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authorphilblunsom@gmail.com <philblunsom@gmail.com@ec762483-ff6d-05da-a07a-a48fb63a330f>2010-06-22 20:34:00 +0000
committerphilblunsom@gmail.com <philblunsom@gmail.com@ec762483-ff6d-05da-a07a-a48fb63a330f>2010-06-22 20:34:00 +0000
commitefe0d24fa7dbca47825638a52f51977456153bd0 (patch)
tree77c1d68ae29e423e1baaca6565a2455ec481955c
parent42e1e2cb20c8f31d9a27bf0be5fe0846f3dde413 (diff)
Initial ci of gi dir
git-svn-id: https://ws10smt.googlecode.com/svn/trunk@5 ec762483-ff6d-05da-a07a-a48fb63a330f
-rwxr-xr-xgi/pyp-topics/scripts/contexts2documents.py29
-rwxr-xr-xgi/pyp-topics/scripts/extract_contexts.py144
-rwxr-xr-xgi/pyp-topics/scripts/extract_contexts_test.py72
-rwxr-xr-xgi/pyp-topics/scripts/extract_leaves.py49
-rwxr-xr-xgi/pyp-topics/scripts/map-documents.py20
-rwxr-xr-xgi/pyp-topics/scripts/map-terms.py20
-rwxr-xr-xgi/pyp-topics/scripts/score-mkcls.py61
-rwxr-xr-xgi/pyp-topics/scripts/score-topics.py64
-rwxr-xr-xgi/pyp-topics/scripts/spans2labels.py46
-rwxr-xr-xgi/pyp-topics/scripts/topics.py20
-rw-r--r--gi/pyp-topics/src/Makefile30
-rw-r--r--gi/pyp-topics/src/corpus.cc103
-rw-r--r--gi/pyp-topics/src/corpus.hh101
-rw-r--r--gi/pyp-topics/src/gammadist.c247
-rw-r--r--gi/pyp-topics/src/gammadist.h72
-rw-r--r--gi/pyp-topics/src/gzstream.cc165
-rw-r--r--gi/pyp-topics/src/gzstream.hh121
-rw-r--r--gi/pyp-topics/src/log_add.h30
-rw-r--r--gi/pyp-topics/src/makefile.darwin15
-rw-r--r--gi/pyp-topics/src/makefile.depend1250
-rw-r--r--gi/pyp-topics/src/mt19937ar.c194
-rw-r--r--gi/pyp-topics/src/mt19937ar.h44
-rw-r--r--gi/pyp-topics/src/pyp-topics.cc224
-rw-r--r--gi/pyp-topics/src/pyp-topics.hh52
-rw-r--r--gi/pyp-topics/src/pyp.hh477
-rw-r--r--gi/pyp-topics/src/slice-sampler.h192
-rw-r--r--gi/pyp-topics/src/train.cc136
-rw-r--r--gi/pyp-topics/src/utility.h962
28 files changed, 4940 insertions, 0 deletions
diff --git a/gi/pyp-topics/scripts/contexts2documents.py b/gi/pyp-topics/scripts/contexts2documents.py
new file mode 100755
index 00000000..c625d17d
--- /dev/null
+++ b/gi/pyp-topics/scripts/contexts2documents.py
@@ -0,0 +1,29 @@
+#!/usr/bin/python
+
+import sys
+from operator import itemgetter
+
+if len(sys.argv) > 2:
+ print "Usage: contexts2documents.py [contexts_index_out]"
+ exit(1)
+
+context_index = {}
+for line in sys.stdin:
+ phrase, line_tail = line.split('\t')
+
+ raw_contexts = line_tail.split('|||')
+ contexts = [c.strip() for x,c in enumerate(raw_contexts) if x%2 == 0]
+ counts = [int(c.split('=')[1].strip()) for x,c in enumerate(raw_contexts) if x%2 != 0]
+
+ print len(contexts),
+ for context,count in zip(contexts,counts):
+ c = context_index.setdefault(context, len(context_index))
+ print "%d:%d" % (c,count),
+ print
+if len(sys.argv) == 2:
+ contexts_out = open(sys.argv[1],'w')
+ contexts = context_index.items()
+ contexts.sort(key = itemgetter(1))
+ for context in contexts:
+ print >>contexts_out, context[0]
+ contexts_out.close()
diff --git a/gi/pyp-topics/scripts/extract_contexts.py b/gi/pyp-topics/scripts/extract_contexts.py
new file mode 100755
index 00000000..b2723f2a
--- /dev/null
+++ b/gi/pyp-topics/scripts/extract_contexts.py
@@ -0,0 +1,144 @@
+#!/usr/bin/python
+
+import sys,collections
+
+def extract_backoff(context_list, order):
+ assert len(context_list) == (2*order)
+ backoffs = []
+ for i in range(1,order+1):
+ if i == order:
+ backoffs.append(([context_list[i-1]+"|"], ["|"+context_list[i]]))
+ else:
+ right_limit = 2*order-i
+ core = context_list[i:right_limit]
+ left = [context_list[i-1]+"|"*(order-i+1)]
+ right = ["|"*(order-i+1)+context_list[right_limit]]
+ backoffs.append((core, left, right))
+# print context_list, backoffs
+ return backoffs
+
+def tuple_to_str(t):
+ s=""
+ for i,x in enumerate(t):
+ if i > 0: s += "|"
+ s += str(x)
+ return s
+
+if len(sys.argv) < 3:
+ print "Usage: extract-contexts.py output_filename order cutoff lowercase"
+ exit(1)
+
+output_filename = sys.argv[1]
+order = int(sys.argv[2])
+cutoff = 0
+if len(sys.argv) > 3:
+ cutoff = int(sys.argv[3])
+lowercase = False
+if len(sys.argv) > 4:
+ lowercase = bool(sys.argv[4])
+
+contexts_dict={}
+contexts_list=[]
+contexts_freq=collections.defaultdict(int)
+contexts_backoff={}
+
+token_dict={}
+token_list=[]
+documents_dict=collections.defaultdict(dict)
+
+contexts_at_order = [i for i in range(order+1)]
+
+prefix = ["<s%d>|<s>"%i for i in range(order)]
+suffix = ["</s%d>|</s>"%i for i in range(order)]
+
+for line in sys.stdin:
+ tokens = list(prefix)
+ tokens.extend(line.split())
+ tokens.extend(suffix)
+ if lowercase:
+ tokens = map(lambda x: x.lower(), tokens)
+
+ for i in range(order, len(tokens)-order):
+ context_list = []
+ term=""
+ for j in range(i-order, i+order+1):
+ token,tag = tokens[j].rsplit('|',2)
+ if j != i:
+ context_list.append(token)
+ else:
+ if token not in token_dict:
+ token_dict[token] = len(token_dict)
+ token_list.append(token)
+ term = token_dict[token]
+
+ context = tuple_to_str(tuple(context_list))
+
+ if context not in contexts_dict:
+ context_index = len(contexts_dict)
+ contexts_dict[context] = context_index
+ contexts_list.append(context)
+ contexts_at_order[0] += 1
+
+ # handle backoff
+ backoff_contexts = extract_backoff(context_list, order)
+ bo_indexes=[(context_index,)]
+# bo_indexes=[(context,)]
+ for i,bo in enumerate(backoff_contexts):
+ factor_indexes=[]
+ for factor in bo:
+ bo_tuple = tuple_to_str(tuple(factor))
+ if bo_tuple not in contexts_dict:
+ contexts_dict[bo_tuple] = len(contexts_dict)
+ contexts_list.append(bo_tuple)
+ contexts_at_order[i+1] += 1
+# factor_indexes.append(bo_tuple)
+ factor_indexes.append(contexts_dict[bo_tuple])
+ bo_indexes.append(tuple(factor_indexes))
+
+ for i in range(len(bo_indexes)-1):
+ contexts_backoff[bo_indexes[i][0]] = bo_indexes[i+1]
+
+ context_index = contexts_dict[context]
+ contexts_freq[context_index] += 1
+
+ if context_index not in documents_dict[term]:
+ documents_dict[term][context_index] = 1
+ else:
+ documents_dict[term][context_index] += 1
+
+term_file = open(output_filename+".terms",'w')
+for t in token_list: print >>term_file, t
+term_file.close()
+
+contexts_file = open(output_filename+".contexts",'w')
+for c in contexts_list:
+ print >>contexts_file, c
+contexts_file.close()
+
+data_file = open(output_filename+".data",'w')
+for t in range(len(token_list)):
+ line=""
+ num_active=0
+ for c in documents_dict[t]:
+ count = documents_dict[t][c]
+ if contexts_freq[c] >= cutoff:
+ line += (' ' + str(c) + ':' + str(count))
+ num_active += 1
+ if num_active > 0:
+ print >>data_file, "%d%s" % (num_active,line)
+data_file.close()
+
+contexts_backoff_file = open(output_filename+".contexts_backoff",'w')
+print >>contexts_backoff_file, len(contexts_list), order,
+#for x in contexts_at_order:
+# print >>contexts_backoff_file, x,
+#print >>contexts_backoff_file
+for x in range(order-1):
+ print >>contexts_backoff_file, 3,
+print >>contexts_backoff_file, 2
+
+for x in contexts_backoff:
+ print >>contexts_backoff_file, x,
