Merge remote-tracking branch 'upstream/master'

7 files changed, 2036 insertions, 15 deletions

diff --git a/training/Makefile.am b/training/Makefile.am
index e95e045f..8ef3c939 100644
--- a/training/Makefile.am
+++ b/training/Makefile.am
@@ -6,6 +6,7 @@ SUBDIRS = \
   dpmert \
   pro \
   dtrain \
+  latent_svm \
   mira \
   rampion
 
diff --git a/training/latent_svm/Makefile.am b/training/latent_svm/Makefile.am
new file mode 100644
index 00000000..65c5e038
--- /dev/null
+++ b/training/latent_svm/Makefile.am
@@ -0,0 +1,6 @@
+bin_PROGRAMS = latent_svm
+
+latent_svm_SOURCES = latent_svm.cc
+latent_svm_LDADD = ../..//decoder/libcdec.a ../../klm/search/libksearch.a ../../mteval/libmteval.a ../../utils/libutils.a ../../klm/lm/libklm.a ../../klm/util/libklm_util.a ../../klm/util/double-conversion/libklm_util_double.a
+
+AM_CPPFLAGS = -W -Wall -Wno-sign-compare -I$(top_srcdir)/utils -I$(top_srcdir)/decoder -I$(top_srcdir)/mteval
diff --git a/training/latent_svm/latent_svm.cc b/training/latent_svm/latent_svm.cc
new file mode 100644
index 00000000..ab9c1d5d
--- /dev/null
+++ b/training/latent_svm/latent_svm.cc
@@ -0,0 +1,412 @@
+/*
+Points to note regarding variable names:
+total_loss and prev_loss actually refer not to loss, but the metric (usually BLEU)
+*/
+#include <sstream>
+#include <iostream>
+#include <vector>
+#include <cassert>
+#include <cmath>
+
+//boost libraries
+#include <boost/shared_ptr.hpp>
+#include <boost/program_options.hpp>
+#include <boost/program_options/variables_map.hpp>
+
+//cdec libraries
+#include "config.h"
+#include "hg_sampler.h"
+#include "sentence_metadata.h"
+#include "scorer.h"
+#include "verbose.h"
+#include "viterbi.h"
+#include "hg.h"
+#include "prob.h"
+#include "kbest.h"
+#include "ff_register.h"
+#include "decoder.h"
+#include "filelib.h"
+#include "fdict.h"
+#include "weights.h"
+#include "sparse_vector.h"
+#include "sampler.h"
+
+using namespace std;
+using boost::shared_ptr;
+namespace po = boost::program_options;
+
+bool invert_score; 
+boost::shared_ptr<MT19937> rng; //random seed ptr
+
+void RandomPermutation(int len, vector<int>* p_ids) {
+  vector<int>& ids = *p_ids;
+  ids.resize(len);
+  for (int i = 0; i < len; ++i) ids[i] = i;
+  for (int i = len; i > 0; --i) {
+    int j = rng->next() * i;
+    if (j == i) i--;
+    swap(ids[i-1], ids[j]);
+  }  
+}
+
+bool InitCommandLine(int argc, char** argv, po::variables_map* conf) {
+  po::options_description opts("Configuration options");
+  opts.add_options()
+        ("weights,w",po::value<string>(),"[REQD] Input feature weights file")
+        ("input,i",po::value<string>(),"[REQD] Input source file for development set")
+        ("passes,p", po::value<int>()->default_value(15), "Number of passes through the training data")
+        ("weights_write_interval,n", po::value<int>()->default_value(1000), "Number of lines between writing out weights")
+        ("reference,r",po::value<vector<string> >(), "[REQD] Reference translation(s) (tokenized text file)")
+        ("mt_metric,m",po::value<string>()->default_value("ibm_bleu"), "Scoring metric (ibm_bleu, nist_bleu, koehn_bleu, ter, combi)")
+        ("regularizer_strength,C", po::value<double>()->default_value(0.01), "regularization strength")
+        ("mt_metric_scale,s", po::value<double>()->default_value(1.0), "Cost function is -mt_metric_scale*BLEU")
+        ("costaug_log_bleu,l", "Flag converts BLEU to log space. Cost function is thus -mt_metric_scale*log(BLEU). Not on by default")
+        ("average,A", "Average the weights (this is a weighted average due to the scaling factor)")
+        ("mu,u", po::value<double>()->default_value(0.0), "weight (between 0 and 1) to scale model score by for oracle selection")
+        ("stepsize_param,a", po::value<double>()->default_value(0.01), "Stepsize parameter, during optimization")
+        ("stepsize_reduce,t", "Divide step size by sqrt(number of examples seen so far), as per Ratliff et al., 2007")
+	("metric_threshold,T", po::value<double>()->default_value(0.0), "Threshold for diff between oracle BLEU and cost-aug BLEU for updating the weights")
+	("check_positive,P", "Check that the loss is positive before updating")
+        ("k_best_size,k", po::value<int>()->default_value(250), "Size of hypothesis list to search for oracles")
+        ("best_ever,b", "Keep track of the best hypothesis we've ever seen (metric score), and use that as the reference")
+        ("random_seed,S", po::value<uint32_t>(), "Random seed (if not specified, /dev/random will be used)")
+        ("decoder_config,c",po::value<string>(),"Decoder configuration file");
+  po::options_description clo("Command line options");
+  clo.add_options()
+        ("config", po::value<string>(), "Configuration file")
+        ("help,h", "Print this help message and exit");
+  po::options_description dconfig_options, dcmdline_options;
+  dconfig_options.add(opts);
+  dcmdline_options.add(opts).add(clo);
+  
+  po::store(parse_command_line(argc, argv, dcmdline_options), *conf);
+  if (conf->count("config")) {
+    ifstream config((*conf)["config"].as<string>().c_str());
+    po::store(po::parse_config_file(config, dconfig_options), *conf);
+  }
+  po::notify(*conf);
+
+  if (conf->count("help") || !conf->count("weights") || !conf->count("input") || !conf->count("decoder_config") || !conf->count("reference")) {
+    cerr << dcmdline_options << endl;
+    return false;
+  }
+  return true;
+}
+
+double scaling_trick = 1; // see http://blog.smola.org/post/940672544/fast-quadratic-regularization-for-online-learning
+/*computes and returns cost augmented score for negative example selection*/
+double cost_augmented_score(const LogVal<double> model_score, const double mt_metric_score, const double mt_metric_scale, const bool logbleu) {
+  if(logbleu) {
+    if(mt_metric_score != 0)
+      // NOTE: log(model_score) is just the model score feature weights * features
+      return log(model_score) * scaling_trick + (- mt_metric_scale * log(mt_metric_score));
+    else
+      return -1000000;
+  }
+  // NOTE: log(model_score) is just the model score feature weights * features
+  return log(model_score) * scaling_trick + (- mt_metric_scale * mt_metric_score);
+}
+
+/*computes and returns mu score, for oracle selection*/
+double muscore(const vector<weight_t>& feature_weights, const SparseVector<double>& feature_values, const double mt_metric_score, const double mu, const bool logbleu) {
+  if(logbleu) {
+    if(mt_metric_score != 0)
+      return feature_values.dot(feature_weights) * mu + (1 - mu) * log(mt_metric_score);
+    else
+      return feature_values.dot(feature_weights) * mu + (1 - mu) * (-1000000);  // log(0) is -inf
+  }
+  return feature_values.dot(feature_weights) * mu + (1 - mu) * mt_metric_score;
+}
+
+static const double kMINUS_EPSILON = -1e-6;
+
+struct HypothesisInfo {
+  SparseVector<double> features;
+  double mt_metric_score;
+  // The model score changes when the feature weights change, so it is not stored here
+  // It must be recomputed every time
+};
+
+struct GoodOracle {
+  shared_ptr<HypothesisInfo> good;
+};
+
+struct TrainingObserver : public DecoderObserver {
+  TrainingObserver(const int k,
+                   const DocScorer& d,
+                   vector<GoodOracle>* o,
+                   const vector<weight_t>& feat_weights,
+                   const double metric_scale,
+                   const double Mu,
+                   const bool bestever,
+                   const bool LogBleu) : ds(d), feature_weights(feat_weights), oracles(*o), kbest_size(k), mt_metric_scale(metric_scale), mu(Mu), best_ever(bestever), log_bleu(LogBleu) {}
+  const DocScorer& ds;
+  const vector<weight_t>& feature_weights;
+  vector<GoodOracle>& oracles;
+  shared_ptr<HypothesisInfo> cur_best;
+  shared_ptr<HypothesisInfo> cur_costaug_best;
+  shared_ptr<HypothesisInfo> cur_ref; 
+  const int kbest_size;
+  const double mt_metric_scale;
+  const double mu;
+  const bool best_ever;
+  const bool log_bleu;
+
+  const HypothesisInfo& GetCurrentBestHypothesis() const {
+    return *cur_best;
+  }
+
+  const HypothesisInfo& GetCurrentCostAugmentedHypothesis() const {
+    return *cur_costaug_best;
+  }
+
+  const HypothesisInfo& GetCurrentReference() const {
+    return *cur_ref; 
+  }
+
+  virtual void NotifyTranslationForest(const SentenceMetadata& smeta, Hypergraph* hg) {
+    UpdateOracles(smeta.GetSentenceID(), *hg);
+  }
+
+  shared_ptr<HypothesisInfo> MakeHypothesisInfo(const SparseVector<double>& feats, const double metric) {
+    shared_ptr<HypothesisInfo> h(new HypothesisInfo);
+    h->features = feats;
+    h->mt_metric_score = metric;
+    return h;
+  }
+
+  void UpdateOracles(int sent_id, const Hypergraph& forest) {
+    //shared_ptr<HypothesisInfo>& cur_ref = oracles[sent_id].good;
+    cur_ref = oracles[sent_id].good; 
+    if(!best_ever)
+      cur_ref.reset();
+
+    KBest::KBestDerivations<vector<WordID>, ESentenceTraversal> kbest(forest, kbest_size);
+    double costaug_best_score = 0;
+
+    for (int i = 0; i < kbest_size; ++i) {
+      const KBest::KBestDerivations<vector<WordID>, ESentenceTraversal>::Derivation* d =
+        kbest.LazyKthBest(forest.nodes_.size() - 1, i);
+      if (!d) break;
+      double mt_metric_score = ds[sent_id]->ScoreCandidate(d->yield)->ComputeScore(); //this might need to change!!
