Merge remote branch 'upstream/master'

Conflicts:
	Jamroot
	bjam
	decoder/Jamfile
	decoder/cdec.cc
	dpmert/Jamfile
	jam-files/sanity.jam
	klm/lm/Jamfile
	klm/util/Jamfile
	mira/Jamfile

1 files changed, 0 insertions, 466 deletions

diff --git a/gi/pyp-topics/src/mpi-pyp-topics.cc b/gi/pyp-topics/src/mpi-pyp-topics.cc
deleted file mode 100644
index d6e22af6..00000000
--- a/gi/pyp-topics/src/mpi-pyp-topics.cc
+++ /dev/null
@@ -1,466 +0,0 @@
-#include <boost/mpi/communicator.hpp>
-
-#include "timing.h"
-#include "mpi-pyp-topics.hh"
-
-//#include <boost/date_time/posix_time/posix_time_types.hpp>
-void MPIPYPTopics::sample_corpus(const MPICorpus& corpus, int samples,
-                              int freq_cutoff_start, int freq_cutoff_end,
-                              int freq_cutoff_interval,
-                              int max_contexts_per_document) {
-  Timer timer;
-
-  //int documents = corpus.num_documents();
-  /*
-  m_mpi_start = 0;
-  m_mpi_end = documents;
-  if (m_size != 1) {
-      assert(documents < std::numeric_limits<int>::max());
-      m_mpi_start = (documents / m_size) * m_rank;
-      if (m_rank == m_size-1) m_mpi_end = documents;
-      else m_mpi_end = (documents / m_size)*(m_rank+1);
-  }
-  */
-  corpus.bounds(&m_mpi_start, &m_mpi_end);
-  int local_documents = m_mpi_end - m_mpi_start;
-
-  if (!m_backoff.get()) {
-    m_word_pyps.clear();
-    m_word_pyps.push_back(MPIPYPs());
-  }
-
-  if (m_am_root) std::cerr << "\n Training with " << m_word_pyps.size()-1 << " backoff level"
-    << (m_word_pyps.size()>1 ? ":" : "s:") << std::endl;
-
-  for (int i=0; i<(int)m_word_pyps.size(); ++i) {
-    m_word_pyps.at(i).reserve(m_num_topics);
-    for (int j=0; j<m_num_topics; ++j)
-      m_word_pyps.at(i).push_back(new MPIPYP<int>(0.5, 1.0));
-  }
-  if (m_am_root) std::cerr << std::endl;
-
-  m_document_pyps.reserve(local_documents);
-  //m_document_pyps.reserve(corpus.num_documents());
-  //for (int j=0; j<corpus.num_documents(); ++j)
-  for (int j=0; j<local_documents; ++j)
-    m_document_pyps.push_back(new PYP<int>(0.5, 1.0));
-
-  m_topic_p0 = 1.0/m_num_topics;
-  m_term_p0 = 1.0/corpus.num_types();
-  m_backoff_p0 = 1.0/corpus.num_documents();
-
-  if (m_am_root) std::cerr << " Documents: " << corpus.num_documents() << "(" 
-    << local_documents << ")" << " Terms: " << corpus.num_types() << std::endl;
-
-  int frequency_cutoff = freq_cutoff_start;
-  if (m_am_root) std::cerr << " Context frequency cutoff set to " << frequency_cutoff << std::endl;
-
-  timer.Reset();
-  // Initialisation pass
-  int document_id=0, topic_counter=0;
-  for (int i=0; i<local_documents; ++i) {
-    document_id = i+m_mpi_start;
-
-  //for (Corpus::const_iterator corpusIt=corpus.begin();
-  //     corpusIt != corpus.end(); ++corpusIt, ++document_id) {
-    m_corpus_topics.push_back(DocumentTopics(corpus.at(document_id).size(), 0));
-
-    int term_index=0;
-    for (Document::const_iterator docIt=corpus.at(document_id).begin();
-         docIt != corpus.at(document_id).end(); ++docIt, ++term_index) {
-      topic_counter++;
-      Term term = *docIt;
-
-      // sample a new_topic
-      //int new_topic = (topic_counter % m_num_topics);
-      int freq = corpus.context_count(term);
-      int new_topic = -1;
-      if (freq > frequency_cutoff
-          && (!max_contexts_per_document || term_index < max_contexts_per_document)) {
-        new_topic = sample(i, term);
-        //new_topic = document_id % m_num_topics;
-
-        // add the new topic to the PYPs
-        increment(term, new_topic);
-
-        if (m_use_topic_pyp) {
-          F p0 = m_topic_pyp.prob(new_topic, m_topic_p0);
-          int table_delta = m_document_pyps.at(i).increment(new_topic, p0);
-          if (table_delta)
-            m_topic_pyp.increment(new_topic, m_topic_p0, rnd);
-        }
-        else m_document_pyps.at(i).increment(new_topic, m_topic_p0);
-      }
-
-      m_corpus_topics.at(i).at(term_index) = new_topic;
-    }
-  }
-
-  // Synchronise the topic->word counds across the processes.