+ for y in contexts_backoff[x]: print >>contexts_backoff_file, y,
+ print >>contexts_backoff_file
+contexts_backoff_file.close()
diff --git a/gi/pyp-topics/scripts/extract_contexts_test.py b/gi/pyp-topics/scripts/extract_contexts_test.py
new file mode 100755
index 00000000..693b6e0b
--- /dev/null
+++ b/gi/pyp-topics/scripts/extract_contexts_test.py
@@ -0,0 +1,72 @@
+#!/usr/bin/python
+
+import sys,collections
+
+def tuple_to_str(t):
+ s=""
+ for i,x in enumerate(t):
+ if i > 0: s += "|"
+ s += str(x)
+ return s
+
+if len(sys.argv) < 5:
+ print "Usage: extract-contexts_test.py output_filename vocab contexts order lowercase"
+ exit(1)
+
+output_filename = sys.argv[1]
+output = open(output_filename+".test_data",'w')
+
+unk_term="-UNK-"
+vocab_dict={}
+for i,x in enumerate(file(sys.argv[2], 'r').readlines()):
+ vocab_dict[x.strip()]=i
+
+contexts_dict={}
+contexts_list=[]
+for i,x in enumerate(file(sys.argv[3], 'r').readlines()):
+ contexts_dict[x.strip()]=i
+ contexts_list.append(x.strip())
+
+order = int(sys.argv[4])
+
+lowercase = False
+if len(sys.argv) > 5:
+ lowercase = bool(sys.argv[5])
+if lowercase: unk_term = unk_term.lower()
+
+prefix = ["<s%d>|<s>"%i for i in range(order)]
+suffix = ["</s%d>|</s>"%i for i in range(order)]
+
+assert unk_term in vocab_dict
+for line in sys.stdin:
+ tokens = list(prefix)
+ tokens.extend(line.split())
+ tokens.extend(suffix)
+ if lowercase:
+ tokens = map(lambda x: x.lower(), tokens)
+
+ for i in range(order, len(tokens)-order):
+ context_list=[]
+ term=""
+ for j in range(i-order, i+order+1):
+ token,tag = tokens[j].rsplit('|',2)
+ if j != i:
+ context_list.append(token)
+ else:
+ if token not in vocab_dict:
+ term = vocab_dict[unk_term]
+ else:
+ term = vocab_dict[token]
+ context = tuple_to_str(context_list)
+ if context not in contexts_dict:
+ contexts_dict[context] = len(contexts_dict)
+ contexts_list.append(context)
+ context_index = contexts_dict[context]
+ print >>output, "%d:%d" % (term,context_index),
+ print >>output
+output.close()
+
+contexts_file = open(output_filename+".test_contexts",'w')
+for c in contexts_list:
+ print >>contexts_file, c
+contexts_file.close()
diff --git a/gi/pyp-topics/scripts/extract_leaves.py b/gi/pyp-topics/scripts/extract_leaves.py
new file mode 100755
index 00000000..14783b36
--- /dev/null
+++ b/gi/pyp-topics/scripts/extract_leaves.py
@@ -0,0 +1,49 @@
+#!/usr/bin/python
+
+import nltk
+import nltk.probability
+import sys
+import getopt
+
+lexicalise=False
+rm_traces=False
+cutoff=100
+length_cutoff=10000
+try:
+ opts, args = getopt.getopt(sys.argv[1:], "hs:c:l", ["help", "lexicalise", "cutoff","sentence-length","remove-traces"])
+except getopt.GetoptError:
+ print "Usage: extract_leaves.py [-lsc]"
+ sys.exit(2)
+for opt, arg in opts:
+ if opt in ("-h", "--help"):
+ print "Usage: extract_leaves.py [-lsc]"
+ sys.exit()
+ elif opt in ("-l", "--lexicalise"):
+ lexicalise = True
+ elif opt in ("-c", "--cutoff"):
+ cutoff = int(arg)
+ elif opt in ("-s", "--sentence-length"):
+ length_cutoff = int(arg)
+ elif opt in ("--remove-traces"):
+ rm_traces = True
+
+token_freq = nltk.probability.FreqDist()
+lines = []
+for line in sys.stdin:
+ t = nltk.Tree.parse(line)
+ pos = t.pos()
+ if len(pos) <= length_cutoff:
+ lines.append(pos)
+ for token, tag in pos:
+ token_freq.inc(token)
+
+for line in lines:
+ for token,tag in line:
+ if not (rm_traces and tag == "-NONE-"):
+ if lexicalise:
+ if token_freq[token] < cutoff:
+ token = '-UNK-'
+ print '%s|%s' % (token,tag),
+ else:
+ print '%s' % tag,
+ print
diff --git a/gi/pyp-topics/scripts/map-documents.py b/gi/pyp-topics/scripts/map-documents.py
new file mode 100755
index 00000000..703de312
--- /dev/null
+++ b/gi/pyp-topics/scripts/map-documents.py
@@ -0,0 +1,20 @@
+#!/usr/bin/python
+
+import sys
+
+if len(sys.argv) != 2:
+ print "Usage: map-documents.py vocab-file"
+ exit(1)
+
+vocab = file(sys.argv[1], 'r').readlines()
+term_dict = map(lambda x: x.strip(), vocab)
+
+for line in sys.stdin:
+ tokens = line.split()
+ for token in tokens:
+ elements = token.split(':')
+ if len(elements) == 1:
+ print "%s" % (term_dict[int(elements[0])]),
+ else:
+ print "%s:%s" % (term_dict[int(elements[0])], elements[1]),
+ print
diff --git a/gi/pyp-topics/scripts/map-terms.py b/gi/pyp-topics/scripts/map-terms.py
new file mode 100755
index 00000000..eb0298d7
--- /dev/null
+++ b/gi/pyp-topics/scripts/map-terms.py
@@ -0,0 +1,20 @@
+#!/usr/bin/python
+
+import sys
+
+if len(sys.argv) != 2:
+ print "Usage: map-terms.py vocab-file"
+ exit(1)
+
+vocab = file(sys.argv[1], 'r').readlines()
+term_dict = map(lambda x: x.strip().replace(' ','_'), vocab)
+
+for line in sys.stdin:
+ tokens = line.split()
+ for token in tokens:
+ elements = token.split(':')
+ if len(elements) == 1:
+ print "%s" % (term_dict[int(elements[0])]),
+ else:
+ print "%s:%s" % (term_dict[int(elements[0])], elements[1]),
+ print
diff --git a/gi/pyp-topics/scripts/score-mkcls.py b/gi/pyp-topics/scripts/score-mkcls.py
new file mode 100755
index 00000000..6bd33fc5
--- /dev/null
+++ b/gi/pyp-topics/scripts/score-mkcls.py
@@ -0,0 +1,61 @@
+#!/usr/bin/python
+
+import sys
+from collections import defaultdict
+
+def dict_max(d):
+ max_val=-1
+ max_key=None
+ for k in d:
+ if d[k] > max_val:
+ max_val = d[k]
+ max_key = k
+ assert max_key
+ return max_key
+
+if len(sys.argv) != 3:
+ print "Usage: score-mkcls.py gold classes"
+ exit(1)
+
+gold_file=open(sys.argv[1],'r')
+
+term_to_topics = {}
+for line in open(sys.argv[2],'r'):
+ term,cls = line.split()
+ term_to_topics[term] = cls
+
+gold_to_topics = defaultdict(dict)
+topics_to_gold = defaultdict(dict)
+
+for gold_line in gold_file:
+ gold_tokens = gold_line.split()
+ for gold_token in gold_tokens:
+ gold_term,gold_tag = gold_token.rsplit('|',1)
+ pred_token = term_to_topics[gold_term]
+ gold_to_topics[gold_tag][pred_token] \
+ = gold_to_topics[gold_tag].get(pred_token, 0) + 1
+ topics_to_gold[pred_token][gold_tag] \
+ = topics_to_gold[pred_token].get(gold_tag, 0) + 1
+
+pred=0
+correct=0
+gold_file=open(sys.argv[1],'r')
+for gold_line in gold_file:
+ gold_tokens = gold_line.split()
+
+ for gold_token in gold_tokens:
+ gold_term,gold_tag = gold_token.rsplit('|',1)
+ pred_token = term_to_topics[gold_term]
+ print "%s|%s|%s" % (gold_token, pred_token, dict_max(topics_to_gold[pred_token])),
+ pred += 1
+ if gold_tag == dict_max(topics_to_gold[pred_token]):
+ correct += 1
+ print
+print >>sys.stderr, "Many-to-One Accuracy = %f" % (float(correct) / pred)
+#for x in gold_to_topics:
+# print x,dict_max(gold_to_topics[x])
+#print "###################################################"
+#for x in range(len(topics_to_gold)):
+# print x,dict_max(topics_to_gold[str(x)])
+# print x,topics_to_gold[str(x)]
+#print term_to_topics
diff --git a/gi/pyp-topics/scripts/score-topics.py b/gi/pyp-topics/scripts/score-topics.py
new file mode 100755
index 00000000..1d8a1fcd
--- /dev/null
+++ b/gi/pyp-topics/scripts/score-topics.py
@@ -0,0 +1,64 @@