+      const SparseVector<double>& feature_vals = d->feature_values; 
+      double costaugmented_score = cost_augmented_score(d->score, mt_metric_score, mt_metric_scale, log_bleu); //note that d->score, i.e., model score, is passed in
+      if (i == 0) { //i.e., setting up cur_best to be model score highest, and initializing costaug_best
+        cur_best = MakeHypothesisInfo(feature_vals, mt_metric_score);
+        cur_costaug_best = cur_best;
+        costaug_best_score = costaugmented_score; 
+      }
+      if (costaugmented_score > costaug_best_score) {   // kbest_mira's cur_bad, i.e., "fear" derivation
+        cur_costaug_best = MakeHypothesisInfo(feature_vals, mt_metric_score);
+        costaug_best_score = costaugmented_score;
+      }
+      double cur_muscore = mt_metric_score;
+      if (!cur_ref)   // kbest_mira's cur_good, i.e., "hope" derivation
+        cur_ref =  MakeHypothesisInfo(feature_vals, cur_muscore);
+      else {
+          double cur_ref_muscore = cur_ref->mt_metric_score;
+          if(mu > 0) { //select oracle with mixture of model score and BLEU
+              cur_ref_muscore =  muscore(feature_weights, cur_ref->features, cur_ref->mt_metric_score, mu, log_bleu);
+              cur_muscore = muscore(feature_weights, d->feature_values, mt_metric_score, mu, log_bleu);
+          }
+          if (cur_muscore > cur_ref_muscore) //replace oracle
+            cur_ref = MakeHypothesisInfo(feature_vals, mt_metric_score);
+      }
+    }
+  }
+};
+
+void ReadTrainingCorpus(const string& fname, vector<string>* c) {
+  ReadFile rf(fname);
+  istream& in = *rf.stream();
+  string line;
+  while(in) {
+    getline(in, line);
+    if (!in) break;
+    c->push_back(line);
+  }
+}
+
+bool ApproxEqual(double a, double b) {
+  if (a == b) return true;
+  return (fabs(a-b)/fabs(b)) < 0.000001;
+}
+
+int main(int argc, char** argv) {
+  register_feature_functions();
+  SetSilent(true);  // turn off verbose decoder output
+
+  po::variables_map conf;
+  if (!InitCommandLine(argc, argv, &conf)) return 1;
+
+  if (conf.count("random_seed"))
+    rng.reset(new MT19937(conf["random_seed"].as<uint32_t>()));
+  else
+    rng.reset(new MT19937);
+
+  const bool best_ever = conf.count("best_ever") > 0;
+  vector<string> corpus;
+  ReadTrainingCorpus(conf["input"].as<string>(), &corpus);
+
+  const string metric_name = conf["mt_metric"].as<string>(); //set up scoring; this may need to be changed!!
+  
+  ScoreType type = ScoreTypeFromString(metric_name);
+  if (type == TER) {
+    invert_score = true;
+  } else {
+    invert_score = false;
+  } 
+  DocScorer ds(type, conf["reference"].as<vector<string> >(), "");
+  cerr << "Loaded " << ds.size() << " references for scoring with " << metric_name << endl;
+  if (ds.size() != corpus.size()) {
+    cerr << "Mismatched number of references (" << ds.size() << ") and sources (" << corpus.size() << ")\n";
+    return 1;
+  }
+
+  ReadFile ini_rf(conf["decoder_config"].as<string>());
+  Decoder decoder(ini_rf.stream());
+
+  // load initial weights
+  vector<weight_t>& decoder_weights = decoder.CurrentWeightVector(); //equivalent to "dense_weights" vector in kbest_mira.cc
+  SparseVector<weight_t> sparse_weights; //equivaelnt to  kbest_mira.cc "lambdas"
+  Weights::InitFromFile(conf["weights"].as<string>(), &decoder_weights);
+  Weights::InitSparseVector(decoder_weights, &sparse_weights);
+
+  //initializing other algorithm and output parameters
+  const double c = conf["regularizer_strength"].as<double>();
+  const int weights_write_interval = conf["weights_write_interval"].as<int>();
+  const double mt_metric_scale = conf["mt_metric_scale"].as<double>();
+  const double mu = conf["mu"].as<double>();
+  const double metric_threshold = conf["metric_threshold"].as<double>();
+  const double stepsize_param = conf["stepsize_param"].as<double>(); //step size in structured SGD optimization step
+  const bool stepsize_reduce = conf.count("stepsize_reduce") > 0; 
+  const bool costaug_log_bleu = conf.count("costaug_log_bleu") > 0;
+  const bool average = conf.count("average") > 0;
+  const bool checkpositive = conf.count("check_positive") > 0;
+
+  assert(corpus.size() > 0);
+  vector<GoodOracle> oracles(corpus.size());
+  TrainingObserver observer(conf["k_best_size"].as<int>(),  // kbest size
+                            ds,                             // doc scorer
+                            &oracles,
+                            decoder_weights,
+                            mt_metric_scale,
+                            mu,
+                            best_ever,
+                            costaug_log_bleu);
+  int cur_sent = 0;
+  int line_count = 0;
+  int normalizer = 0; 
+  double total_loss = 0;
+  double prev_loss = 0;
+  int dots = 0;             // progess bar
+  int cur_pass = 0;
+  SparseVector<double> tot;
+  tot += sparse_weights; //add initial weights to total
+  normalizer++; //add 1 to normalizer
+  int max_iteration = conf["passes"].as<int>();
+  string msg = "# LatentSVM tuned weights";
+  vector<int> order;
+  int interval_counter = 0;
+  RandomPermutation(corpus.size(), &order); //shuffle corpus
+  while (line_count <= max_iteration * corpus.size()) { //loop over all (passes * num sentences) examples
+    //if ((interval_counter * 40 / weights_write_interval) > dots) { ++dots; cerr << '.'; } //check this
+    if ((cur_sent * 40 / corpus.size()) > dots) { ++dots; cerr << '.';}
+    if (interval_counter == weights_write_interval) { //i.e., we need to write out weights
+      sparse_weights *= scaling_trick;
+      tot *= scaling_trick;
+      scaling_trick = 1;
+      cerr << " [SENTENCE NUMBER= " << cur_sent << "\n";
+      cerr << " [AVG METRIC LAST INTERVAL =" << ((total_loss - prev_loss) / weights_write_interval) << "]\n";
+      cerr << " [AVG METRIC THIS PASS THUS FAR =" << (total_loss / cur_sent) << "]\n";
+      cerr << " [TOTAL LOSS: =" << total_loss << "\n";
+      Weights::ShowLargestFeatures(decoder_weights);
+      //dots = 0;
+      interval_counter = 0;
+      prev_loss = total_loss;
+      if (average){
+	SparseVector<double> x = tot;
+	x /= normalizer;
+	ostringstream sa;
+	sa << "weights.latentsvm-" << line_count/weights_write_interval << "-avg.gz";
+	x.init_vector(&decoder_weights);
+	Weights::WriteToFile(sa.str(), decoder_weights, true, &msg); 
+      }
+      else {
+	ostringstream os;
+	os << "weights.latentsvm-" << line_count/weights_write_interval << ".gz";
+	sparse_weights.init_vector(&decoder_weights);
+	Weights::WriteToFile(os.str(), decoder_weights, true, &msg);
+      }
+    }
+    if (corpus.size() == cur_sent) { //i.e., finished a pass
+      //cerr << " [AVG METRIC LAST PASS=" << (document_metric_score / corpus.size()) << "]\n";
+      cerr << " [AVG METRIC LAST PASS=" << (total_loss / corpus.size()) << "]\n";
+      cerr << " TOTAL LOSS: " << total_loss << "\n";
+      Weights::ShowLargestFeatures(decoder_weights);
+      cur_sent = 0;
+      total_loss = 0;
+      dots = 0;
+      if(average) {
+        SparseVector<double> x = tot; 
+        x /= normalizer;
+        ostringstream sa;
+        sa << "weights.latentsvm-pass" << (cur_pass < 10 ? "0" : "") << cur_pass << "-avg.gz";
+        x.init_vector(&decoder_weights);
+        Weights::WriteToFile(sa.str(), decoder_weights, true, &msg);
+      }
+      else {
+	ostringstream os;
+	os << "weights.latentsvm-pass" << (cur_pass < 10 ? "0" : "") << cur_pass << ".gz";
+	Weights::WriteToFile(os.str(), decoder_weights, true, &msg);	
+      }
+      cur_pass++;
+      RandomPermutation(corpus.size(), &order);
+    }
+    if (cur_sent == 0) { //i.e., starting a new pass
+      cerr << "PASS " << (line_count / corpus.size() + 1) << endl;
+    }
+    sparse_weights.init_vector(&decoder_weights);   // copy sparse_weights to the decoder weights
+    decoder.SetId(order[cur_sent]); //assign current sentence
+    decoder.Decode(corpus[order[cur_sent]], &observer);  // decode/update oracles
+
+    const HypothesisInfo& cur_best = observer.GetCurrentBestHypothesis(); //model score best
+    const HypothesisInfo& cur_costaug = observer.GetCurrentCostAugmentedHypothesis(); //(model + cost) best; cost = -metric_scale*log(BLEU) or -metric_scale*BLEU
+    //const HypothesisInfo& cur_ref = *oracles[order[cur_sent]].good; //this oracle-best line only picks based on BLEU
+    const HypothesisInfo& cur_ref = observer.GetCurrentReference();  //if mu > 0, this mu-mixed oracle will be picked; otherwise, only on BLEU
+    total_loss += cur_best.mt_metric_score; 
+
+    double step_size = stepsize_param;
+    if (stepsize_reduce){       // w_{t+1} = w_t - stepsize_t * grad(Loss) 
+        step_size  /= (sqrt(cur_sent+1.0)); 
+    }
+    //actual update step - compute gradient, and modify sparse_weights
+    if(cur_ref.mt_metric_score - cur_costaug.mt_metric_score > metric_threshold) {
+      const double loss = (cur_costaug.features.dot(decoder_weights) - cur_ref.features.dot(decoder_weights)) * scaling_trick + mt_metric_scale * (cur_ref.mt_metric_score - cur_costaug.mt_metric_score);
+      if (!checkpositive || loss > 0.0) { //can update either all the time if check positive is off, or only when loss > 0 if it's on
+	sparse_weights -= cur_costaug.features * step_size / ((1.0-2.0*step_size*c)*scaling_trick);    // cost augmented hyp orig -
+	sparse_weights += cur_ref.features * step_size / ((1.0-2.0*step_size*c)*scaling_trick);        // ref orig +
+      }
+    }
+    scaling_trick *= (1.0 - 2.0 * step_size * c);
+
+    tot += sparse_weights; //for averaging purposes
+    normalizer++; //for averaging purposes
+    line_count++;
+    interval_counter++;
+    cur_sent++;
