
-      --num_tables_;
-      --num_customers_;
-      return -1;
-    } else {
-      int delta = 0;
-      // sample customer to remove UNIFORMLY. that is, do NOT use the discount
-      // here. if you do, it will introduce (unwanted) bias!
-      double r = rng->next() * loc.total_dish_count_;
-      --loc.total_dish_count_;
-      for (typename std::list<unsigned>::iterator ti = loc.table_counts_.begin();
-           ti != loc.table_counts_.end(); ++ti) {
-        r -= *ti;
-        if (r <= 0.0) {
-          if ((--(*ti)) == 0) {
-            --num_tables_;
-            delta = -1;
-            loc.table_counts_.erase(ti);
-          }
-          break;
-        }
-      }
-      if (r > 0.0) {
-        std::cerr << "Serious error: r=" << r << std::endl;
-        Print(&std::cerr);
-        assert(r <= 0.0);
-      }
-      --num_customers_;
-      return delta;
-    }
-  }
-
-  double prob(const Dish& dish, const double& p0) const {
-    const typename std::tr1::unordered_map<Dish, DishLocations, DishHash>::const_iterator it = dish_locs_.find(dish);
-    const double r = num_tables_ * discount_ + concentration_;
-    if (it == dish_locs_.end()) {
-      return r * p0 / (num_customers_ + concentration_);
-    } else {
-      return (it->second.total_dish_count_ - discount_ * it->second.table_counts_.size() + r * p0) /
-               (num_customers_ + concentration_);
-    }
-  }
-
-  double log_crp_prob() const {
-    return log_crp_prob(discount_, concentration_);
-  }
-
-  static double log_beta_density(const double& x, const double& alpha, const double& beta) {
-    assert(x > 0.0);
-    assert(x < 1.0);
-    assert(alpha > 0.0);
-    assert(beta > 0.0);
-    const double lp = (alpha-1)*log(x)+(beta-1)*log(1-x)+lgamma(alpha+beta)-lgamma(alpha)-lgamma(beta);
-    return lp;
-  }
-
-  static double log_gamma_density(const double& x, const double& shape, const double& rate) {
-    assert(x >= 0.0);
-    assert(shape > 0.0);
-    assert(rate > 0.0);
-    const double lp = (shape-1)*log(x) - shape*log(rate) - x/rate - lgamma(shape);
-    return lp;
-  }
-
-  // taken from http://en.wikipedia.org/wiki/Chinese_restaurant_process
-  // does not include P_0's
-  double log_crp_prob(const double& discount, const double& concentration) const {
-    double lp = 0.0;
-    if (has_discount_prior())
-      lp = log_beta_density(discount, discount_prior_alpha_, discount_prior_beta_);
-    if (has_concentration_prior())
-      lp += log_gamma_density(concentration, concentration_prior_shape_, concentration_prior_rate_);
-    assert(lp <= 0.0);
-    if (num_customers_) {
-      if (discount > 0.0) {
-        const double r = lgamma(1.0 - discount);
-        lp += lgamma(concentration) - lgamma(concentration + num_customers_)
-             + num_tables_ * log(discount) + lgamma(concentration / discount + num_tables_)
-             - lgamma(concentration / discount);
-        assert(std::isfinite(lp));
-        for (typename std::tr1::unordered_map<Dish, DishLocations, DishHash>::const_iterator it = dish_locs_.begin();
-             it != dish_locs_.end(); ++it) {
-          const DishLocations& cur = it->second;
-          for (std::list<unsigned>::const_iterator ti = cur.table_counts_.begin(); ti != cur.table_counts_.end(); ++ti) {
-            lp += lgamma(*ti - discount) - r;
-          }
-        }
-      } else {
-        assert(!"not implemented yet");
-      }
-    }
-    assert(std::isfinite(lp));
-    return lp;
-  }
-
-  void resample_hyperparameters(MT19937* rng) {
-    assert(has_discount_prior() || has_concentration_prior());
-    DiscountResampler dr(*this);
-    ConcentrationResampler cr(*this);
-    const int niterations = 10;
-    double gamma_upper = std::numeric_limits<double>::infinity();
-    for (int iter = 0; iter < 5; ++iter) {
-      if (has_concentration_prior()) {
-        concentration_ = slice_sampler1d(cr, concentration_, *rng, 0.0,
-                               gamma_upper, 0.0, niterations, 100*niterations);
-      }
-      if (has_discount_prior()) {
-        discount_ = slice_sampler1d(dr, discount_, *rng, std::numeric_limits<double>::min(),
-                               1.0, 0.0, niterations, 100*niterations);
-      }
-    }
-    concentration_ = slice_sampler1d(cr, concentration_, *rng, 0.0,
-                             gamma_upper, 0.0, niterations, 100*niterations);
-  }
-
-  struct DiscountResampler {
-    DiscountResampler(const CCRP& crp) : crp_(crp) {}
-    const CCRP& crp_;
-    double operator()(const double& proposed_discount) const {
-      return crp_.log_crp_prob(proposed_discount, crp_.concentration_);
-    }
-  };
-
-  struct ConcentrationResampler {
-    ConcentrationResampler(const CCRP& crp) : crp_(crp) {}
-    const CCRP& crp_;
-    double operator()(const double& proposed_concentration) const {
-      return crp_.log_crp_prob(crp_.discount_, proposed_concentration);
-    }
-  };
-
-  struct DishLocations {
-    DishLocations() : total_dish_count_() {}
-    unsigned total_dish_count_;        // customers at all tables with this dish
-    std::list<unsigned> table_counts_; // list<> gives O(1) deletion and insertion, which we want
-                                       // .size() is the number of tables for this dish
-  };
-
-  void Print(std::ostream* out) const {
-    for (typename std::tr1::unordered_map<Dish, DishLocations, DishHash>::const_iterator it = dish_locs_.begin();
-         it != dish_locs_.end(); ++it) {
-      (*out) << it->first << " (" << it->second.total_dish_count_ << " on " << it->second.table_counts_.size() << " tables): ";
-      for (typename std::list<unsigned>::const_iterator i = it->second.table_counts_.begin();
-           i != it->second.table_counts_.end(); ++i) {
-        (*out) << " " << *i;
-      }
-      (*out) << std::endl;
-    }
-  }
-
-  typedef typename std::tr1::unordered_map<Dish, DishLocations, DishHash>::const_iterator const_iterator;
-  const_iterator begin() const {
-    return dish_locs_.begin();
-  }
-  const_iterator end() const {
-    return dish_locs_.end();
-  }
-
-  unsigned num_tables_;
-  unsigned num_customers_;
-  std::tr1::unordered_map<Dish, DishLocations, DishHash> dish_locs_;
-
-  double discount_;
-  double concentration_;
-
-  // optional beta prior on discount_ (NaN if no prior)
-  double discount_prior_alpha_;
-  double discount_prior_beta_;
-
-  // optional gamma prior on concentration_ (NaN if no prior)
-  double concentration_prior_shape_;
-  double concentration_prior_rate_;
-};
-
-template <typename T,typename H>
-std::ostream& operator<<(std::ostream& o, const CCRP<T,H>& c) {
-  c.Print(&o);
-  return o;
-}
-
-#endif