+#!/usr/bin/python
+
+import sys
+from collections import defaultdict
+
+def dict_max(d):
+ max_val=-1
+ max_key=None
+ for k in d:
+ if d[k] > max_val:
+ max_val = d[k]
+ max_key = k
+ assert max_key
+ return max_key
+
+if len(sys.argv) != 3:
+ print "Usage: score-topics.py gold pred"
+ exit(1)
+
+gold_file=open(sys.argv[1],'r')
+pred_file=open(sys.argv[2],'r')
+
+gold_to_topics = defaultdict(dict)
+topics_to_gold = defaultdict(dict)
+term_to_topics = defaultdict(dict)
+
+for gold_line,pred_line in zip(gold_file,pred_file):
+ gold_tokens = gold_line.split()
+ pred_tokens = pred_line.split()
+ assert len(gold_tokens) == len(pred_tokens)
+
+ for gold_token,pred_token in zip(gold_tokens,pred_tokens):
+ gold_term,gold_tag = gold_token.rsplit('|',1)
+ gold_to_topics[gold_tag][pred_token] \
+ = gold_to_topics[gold_tag].get(pred_token, 0) + 1
+ term_to_topics[gold_term][pred_token] \
+ = term_to_topics[gold_term].get(pred_token, 0) + 1
+ topics_to_gold[pred_token][gold_tag] \
+ = topics_to_gold[pred_token].get(gold_tag, 0) + 1
+
+pred=0
+correct=0
+gold_file=open(sys.argv[1],'r')
+pred_file=open(sys.argv[2],'r')
+for gold_line,pred_line in zip(gold_file,pred_file):
+ gold_tokens = gold_line.split()
+ pred_tokens = pred_line.split()
+
+ for gold_token,pred_token in zip(gold_tokens,pred_tokens):
+ gold_term,gold_tag = gold_token.rsplit('|',1)
+# print "%s|%s" % (gold_token, dict_max(gold_to_topics[gold_tag])),
+ print "%s|%s|%s" % (gold_token, pred_token, dict_max(topics_to_gold[pred_token])),
+ pred += 1
+ if gold_tag == dict_max(topics_to_gold[pred_token]):
+ correct += 1
+ print
+print >>sys.stderr, "Many-to-One Accuracy = %f" % (float(correct) / pred)
+#for x in gold_to_topics:
+# print x,dict_max(gold_to_topics[x])
+#print "###################################################"
+#for x in range(len(topics_to_gold)):
+# print x,dict_max(topics_to_gold[str(x)])
+# print x,topics_to_gold[str(x)]
+#print term_to_topics
diff --git a/gi/pyp-topics/scripts/spans2labels.py b/gi/pyp-topics/scripts/spans2labels.py
new file mode 100755
index 00000000..b523e191
--- /dev/null
+++ b/gi/pyp-topics/scripts/spans2labels.py
@@ -0,0 +1,46 @@
+#!/usr/bin/python
+
+import sys
+from operator import itemgetter
+
+if len(sys.argv) != 4:
+ print "Usage: spans2labels.py phrase_index context_index phrase_context_index"
+ exit(1)
+
+phrase_index = dict(map(lambda x: (x[1].strip(),x[0]), enumerate(file(sys.argv[1], 'r').readlines())))
+context_index = dict(map(lambda x: (x[1].strip(),x[0]), enumerate(file(sys.argv[2], 'r').readlines())))
+
+phrase_context_index = {}
+for i,line in enumerate(file(sys.argv[3], 'r').readlines()):
+ for c,l in map(lambda x: x.split(':'), line.split()[1:]):
+ phrase_context_index[(int(i),int(c))] = l
+
+for line in sys.stdin:
+ line_segments = line.split('|||')
+ source = ['<s>'] + line_segments[0].split() + ['</s>']
+ target = ['<s>'] + line_segments[1].split() + ['</s>']
+ phrases = [ [int(i) for i in x.split('-')] for x in line_segments[2].split()]
+
+# for x in source[1:-1]:
+# print x,
+# print "|||",
+# for x in target[1:-1]:
+# print x,
+ print "|||",
+
+ for s1,s2,t1,t2 in phrases:
+ s1 += 1
+ s2 += 1
+ t1 += 1
+ t2 += 1
+
+ phrase = reduce(lambda x, y: x+y+" ", target[t1:t2], "").strip()
+ context = "%s <PHRASE> %s" % (target[t1-1], target[t2])
+
+ pi = phrase_index[phrase]
+ ci = context_index[context]
+ label = phrase_context_index[(pi,ci)]
+ print "%s-%s:%s" % (t1-1,t2-1,label),
+# print phrase, pi, context, ci
+# print phrase_context_index[(pi,ci)]
+ print
diff --git a/gi/pyp-topics/scripts/topics.py b/gi/pyp-topics/scripts/topics.py
new file mode 100755
index 00000000..0db1af71
--- /dev/null
+++ b/gi/pyp-topics/scripts/topics.py
@@ -0,0 +1,20 @@
+#!/usr/bin/python
+
+import sys
+
+if len(sys.argv) != 2:
+ print "Usage: topics.py words-per-topic"
+ exit(1)
+
+for t,line in enumerate(sys.stdin):
+ tokens = line.split()
+ terms = []
+ for token in tokens:
+ elements = token.rsplit(':',1)
+ terms.append((int(elements[1]),elements[0]))
+ terms.sort()
+ terms.reverse()
+
+ print "Topic %d:" % t
+ map(lambda (x,y) : sys.stdout.write(" %s:%s\n" % (y,x)), terms[:int(sys.argv[1])])
+ print
diff --git a/gi/pyp-topics/src/Makefile b/gi/pyp-topics/src/Makefile
new file mode 100644
index 00000000..1d1391ae
--- /dev/null
+++ b/gi/pyp-topics/src/Makefile
@@ -0,0 +1,30 @@
+-include makefile.darwin
+
+local_objs = ../obj/corpus.o ../obj/gzstream.o ../obj/mt19937ar.o ../obj/pyp-topics.o ../obj/gammadist.o
+
+all: ../bin/pyp-topics-train
+
+-include makefile.depend
+
+#-----------------------#
+# Local stuff
+#-----------------------#
+
+../bin/pyp-topics-train: ../obj/train.o $(local_objs)
+ $(CXX) -o $@ $^ $(LDFLAGS)
+
+../obj/%.o: %.cc
+ ${CXX} $(CXXFLAGS) -c $< -o $@
+
+../obj/%.o: %.c
+ ${CC} $(CFLAGS) -c $< -o $@
+
+.PHONY: depend
+depend:
+ $(CXX) -MM $(CXXFLAGS) *.cc | sed 's/^\(.*\.o:\)/obj\/\1/' > makefile.depend
+
+clean:
+ rm -f ../obj/*.o
+
+#clobber: clean
+# rm makefile.depend ../bin/${ARCH}/*
diff --git a/gi/pyp-topics/src/corpus.cc b/gi/pyp-topics/src/corpus.cc
new file mode 100644
index 00000000..93910ea3
--- /dev/null
+++ b/gi/pyp-topics/src/corpus.cc
@@ -0,0 +1,103 @@
+#include <sstream>
+#include <iostream>
+#include <set>
+
+#include "corpus.hh"
+#include "gzstream.hh"
+
+using namespace std;
+
+//////////////////////////////////////////////////
+// Corpus
+//////////////////////////////////////////////////
+
+Corpus::Corpus() {}
+
+unsigned Corpus::read(const std::string &filename) {
+ m_num_terms = 0;
+ m_num_types = 0;
+ std::set<int> seen_types;
+
+ igzstream in(filename.c_str());
+
+ string buf;
+ int token;
+ unsigned count=0;
+ while (getline(in, buf)) {
+ Document* doc(new Document());
+ istringstream ss(buf);
+
+ ss >> token; // the number of unique terms
+
+ char delimeter;
+ int count;
+ while(ss >> token >> delimeter >> count) {
+ for (int i=0; i<count; ++i)
+ doc->push_back(token);
+ m_num_terms += count;
+ seen_types.insert(token);
+ }
+
+ m_documents.push_back(doc);
+ count++;
+ }
+
+ m_num_types = seen_types.size();
+
+ return count;
+}
+
+//////////////////////////////////////////////////
+// TestCorpus
+//////////////////////////////////////////////////
+
+TestCorpus::TestCorpus() {}
+
+void TestCorpus::read(const std::string &filename) {
+ igzstream in(filename.c_str());
+
+ string buf;
+ Term term;
+ DocumentId doc;
+ char delimeter;
+ while (getline(in, buf)) {
+ DocumentTerms* line(new DocumentTerms());
+ istringstream ss(buf);
+
+ while(ss >> doc >> delimeter >> term)
+ line->push_back(DocumentTerm(doc, term));
+
+ m_lines.push_back(line);
+ }
+}
+
+//////////////////////////////////////////////////
+// TermBackoff
+//////////////////////////////////////////////////
+
+void TermBackoff::read(const std::string &filename) {
+ igzstream in(filename.c_str());
+
+ string buf;
+ int num_terms;
+ getline(in, buf);
+ istringstream ss(buf);
+ ss >> num_terms >> m_backoff_order;
+
+ m_dict.resize(num_terms, -1);