+  }
+  cerr << endl;
+  if(average) {
+    tot /= normalizer;
+    tot.init_vector(decoder_weights);
+    msg = "# Latent SSVM tuned weights (averaged vector)";
+    Weights::WriteToFile("weights.latentsvm-final-avg.gz", decoder_weights, true, &msg); 
+    cerr << "Optimization complete.\n" << "AVERAGED WEIGHTS: weights.latentsvm-final-avg.gz\n";
+  } else {
+    Weights::WriteToFile("weights.latentsvm-final.gz", decoder_weights, true, &msg);    
+    cerr << "Optimization complete.\n";
+  }
+  return 0;
+}
+
diff --git a/training/mira/Makefile.am b/training/mira/Makefile.am
index fa4fb22d..8cddc2d7 100644
--- a/training/mira/Makefile.am
+++ b/training/mira/Makefile.am
@@ -1,6 +1,11 @@
-bin_PROGRAMS = kbest_mira
+bin_PROGRAMS = kbest_mira \
+		kbest_cut_mira 
 
 kbest_mira_SOURCES = kbest_mira.cc
 kbest_mira_LDADD = ../../decoder/libcdec.a ../../klm/search/libksearch.a ../../mteval/libmteval.a ../../utils/libutils.a ../../klm/lm/libklm.a ../../klm/util/libklm_util.a ../../klm/util/double-conversion/libklm_util_double.a
 
+
+kbest_cut_mira_SOURCES = kbest_cut_mira.cc
+kbest_cut_mira_LDADD = ../../decoder/libcdec.a ../../klm/search/libksearch.a ../../mteval/libmteval.a ../../utils/libutils.a ../../klm/lm/libklm.a ../../klm/util/libklm_util.a ../../klm/util/double-conversion/libklm_util_double.a
+
 AM_CPPFLAGS = -W -Wall -Wno-sign-compare -I$(top_srcdir)/utils -I$(top_srcdir)/decoder -I$(top_srcdir)/mteval
diff --git a/training/mira/kbest_cut_mira.cc b/training/mira/kbest_cut_mira.cc
new file mode 100644
index 00000000..7df9a18f
--- /dev/null
+++ b/training/mira/kbest_cut_mira.cc
@@ -0,0 +1,954 @@
+#include <sstream>
+#include <iostream>
+#include <vector>
+#include <cassert>
+#include <cmath>
+#include <algorithm>
+
+#include "config.h"
+
+
+#include <boost/shared_ptr.hpp>
+#include <boost/program_options.hpp>
+#include <boost/program_options/variables_map.hpp>
+
+#include "sentence_metadata.h"
+#include "scorer.h"
+#include "verbose.h"
+#include "viterbi.h"
+#include "hg.h"
+#include "prob.h"
+#include "kbest.h"
+#include "ff_register.h"
+#include "decoder.h"
+#include "filelib.h"
+#include "fdict.h"
+#include "time.h"
+#include "sampler.h"
+
+#include "weights.h"
+#include "sparse_vector.h"
+
+using namespace std;
+using boost::shared_ptr;
+namespace po = boost::program_options;
+
+bool invert_score;
+boost::shared_ptr<MT19937> rng;
+bool approx_score;
+bool no_reweight;
+bool no_select;
+bool unique_kbest;
+int update_list_size;
+vector<weight_t> dense_w_local;
+double mt_metric_scale;
+int optimizer;
+int fear_select;
+int hope_select;
+bool pseudo_doc;
+bool sent_approx;
+bool checkloss;
+
+void SanityCheck(const vector<double>& w) {
+  for (int i = 0; i < w.size(); ++i) {
+    assert(!isnan(w[i]));
+    assert(!isinf(w[i]));
+  }
+}
+
+struct FComp {
+  const vector<double>& w_;
+  FComp(const vector<double>& w) : w_(w) {}
+  bool operator()(int a, int b) const {
+    return fabs(w_[a]) > fabs(w_[b]);
+  }
+};
+
+void ShowLargestFeatures(const vector<double>& w) {
+  vector<int> fnums(w.size());
+  for (int i = 0; i < w.size(); ++i)
+    fnums[i] = i;
+  vector<int>::iterator mid = fnums.begin();
+  mid += (w.size() > 10 ? 10 : w.size());
+  partial_sort(fnums.begin(), mid, fnums.end(), FComp(w));
+  cerr << "TOP FEATURES:";
+  for (vector<int>::iterator i = fnums.begin(); i != mid; ++i) {
+    cerr << ' ' << FD::Convert(*i) << '=' << w[*i];
+  }
+  cerr << endl;
+}
+
+bool InitCommandLine(int argc, char** argv, po::variables_map* conf) {
+  po::options_description opts("Configuration options");
+  opts.add_options()
+    ("input_weights,w",po::value<string>(),"Input feature weights file")
+    ("source,i",po::value<string>(),"Source file for development set")
+    ("pass,p", po::value<int>()->default_value(15), "Current pass through the training data")
+    ("reference,r",po::value<vector<string> >(), "[REQD] Reference translation(s) (tokenized text file)")
+    ("mt_metric,m",po::value<string>()->default_value("ibm_bleu"), "Scoring metric (ibm_bleu, nist_bleu, koehn_bleu, ter, combi)")
+    ("optimizer,o",po::value<int>()->default_value(1), "Optimizer (SGD=1, PA MIRA w/Delta=2, Cutting Plane MIRA=3, PA MIRA=4, Triple nbest list MIRA=5)")
+    ("fear,f",po::value<int>()->default_value(1), "Fear selection (model-cost=1, maxcost=2, maxscore=3)")
+    ("hope,h",po::value<int>()->default_value(1), "Hope selection (model+cost=1, mincost=2)")
+    ("max_step_size,C", po::value<double>()->default_value(0.01), "regularization strength (C)")
+    ("random_seed,S", po::value<uint32_t>(), "Random seed (if not specified, /dev/random will be used)")
+    ("mt_metric_scale,s", po::value<double>()->default_value(1.0), "Amount to scale MT loss function by")
+    ("sent_approx,a", "Use smoothed sentence-level BLEU score for approximate scoring")
+    ("pseudo_doc,e", "Use pseudo-document BLEU score for approximate scoring")
+    ("no_reweight,d","Do not reweight forest for cutting plane")
+    ("no_select,n", "Do not use selection heuristic")
+    ("k_best_size,k", po::value<int>()->default_value(250), "Size of hypothesis list to search for oracles")
+    ("update_k_best,b", po::value<int>()->default_value(1), "Size of good, bad lists to perform update with")
+    ("unique_k_best,u", "Unique k-best translation list")
+    ("weights_output,O",po::value<string>(),"Directory to write weights to")
+    ("output_dir,D",po::value<string>(),"Directory to place output in")
+    ("decoder_config,c",po::value<string>(),"Decoder configuration file");
+  po::options_description clo("Command line options");
+  clo.add_options()
+    ("config", po::value<string>(), "Configuration file")
+    ("help,H", "Print this help message and exit");
+  po::options_description dconfig_options, dcmdline_options;
+  dconfig_options.add(opts);
+  dcmdline_options.add(opts).add(clo);
+  
+  po::store(parse_command_line(argc, argv, dcmdline_options), *conf);
+  if (conf->count("config")) {
+    ifstream config((*conf)["config"].as<string>().c_str());
+    po::store(po::parse_config_file(config, dconfig_options), *conf);
+  }
+  po::notify(*conf);
+
+  if (conf->count("help") || !conf->count("input_weights") || !conf->count("decoder_config") || !conf->count("reference")) {
+    cerr << dcmdline_options << endl;
+    return false;
+  }
+  return true;
+}
+
+//load previous translation, store array of each sentences score, subtract it from current sentence and replace with new translation score
+
+
+static const double kMINUS_EPSILON = -1e-6;
+static const double EPSILON = 0.000001;
+static const double SMO_EPSILON = 0.0001;
+static const double PSEUDO_SCALE = 0.95;
+static const int MAX_SMO = 10;
+int cur_pass;
+
+struct HypothesisInfo {
+  SparseVector<double> features;
+  vector<WordID> hyp;
+  double mt_metric;
+  double hope;
+  double fear;
+  double alpha;
+  double oracle_loss;
+  SparseVector<double> oracle_feat_diff;
+  shared_ptr<HypothesisInfo> oracleN;
+};
+
+bool ApproxEqual(double a, double b) {
+  if (a == b) return true;
+  return (fabs(a-b)/fabs(b)) < EPSILON;
+}
+
+typedef shared_ptr<HypothesisInfo> HI;
+bool HypothesisCompareB(const HI& h1, const HI& h2 ) 
+{
+  return h1->mt_metric > h2->mt_metric;
+};
+
+
+bool HopeCompareB(const HI& h1, const HI& h2 ) 
+{
+  return h1->hope > h2->hope;
+};
+
+bool FearCompareB(const HI& h1, const HI& h2 ) 
+{
+  return h1->fear > h2->fear;
+};
+
+bool FearComparePred(const HI& h1, const HI& h2 ) 
+{
+  return h1->features.dot(dense_w_local) > h2->features.dot(dense_w_local);
+};
+
+bool HypothesisCompareG(const HI& h1, const HI& h2 ) 
+{
+  return h1->mt_metric < h2->mt_metric;
+};
+
+
+void CuttingPlane(vector<shared_ptr<HypothesisInfo> >* cur_c, bool* again, vector<shared_ptr<HypothesisInfo> >& all_hyp, vector<weight_t> dense_weights)
+{
+  bool DEBUG_CUT = false;
+  shared_ptr<HypothesisInfo> max_fear, max_fear_in_set;
+  vector<shared_ptr<HypothesisInfo> >& cur_constraint = *cur_c;
+
+  if(no_reweight)
+    {
+      //find new hope hypothesis
+      for(int u=0;u!=all_hyp.size();u++)	
+	{ 
+	  double t_score = all_hyp[u]->features.dot(dense_weights);
+	  all_hyp[u]->hope = 1 * all_hyp[u]->mt_metric + t_score;
+	}
+      
+      //sort hyps by hope score
+      sort(all_hyp.begin(),all_hyp.end(),HopeCompareB);    
+      
+      double hope_score = all_hyp[0]->features.dot(dense_weights);
+      if(DEBUG_CUT) cerr << "New hope derivation score " << hope_score << endl;
+     
+      for(int u=0;u!=all_hyp.size();u++)	
+	{ 
+	  double t_score = all_hyp[u]->features.dot(dense_weights);
+	  all_hyp[u]->fear = -1*all_hyp[u]->mt_metric + 1*all_hyp[0]->mt_metric - hope_score + t_score; //relative loss
+	}
+    
+      sort(all_hyp.begin(),all_hyp.end(),FearCompareB);
+      
+    }
+  //assign maximum fear derivation from all derivations
+  max_fear = all_hyp[0];
+  
+  if(DEBUG_CUT) cerr <<"Cutting Plane Max Fear "<<max_fear->fear ;
+  for(int i=0; i < cur_constraint.size();i++) //select maximal violator already in constraint set
+    {
+      if (!max_fear_in_set || cur_constraint[i]->fear > max_fear_in_set->fear)
+	max_fear_in_set = cur_constraint[i];
+    }
+  if(DEBUG_CUT) cerr << "Max Fear in constraint set " << max_fear_in_set->fear << endl;
+  
+  if(max_fear->fear > max_fear_in_set->fear + SMO_EPSILON)
+    {
+      cur_constraint.push_back(max_fear);
+      *again = true;
+      if(DEBUG_CUT) cerr << "Optimize Again " << *again << endl;
+    }
+}
+
+
+double ComputeDelta(vector<shared_ptr<HypothesisInfo> >* cur_p, double max_step_size,vector<weight_t> dense_weights )
+{
+  vector<shared_ptr<HypothesisInfo> >& cur_pair = *cur_p;