-  synchronise();
-
-  if (m_am_root) std::cerr << "  Initialized in " << timer.Elapsed() << " seconds\n";
-
-  int* randomDocIndices = new int[local_documents];
-  for (int i = 0; i < local_documents; ++i)
-	  randomDocIndices[i] = i;
-
-  // Sampling phase
-  for (int curr_sample=0; curr_sample < samples; ++curr_sample) {
-    if (freq_cutoff_interval > 0 && curr_sample != 1
-        && curr_sample % freq_cutoff_interval == 1
-        && frequency_cutoff > freq_cutoff_end) {
-      frequency_cutoff--;
-      if (m_am_root) std::cerr << "\n Context frequency cutoff set to " << frequency_cutoff << std::endl;
-    }
-
-    if (m_am_root) std::cerr << "\n  -- Sample " << curr_sample << " "; std::cerr.flush();
-
-    // Randomize the corpus indexing array
-    int tmp;
-    int processed_terms=0;
-    for (int i = (local_documents-1); i > 0; --i) {
-      //i+1 since j \in [0,i] but rnd() \in [0,1)
-    	int j = (int)(rnd() * (i+1));
-      assert(j >= 0 && j <= i);
-     	tmp = randomDocIndices[i];
-    	randomDocIndices[i] = randomDocIndices[j];
-    	randomDocIndices[j] = tmp;
-    }
-
-    // for each document in the corpus
-    for (int rand_doc=0; rand_doc<local_documents; ++rand_doc) {
-    	int doc_index = randomDocIndices[rand_doc];
-    	int document_id = doc_index + m_mpi_start;
-      const Document& doc = corpus.at(document_id);
-
-      // for each term in the document
-      int term_index=0;
-      Document::const_iterator docEnd = doc.end();
-      for (Document::const_iterator docIt=doc.begin();
-           docIt != docEnd; ++docIt, ++term_index) {
-
-        if (max_contexts_per_document && term_index > max_contexts_per_document)
-          break;
-        
-        Term term = *docIt;
-        int freq = corpus.context_count(term);
-        if (freq < frequency_cutoff)
-          continue;
-
-        processed_terms++;
-
-        // remove the prevous topic from the PYPs
-        int current_topic = m_corpus_topics.at(doc_index).at(term_index);
-        // a negative label mean that term hasn't been sampled yet
-        if (current_topic >= 0) {
-          decrement(term, current_topic);
-
-          int table_delta = m_document_pyps.at(doc_index).decrement(current_topic);
-          if (m_use_topic_pyp && table_delta < 0)
-            m_topic_pyp.decrement(current_topic, rnd);
-        }
-
-        // sample a new_topic
-        int new_topic = sample(doc_index, term);
-
-        // add the new topic to the PYPs
-        m_corpus_topics.at(doc_index).at(term_index) = new_topic;
-        increment(term, new_topic);
-
-        if (m_use_topic_pyp) {
-          F p0 = m_topic_pyp.prob(new_topic, m_topic_p0);
-          int table_delta = m_document_pyps.at(doc_index).increment(new_topic, p0);
-          if (table_delta)
-            m_topic_pyp.increment(new_topic, m_topic_p0, rnd);
-        }
-        else m_document_pyps.at(doc_index).increment(new_topic, m_topic_p0);
-      }
-      if (document_id && document_id % 10000 == 0) {
-        if (m_am_root) std::cerr << "."; std::cerr.flush();
-      }
-    }
-    std::cerr << "|"; std::cerr.flush();  
-
-    // Synchronise the topic->word counds across the processes.