+ for (int i=0; i<m_backoff_order; ++i) {
+ int count; ss >> count;
+ m_terms_at_order.push_back(count);
+ }
+
+ Term term, backoff;
+ while (getline(in, buf)) {
+ istringstream ss(buf);
+ ss >> term >> backoff;
+
+ assert(term < num_terms);
+ assert(term >= 0);
+
+ m_dict[term] = backoff;
+ }
+}
diff --git a/gi/pyp-topics/src/corpus.hh b/gi/pyp-topics/src/corpus.hh
new file mode 100644
index 00000000..3dd17cf9
--- /dev/null
+++ b/gi/pyp-topics/src/corpus.hh
@@ -0,0 +1,101 @@
+#ifndef _CORPUS_HH
+#define _CORPUS_HH
+
+#include <vector>
+#include <string>
+#include <map>
+
+#include <boost/ptr_container/ptr_vector.hpp>
+
+////////////////////////////////////////////////////////////////
+// Corpus
+////////////////////////////////////////////////////////////////
+typedef int Term;
+
+typedef std::vector<Term> Document;
+typedef std::vector<Term> Terms;
+
+class Corpus {
+public:
+ typedef boost::ptr_vector<Document>::const_iterator const_iterator;
+
+public:
+ Corpus();
+ ~Corpus() {}
+
+ unsigned read(const std::string &filename);
+
+ const_iterator begin() const { return m_documents.begin(); }
+ const_iterator end() const { return m_documents.end(); }
+
+ int num_documents() const { return m_documents.size(); }
+ int num_terms() const { return m_num_terms; }
+ int num_types() const { return m_num_types; }
+
+protected:
+ int m_num_terms, m_num_types;
+ boost::ptr_vector<Document> m_documents;
+};
+
+typedef int DocumentId;
+struct DocumentTerm {
+ DocumentTerm(DocumentId d, Term t) : term(t), doc(d) {}
+ Term term;
+ DocumentId doc;
+};
+typedef std::vector<DocumentTerm> DocumentTerms;
+
+class TestCorpus {
+public:
+ typedef boost::ptr_vector<DocumentTerms>::const_iterator const_iterator;
+
+public:
+ TestCorpus();
+ ~TestCorpus() {}
+
+ void read(const std::string &filename);
+
+ const_iterator begin() const { return m_lines.begin(); }
+ const_iterator end() const { return m_lines.end(); }
+
+ int num_instances() const { return m_lines.size(); }
+
+protected:
+ boost::ptr_vector<DocumentTerms> m_lines;
+};
+
+class TermBackoff {
+public:
+ typedef std::vector<Term> dictionary_type;
+ typedef dictionary_type::const_iterator const_iterator;
+
+public:
+ TermBackoff() : m_backoff_order(-1) {}
+ ~TermBackoff() {}
+
+ void read(const std::string &filename);
+
+ const_iterator begin() const { return m_dict.begin(); }
+ const_iterator end() const { return m_dict.end(); }
+
+ const Term& operator[](const Term& t) const {
+ assert(t < static_cast<int>(m_dict.size()));
+ return m_dict[t];
+ }
+
+ int order() const { return m_backoff_order; }
+// int levels() const { return m_terms_at_order.size(); }
+ bool is_null(const Term& term) const { return term < 0; }
+ int terms_at_level(int level) const {
+ assert (level < (int)m_terms_at_order.size());
+ return m_terms_at_order[level];
+ }
+
+ int size() const { return m_dict.size(); }
+
+protected:
+ dictionary_type m_dict;
+ int m_backoff_order;
+ std::vector<int> m_terms_at_order;
+};
+#endif // _CORPUS_HH
diff --git a/gi/pyp-topics/src/gammadist.c b/gi/pyp-topics/src/gammadist.c
new file mode 100644
index 00000000..4e260db8
--- /dev/null
+++ b/gi/pyp-topics/src/gammadist.c
@@ -0,0 +1,247 @@
+/* gammadist.c -- computes probability of samples under / produces samples from a Gamma distribution
+ *
+ * Mark Johnson, 22nd March 2008
+ *
+ * WARNING: you need to set the flag -std=c99 to compile
+ *
+ * gammavariate() was translated from random.py in Python library
+ *
+ * The Gamma distribution is:
+ *
+ * Gamma(x | alpha, beta) = pow(x/beta, alpha-1) * exp(-x/beta) / (gamma(alpha)*beta)
+ *
+ * shape parameter alpha > 0 (also called c), scale parameter beta > 0 (also called s);
+ * mean is alpha*beta, variance is alpha*beta**2
+ *
+ * Note that many parameterizations of the Gamma function are in terms of an _inverse_
+ * scale parameter beta, which is the inverse of the beta given here.
+ *
+ * To define a main() that tests the routines, uncomment the following #define:
+ */
+/* #define GAMMATEST */
+
+#include <assert.h>
+#include <math.h>
+
+#include "gammadist.h"
+#include "mt19937ar.h"
+
+/* gammadist() returns the probability density of x under a Gamma(alpha,beta)
+ * distribution
+ */
+
+long double gammadist(long double x, long double alpha, long double beta) {
+ assert(alpha > 0);
+ assert(beta > 0);
+ return pow(x/beta, alpha-1) * exp(-x/beta) / (tgamma(alpha)*beta);
+}
+
+/* lgammadist() returns the log probability density of x under a Gamma(alpha,beta)
+ * distribution
+ */
+
+long double lgammadist(long double x, long double alpha, long double beta) {
+ assert(alpha > 0);
+ assert(beta > 0);
+ return (alpha-1)*log(x) - alpha*log(beta) - x/beta - lgamma(alpha);
+}
+
+/* This definition of gammavariate is from Python code in
+ * the Python random module.
+ */
+
+long double gammavariate(long double alpha, long double beta) {
+
+ assert(alpha > 0);
+ assert(beta > 0);
+
+ if (alpha > 1.0) {
+
+ /* Uses R.C.H. Cheng, "The generation of Gamma variables with
+ non-integral shape parameters", Applied Statistics, (1977), 26,
+ No. 1, p71-74 */
+
+ long double ainv = sqrt(2.0 * alpha - 1.0);
+ long double bbb = alpha - log(4.0);
+ long double ccc = alpha + ainv;
+
+ while (1) {
+ long double u1 = mt_genrand_real3();
+ if (u1 > 1e-7 || u1 < 0.9999999) {
+ long double u2 = 1.0 - mt_genrand_real3();
+ long double v = log(u1/(1.0-u1))/ainv;
+ long double x = alpha*exp(v);
+ long double z = u1*u1*u2;
+ long double r = bbb+ccc*v-x;
+ if (r + (1.0+log(4.5)) - 4.5*z >= 0.0 || r >= log(z))
+ return x * beta;
+ }
+ }
+ }
+ else if (alpha == 1.0) {
+ long double u = mt_genrand_real3();
+ while (u <= 1e-7)
+ u = mt_genrand_real3();
+ return -log(u) * beta;
+ }
+ else {
+ /* alpha is between 0 and 1 (exclusive)
+ Uses ALGORITHM GS of Statistical Computing - Kennedy & Gentle */
+
+ while (1) {
+ long double u = mt_genrand_real3();
+ long double b = (exp(1) + alpha)/exp(1);
+ long double p = b*u;
+ long double x = (p <= 1.0) ? pow(p, 1.0/alpha) : -log((b-p)/alpha);
+ long double u1 = mt_genrand_real3();
+ if (! (((p <= 1.0) && (u1 > exp(-x))) ||
+ ((p > 1.0) && (u1 > pow(x, alpha - 1.0)))))
+ return x * beta;
+ }
+ }
+}
+
+/* betadist() returns the probability density of x under a Beta(alpha,beta)
+ * distribution.
+ */
+
+long double betadist(long double x, long double alpha, long double beta) {
+ assert(x >= 0);
+ assert(x <= 1);
+ assert(alpha > 0);
+ assert(beta > 0);
+ return pow(x,alpha-1)*pow(1-x,beta-1)*tgamma(alpha+beta)/(tgamma(alpha)*tgamma(beta));
+}
+
+/* lbetadist() returns the log probability density of x under a Beta(alpha,beta)
+ * distribution.
+ */
+
+long double lbetadist(long double x, long double alpha, long double beta) {
+ assert(x > 0);
+ assert(x < 1);
+ assert(alpha > 0);
+ assert(beta > 0);
+ return (alpha-1)*log(x)+(beta-1)*log(1-x)+lgamma(alpha+beta)-lgamma(alpha)-lgamma(beta);
+}
+
+/* betavariate() generates a sample from a Beta distribution with
+ * parameters alpha and beta.