+   double loss = cur_pair[0]->oracle_loss - cur_pair[1]->oracle_loss;
+
+   double margin = -(cur_pair[0]->oracleN->features.dot(dense_weights)- cur_pair[0]->features.dot(dense_weights)) + (cur_pair[1]->oracleN->features.dot(dense_weights) - cur_pair[1]->features.dot(dense_weights));
+   const double num = margin +  loss;
+   cerr << "LOSS: " << num << " Margin:" << margin << " BLEUL:" << loss << " " << cur_pair[1]->features.dot(dense_weights) << " " << cur_pair[0]->features.dot(dense_weights) <<endl;
+   
+
+  SparseVector<double> diff = cur_pair[0]->features;
+  diff -= cur_pair[1]->features;
+  double diffsqnorm = diff.l2norm_sq();
+  double delta;
+  if (diffsqnorm > 0)
+    delta = num / (diffsqnorm * max_step_size);
+  else
+    delta = 0;
+  cerr << " D1:" << delta;
+  //clip delta (enforce margin constraints)
+  delta = max(-cur_pair[0]->alpha, min(delta, cur_pair[1]->alpha));
+  cerr << " D2:" << delta;
+  return delta;
+}
+
+
+vector<shared_ptr<HypothesisInfo> > SelectPair(vector<shared_ptr<HypothesisInfo> >* cur_c)
+{
+  bool DEBUG_SELECT= false;
+  vector<shared_ptr<HypothesisInfo> >& cur_constraint = *cur_c;
+  
+  vector<shared_ptr<HypothesisInfo> > pair;
+
+  if (no_select || optimizer == 2){ //skip heuristic search and return oracle and fear for pa-mira
+
+      pair.push_back(cur_constraint[0]);
+      pair.push_back(cur_constraint[1]);
+      return pair;
+
+    }
+  
+  for(int u=0;u != cur_constraint.size();u++)	
+    {
+      shared_ptr<HypothesisInfo> max_fear;
+      
+      if(DEBUG_SELECT) cerr<< "cur alpha " << u  << " " << cur_constraint[u]->alpha;
+      for(int i=0; i < cur_constraint.size();i++) //select maximal violator
+	{
+	  if(i != u)
+	    if (!max_fear || cur_constraint[i]->fear > max_fear->fear)
+	      max_fear = cur_constraint[i];
+	}
+      if(!max_fear) return pair; //
+      
+      
+      if ((cur_constraint[u]->alpha == 0) && (cur_constraint[u]->fear > max_fear->fear + SMO_EPSILON))
+	{
+	  for(int i=0; i < cur_constraint.size();i++) //select maximal violator
+	    {
+	      if(i != u)
+		if (cur_constraint[i]->alpha > 0)
+		  {
+		    pair.push_back(cur_constraint[u]);
+		    pair.push_back(cur_constraint[i]);		    
+		    return pair;
+		  }
+	    }
+	}	       
+      if ((cur_constraint[u]->alpha > 0) && (cur_constraint[u]->fear < max_fear->fear - SMO_EPSILON))
+	{
+	  for(int i=0; i < cur_constraint.size();i++) //select maximal violator
+	    {
+	      if(i != u)	
+		if (cur_constraint[i]->fear > cur_constraint[u]->fear)
+		  {
+		    pair.push_back(cur_constraint[u]);
+		    pair.push_back(cur_constraint[i]);
+		    return pair;
+		  }
+	    }  
+	}
+    
+    } 
+  return pair; //no more constraints to optimize, we're done here
+
+}
+
+struct GoodBadOracle {
+  vector<shared_ptr<HypothesisInfo> > good;
+  vector<shared_ptr<HypothesisInfo> > bad;
+};
+
+struct TrainingObserver : public DecoderObserver {
+  TrainingObserver(const int k, const DocScorer& d, vector<GoodBadOracle>* o, vector<ScoreP>* cbs) : ds(d), oracles(*o), corpus_bleu_sent_stats(*cbs), kbest_size(k) {
+    
+
+    if(!pseudo_doc && !sent_approx)
+    if(cur_pass > 0)     //calculate corpus bleu score from previous iterations 1-best for BLEU gain
+      {
+	ScoreP acc;
+	for (int ii = 0; ii < corpus_bleu_sent_stats.size(); ii++) {
+	  if (!acc) { acc = corpus_bleu_sent_stats[ii]->GetZero(); }
+	  acc->PlusEquals(*corpus_bleu_sent_stats[ii]);
+	  
+	}
+	corpus_bleu_stats = acc;
+	corpus_bleu_score = acc->ComputeScore();
+      }
+
+}
+  const DocScorer& ds;
+  vector<ScoreP>& corpus_bleu_sent_stats;
+  vector<GoodBadOracle>& oracles;
+  vector<shared_ptr<HypothesisInfo> > cur_best;
+  shared_ptr<HypothesisInfo> cur_oracle;
+  const int kbest_size;
+  Hypergraph forest;
+  int cur_sent;
+  ScoreP corpus_bleu_stats;
+  float corpus_bleu_score;
+
+  float corpus_src_length;
+  float curr_src_length;
+
+  const int GetCurrentSent() const {
+    return cur_sent;
+  }
+
+  const HypothesisInfo& GetCurrentBestHypothesis() const {
+    return *cur_best[0];
+  }
+
+  const vector<shared_ptr<HypothesisInfo> > GetCurrentBest() const {
+    return cur_best;
+  }
+  
+ const HypothesisInfo& GetCurrentOracle() const {
+    return *cur_oracle;
+  }
+  
+  const Hypergraph& GetCurrentForest() const {
+    return forest;
+  }
+  
+
+  virtual void NotifyTranslationForest(const SentenceMetadata& smeta, Hypergraph* hg) {
+    cur_sent = smeta.GetSentenceID();
+    curr_src_length = (float) smeta.GetSourceLength();
+
+    if(unique_kbest)
+      UpdateOracles<KBest::FilterUnique>(smeta.GetSentenceID(), *hg);
+    else
+      UpdateOracles<KBest::NoFilter<std::vector<WordID> > >(smeta.GetSentenceID(), *hg);
+    forest = *hg;
+    
+  }
+
+  shared_ptr<HypothesisInfo> MakeHypothesisInfo(const SparseVector<double>& feats, const double score, const vector<WordID>& hyp) {
+    shared_ptr<HypothesisInfo> h(new HypothesisInfo);
+    h->features = feats;
+    h->mt_metric = score;
+    h->hyp = hyp;
+    return h;
+  }
+
+  template <class Filter>  
+  void UpdateOracles(int sent_id, const Hypergraph& forest) {
+
+    bool PRINT_LIST= false;    
+    vector<shared_ptr<HypothesisInfo> >& cur_good = oracles[sent_id].good;
+    vector<shared_ptr<HypothesisInfo> >& cur_bad = oracles[sent_id].bad;
+    //TODO: look at keeping previous iterations hypothesis lists around
+    cur_best.clear();
+    cur_good.clear();
+    cur_bad.clear();
+
+    vector<shared_ptr<HypothesisInfo> > all_hyp;
+
+    typedef KBest::KBestDerivations<vector<WordID>, ESentenceTraversal,Filter> K;
+    K kbest(forest,kbest_size);
+    
+    for (int i = 0; i < kbest_size; ++i) {
+
+      typename K::Derivation *d =
+        kbest.LazyKthBest(forest.nodes_.size() - 1, i);
+      if (!d) break;
+
+      float sentscore;
+	  if(cur_pass > 0 && !pseudo_doc && !sent_approx)
+	    {
+	      ScoreP sent_stats = ds[sent_id]->ScoreCandidate(d->yield);
+	      ScoreP corpus_no_best = corpus_bleu_stats->GetZero();
+
+	      corpus_bleu_stats->Subtract(*corpus_bleu_sent_stats[sent_id], &*corpus_no_best);
+	      sent_stats->PlusEquals(*corpus_no_best, 0.5);
+	      
+	      //compute gain from new sentence in 1-best corpus
+	      sentscore = mt_metric_scale * (sent_stats->ComputeScore() - corpus_no_best->ComputeScore());// - corpus_bleu_score);
+	    }
+	  else if(pseudo_doc)   //pseudo-corpus smoothing 
+	    {
+	      float src_scale = corpus_src_length + curr_src_length;
+	      ScoreP sent_stats = ds[sent_id]->ScoreCandidate(d->yield);
+	      if(!corpus_bleu_stats){ corpus_bleu_stats = sent_stats->GetZero();}
+	      
+	      sent_stats->PlusEquals(*corpus_bleu_stats);
+	      sentscore =  mt_metric_scale  * src_scale * sent_stats->ComputeScore();
+
+	    }
+	  else //use sentence-level smoothing ( used when cur_pass=0 if not pseudo_doc)
+	    {
+	     
+	      sentscore = mt_metric_scale * (ds[sent_id]->ScoreCandidate(d->yield)->ComputeScore());
+	    }
+	
+      if (invert_score) sentscore *= -1.0;
+      
+      if (i < update_list_size){ 
+	if(PRINT_LIST)cerr << TD::GetString(d->yield) << " ||| " << d->score << " ||| " << sentscore << endl; 
+	cur_best.push_back( MakeHypothesisInfo(d->feature_values, sentscore, d->yield));
+      }
+      
+      all_hyp.push_back(MakeHypothesisInfo(d->feature_values, sentscore,d->yield));   //store all hyp to extract hope and fear         
+    }
+    
+    if(pseudo_doc){
+    //update psuedo-doc stats
+      string details, details2;     
+      corpus_bleu_stats->ScoreDetails(&details2);   
+      ScoreP sent_stats = ds[sent_id]->ScoreCandidate(cur_best[0]->hyp);
+      corpus_bleu_stats->PlusEquals(*sent_stats);
+      
+      sent_stats->ScoreDetails(&details);
+      sent_stats = corpus_bleu_stats;
+      corpus_bleu_stats = sent_stats->GetZero();
+      corpus_bleu_stats->PlusEquals(*sent_stats, PSEUDO_SCALE);
+            
+      corpus_src_length = PSEUDO_SCALE * (corpus_src_length + curr_src_length);
+      cerr << "ps corpus size: " << corpus_src_length << " " << curr_src_length << "\n" << details << "\n" << details2 << endl;
+    }
+
+    //figure out how many hyps we can keep maximum
+    int temp_update_size = update_list_size;
+    if (all_hyp.size() < update_list_size){ temp_update_size = all_hyp.size();}
+
+    //sort all hyps by sentscore (eg. bleu)
+    sort(all_hyp.begin(),all_hyp.end(),HypothesisCompareB);
+    
+    if(PRINT_LIST){  cerr << "Sorting " << endl; for(int u=0;u!=all_hyp.size();u++)  
+						   cerr << all_hyp[u]->mt_metric << " " << all_hyp[u]->features.dot(dense_w_local) << endl; }
+    
+    if(hope_select == 1)
+      {
+	//find hope hypothesis using model + bleu
+	if (PRINT_LIST) cerr << "HOPE " << endl;
+	for(int u=0;u!=all_hyp.size();u++)	
+	  { 
+	    double t_score = all_hyp[u]->features.dot(dense_w_local);
+	    all_hyp[u]->hope = all_hyp[u]->mt_metric + t_score;
+	    if (PRINT_LIST) cerr << all_hyp[u]->mt_metric << " H:" << all_hyp[u]->hope << " S:" << t_score << endl; 
+	    
+	  }
+	
+	//sort hyps by hope score
+	sort(all_hyp.begin(),all_hyp.end(),HopeCompareB);
+      }        
+
+    //assign cur_good the sorted list
+    cur_good.insert(cur_good.begin(), all_hyp.begin(), all_hyp.begin()+temp_update_size);    
+    if(PRINT_LIST) { cerr << "GOOD" << endl;  for(int u=0;u!=cur_good.size();u++) cerr << cur_good[u]->mt_metric << " " << cur_good[u]->hope << endl;}     
+
+    //use hope for fear selection
+    shared_ptr<HypothesisInfo>& oracleN = cur_good[0];
+
+    if(fear_select == 1){   //compute fear hyps with model - bleu
+      if (PRINT_LIST) cerr << "FEAR " << endl;
+      double hope_score = oracleN->features.dot(dense_w_local);
+