-    synchronise();
-
-    if (m_am_root) std::cerr << " ||| sampled " << processed_terms << " terms.";
-
-    if (curr_sample != 0 && curr_sample % 10 == 0) {
-      if (m_am_root) std::cerr << " ||| time=" << (timer.Elapsed() / 10.0) << " sec/sample" << std::endl;
-      timer.Reset();
-      if (m_am_root) std::cerr << "     ... Resampling hyperparameters"; std::cerr.flush();
-
-      // resample the hyperparamters
-      F log_p=0.0;
-      for (std::vector<MPIPYPs>::iterator levelIt=m_word_pyps.begin();
-           levelIt != m_word_pyps.end(); ++levelIt) {
-        for (MPIPYPs::iterator pypIt=levelIt->begin();
-             pypIt != levelIt->end(); ++pypIt) {
-          pypIt->resample_prior(rnd);
-          log_p += pypIt->log_restaurant_prob();
-        }
-      }
-
-      for (PYPs::iterator pypIt=m_document_pyps.begin();
-           pypIt != m_document_pyps.end(); ++pypIt) {
-        pypIt->resample_prior(rnd);
-        log_p += pypIt->log_restaurant_prob();
-      }
-
-      if (m_use_topic_pyp) {
-        m_topic_pyp.resample_prior(rnd);
-        log_p += m_topic_pyp.log_restaurant_prob();
-      }
-
-      std::cerr.precision(10);
-      if (m_am_root) std::cerr << " ||| LLH=" << log_p << " ||| resampling time=" << timer.Elapsed() << " sec" << std::endl;
-      timer.Reset();
-
-      int k=0;
-      if (m_am_root) std::cerr << "Topics distribution: ";
-      std::cerr.precision(2);
-      for (MPIPYPs::iterator pypIt=m_word_pyps.front().begin();
-           pypIt != m_word_pyps.front().end(); ++pypIt, ++k) {
-        if (m_am_root && k % 5 == 0) std::cerr << std::endl << '\t';
-        if (m_am_root) std::cerr << "<" << k << ":" << pypIt->num_customers() << ","
-          << pypIt->num_types() << "," << m_topic_pyp.prob(k, m_topic_p0) << "> ";
-      }
-      std::cerr.precision(4);
-      if (m_am_root) std::cerr << std::endl;
-    }
-  }
-  delete [] randomDocIndices;
-}
-
-void MPIPYPTopics::synchronise() {
-  // Synchronise the topic->word counds across the processes.
-  //for (std::vector<MPIPYPs>::iterator levelIt=m_word_pyps.begin();
-  //     levelIt != m_word_pyps.end(); ++levelIt) {
-//  std::vector<MPIPYPs>::iterator levelIt=m_word_pyps.begin(); 
-//  {
-//    for (MPIPYPs::iterator pypIt=levelIt->begin(); pypIt != levelIt->end(); ++pypIt) {
-    for (size_t label=0; label < m_word_pyps.at(0).size(); ++label) {
-      MPIPYP<int>& pyp = m_word_pyps.at(0).at(label);
-
-      //if (!m_am_root) boost::mpi::communicator().barrier();
-      //std::cerr << "Before Sync Process " << m_rank << ":";
-      //pyp.debug_info(std::cerr); std::cerr << std::endl;
-      //if (m_am_root) boost::mpi::communicator().barrier();
-
-      MPIPYP<int>::dish_delta_type delta;
-      pyp.synchronise(&delta);
-
-      for (MPIPYP<int>::dish_delta_type::const_iterator it=delta.begin(); it != delta.end(); ++it) {
-        int count = it->second;
-        if (count > 0)
-          for (int i=0; i < count; ++i) increment(it->first, label);
-        if (count < 0)
-          for (int i=0; i > count; --i) decrement(it->first, label);
-      }
-      pyp.reset_deltas();
-
-      //if (!m_am_root) boost::mpi::communicator().barrier();
-      //std::cerr << "After Sync Process " << m_rank << ":";
-      //pyp.debug_info(std::cerr); std::cerr << std::endl;