+ *
+ * 0 < alpha < 1, 0 < beta < 1, mean is alpha/(alpha+beta)
+ */
+
+long double betavariate(long double alpha, long double beta) {
+ long double x = gammavariate(alpha, 1);
+ long double y = gammavariate(beta, 1);
+ return x/(x+y);
+}
+
+#ifdef GAMMATEST
+#include <stdio.h>
+
+int main(int argc, char **argv) {
+ int iteration, niterations = 1000;
+
+ for (iteration = 0; iteration < niterations; ++iteration) {
+ long double alpha = 100*mt_genrand_real3();
+ long double gv = gammavariate(alpha, 1);
+ long double pgv = gammadist(gv, alpha, 1);
+ long double pgvl = exp(lgammadist(gv, alpha, 1));
+ fprintf(stderr, "iteration = %d, gammavariate(%lg,1) = %lg, gammadist(%lg,%lg,1) = %lg, exp(lgammadist(%lg,%lg,1) = %lg\n",
+ iteration, alpha, gv, gv, alpha, pgv, gv, alpha, pgvl);
+ }
+ return 0;
+}
+
+#endif /* GAMMATEST */
+
+
+/* Other routines I tried, but which weren't as good as the ones above */
+
+#if 0
+
+/*! gammavariate() returns samples from a Gamma distribution
+ *! where alpha is the shape parameter and beta is the scale
+ *! parameter, using the algorithm described on p. 94 of
+ *! Gentle (1998) Random Number Generation and Monte Carlo Methods,
+ *! Springer.
+ */
+
+long double gammavariate(long double alpha) {
+
+ assert(alpha > 0);
+
+ if (alpha > 1.0) {
+ while (1) {
+ long double u1 = mt_genrand_real3();
+ long double u2 = mt_genrand_real3();
+ long double v = (alpha - 1/(6*alpha))*u1/(alpha-1)*u2;
+ if (2*(u2-1)/(alpha-1) + v + 1/v <= 2
+ || 2*log(u2)/(alpha-1) - log(v) + v <= 1)
+ return (alpha-1)*v;
+ }
+ } else if (alpha < 1.0) {
+ while (1) {
+ long double t = 0.07 + 0.75*sqrt(1-alpha);
+ long double b = alpha + exp(-t)*alpha/t;
+ long double u1 = mt_genrand_real3();
+ long double u2 = mt_genrand_real3();
+ long double v = b*u1;
+ if (v <= 1) {
+ long double x = t*pow(v, 1/alpha);
+ if (u2 <= (2 - x)/(2 + x))
+ return x;
+ if (u2 <= exp(-x))
+ return x;
+ }
+ else {
+ long double x = log(t*(b-v)/alpha);
+ long double y = x/t;
+ if (u2*(alpha + y*(1-alpha)) <= 1)
+ return x;
+ if (u2 <= pow(y,alpha-1))
+ return x;
+ }
+ }
+ }
+ else
+ return -log(mt_genrand_real3());
+}
+
+
+/*! gammavariate() returns a deviate distributed as a gamma
+ *! distribution of order alpha, beta, i.e., a waiting time to the alpha'th
+ *! event in a Poisson process of unit mean.
+ *!
+ *! Code from Numerical Recipes
+ */
+
+long double nr_gammavariate(long double ia) {
+ int j;
+ long double am,e,s,v1,v2,x,y;
+ assert(ia > 0);
+ if (ia < 10) {
+ x=1.0;
+ for (j=1;j<=ia;j++)
+ x *= mt_genrand_real3();
+ x = -log(x);
+ } else {
+ do {
+ do {
+ do {
+ v1=mt_genrand_real3();
+ v2=2.0*mt_genrand_real3()-1.0;
+ } while (v1*v1+v2*v2 > 1.0);
+ y=v2/v1;
+ am=ia-1;
+ s=sqrt(2.0*am+1.0);
+ x=s*y+am;
+ } while (x <= 0.0);
+ e=(1.0+y*y)*exp(am*log(x/am)-s*y);
+ } while (mt_genrand_real3() > e);
+ }
+ return x;
+}
+
+#endif
diff --git a/gi/pyp-topics/src/gammadist.h b/gi/pyp-topics/src/gammadist.h
new file mode 100644
index 00000000..b6ad6c40
--- /dev/null
+++ b/gi/pyp-topics/src/gammadist.h
@@ -0,0 +1,72 @@
+/* gammadist.h -- computes probability of samples under / produces samples from a Gamma distribution
+ *
+ * Mark Johnson, 22nd March 2008
+ *
+ * gammavariate() was translated from random.py in Python library
+ *
+ * The Gamma distribution is:
+ *
+ * Gamma(x | alpha, beta) = pow(x/beta, alpha-1) * exp(-x/beta) / (gamma(alpha)*beta)
+ *
+ * shape parameter alpha > 0 (also called c), scale parameter beta > 0 (also called s);
+ * mean is alpha*beta, variance is alpha*beta**2
+ *
+ * Note that many parameterizations of the Gamma function are in terms of an _inverse_
+ * scale parameter beta, which is the inverse of the beta given here.
+ */
+
+#ifndef GAMMADIST_H
+#define GAMMADIST_H
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+ /* gammadist() returns the probability density of x under a Gamma(alpha,beta)
+ * distribution
+ */
+
+ long double gammadist(long double x, long double alpha, long double beta);
+
+ /* lgammadist() returns the log probability density of x under a Gamma(alpha,beta)
+ * distribution
+ */
+
+ long double lgammadist(long double x, long double alpha, long double beta);
+
+ /* gammavariate() generates samples from a Gamma distribution
+ * conditioned on the parameters alpha and beta.
+ *
+ * alpha > 0, beta > 0, mean is alpha*beta, variance is alpha*beta**2
+ *
+ * Warning: a few older sources define the gamma distribution in terms
+ * of alpha > -1.0
+ */
+
+ long double gammavariate(long double alpha, long double beta);
+
+ /* betadist() returns the probability density of x under a Beta(alpha,beta)
+ * distribution.
+ */
+
+ long double betadist(long double x, long double alpha, long double beta);
+
+ /* lbetadist() returns the log probability density of x under a Beta(alpha,beta)
+ * distribution.
+ */
+
+ long double lbetadist(long double x, long double alpha, long double beta);
+
+ /* betavariate() generates a sample from a Beta distribution with
+ * parameters alpha and beta.
+ *
+ * 0 < alpha < 1, 0 < beta < 1, mean is alpha/(alpha+beta)
+ */
+
+ long double betavariate(long double alpha, long double beta);
+
+#ifdef __cplusplus
+};
+#endif
+
+#endif /* GAMMADIST_H */
diff --git a/gi/pyp-topics/src/gzstream.cc b/gi/pyp-topics/src/gzstream.cc
new file mode 100644
index 00000000..7c4d3a12
--- /dev/null
+++ b/gi/pyp-topics/src/gzstream.cc
@@ -0,0 +1,165 @@
+// ============================================================================
+// gzstream, C++ iostream classes wrapping the zlib compression library.
+// Copyright (C) 2001 Deepak Bandyopadhyay, Lutz Kettner
+//
+// This library is free software; you can redistribute it and/or
+// modify it under the terms of the GNU Lesser General Public
+// License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+//
+// This library is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+// Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public
+// License along with this library; if not, write to the Free Software
+// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+// ============================================================================
+//
+// File : gzstream.C
+// Revision : $Revision: 1.1 $
+// Revision_date : $Date: 2006/03/30 04:05:52 $
+// Author(s) : Deepak Bandyopadhyay, Lutz Kettner
+//
+// Standard streambuf implementation following Nicolai Josuttis, "The
+// Standard C++ Library".
+// ============================================================================
+
+#include "gzstream.hh"
+#include <iostream>
+#include <string.h> // for memcpy
+
+#ifdef GZSTREAM_NAMESPACE
+namespace GZSTREAM_NAMESPACE {
+#endif
+
+// ----------------------------------------------------------------------------
+// Internal classes to implement gzstream. See header file for user classes.
+// ----------------------------------------------------------------------------
+
+// --------------------------------------
+// class gzstreambuf:
+// --------------------------------------
+
+gzstreambuf* gzstreambuf::open( const char* name, int open_mode) {
+ if ( is_open())
+ return (gzstreambuf*)0;
+ mode = open_mode;
+ // no append nor read/write mode
+ if ((mode & std::ios::ate) || (mode & std::ios::app)
+ || ((mode & std::ios::in) && (mode & std::ios::out)))
+ return (gzstreambuf*)0;
+ char fmode[10];
+ char* fmodeptr = fmode;
+ if ( mode & std::ios::in)
+ *fmodeptr++ = 'r';
+ else if ( mode & std::ios::out)
+ *fmodeptr++ = 'w';
+ *fmodeptr++ = 'b';
+ *fmodeptr = '\0';
+ file = gzopen( name, fmode);
+ if (file == 0)
+ return (gzstreambuf*)0;
+ opened = 1;
+ return this;
+}
+
+gzstreambuf * gzstreambuf::close() {
+ if ( is_open()) {
+ sync();
+ opened = 0;
+ if ( gzclose( file) == Z_OK)
+ return this;
+ }
+ return (gzstreambuf*)0;
+}
+
+int gzstreambuf::underflow() { // used for input buffer only
+ if ( gptr() && ( gptr() < egptr()))
+ return * reinterpret_cast<unsigned char *>( gptr());
+
+ if ( ! (mode & std::ios::in) || ! opened)
+ return EOF;
+ // Josuttis' implementation of inbuf
+ int n_putback = gptr() - eback();
+ if ( n_putback > 4)
+ n_putback = 4;
+ memcpy( buffer + (4 - n_putback), gptr() - n_putback, n_putback);
+
+ int num = gzread( file, buffer+4, bufferSize-4);
+ if (num <= 0) // ERROR or EOF
+ return EOF;
+
+ // reset buffer pointers
+ setg( buffer + (4 - n_putback), // beginning of putback area
+ buffer + 4, // read position
+ buffer + 4 + num); // end of buffer
+
+ // return next character
+ return * reinterpret_cast<unsigned char *>( gptr());
+}
+
+int gzstreambuf::flush_buffer() {
+ // Separate the writing of the buffer from overflow() and
+ // sync() operation.