+      if (PRINT_LIST) cerr << "hope score " << hope_score << endl;
+      for(int u=0;u!=all_hyp.size();u++)	
+	{ 
+	  double t_score = all_hyp[u]->features.dot(dense_w_local);
+
+	  all_hyp[u]->fear = -1*all_hyp[u]->mt_metric + 1*oracleN->mt_metric - hope_score + t_score; //relative loss
+	  all_hyp[u]->oracle_loss = -1*all_hyp[u]->mt_metric + 1*oracleN->mt_metric;
+	  all_hyp[u]->oracle_feat_diff = oracleN->features - all_hyp[u]->features;
+	  all_hyp[u]->oracleN=oracleN;
+	  if (PRINT_LIST) cerr << all_hyp[u]->mt_metric << " H:" << all_hyp[u]->hope << " F:" << all_hyp[u]->fear << endl; 
+	  
+	}
+      
+      sort(all_hyp.begin(),all_hyp.end(),FearCompareB);
+      
+    }
+    else if(fear_select == 2) //select fear based on cost
+      {
+	sort(all_hyp.begin(),all_hyp.end(),HypothesisCompareG);
+      }
+    else //max model score, also known as prediction-based
+      {
+	sort(all_hyp.begin(),all_hyp.end(),FearComparePred);
+      }
+    cur_bad.insert(cur_bad.begin(), all_hyp.begin(), all_hyp.begin()+temp_update_size); 
+
+    if(PRINT_LIST){ cerr<< "BAD"<<endl; for(int u=0;u!=cur_bad.size();u++) cerr << cur_bad[u]->mt_metric << " H:" << cur_bad[u]->hope << " F:" << cur_bad[u]->fear << endl;}
+    
+    cerr << "GOOD (BEST): " << cur_good[0]->mt_metric << endl;
+    cerr << " CUR: " << cur_best[0]->mt_metric << endl;
+    cerr << " BAD (WORST): " << cur_bad[0]->mt_metric << endl;
+  }
+};
+
+void ReadTrainingCorpus(const string& fname, vector<string>* c) {
+
+
+  ReadFile rf(fname);
+  istream& in = *rf.stream();
+  string line;
+  while(in) {
+    getline(in, line);
+    if (!in) break;
+    c->push_back(line);
+  }
+}
+
+void ReadPastTranslationForScore(const int cur_pass, vector<ScoreP>* c, DocScorer& ds, const string& od)
+{
+  cerr << "Reading BLEU gain file ";
+  string fname;
+  if(cur_pass == 0)
+    {
+      fname = od + "/run.raw.init";
+    }
+  else
+    {
+      int last_pass = cur_pass - 1; 
+      fname = od + "/run.raw."  +  boost::lexical_cast<std::string>(last_pass) + ".B";
+    }
+  cerr << fname << "\n";
+  ReadFile rf(fname);
+  istream& in = *rf.stream();
+  ScoreP acc;
+  string line;
+  int lc = 0;
+  while(in) {
+    getline(in, line);
+    if (line.empty() && !in) break;
+    vector<WordID> sent;
+    TD::ConvertSentence(line, &sent);
+    ScoreP sentscore = ds[lc]->ScoreCandidate(sent);
+    c->push_back(sentscore);
+    if (!acc) { acc = sentscore->GetZero(); }
+    acc->PlusEquals(*sentscore);
+    ++lc;
+ 
+  }
+  
+  assert(lc > 0);
+  float score = acc->ComputeScore();
+  string details;
+  acc->ScoreDetails(&details);
+  cerr << "Previous run: " << details << score << endl;
+
+}
+
+
+int main(int argc, char** argv) {
+  register_feature_functions();
+  SetSilent(true);  // turn off verbose decoder output
+
+  po::variables_map conf;
+  if (!InitCommandLine(argc, argv, &conf)) return 1;
+
+  if (conf.count("random_seed"))
+    rng.reset(new MT19937(conf["random_seed"].as<uint32_t>()));
+  else
+    rng.reset(new MT19937);
+  
+  vector<string> corpus;
+
+  const string metric_name = conf["mt_metric"].as<string>();
+  optimizer = conf["optimizer"].as<int>();
+  fear_select = conf["fear"].as<int>();
+  hope_select = conf["hope"].as<int>();
+  mt_metric_scale = conf["mt_metric_scale"].as<double>();
+  approx_score = conf.count("approx_score");
+  no_reweight = conf.count("no_reweight");
+  no_select = conf.count("no_select");
+  update_list_size = conf["update_k_best"].as<int>();
+  unique_kbest = conf.count("unique_k_best");
+  pseudo_doc = conf.count("pseudo_doc");
+  sent_approx = conf.count("sent_approx");
+  cerr << "Using pseudo-doc:" << pseudo_doc << " Sent:" << sent_approx << endl;
+  if(pseudo_doc)
+    mt_metric_scale=1;
+
+  const string weights_dir = conf["weights_output"].as<string>();
+  const string output_dir = conf["output_dir"].as<string>();
+  ScoreType type = ScoreTypeFromString(metric_name);
+
+  //establish metric used for tuning
+  if (type == TER) {
+    invert_score = true;
+  } else {
+    invert_score = false;
+  }
+
+  //load references
+  DocScorer ds(type, conf["reference"].as<vector<string> >(), "");
+  cerr << "Loaded " << ds.size() << " references for scoring with " << metric_name << endl;
+  vector<ScoreP> corpus_bleu_sent_stats;
+  
+  //check training pass,if >0, then use previous iterations corpus bleu stats
+  cur_pass = conf["pass"].as<int>();
+  if(cur_pass > 0)
+    {
+      ReadPastTranslationForScore(cur_pass, &corpus_bleu_sent_stats, ds, output_dir);
+    }
+  
+  cerr << "Using optimizer:" << optimizer << endl;
+    
+  ReadFile ini_rf(conf["decoder_config"].as<string>());
+  Decoder decoder(ini_rf.stream());
+
+  vector<weight_t>& dense_weights = decoder.CurrentWeightVector();
+  
+  SparseVector<weight_t> lambdas;
+  Weights::InitFromFile(conf["input_weights"].as<string>(), &dense_weights);
+  Weights::InitSparseVector(dense_weights, &lambdas);
+
+  const string input = decoder.GetConf()["input"].as<string>();
+  if (!SILENT) cerr << "Reading input from " << ((input == "-") ? "STDIN" : input.c_str()) << endl;
+  ReadFile in_read(input);
+  istream *in = in_read.stream();
+  assert(*in);  
+  string buf;
+  
+  const double max_step_size = conf["max_step_size"].as<double>();
+
+  vector<GoodBadOracle> oracles(ds.size());
+
+  TrainingObserver observer(conf["k_best_size"].as<int>(), ds, &oracles, &corpus_bleu_sent_stats);
+
+  int cur_sent = 0;
+  int lcount = 0;
+  double objective=0;
+  double tot_loss = 0;
+  int dots = 0;
+  SparseVector<double> tot;
+  SparseVector<double> final_tot;
+
+  SparseVector<double> old_lambdas = lambdas;
+  tot.clear();
+  tot += lambdas;
+  cerr << "PASS " << cur_pass << " " << endl << lambdas << endl; 
+  ScoreP acc, acc_h, acc_f;
+  
+  while(*in) {
+      getline(*in, buf);
+      if (buf.empty()) continue;
+      //TODO: allow batch updating
+      lambdas.init_vector(&dense_weights);
+      dense_w_local = dense_weights;
+      decoder.SetId(cur_sent);
+      decoder.Decode(buf, &observer);  // decode the sentence, calling Notify to get the hope,fear, and model best hyps. 
+      
+      cur_sent = observer.GetCurrentSent();
+      cerr << "SENT: " << cur_sent << endl;
+      const HypothesisInfo& cur_hyp = observer.GetCurrentBestHypothesis();
+      const HypothesisInfo& cur_good = *oracles[cur_sent].good[0];
+      const HypothesisInfo& cur_bad = *oracles[cur_sent].bad[0];
+
+      vector<shared_ptr<HypothesisInfo> >& cur_good_v = oracles[cur_sent].good;
+      vector<shared_ptr<HypothesisInfo> >& cur_bad_v = oracles[cur_sent].bad;
+      vector<shared_ptr<HypothesisInfo> > cur_best_v = observer.GetCurrentBest();
+
+      tot_loss += cur_hyp.mt_metric;
+      
+      //score hyps to be able to compute corpus level bleu after we finish this iteration through the corpus
+      ScoreP sentscore = ds[cur_sent]->ScoreCandidate(cur_hyp.hyp);
+      if (!acc) { acc = sentscore->GetZero(); }
+      acc->PlusEquals(*sentscore);
+
+      ScoreP hope_sentscore = ds[cur_sent]->ScoreCandidate(cur_good.hyp);
+      if (!acc_h) { acc_h = hope_sentscore->GetZero(); }
+      acc_h->PlusEquals(*hope_sentscore);
+
+      ScoreP fear_sentscore = ds[cur_sent]->ScoreCandidate(cur_bad.hyp);
+      if (!acc_f) { acc_f = fear_sentscore->GetZero(); }
+      acc_f->PlusEquals(*fear_sentscore);
+      
+      if(optimizer == 4) { //passive-aggresive update (single dual coordinate step)
+      
+	  double margin = cur_bad.features.dot(dense_weights) - cur_good.features.dot(dense_weights);
+	  double mt_loss = (cur_good.mt_metric - cur_bad.mt_metric);
+	  const double loss = margin +  mt_loss;
+	  cerr << "LOSS: " << loss << " Margin:" << margin << " BLEUL:" << mt_loss << " " << cur_bad.features.dot(dense_weights) << " " << cur_good.features.dot(dense_weights) <<endl;
+	  if (loss > 0.0 || !checkloss) {
+	    SparseVector<double> diff = cur_good.features;
+	    diff -= cur_bad.features;	    
+
+	    double diffsqnorm = diff.l2norm_sq();
+	    double delta;
+	    if (diffsqnorm > 0)
+	      delta = loss / (diffsqnorm);
+	    else
+	      delta = 0;
+	    
+	    if (delta > max_step_size) delta = max_step_size;
+	    lambdas += (cur_good.features * delta);
+	    lambdas -= (cur_bad.features * delta);
+	    
+	  }
+      }
+      else if(optimizer == 1) //sgd - nonadapted step size
+	{
+	   
+	  lambdas += (cur_good.features) * max_step_size;
+	  lambdas -= (cur_bad.features) * max_step_size;
+	}
+      else if(optimizer == 5) //full mira with n-best list of constraints from hope, fear, model best
+	{
+	  vector<shared_ptr<HypothesisInfo> > cur_constraint;
+	  cur_constraint.insert(cur_constraint.begin(), cur_bad_v.begin(), cur_bad_v.end());
+	  cur_constraint.insert(cur_constraint.begin(), cur_best_v.begin(), cur_best_v.end());
+	  cur_constraint.insert(cur_constraint.begin(), cur_good_v.begin(), cur_good_v.end());
+
+	  bool optimize_again;
+	  vector<shared_ptr<HypothesisInfo> > cur_pair;
+	  //SMO 
+	  for(int u=0;u!=cur_constraint.size();u++)	
+	    cur_constraint[u]->alpha =0;	      
+	  
+	  cur_constraint[0]->alpha =1; //set oracle to alpha=1
+
+	  cerr <<"Optimizing with " << cur_constraint.size() << " constraints" << endl;
+	  int smo_iter = MAX_SMO, smo_iter2 = MAX_SMO;
+	  int iter, iter2 =0;
+	  bool DEBUG_SMO = false;
+	  while (iter2 < smo_iter2)
+	    {
+	      iter =0;
+	      while (iter < smo_iter)
+		{
+		  optimize_again = true;
+		  for (int i = 0; i< cur_constraint.size(); i++)
+		    for (int j = i+1; j< cur_constraint.size(); j++)
+		      {
+			if(DEBUG_SMO) cerr << "start " << i << " " << j <<  endl;
+			cur_pair.clear();
+			cur_pair.push_back(cur_constraint[j]);
+			cur_pair.push_back(cur_constraint[i]);