-      //if (m_am_root) boost::mpi::communicator().barrier();
-    }
-//  }
-    // Synchronise the hierarchical topic pyp
-    MPIPYP<int>::dish_delta_type topic_delta;
-    m_topic_pyp.synchronise(&topic_delta);
-    for (MPIPYP<int>::dish_delta_type::const_iterator it=topic_delta.begin(); it != topic_delta.end(); ++it) {
-      int count = it->second;
-      if (count > 0)
-        for (int i=0; i < count; ++i) 
-          m_topic_pyp.increment(it->first, m_topic_p0, rnd);
-      if (count < 0)
-        for (int i=0; i > count; --i) 
-          m_topic_pyp.decrement(it->first, rnd);
-    }
-    m_topic_pyp.reset_deltas();
-}
-
-void MPIPYPTopics::decrement(const Term& term, int topic, int level) {
-  //std::cerr << "MPIPYPTopics::decrement(" << term << "," << topic << "," << level << ")" << std::endl;
-  m_word_pyps.at(level).at(topic).decrement(term, rnd);
-  if (m_backoff.get()) {
-    Term backoff_term = (*m_backoff)[term];
-    if (!m_backoff->is_null(backoff_term))
-      decrement(backoff_term, topic, level+1);
-  }
-}
-
-void MPIPYPTopics::increment(const Term& term, int topic, int level) {
-  //std::cerr << "MPIPYPTopics::increment(" << term << "," << topic << "," << level << ")" << std::endl;
-  m_word_pyps.at(level).at(topic).increment(term, word_pyps_p0(term, topic, level), rnd);
-
-  if (m_backoff.get()) {
-    Term backoff_term = (*m_backoff)[term];
-    if (!m_backoff->is_null(backoff_term))
-      increment(backoff_term, topic, level+1);
-  }
-}
-
-int MPIPYPTopics::sample(const DocumentId& doc, const Term& term) {
-  // First pass: collect probs
-  F sum=0.0;
-  std::vector<F> sums;
-  for (int k=0; k<m_num_topics; ++k) {
-    F p_w_k = prob(term, k);
-
-    F topic_prob = m_topic_p0;
-    if (m_use_topic_pyp) topic_prob = m_topic_pyp.prob(k, m_topic_p0);
-
-    //F p_k_d = m_document_pyps[doc].prob(k, topic_prob);
-    F p_k_d = m_document_pyps.at(doc).unnormalised_prob(k, topic_prob);
-
-    sum += (p_w_k*p_k_d);
-    sums.push_back(sum);
-  }
-  // Second pass: sample a topic
-  F cutoff = rnd() * sum;
-  for (int k=0; k<m_num_topics; ++k) {
-    if (cutoff <= sums[k])
-      return k;
-  }
-  std::cerr << cutoff << " " << sum << std::endl;
-  assert(false);
-}
-
-MPIPYPTopics::F MPIPYPTopics::word_pyps_p0(const Term& term, int topic, int level) const {
-  //for (int i=0; i<level+1; ++i) std::cerr << "  ";
-  //std::cerr << "MPIPYPTopics::word_pyps_p0(" << term << "," << topic << "," << level << ")" << std::endl;
-
-  F p0 = m_term_p0;
-  if (m_backoff.get()) {
-    //static F fudge=m_backoff_p0; // TODO
-
-    Term backoff_term = (*m_backoff)[term];
-    if (!m_backoff->is_null(backoff_term)) {
-      assert (level < m_backoff->order());
-      //p0 = (1.0/(double)m_backoff->terms_at_level(level))*prob(backoff_term, topic, level+1);
-      p0 = prob(backoff_term, topic, level+1);
-    }
-    else
-      p0 = m_term_p0;
-  }
-  //for (int i=0; i<level+1; ++i) std::cerr << "  ";
-  //std::cerr << "MPIPYPTopics::word_pyps_p0(" << term << "," << topic << "," << level << ") = " << p0 << std::endl;
-  return p0;
-}
-
-MPIPYPTopics::F MPIPYPTopics::prob(const Term& term, int topic, int level) const {
-  //for (int i=0; i<level+1; ++i) std::cerr << "  ";
-  //std::cerr << "MPIPYPTopics::prob(" << term << "," << topic << "," << level << " " << factor << ")" << std::endl;
-