+ int w = pptr() - pbase();
+ if ( gzwrite( file, pbase(), w) != w)
+ return EOF;
+ pbump( -w);
+ return w;
+}
+
+int gzstreambuf::overflow( int c) { // used for output buffer only
+ if ( ! ( mode & std::ios::out) || ! opened)
+ return EOF;
+ if (c != EOF) {
+ *pptr() = c;
+ pbump(1);
+ }
+ if ( flush_buffer() == EOF)
+ return EOF;
+ return c;
+}
+
+int gzstreambuf::sync() {
+ // Changed to use flush_buffer() instead of overflow( EOF)
+ // which caused improper behavior with std::endl and flush(),
+ // bug reported by Vincent Ricard.
+ if ( pptr() && pptr() > pbase()) {
+ if ( flush_buffer() == EOF)
+ return -1;
+ }
+ return 0;
+}
+
+// --------------------------------------
+// class gzstreambase:
+// --------------------------------------
+
+gzstreambase::gzstreambase( const char* name, int mode) {
+ init( &buf);
+ open( name, mode);
+}
+
+gzstreambase::~gzstreambase() {
+ buf.close();
+}
+
+void gzstreambase::open( const char* name, int open_mode) {
+ if ( ! buf.open( name, open_mode))
+ clear( rdstate() | std::ios::badbit);
+}
+
+void gzstreambase::close() {
+ if ( buf.is_open())
+ if ( ! buf.close())
+ clear( rdstate() | std::ios::badbit);
+}
+
+#ifdef GZSTREAM_NAMESPACE
+} // namespace GZSTREAM_NAMESPACE
+#endif
+
+// ============================================================================
+// EOF //
diff --git a/gi/pyp-topics/src/gzstream.hh b/gi/pyp-topics/src/gzstream.hh
new file mode 100644
index 00000000..ad9785fd
--- /dev/null
+++ b/gi/pyp-topics/src/gzstream.hh
@@ -0,0 +1,121 @@
+// ============================================================================
+// gzstream, C++ iostream classes wrapping the zlib compression library.
+// Copyright (C) 2001 Deepak Bandyopadhyay, Lutz Kettner
+//
+// This library is free software; you can redistribute it and/or
+// modify it under the terms of the GNU Lesser General Public
+// License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+//
+// This library is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+// Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public
+// License along with this library; if not, write to the Free Software
+// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+// ============================================================================
+//
+// File : gzstream.h
+// Revision : $Revision: 1.1 $
+// Revision_date : $Date: 2006/03/30 04:05:52 $
+// Author(s) : Deepak Bandyopadhyay, Lutz Kettner
+//
+// Standard streambuf implementation following Nicolai Josuttis, "The
+// Standard C++ Library".
+// ============================================================================
+
+#ifndef GZSTREAM_H
+#define GZSTREAM_H 1
+
+// standard C++ with new header file names and std:: namespace
+#include <iostream>
+#include <fstream>
+#include <zlib.h>
+
+#ifdef GZSTREAM_NAMESPACE
+namespace GZSTREAM_NAMESPACE {
+#endif
+
+// ----------------------------------------------------------------------------
+// Internal classes to implement gzstream. See below for user classes.
+// ----------------------------------------------------------------------------
+
+class gzstreambuf : public std::streambuf {
+private:
+ static const int bufferSize = 47+256; // size of data buff
+ // totals 512 bytes under g++ for igzstream at the end.
+
+ gzFile file; // file handle for compressed file
+ char buffer[bufferSize]; // data buffer
+ char opened; // open/close state of stream
+ int mode; // I/O mode
+
+ int flush_buffer();
+public:
+ gzstreambuf() : opened(0) {
+ setp( buffer, buffer + (bufferSize-1));
+ setg( buffer + 4, // beginning of putback area
+ buffer + 4, // read position
+ buffer + 4); // end position
+ // ASSERT: both input & output capabilities will not be used together
+ }
+ int is_open() { return opened; }
+ gzstreambuf* open( const char* name, int open_mode);
+ gzstreambuf* close();
+ ~gzstreambuf() { close(); }
+
+ virtual int overflow( int c = EOF);
+ virtual int underflow();
+ virtual int sync();
+};
+
+class gzstreambase : virtual public std::ios {
+protected:
+ gzstreambuf buf;
+public:
+ gzstreambase() { init(&buf); }
+ gzstreambase( const char* name, int open_mode);
+ ~gzstreambase();
+ void open( const char* name, int open_mode);
+ void close();
+ gzstreambuf* rdbuf() { return &buf; }
+};
+
+// ----------------------------------------------------------------------------
+// User classes. Use igzstream and ogzstream analogously to ifstream and
+// ofstream respectively. They read and write files based on the gz*
+// function interface of the zlib. Files are compatible with gzip compression.
+// ----------------------------------------------------------------------------
+
+class igzstream : public gzstreambase, public std::istream {
+public:
+ igzstream() : std::istream( &buf) {}
+ igzstream( const char* name, int open_mode = std::ios::in)
+ : gzstreambase( name, open_mode), std::istream( &buf) {}
+ gzstreambuf* rdbuf() { return gzstreambase::rdbuf(); }
+ void open( const char* name, int open_mode = std::ios::in) {
+ gzstreambase::open( name, open_mode);
+ }
+};
+
+class ogzstream : public gzstreambase, public std::ostream {
+public:
+ ogzstream() : std::ostream( &buf) {}
+ ogzstream( const char* name, int mode = std::ios::out)
+ : gzstreambase( name, mode), std::ostream( &buf) {}
+ gzstreambuf* rdbuf() { return gzstreambase::rdbuf(); }
+ void open( const char* name, int open_mode = std::ios::out) {
+ gzstreambase::open( name, open_mode);
+ }
+};
+
+#ifdef GZSTREAM_NAMESPACE
+} // namespace GZSTREAM_NAMESPACE
+#endif
+
+#endif // GZSTREAM_H
+// ============================================================================
+// EOF //
+
diff --git a/gi/pyp-topics/src/log_add.h b/gi/pyp-topics/src/log_add.h
new file mode 100644
index 00000000..e0620c5a
--- /dev/null
+++ b/gi/pyp-topics/src/log_add.h
@@ -0,0 +1,30 @@
+#ifndef log_add_hh
+#define log_add_hh
+
+#include <limits>
+#include <iostream>
+#include <cassert>
+#include <cmath>
+
+template <typename T>
+struct Log
+{
+ static T zero() { return -std::numeric_limits<T>::infinity(); }
+
+ static T add(T l1, T l2)
+ {
+ if (l1 == zero()) return l2;
+ if (l1 > l2)
+ return l1 + std::log(1 + exp(l2 - l1));
+ else
+ return l2 + std::log(1 + exp(l1 - l2));
+ }
+
+ static T subtract(T l1, T l2)
+ {
+ //std::assert(l1 >= l2);
+ return l1 + log(1 - exp(l2 - l1));
+ }
+};
+
+#endif
diff --git a/gi/pyp-topics/src/makefile.darwin b/gi/pyp-topics/src/makefile.darwin
new file mode 100644
index 00000000..af608fd8
--- /dev/null
+++ b/gi/pyp-topics/src/makefile.darwin
@@ -0,0 +1,15 @@
+CC = /usr/bin/gcc
+CXX = /usr/bin/g++
+LD = /usr/bin/g++
+FC=/usr/bin/g77
+
+ARCH=i686-m64
+CXXFLAGS = -m64 -Wall -I/Users/pblunsom/packages/include
+CFLAGS = -m64 -Wall -I/Users/pblunsom/packages/include
+FFLAGS = -m64 -Wall
+LDFLAGS = -L/Users/pblunsom/packages/lib -lboost_program_options -lm -lz
+
+FFLAGS += -g -O3 -funroll-loops #-pg
+CFLAGS += -g -O3 -funroll-loops #-pg
+CXXFLAGS += -g -O3 -funroll-loops #-pg
+LDFLAGS += -g -O3 -funroll-loops #-pg
diff --git a/gi/pyp-topics/src/makefile.depend b/gi/pyp-topics/src/makefile.depend
new file mode 100644
index 00000000..89bafcf6
--- /dev/null
+++ b/gi/pyp-topics/src/makefile.depend
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diff --git a/gi/pyp-topics/src/mt19937ar.c b/gi/pyp-topics/src/mt19937ar.c
new file mode 100644
index 00000000..6551ea39
--- /dev/null
+++ b/gi/pyp-topics/src/mt19937ar.c
@@ -0,0 +1,194 @@
+/*
+ A C-program for MT19937, with initialization improved 2002/1/26.