+			double delta = ComputeDelta(&cur_pair,max_step_size, dense_weights);
+			
+			if (delta == 0) optimize_again = false;
+			cur_constraint[j]->alpha += delta;
+			cur_constraint[i]->alpha -= delta;
+			double step_size = delta * max_step_size;
+			
+			lambdas += (cur_constraint[i]->features) * step_size;
+			lambdas -= (cur_constraint[j]->features) * step_size;
+			if(DEBUG_SMO) cerr << "SMO opt " << iter << " " << i << " " << j << " " <<  delta << " " << cur_pair[0]->alpha << " " << cur_pair[1]->alpha <<  endl;		
+		      }
+		  iter++;
+		  
+		  if(!optimize_again)
+		    { 
+		      iter = MAX_SMO;
+		      cerr << "Optimization stopped, delta =0" << endl;
+		    }		  
+		}
+	      iter2++;
+	    }	  
+	}
+      else if(optimizer == 2 || optimizer == 3) //PA and Cutting Plane MIRA update
+	  {
+	    bool DEBUG_SMO= true;
+	    vector<shared_ptr<HypothesisInfo> > cur_constraint;
+	    cur_constraint.push_back(cur_good_v[0]); //add oracle to constraint set
+	    bool optimize_again = true;
+	    int cut_plane_calls = 0;
+	    while (optimize_again)
+	      { 
+		if(DEBUG_SMO) cerr<< "optimize again: " << optimize_again << endl;
+		if(optimizer == 2){ //PA
+		  cur_constraint.push_back(cur_bad_v[0]);
+
+		  //check if we have a violation
+		  if(!(cur_constraint[1]->fear > cur_constraint[0]->fear + SMO_EPSILON))
+		    {
+		      optimize_again = false;
+		      cerr << "Constraint not violated" << endl;
+		    }
+		}
+		else
+		  { //cutting plane to add constraints
+		    if(DEBUG_SMO) cerr<< "Cutting Plane " << cut_plane_calls << " with " << lambdas << endl;
+		    optimize_again = false;
+		    cut_plane_calls++;
+		    CuttingPlane(&cur_constraint, &optimize_again, oracles[cur_sent].bad, dense_weights);
+		    if (cut_plane_calls >= MAX_SMO) optimize_again = false;
+		  }
+
+		if(optimize_again)
+		  {
+		    //SMO 
+		    for(int u=0;u!=cur_constraint.size();u++)	
+		      { 
+			cur_constraint[u]->alpha =0;
+		      }
+		    cur_constraint[0]->alpha = 1;
+		    cerr <<" Optimizing with " << cur_constraint.size() << " constraints" << endl;
+		    int smo_iter = MAX_SMO;
+		    int iter =0;
+		    while (iter < smo_iter)
+		      {			
+			//select pair to optimize from constraint set
+			vector<shared_ptr<HypothesisInfo> > cur_pair = SelectPair(&cur_constraint);
+			
+			if(cur_pair.empty()){
+			  iter=MAX_SMO; 
+			  cerr << "Undefined pair " << endl; 
+			  continue;
+			} //pair is undefined so we are done with this smo 
+
+			double delta = ComputeDelta(&cur_pair,max_step_size, dense_weights);
+
+			cur_pair[0]->alpha += delta;
+			cur_pair[1]->alpha -= delta;
+			double step_size = delta * max_step_size;
+			cerr << "step " << step_size << endl;
+
+			lambdas += (cur_pair[1]->features) * step_size;
+			lambdas -= (cur_pair[0]->features) * step_size;
+			cerr << " Lambdas " << lambdas << endl;
+			//reload weights based on update
+
+			dense_weights.clear();
+			lambdas.init_vector(&dense_weights);
+			dense_w_local = dense_weights;
+			iter++;
+					
+			if(DEBUG_SMO) cerr << "SMO opt " << iter << " " << delta << " " << cur_pair[0]->alpha << " " << cur_pair[1]->alpha <<  endl;		
+			if(no_select) //don't use selection heuristic to determine when to stop SMO, rather just when delta =0 
+			  if (delta == 0) iter = MAX_SMO;
+			
+			//only perform one dual coordinate ascent step
+			if(optimizer == 2) 
+			  {
+			    optimize_again = false;
+			    iter = MAX_SMO;
+			  }					
+		      }
+		    if(optimizer == 3)
+		      {
+			if(!no_reweight) //reweight the forest and select a new k-best
+			  {
+			    if(DEBUG_SMO) cerr<< "Decoding with new weights -- now orac are " << oracles[cur_sent].good.size() << endl;
+			    Hypergraph hg = observer.GetCurrentForest();
+			    hg.Reweight(dense_weights);
+			    if(unique_kbest)
+                              observer.UpdateOracles<KBest::FilterUnique>(cur_sent, hg);
+                            else
+                              observer.UpdateOracles<KBest::NoFilter<std::vector<WordID> > >(cur_sent, hg);			    
+			  }
+		      }
+		  }
+		
+	      }
+	   
+	    //print objective after this sentence
+	    double lambda_change = (lambdas - old_lambdas).l2norm_sq();
+	    double max_fear = cur_constraint[cur_constraint.size()-1]->fear;
+	    double temp_objective = 0.5 * lambda_change;// + max_step_size * max_fear;
+
+	    for(int u=0;u!=cur_constraint.size();u++)	
+	      { 
+		cerr << cur_constraint[u]->alpha << " " << cur_constraint[u]->hope << " " << cur_constraint[u]->fear << endl;
+		temp_objective += cur_constraint[u]->alpha * cur_constraint[u]->fear;
+	      }
+	    objective += temp_objective;
+	    
+	    cerr << "SENT OBJ: " << temp_objective << " NEW OBJ: " << objective << endl;
+	  }
+      
+    
+      if ((cur_sent * 40 / ds.size()) > dots) { ++dots; cerr << '.'; }
+      tot += lambdas;
+      ++lcount;
+      cur_sent++;
+      
+      cout << TD::GetString(cur_good_v[0]->hyp) << " ||| " << TD::GetString(cur_best_v[0]->hyp) << " ||| " << TD::GetString(cur_bad_v[0]->hyp) << endl;
+
+    }
+
+    cerr << "FINAL OBJECTIVE: "<< objective << endl;
+    final_tot += tot;
+    cerr << "Translated " << lcount << " sentences " << endl;
+    cerr << " [AVG METRIC LAST PASS=" << (tot_loss / lcount) << "]\n";
+    tot_loss = 0;
+    
+    int node_id = rng->next() * 100000;
+    cerr << " Writing weights to " << node_id << endl;
+    Weights::ShowLargestFeatures(dense_weights);
+    dots = 0;
+    ostringstream os;
+    os << weights_dir << "/weights.mira-pass" << (cur_pass < 10 ? "0" : "") << cur_pass << "." << node_id << ".gz";
+    string msg = "# MIRA tuned weights ||| " + boost::lexical_cast<std::string>(node_id) + " ||| " + boost::lexical_cast<std::string>(lcount);
+    lambdas.init_vector(&dense_weights);
+    Weights::WriteToFile(os.str(), dense_weights, true, &msg);
+
+    SparseVector<double> x = tot;
+    x /= lcount+1;
+    ostringstream sa;
+    string msga = "# MIRA tuned weights AVERAGED ||| " + boost::lexical_cast<std::string>(node_id) + " ||| " + boost::lexical_cast<std::string>(lcount);
+    sa << weights_dir << "/weights.mira-pass" << (cur_pass < 10 ? "0" : "") << cur_pass << "." << node_id << "-avg.gz";
+    x.init_vector(&dense_weights);
+    Weights::WriteToFile(sa.str(), dense_weights, true, &msga);
+    
+    cerr << "Optimization complete.\n";
+    return 0;
+}
+
diff --git a/training/mira/kbest_mira.cc b/training/mira/kbest_mira.cc
index 8b7993dd..d59b4224 100644
--- a/training/mira/kbest_mira.cc
+++ b/training/mira/kbest_mira.cc
@@ -8,9 +8,11 @@
 #include <boost/program_options.hpp>
 #include <boost/program_options/variables_map.hpp>
 
+#include "stringlib.h"
 #include "hg_sampler.h"
 #include "sentence_metadata.h"
-#include "scorer.h"
+#include "ns.h"
+#include "ns_docscorer.h"
 #include "verbose.h"
 #include "viterbi.h"
 #include "hg.h"
@@ -91,8 +93,9 @@ struct GoodBadOracle {
 };
 
 struct TrainingObserver : public DecoderObserver {
-  TrainingObserver(const int k, const DocScorer& d, bool sf, vector<GoodBadOracle>* o) : ds(d), oracles(*o), kbest_size(k), sample_forest(sf) {}
-  const DocScorer& ds;
+  TrainingObserver(const int k, const DocumentScorer& d, const EvaluationMetric& m, bool sf, vector<GoodBadOracle>* o) : ds(d), metric(m), oracles(*o), kbest_size(k), sample_forest(sf) {}
+  const DocumentScorer& ds;
+  const EvaluationMetric& metric;
   vector<GoodBadOracle>& oracles;
   std::tr1::shared_ptr<HypothesisInfo> cur_best;
   const int kbest_size;
@@ -121,13 +124,16 @@ struct TrainingObserver : public DecoderObserver {
     if (sample_forest) {
       vector<WordID> cur_prediction;
       ViterbiESentence(forest, &cur_prediction);
-      float sentscore = ds[sent_id]->ScoreCandidate(cur_prediction)->ComputeScore();
+      SufficientStats sstats;
+      ds[sent_id]->Evaluate(cur_prediction, &sstats);
+      float sentscore = metric.ComputeScore(sstats);
       cur_best = MakeHypothesisInfo(ViterbiFeatures(forest), sentscore);
 
       vector<HypergraphSampler::Hypothesis> samples;
       HypergraphSampler::sample_hypotheses(forest, kbest_size, &*rng, &samples);
       for (unsigned i = 0; i < samples.size(); ++i) {
-        sentscore = ds[sent_id]->ScoreCandidate(samples[i].words)->ComputeScore();
+        ds[sent_id]->Evaluate(samples[i].words, &sstats);
+        float sentscore = metric.ComputeScore(sstats);
         if (invert_score) sentscore *= -1.0;
         if (!cur_good || sentscore > cur_good->mt_metric)
           cur_good = MakeHypothesisInfo(samples[i].fmap, sentscore);
@@ -136,11 +142,13 @@ struct TrainingObserver : public DecoderObserver {
       }
     } else {
       KBest::KBestDerivations<vector<WordID>, ESentenceTraversal> kbest(forest, kbest_size);
+      SufficientStats sstats;
       for (int i = 0; i < kbest_size; ++i) {
         const KBest::KBestDerivations<vector<WordID>, ESentenceTraversal>::Derivation* d =
           kbest.LazyKthBest(forest.nodes_.size() - 1, i);
         if (!d) break;
-        float sentscore = ds[sent_id]->ScoreCandidate(d->yield)->ComputeScore();
+        ds[sent_id]->Evaluate(d->yield, &sstats);
+        float sentscore = metric.ComputeScore(sstats);
         if (invert_score) sentscore *= -1.0;
         // cerr << TD::GetString(d->yield) << " ||| " << d->score << " ||| " << sentscore << endl;
         if (i == 0)
@@ -192,15 +200,20 @@ int main(int argc, char** argv) {
   }
   vector<string> corpus;
   ReadTrainingCorpus(conf["source"].as<string>(), &corpus);
-  const string metric_name = conf["mt_metric"].as<string>();
-  ScoreType type = ScoreTypeFromString(metric_name);
-  if (type == TER) {
-    invert_score = true;