-  F p0 = word_pyps_p0(term, topic, level);
-  F p_w_k = m_word_pyps.at(level).at(topic).prob(term, p0);
-
-  //for (int i=0; i<level+1; ++i) std::cerr << "  ";
-  //std::cerr << "MPIPYPTopics::prob(" << term << "," << topic << "," << level << ") = " << p_w_k << std::endl;
-
-  return p_w_k;
-}
-
-int MPIPYPTopics::max_topic() const {
-  if (!m_use_topic_pyp)
-    return -1;
-
-  F current_max=0.0;
-  int current_topic=-1;
-  for (int k=0; k<m_num_topics; ++k) {
-    F prob = m_topic_pyp.prob(k, m_topic_p0);
-    if (prob > current_max) {
-      current_max = prob;
-      current_topic = k;
-    }
-  }
-  assert(current_topic >= 0);
-  assert(current_max >= 0);
-  return current_max;
-}
-
-std::pair<int,MPIPYPTopics::F> MPIPYPTopics::max(const DocumentId& true_doc) const {
-  //std::cerr << "MPIPYPTopics::max(" << doc << "," << term << ")" << std::endl;
-  // collect probs
-  F current_max=0.0;
-  DocumentId local_doc = true_doc - m_mpi_start;
-  int current_topic=-1;
-  for (int k=0; k<m_num_topics; ++k) {
-    //F p_w_k = prob(term, k);
-
-    F topic_prob = m_topic_p0;
-    if (m_use_topic_pyp)
-      topic_prob = m_topic_pyp.prob(k, m_topic_p0);
-
-    F prob = 0;
-    if (local_doc < 0) prob = topic_prob;
-    else               prob = m_document_pyps.at(local_doc).prob(k, topic_prob);
-
-    if (prob > current_max) {
-      current_max = prob;
-      current_topic = k;
-    }
-  }
-  assert(current_topic >= 0);
-  assert(current_max >= 0);
-  return std::make_pair(current_topic, current_max);
-}
-
-std::pair<int,MPIPYPTopics::F> MPIPYPTopics::max(const DocumentId& true_doc, const Term& term) const {
-  //std::cerr << "MPIPYPTopics::max(" << doc << "," << term << ")" << std::endl;
-  // collect probs
-  F current_max=0.0;
-  DocumentId local_doc = true_doc - m_mpi_start;
-  int current_topic=-1;
-  for (int k=0; k<m_num_topics; ++k) {
-    F p_w_k = prob(term, k);
-
-    F topic_prob = m_topic_p0;
-    if (m_use_topic_pyp)
-      topic_prob = m_topic_pyp.prob(k, m_topic_p0);
-
-    F p_k_d = 0;
-    if (local_doc < 0) p_k_d = topic_prob;
-    else               p_k_d = m_document_pyps.at(local_doc).prob(k, topic_prob);
-
-    F prob = (p_w_k*p_k_d);
-    if (prob > current_max) {
-      current_max = prob;
-      current_topic = k;
-    }
-  }
-  assert(current_topic >= 0);
-  assert(current_max >= 0);
-  return std::make_pair(current_topic, current_max);
-}
-
-std::ostream& MPIPYPTopics::print_document_topics(std::ostream& out) const {
-  for (CorpusTopics::const_iterator corpusIt=m_corpus_topics.begin();
-       corpusIt != m_corpus_topics.end(); ++corpusIt) {
-    int term_index=0;
-    for (DocumentTopics::const_iterator docIt=corpusIt->begin();
-         docIt != corpusIt->end(); ++docIt, ++term_index) {
-      if (term_index) out << " ";
-      out << *docIt;
-    }
-    out << std::endl;
-  }
-  return out;
-}
-
-std::ostream& MPIPYPTopics::print_topic_terms(std::ostream& out) const {
-  for (PYPs::const_iterator pypsIt=m_word_pyps.front().begin();
-       pypsIt != m_word_pyps.front().end(); ++pypsIt) {
-    int term_index=0;
-    for (PYP<int>::const_iterator termIt=pypsIt->begin();
-         termIt != pypsIt->end(); ++termIt, ++term_index) {
-      if (term_index) out << " ";
-      out << termIt->first << ":" << termIt->second;
-    }
-    out << std::endl;
-  }
-  return out;
-}