+ Coded by Takuji Nishimura and Makoto Matsumoto.
+
+ Before using, initialize the state by using mt_init_genrand(seed)
+ or mt_init_by_array(init_key, key_length).
+
+ Copyright (C) 1997 - 2002, Makoto Matsumoto and Takuji Nishimura,
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in the
+ documentation and/or other materials provided with the distribution.
+
+ 3. The names of its contributors may not be used to endorse or promote
+ products derived from this software without specific prior written
+ permission.
+
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+ A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+ EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+ PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+ PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+ LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+ NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+
+ Any feedback is very welcome.
+ http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/emt.html
+ email: m-mat @ math.sci.hiroshima-u.ac.jp (remove space)
+*/
+
+#include "mt19937ar.h" /* XXX MJ 17th March 2006 */
+
+/* Period parameters */
+#define N 624
+#define M 397
+#define MATRIX_A 0x9908b0dfUL /* constant vector a */
+#define UPPER_MASK 0x80000000UL /* most significant w-r bits */
+#define LOWER_MASK 0x7fffffffUL /* least significant r bits */
+
+static unsigned long mt[N]; /* the array for the state vector */
+static int mti=N+1; /* mti==N+1 means mt[N] is not initialized */
+
+/* initializes mt[N] with a seed */
+void mt_init_genrand(unsigned long s)
+{
+ mt[0]= s & 0xffffffffUL;
+ for (mti=1; mti<N; mti++) {
+ mt[mti] =
+ (1812433253UL * (mt[mti-1] ^ (mt[mti-1] >> 30)) + mti);
+ /* See Knuth TAOCP Vol2. 3rd Ed. P.106 for multiplier. */
+ /* In the previous versions, MSBs of the seed affect */
+ /* only MSBs of the array mt[]. */
+ /* 2002/01/09 modified by Makoto Matsumoto */
+ mt[mti] &= 0xffffffffUL;
+ /* for >32 bit machines */
+ }
+}
+
+/* initialize by an array with array-length */
+/* init_key is the array for initializing keys */
+/* key_length is its length */
+/* slight change for C++, 2004/2/26 */
+void mt_init_by_array(unsigned long init_key[], int key_length)
+{
+ int i, j, k;
+ mt_init_genrand(19650218UL);
+ i=1; j=0;
+ k = (N>key_length ? N : key_length);
+ for (; k; k--) {
+ mt[i] = (mt[i] ^ ((mt[i-1] ^ (mt[i-1] >> 30)) * 1664525UL))
+ + init_key[j] + j; /* non linear */
+ mt[i] &= 0xffffffffUL; /* for WORDSIZE > 32 machines */
+ i++; j++;
+ if (i>=N) { mt[0] = mt[N-1]; i=1; }
+ if (j>=key_length) j=0;
+ }
+ for (k=N-1; k; k--) {
+ mt[i] = (mt[i] ^ ((mt[i-1] ^ (mt[i-1] >> 30)) * 1566083941UL))
+ - i; /* non linear */
+ mt[i] &= 0xffffffffUL; /* for WORDSIZE > 32 machines */
+ i++;
+ if (i>=N) { mt[0] = mt[N-1]; i=1; }
+ }
+
+ mt[0] = 0x80000000UL; /* MSB is 1; assuring non-zero initial array */
+}
+
+/* generates a random number on [0,0xffffffff]-interval */
+unsigned long mt_genrand_int32(void)
+{
+ unsigned long y;
+ static unsigned long mag01[2]={0x0UL, MATRIX_A};
+ /* mag01[x] = x * MATRIX_A for x=0,1 */
+
+ if (mti >= N) { /* generate N words at one time */
+ int kk;
+
+ if (mti == N+1) /* if mt_init_genrand() has not been called, */
+ mt_init_genrand(5489UL); /* a default initial seed is used */
+
+ for (kk=0;kk<N-M;kk++) {
+ y = (mt[kk]&UPPER_MASK)|(mt[kk+1]&LOWER_MASK);
+ mt[kk] = mt[kk+M] ^ (y >> 1) ^ mag01[y & 0x1UL];
+ }
+ for (;kk<N-1;kk++) {
+ y = (mt[kk]&UPPER_MASK)|(mt[kk+1]&LOWER_MASK);
+ mt[kk] = mt[kk+(M-N)] ^ (y >> 1) ^ mag01[y & 0x1UL];
+ }
+ y = (mt[N-1]&UPPER_MASK)|(mt[0]&LOWER_MASK);
+ mt[N-1] = mt[M-1] ^ (y >> 1) ^ mag01[y & 0x1UL];
+
+ mti = 0;
+ }
+
+ y = mt[mti++];
+
+ /* Tempering */
+ y ^= (y >> 11);
+ y ^= (y << 7) & 0x9d2c5680UL;
+ y ^= (y << 15) & 0xefc60000UL;
+ y ^= (y >> 18);
+
+ return y;
+}
+
+/* generates a random number on [0,0x7fffffff]-interval */
+long mt_genrand_int31(void)
+{
+ return (long)( mt_genrand_int32()>>1);
+}
+
+/* generates a random number on [0,1]-real-interval */
+double mt_genrand_real1(void)
+{
+ return mt_genrand_int32()*(1.0/4294967295.0);
+ /* divided by 2^32-1 */
+}
+
+/* generates a random number on [0,1)-real-interval */
+double mt_genrand_real2(void)
+{
+ return mt_genrand_int32()*(1.0/4294967296.0);
+ /* divided by 2^32 */
+}
+
+/* generates a random number on (0,1)-real-interval */
+double mt_genrand_real3(void)
+{
+ return (((double) mt_genrand_int32()) + 0.5)*(1.0/4294967296.0);
+ /* divided by 2^32 */
+}
+
+/* generates a random number on [0,1) with 53-bit resolution*/
+double mt_genrand_res53(void)
+{
+ unsigned long a=mt_genrand_int32()>>5, b=mt_genrand_int32()>>6;
+ return(a*67108864.0+b)*(1.0/9007199254740992.0);
+}
+/* These real versions are due to Isaku Wada, 2002/01/09 added */
+
+/*
+#include <stdio.h>
+
+int main(void)
+{
+ int i;
+ unsigned long init[4]={0x123, 0x234, 0x345, 0x456}, length=4;
+ mt_init_by_array(init, length);
+ printf("1000 outputs of genrand_int32()\n");
+ for (i=0; i<1000; i++) {
+ printf("%10lu ", mt_genrand_int32());
+ if (i%5==4) printf("\n");
+ }
+ printf("\n1000 outputs of genrand_real2()\n");
+ for (i=0; i<1000; i++) {
+ printf("%10.8f ", mt_genrand_real2());
+ if (i%5==4) printf("\n");
+ }
+ return 0;
+}
+*/
diff --git a/gi/pyp-topics/src/mt19937ar.h b/gi/pyp-topics/src/mt19937ar.h
new file mode 100644
index 00000000..caab4045
--- /dev/null
+++ b/gi/pyp-topics/src/mt19937ar.h
@@ -0,0 +1,44 @@
+/* mt19937ar.h
+ *
+ * Mark Johnson, 17th March 2006
+ */
+
+#ifndef MT19937AR_H
+#define MT19937AR_H
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+ /* initializes mt[N] with a seed */
+ void mt_init_genrand(unsigned long s);
+
+ /* initialize by an array with array-length */
+ /* init_key is the array for initializing keys */
+ /* key_length is its length */
+ /* slight change for C++, 2004/2/26 */
+ void mt_init_by_array(unsigned long init_key[], int key_length);
+
+ /* generates a random number on [0,0xffffffff]-interval */
+ unsigned long mt_genrand_int32(void);
+
+ /* generates a random number on [0,0x7fffffff]-interval */
+ long mt_genrand_int31(void);
+
+ /* generates a random number on [0,1]-real-interval */
+ double mt_genrand_real1(void);
+
+ /* generates a random number on [0,1)-real-interval */
+ double mt_genrand_real2(void);
+
+ /* generates a random number on (0,1)-real-interval */
+ double mt_genrand_real3(void);
+
+ /* generates a random number on [0,1) with 53-bit resolution*/
+ double mt_genrand_res53(void);
+
+#ifdef __cplusplus
+};
+#endif
+
+#endif /* MT19937AR_H */
diff --git a/gi/pyp-topics/src/pyp-topics.cc b/gi/pyp-topics/src/pyp-topics.cc
new file mode 100644
index 00000000..9b43d6d1
--- /dev/null
+++ b/gi/pyp-topics/src/pyp-topics.cc
@@ -0,0 +1,224 @@
+#include "pyp-topics.hh"
+
+void PYPTopics::sample(const Corpus& corpus, int samples) {
+ if (!m_backoff.get()) {
+ m_word_pyps.clear();
+ m_word_pyps.push_back(PYPs());
+ }
+
+ std::cerr << " Training with " << m_word_pyps.size()-1 << " backoff level"
+ << (m_word_pyps.size()==2 ? ":" : "s:") << std::endl;
+
+ for (int i=0; i<(int)m_word_pyps.size(); ++i)