-  } else {
-    invert_score = false;
+
+  string metric_name = UppercaseString(conf["mt_metric"].as<string>());
+  if (metric_name == "COMBI") {
+    cerr << "WARNING: 'combi' metric is no longer supported, switching to 'COMB:TER=-0.5;IBM_BLEU=0.5'\n";
+    metric_name = "COMB:TER=-0.5;IBM_BLEU=0.5";
+  } else if (metric_name == "BLEU") {
+    cerr << "WARNING: 'BLEU' is ambiguous, assuming 'IBM_BLEU'\n";
+    metric_name = "IBM_BLEU";
   }
-  DocScorer ds(type, conf["reference"].as<vector<string> >(), "");
+  EvaluationMetric* metric = EvaluationMetric::Instance(metric_name);
+  DocumentScorer ds(metric, conf["reference"].as<vector<string> >());
   cerr << "Loaded " << ds.size() << " references for scoring with " << metric_name << endl;
+  invert_score = metric->IsErrorMetric();
+
   if (ds.size() != corpus.size()) {
     cerr << "Mismatched number of references (" << ds.size() << ") and sources (" << corpus.size() << ")\n";
     return 1;
@@ -221,7 +234,7 @@ int main(int argc, char** argv) {
   assert(corpus.size() > 0);
   vector<GoodBadOracle> oracles(corpus.size());
 
-  TrainingObserver observer(conf["k_best_size"].as<int>(), ds, sample_forest, &oracles);
+  TrainingObserver observer(conf["k_best_size"].as<int>(), ds, *metric, sample_forest, &oracles);
   int cur_sent = 0;
   int lcount = 0;
   int normalizer = 0;
diff --git a/training/mira/run_mira.pl b/training/mira/run_mira.pl
new file mode 100755
index 00000000..d71590ba
--- /dev/null
+++ b/training/mira/run_mira.pl
@@ -0,0 +1,630 @@
+#!/usr/bin/env perl
+use strict;
+my @ORIG_ARGV=@ARGV;
+use Cwd qw(getcwd);
+my $SCRIPT_DIR; BEGIN { use Cwd qw/ abs_path /; use File::Basename; $SCRIPT_DIR = dirname(abs_path($0));
+push @INC, $SCRIPT_DIR, "$SCRIPT_DIR/../../environment"; }
+
+# Skip local config (used for distributing jobs) if we're running in local-only mode
+use LocalConfig;
+use Getopt::Long;
+use IPC::Open2;
+use POSIX ":sys_wait_h";
+my $QSUB_CMD = qsub_args(mert_memory());
+my $default_jobs = env_default_jobs();
+
+my $srcFile;
+my $refFiles;
+my $bin_dir = $SCRIPT_DIR;
+die "Bin directory $bin_dir missing/inaccessible" unless -d $bin_dir;
+my $FAST_SCORE="$bin_dir/../../mteval/fast_score";
+die "Can't execute $FAST_SCORE" unless -x $FAST_SCORE;
+
+my $iteration = 0.0;
+my $max_iterations = 10;
+my $metric = "ibm_bleu";
+my $iniFile;
+my $weights;
+my $initialWeights;
+my $jobs = $default_jobs;   # number of decode nodes
+my $pmem = "1g";
+my $dir;
+
+my $SCORER = $FAST_SCORE;
+
+my $UTILS_DIR="$SCRIPT_DIR/../utils";
+require "$UTILS_DIR/libcall.pl";
+
+my $parallelize = "$UTILS_DIR/parallelize.pl";
+my $libcall = "$UTILS_DIR/libcall.pl";
+my $sentserver = "$UTILS_DIR/sentserver";
+my $sentclient = "$UTILS_DIR/sentclient";
+
+my $run_local = 0;
+my $pass_suffix = '';
+
+my $cdec ="$bin_dir/kbest_cut_mira"; 
+
+die "Can't find decoder in $cdec" unless -x $cdec;
+my $decoder = $cdec;
+my $decoderOpt;
+my $update_size;
+my $approx_score;
+my $kbest_size=250;
+my $metric_scale=1;
+my $optimizer=2;
+my $disable_clean = 0;
+my $use_make=0;  
+my $density_prune;
+my $cpbin=1;
+my $help = 0;
+my $epsilon = 0.0001;
+my $step_size = 0.01;
+my $gpref;
+my $unique_kbest;
+my $freeze;
+my $hopes=1;
+my $fears=1;
+my $sent_approx=0;
+my $pseudo_doc=0;
+
+my $range = 35000;
+my $minimum = 15000;
+my $portn = int(rand($range)) + $minimum;
+
+
+# Process command-line options
+Getopt::Long::Configure("no_auto_abbrev");
+if (GetOptions(
+        "decoder=s" => \$decoderOpt,
+        "jobs=i" => \$jobs,
+        "density-prune=f" => \$density_prune,
+        "dont-clean" => \$disable_clean,
+        "pass-suffix=s" => \$pass_suffix,
+        "epsilon=s" => \$epsilon,
+        "help" => \$help,
+        "local" => \$run_local,
+        "use-make=i" => \$use_make,
+        "max-iterations=i" => \$max_iterations,
+        "pmem=s" => \$pmem,
+        "cpbin!" => \$cpbin,
+        "ref-files=s" => \$refFiles,
+        "metric=s" => \$metric,
+        "source-file=s" => \$srcFile,
+        "weights=s" => \$initialWeights,
+	"optimizer=i" => \$optimizer,
+	"metric-scale=i" => \$metric_scale,
+	"kbest-size=i" => \$kbest_size,
+	"update-size=i" => \$update_size,
+	"step-size=f" => \$step_size,
+	"hope-select=i" => \$hopes,
+	"fear-select=i" => \$fears,
+	"sent-approx" => \$sent_approx,
+        "pseudo-doc" => \$pseudo_doc,
+	"unique-kbest" => \$unique_kbest,
+        "grammar-prefix=s" => \$gpref,
+	"freeze" => \$freeze,
+        "workdir=s" => \$dir,
+	) == 0 || @ARGV!=1 || $help) {
+        print_help();
+        exit;
+}
+
+($iniFile) = @ARGV;
+
+
+sub write_config;
+sub enseg;
+sub print_help;
+
+my $nodelist;
+my $host =check_output("hostname"); chomp $host;
+my $bleu;
+my $interval_count = 0;
+my $logfile;
+my $projected_score;
+
+
+#my $refs_comma_sep = get_comma_sep_refs($refFiles);
+my $refs_comma_sep = get_comma_sep_refs('r',$refFiles);
+
+#my $refs_comma_sep_4cdec = get_comma_sep_refs_4cdec($refFiles);
+
+unless ($dir){
+        $dir = "mira";
+}
+unless ($dir =~ /^\//){  # convert relative path to absolute path
+        my $basedir = check_output("pwd");
+        chomp $basedir;
+        $dir = "$basedir/$dir";
+}
+
+if ($decoderOpt){ $decoder = $decoderOpt; }
+
+# Initializations and helper functions
+srand;
+
+my @childpids = ();
+my @cleanupcmds = ();
+
+sub cleanup {
+        print STDERR "Cleanup...\n";
+        for my $pid (@childpids){ unchecked_call("kill $pid"); }
+        for my $cmd (@cleanupcmds){ unchecked_call("$cmd"); }
+        exit 1;
+};
+
+# Always call cleanup, no matter how we exit
+*CORE::GLOBAL::exit =
+    sub{ cleanup(); };
+$SIG{INT} = "cleanup";
+$SIG{TERM} = "cleanup";
+$SIG{HUP} = "cleanup";
+
+
+my $decoderBase = check_output("basename $decoder"); chomp $decoderBase;
+my $newIniFile = "$dir/$decoderBase.ini";
+my $inputFileName = "$dir/input";
+my $user = $ENV{"USER"};
+
+
+# process ini file
+-e $iniFile || die "Error: could not open $iniFile for reading\n";
+open(INI, $iniFile);
+
+use File::Basename qw(basename);
+#pass bindir, refs to vars holding bin
+sub modbin {
+    local $_;
+    my $bindir=shift;
+    check_call("mkdir -p $bindir");
+    -d $bindir || die "couldn't make bindir $bindir";
+    for (@_) {
+        my $src=$$_;
+        $$_="$bindir/".basename($src);
+        check_call("cp -p $src $$_");
+    }
+}
+sub dirsize {
+    opendir ISEMPTY,$_[0];
+    return scalar(readdir(ISEMPTY))-1;
+}
+
+
+
+
+if (-e $dir && dirsize($dir)>1 && -e "$dir/weights" ){ # allow preexisting logfile, binaries, but not dist-vest.pl outputs
+    die "ERROR: working dir $dir already exists\n\n";
+} else {
+    -e $dir || mkdir $dir;
+    mkdir "$dir/scripts";
+    my $cmdfile="$dir/rerun-mira.sh";
+    open CMD,'>',$cmdfile;
+    print CMD "cd ",&getcwd,"\n";
+    my $cline=&cmdline."\n";
+    print CMD $cline;
+    close CMD;
+    print STDERR $cline;
+    chmod(0755,$cmdfile);
+    unless (-e $initialWeights) {
+        print STDERR "Please specify an initial weights file with --initial-weights\n";
+        print_help();
+        exit;
+    }
+    check_call("cp $initialWeights $dir/weights.0");
+    die "Can't find weights.0" unless (-e "$dir/weights.0");
+}
+write_config(*STDERR);
+
+# Generate initial files and values
+check_call("cp $iniFile $newIniFile");
+$iniFile = $newIniFile;
+
+my $newsrc = "$dir/dev.input";
+enseg($srcFile, $newsrc, $gpref);
+
+$srcFile = $newsrc;
+my $devSize = 0;
+open F, "<$srcFile" or die "Can't read $srcFile: $!";
+while(<F>) { $devSize++; }
+close F;
+
+my $lastPScore = 0;
+my $lastWeightsFile;
+my $bestScoreIter=-1;
+my $bestScore=-1;
+unless ($update_size){$update_size = $kbest_size;}
+# main optimization loop
+#while (1){
+for (my $opt_iter=0; $opt_iter<$max_iterations; $opt_iter++) {
+
+	print STDERR "\n\nITERATION $opt_iter\n==========\n";
+	print STDERR "Using port $portn\n";
+
+	# iteration-specific files
+	my $runFile="$dir/run.raw.$opt_iter";
+	my $onebestFile="$dir/1best.$opt_iter";
+	my $logdir="$dir/logs.$opt_iter";
+	my $decoderLog="$logdir/decoder.sentserver.log.$opt_iter";
+	my $scorerLog="$logdir/scorer.log.$opt_iter";
+	my $weightdir="$dir/weights.pass$opt_iter/";
+	check_call("mkdir -p $logdir");
+	check_call("mkdir -p $weightdir");
+
+	#decode
+	print STDERR "RUNNING DECODER AT ";
+	print STDERR unchecked_output("date");
+#	my $im1 = $opt_iter - 1;
+	my $weightsFile="$dir/weights.$opt_iter";
+	print "ITER $iteration " ;
+	my $cur_pass = "-p 0$opt_iter";
+	my $decoder_cmd = "$decoder -c $iniFile -w $weightsFile $refs_comma_sep -m $metric -s $metric_scale -b $update_size -k $kbest_size -o $optimizer $cur_pass -O $weightdir -D $dir  -h $hopes -f $fears -C $step_size";
+	if($unique_kbest){
+		$decoder_cmd .= " -u";
+	}
+	if($sent_approx){
+		$decoder_cmd .= " -a";
+	}
+	if($pseudo_doc){
+                $decoder_cmd .= " -e";
+        }
+	if ($density_prune) {
+		$decoder_cmd .= " --density_prune $density_prune";
+	}
+	my $pcmd;
+	if ($run_local) {
+		$pcmd = "cat $srcFile |";
+	} elsif ($use_make) {
+	    # TODO: Throw error when jobs is speong with use_make
+		$pcmd = "cat $srcFile | $parallelize --use-fork -p $pmem -e $logdir -j $use_make --";
+	} 
+	else {
+	    $pcmd = "cat $srcFile | $parallelize -p $pmem -e $logdir -j $jobs --baseport $portn --";
+	}
+	my $cmd = "$pcmd $decoder_cmd 2> $decoderLog 1> $runFile";
+	print STDERR "COMMAND:\n$cmd\n";
+	check_bash_call($cmd);
+
+	my $retries = 0;
+        my $num_topbest;
+        while($retries < 6) {
+            $num_topbest = check_output("wc -l < $runFile");
+            print STDERR "NUMBER OF TOP-BEST HYPs: $num_topbest\n";
+            if($devSize == $num_topbest) {
+                last;
+            } else {
+                print STDERR "Incorrect number of topbest. Waiting for distributed filesystem and retrying...\n";
+                sleep(10);
+            }
+            $retries++;
+        }
+	 die "Dev set contains $devSize sentences, but we don't have topbest for all these! Decoder failure? Check $decoderLog\n" if ($devSize != $num_topbest);
+
+
+	#score the output from this iteration
+	open RUN, "<$runFile" or die "Can't read $runFile: $!";
+	open H, ">$runFile.H" or die;
+	open F, ">$runFile.F" or die;
+	open B, ">$runFile.B" or die;
+	while(<RUN>) {
+	    chomp();
+	    (my $hope,my $best,my $fear) = split(/ \|\|\| /);
+	    print H "$hope \n"; 	    
+	    print B "$best \n";
+ 	    print F "$fear \n";
+	}
+	close RUN;
+	close F; close B; close H;
+	
+	my $dec_score = check_output("cat $runFile.B | $SCORER $refs_comma_sep -m $metric");
+	my $dec_score_h = check_output("cat $runFile.H | $SCORER $refs_comma_sep -m $metric");
+	my $dec_score_f = check_output("cat $runFile.F | $SCORER $refs_comma_sep -m $metric");
+	chomp $dec_score; chomp $dec_score_h; chomp $dec_score_f;
+	print STDERR "DECODER SCORE: $dec_score HOPE: $dec_score_h FEAR: $dec_score_f\n";
+	if ($dec_score> $bestScore){
+		$bestScoreIter=$opt_iter; 
+		$bestScore=$dec_score;
+	}
+	# save space
+	check_call("gzip -f $runFile");
+	check_call("gzip -f $decoderLog");
+		my $iter_filler="";
+	if($opt_iter < 10)
+	{$iter_filler="0";}
+
+	my $nextIter = $opt_iter + 1;
+	my $newWeightsFile = "$dir/weights.$nextIter";
+	$lastWeightsFile = "$dir/weights.$opt_iter";
+
+	average_weights("$weightdir/weights.mira-pass*.*[0-9].gz", $newWeightsFile, $logdir);
+	system("gzip -f $logdir/kbes*");
+	print STDERR "\n==========\n";
+	$iteration++;
+}
+print STDERR "\nBEST ITER: $bestScoreIter :: $bestScore\n\n\n";
+
+print STDOUT "$lastWeightsFile\n";
+
+sub get_lines {
+  my $fn = shift @_;
+  open FL, "<$fn" or die "Couldn't read $fn: $!";
+  my $lc = 0;
+  while(<FL>) { $lc++; }
+  return $lc;
+}
+
+sub get_comma_sep_refs {
+  my ($r,$p) = @_;
+  my $o = check_output("echo $p");
+  chomp $o;
+  my @files = split /\s+/, $o;
+  return "-$r " . join(" -$r ", @files);
+}
+
+
+sub read_weights_file {
+  my ($file) = @_;
+  open F, "<$file" or die "Couldn't read $file: $!";
+  my @r = ();
+  my $pm = -1;
+  while(<F>) {
+    next if /^#/;
+    next if /^\s*$/;
+    chomp;
+    if (/^(.+)\s+(.+)$/) {
+      my $m = $1;
+      my $w = $2;
+      die "Weights out of order: $m <= $pm" unless $m > $pm;
+      push @r, $w;
+    } else {
+      warn "Unexpected feature name in weight file: $_";
+    }
+  }
+  close F;
+  return join ' ', @r;
+}
+
+sub write_config {
+	my $fh = shift;
+	my $cleanup = "yes";
+	if ($disable_clean) {$cleanup = "no";}
+
+	print $fh "\n";
+	print $fh "DECODER:          $decoder\n";
+	print $fh "INI FILE:         $iniFile\n";
+	print $fh "WORKING DIR:      $dir\n";
+	print $fh "SOURCE (DEV):     $srcFile\n";
+	print $fh "REFS (DEV):       $refFiles\n";
+	print $fh "EVAL METRIC:      $metric\n";
+	print $fh "START ITERATION:  $iteration\n";
+	print $fh "MAX ITERATIONS:   $max_iterations\n";
+	print $fh "DECODE NODES:     $jobs\n";
+	print $fh "HEAD NODE:        $host\n";
+	print $fh "PMEM (DECODING):  $pmem\n";
+	print $fh "CLEANUP:          $cleanup\n";
+	print $fh "INITIAL WEIGHTS:  $initialWeights\n";
+        print $fh "GRAMMAR PREFIX:   $gpref\n";
+}
+
+sub update_weights_file {
+  my ($neww, $rfn, $rpts) = @_;
+  my @feats = @$rfn;
+  my @pts = @$rpts;
+  my $num_feats = scalar @feats;
+  my $num_pts = scalar @pts;
+  die "$num_feats (num_feats) != $num_pts (num_pts)" unless $num_feats == $num_pts;
+  open G, ">$neww" or die;
+  for (my $i = 0; $i < $num_feats; $i++) {
+    my $f = $feats[$i];
+    my $lambda = $pts[$i];
+    print G "$f $lambda\n";
+  }
+  close G;
+}
+
+sub enseg {
+    my $src = shift;
+    my $newsrc = shift;
+    my $grammarpref = shift;
+
+    open(SRC, $src);
+    open(NEWSRC, ">$newsrc");
+    my $i=0;
+    while (my $line=<SRC>){
+	chomp $line;
+	if ($line =~ /^\s*<seg/i) {
+	    if($line =~ /id="[0-9]+"/) {
+		print NEWSRC "$line\n";
+	    } else {
+		die "When using segments with pre-generated <seg> tags, you must include a zero-based id attribute";
+	    }
+	}
+	elsif (defined $grammarpref) {
+	    print NEWSRC "<seg id=\"$i\" grammar=\"$grammarpref.$i.gz\">$line</seg>\n";}
+	else {
+	    print NEWSRC "<seg id=\"$i\">$line</seg>\n";
+	}
+	$i++;
+    }
+    close SRC;
+    close NEWSRC;
+}
+
+sub print_help {
+ my $executable = check_output("basename $0"); chomp $executable;
+        print << "Help";
+
+Usage: $executable [options] <ini file>
+        Runs a complete MIRA optimization using the ini file specified.
+	Example invocation:
+	run_mira.pl \
+        --pmem 3g \
+        --max-iterations 20 \
+        --optimizer 2 \
+        --unique-kbest \
+        --jobs 15 \
+        --kbest-size 500 \
+        --hope-select 1 \
+        --fear-select 1  \
+        --ref-files "ref.0.soseos ref.1.soseos" \
+        --source-file src.soseos \
+        --weights weights.init \
+        --workdir workdir \
+        --grammar-prefix grammars/grammar \
+        --step-size 0.01 \
+        --metric-scale 10000 \
+
+Required:
+
+        --ref-files <files>
+                Dev set ref files.  This option takes only a single string argument.
+                To use multiple files (including file globbing), this argument should
+                be quoted.
+        --source-file <file>
+                Dev set source file.
+        --weights <file>
+                Initial weights file
+
+General options:
+
+        --help
+                Print this message and exit.
+
+       --max-iterations <M>
+                Maximum number of iterations to run.  If not specified, defaults
+                to $max_iterations.
+
+        --metric <method>
+                Metric to optimize.
+                Example values: IBM_BLEU, NIST_BLEU, Koehn_BLEU, TER, Combi
+
+        --workdir <dir>
+                Directory for intermediate and output files.  If not specified, the
+                name is derived from the ini filename.  Assuming that the ini
+                filename begins with the decoder name and ends with ini, the default
+                name of the working directory is inferred from the middle part of
+                the filename.  E.g. an ini file named decoder.foo.ini would have
+                a default working directory name foo.
+	--optimizer <I>
+		Learning method to use for weight update. Choice are 1) SGD, 2) PA MIRA with Selection from Cutting Plane, 3) Cutting Plane MIRA, 4) PA MIRA,5) nbest MIRA with hope, fear, and model constraints
+	--metric-scale <I>
+		Scale MT loss by this amount when computing hope/fear candidates
+	--kbest-size <I>
+		Size of k-best list to extract from forest
+	--update-size <I>
+		Size of k-best list to use for update (applies to optimizer 5)
+	--step-size <F>
+		Controls aggresiveness of update (C) 
+	--hope-select<I>
+		How to select hope candidate. Choices are 1) model score - cost, 2) min cost
+	--fear-select <I>
+		How to select fear candodate. Choices are 1) model score + cost, 2) max cost, 3) max score
+	--sent-approx
+		Use smoothed sentence-level MT metric
+	--pseudo-doc
+		Use pseudo document to approximate MT metric
+	--unique-kbest
+		Extract unique k-best from forest
+	--grammar-prefix <path>
+		Path to sentence-specific grammar files
+
+Job control options:
+
+        --jobs <I>
+                Number of decoder processes to run in parallel. [default=$default_jobs]
+
+        --pmem <N>
+                Amount of physical memory requested for parallel decoding jobs
+                (used with qsub requests only)
+
+	--local 
+		Run single learner
+	--use-make <I>
+		Run parallel learners on a single machine through fork.
+
+
+Help
+}
+
+
+sub cmdline {
+    return join ' ',($0,@ORIG_ARGV);
+}
+
+#buggy: last arg gets quoted sometimes?
+my $is_shell_special=qr{[ \t\n\\><|&;"'`~*?{}$!()]};
+my $shell_escape_in_quote=qr{[\\"\$`!]};
+
+sub escape_shell {
+    my ($arg)=@_;
+    return undef unless defined $arg;
+    if ($arg =~ /$is_shell_special/) {
+        $arg =~ s/($shell_escape_in_quote)/\\$1/g;
+        return "\"$arg\"";
+    }
+    return $arg;
+}
+
+sub escaped_shell_args {
+    return map {local $_=$_;chomp;escape_shell($_)} @_;
+}
+
+sub escaped_shell_args_str {
+    return join ' ',&escaped_shell_args(@_);
+}
+
+sub escaped_cmdline {
+    return "$0 ".&escaped_shell_args_str(@ORIG_ARGV);
+}
+
+sub average_weights {
+
+    my $path = shift;
+    my $out = shift;
+    my $logpath = shift;
+    print "AVERAGE $path $out\n";
+    my %feature_weights= ();
+    my $total =0;
+    my $total_mult =0;
+    sleep(10);
+    foreach my $file (glob "$path")
+    {
+	$file =~ /\/([^\/]+).gz$/;
+	my $fname = $1;
+	my $cmd = "gzip -d $file";
+	$file =~ s/\.gz//;
+	check_bash_call($cmd);
+	my $mult = 0;
+	print "FILE $file \n";
+	open SCORE, "< $file" or next;
+	$total++;
+	while( <SCORE> ) {
+	    my $line = $_;
+	    if ($line !~ m/^\#/)
+	    {
+		my @s = split(" ",$line);
+		$feature_weights{$s[0]}+= $mult * $s[1];
+	    }
+	    else
+	    {
+		(my $msg,my $ran,$mult) = split(/ \|\|\| /);
+		print "Processing $ran $mult\n";
+	    }
+	}
+	$total_mult += $mult;
+	
+	close SCORE;
+	$cmd = "gzip $file"; check_bash_call($cmd);
+    }
+    
+#print out new averaged weights
+    open OUT, "> $out" or next;
+    for my $f ( keys %feature_weights ) {
+	print "$f $feature_weights{$f} $total_mult\n";
+	my $ave = $feature_weights{$f} / $total_mult;
+	
+	print "Printing $f $ave ||| ";
+	print OUT "$f $ave\n";
+    }
+    
+}