+ m_word_pyps.at(i).resize(m_num_topics, PYP<int>(0.5, 1.0));
+ std::cerr << std::endl;
+
+ m_document_pyps.resize(corpus.num_documents(), 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();
+
+ std::cerr << " Documents: " << corpus.num_documents() << " Terms: "
+ << corpus.num_types() << std::endl;
+
+ // Initialisation pass
+ int document_id=0, topic_counter=0;
+ for (Corpus::const_iterator corpusIt=corpus.begin();
+ corpusIt != corpus.end(); ++corpusIt, ++document_id) {
+ m_corpus_topics.push_back(DocumentTopics(corpusIt->size(), 0));
+
+ int term_index=0;
+ for (Document::const_iterator docIt=corpusIt->begin();
+ docIt != corpusIt->end(); ++docIt, ++term_index) {
+ topic_counter++;
+ Term term = *docIt;
+
+ // sample a new_topic
+ //int new_topic = (topic_counter % m_num_topics);
+ int new_topic = (document_id % m_num_topics);
+
+ // add the new topic to the PYPs
+ m_corpus_topics[document_id][term_index] = new_topic;
+ increment(term, new_topic);
+ m_document_pyps[document_id].increment(new_topic, m_topic_p0);
+ }
+ }
+
+ // Sampling phase
+ for (int curr_sample=0; curr_sample < samples; ++curr_sample) {
+ std::cerr << "\n -- Sample " << curr_sample << " "; std::cerr.flush();
+
+ // for each document in the corpus
+ int document_id=0;
+ for (Corpus::const_iterator corpusIt=corpus.begin();
+ corpusIt != corpus.end(); ++corpusIt, ++document_id) {
+ // for each term in the document
+ int term_index=0;
+ for (Document::const_iterator docIt=corpusIt->begin();
+ docIt != corpusIt->end(); ++docIt, ++term_index) {
+ Term term = *docIt;
+
+ // remove the prevous topic from the PYPs
+ int current_topic = m_corpus_topics[document_id][term_index];
+ decrement(term, current_topic);
+ m_document_pyps[document_id].decrement(current_topic);
+
+ // sample a new_topic
+ int new_topic = sample(document_id, term);
+
+ // add the new topic to the PYPs
+ m_corpus_topics[document_id][term_index] = new_topic;
+ increment(term, new_topic);
+ m_document_pyps[document_id].increment(new_topic, m_topic_p0);
+ }
+ if (document_id && document_id % 10000 == 0) {
+ std::cerr << "."; std::cerr.flush();
+ }
+ }
+
+ if (curr_sample != 0 && curr_sample % 10 == 0) {
+ std::cerr << " ||| Resampling hyperparameters "; std::cerr.flush();
+ // resample the hyperparamters
+ F log_p=0.0; int resample_counter=0;
+ for (std::vector<PYPs>::iterator levelIt=m_word_pyps.begin();
+ levelIt != m_word_pyps.end(); ++levelIt) {
+ for (PYPs::iterator pypIt=levelIt->begin();
+ pypIt != levelIt->end(); ++pypIt) {
+ pypIt->resample_prior();
+ log_p += pypIt->log_restaurant_prob();
+ if (resample_counter++ % 100 == 0) {
+ std::cerr << "."; std::cerr.flush();
+ }
+ }
+ }
+
+ for (PYPs::iterator pypIt=m_document_pyps.begin();
+ pypIt != m_document_pyps.end(); ++pypIt) {
+ pypIt->resample_prior();
+ log_p += pypIt->log_restaurant_prob();
+ }
+ std::cerr << " ||| LLH=" << log_p << std::endl;
+ }
+ }
+}
+
+void PYPTopics::decrement(const Term& term, int topic, int level) {
+ //std::cerr << "PYPTopics::decrement(" << term << "," << topic << "," << level << ")" << std::endl;
+ m_word_pyps.at(level).at(topic).decrement(term);
+ if (m_backoff.get()) {
+ Term backoff_term = (*m_backoff)[term];
+ if (!m_backoff->is_null(backoff_term))
+ decrement(backoff_term, topic, level+1);
+ }
+}
+
+void PYPTopics::increment(const Term& term, int topic, int level) {
+ //std::cerr << "PYPTopics::increment(" << term << "," << topic << "," << level << ")" << std::endl;
+ m_word_pyps.at(level).at(topic).increment(term, word_pyps_p0(term, topic, level));
+
+ if (m_backoff.get()) {
+ Term backoff_term = (*m_backoff)[term];
+ if (!m_backoff->is_null(backoff_term))
+ increment(backoff_term, topic, level+1);
+ }
+}
+
+int PYPTopics::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 p_k_d = m_document_pyps[doc].prob(k, m_topic_p0);
+ sum += (p_w_k*p_k_d);
+ sums.push_back(sum);
+ }
+ // Second pass: sample a topic
+ F cutoff = mt_genrand_res53() * sum;
+ for (int k=0; k<m_num_topics; ++k) {
+ if (cutoff <= sums[k])
+ return k;
+ }
+ assert(false);
+}
+
+PYPTopics::F PYPTopics::word_pyps_p0(const Term& term, int topic, int level) const {
+ //for (int i=0; i<level+1; ++i) std::cerr << " ";
+ //std::cerr << "PYPTopics::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 = m_backoff->terms_at_level(level)*prob(backoff_term, topic, level+1);
+ }
+ else
+ p0 = m_term_p0;
+ }
+ //for (int i=0; i<level+1; ++i) std::cerr << " ";
+ //std::cerr << "PYPTopics::word_pyps_p0(" << term << "," << topic << "," << level << ") = " << p0 << std::endl;
+ return p0;
+}
+
+PYPTopics::F PYPTopics::prob(const Term& term, int topic, int level) const {
+ //for (int i=0; i<level+1; ++i) std::cerr << " ";
+ //std::cerr << "PYPTopics::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 << "PYPTopics::prob(" << term << "," << topic << "," << level << ") = " << p_w_k << std::endl;
+
+ return p_w_k;
+}
+
+int PYPTopics::max(const DocumentId& doc, const Term& term) {
+ //std::cerr << "PYPTopics::max(" << doc << "," << term << ")" << std::endl;
+ // collect probs
+ F current_max=0.0;
+ int current_topic=-1;
+ for (int k=0; k<m_num_topics; ++k) {
+ F p_w_k = prob(term, k);
+ F p_k_d = m_document_pyps[doc].prob(k, m_topic_p0);
+ F prob = (p_w_k*p_k_d);
+ if (prob > current_max) {
+ current_max = prob;
+ current_topic = k;
+ }
+ }
+ assert(current_topic >= 0);
+ return current_topic;
+}
+
+std::ostream& PYPTopics::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& PYPTopics::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;
+}
diff --git a/gi/pyp-topics/src/pyp-topics.hh b/gi/pyp-topics/src/pyp-topics.hh
new file mode 100644
index 00000000..4036985a
--- /dev/null
+++ b/gi/pyp-topics/src/pyp-topics.hh
@@ -0,0 +1,52 @@
+#ifndef PYP_TOPICS_HH
+#define PYP_TOPICS_HH
+
+#include <vector>
+#include <iostream>
+
+#include "pyp.hh"
+#include "corpus.hh"
+
+
+class PYPTopics {
+public:
+ typedef std::vector<int> DocumentTopics;
+ typedef std::vector<DocumentTopics> CorpusTopics;
+ typedef long double F;
+
+public:
+ PYPTopics(int num_topics) : m_num_topics(num_topics), m_word_pyps(1), m_backoff(0) {}
+
+ void sample(const Corpus& corpus, int samples);
+ int sample(const DocumentId& doc, const Term& term);
+ int max(const DocumentId& doc, const Term& term);
+
+ void set_backoff(const std::string& filename) {
+ m_backoff.reset(new TermBackoff);
+ m_backoff->read(filename);
+ m_word_pyps.clear();
+ m_word_pyps.resize(m_backoff->order(), PYPs());
+ }
+
+ F prob(const Term& term, int topic, int level=0) const;
+ void decrement(const Term& term, int topic, int level=0);
+ void increment(const Term& term, int topic, int level=0);
+
+ std::ostream& print_document_topics(std::ostream& out) const;
+ std::ostream& print_topic_terms(std::ostream& out) const;
+
+private:
+ F word_pyps_p0(const Term& term, int topic, int level) const;
+
+ int m_num_topics;
+ F m_term_p0, m_topic_p0, m_backoff_p0;
+
+ CorpusTopics m_corpus_topics;
+ typedef std::vector< PYP<int> > PYPs;
+ PYPs m_document_pyps;
+ std::vector<PYPs> m_word_pyps;
+
+ std::auto_ptr<TermBackoff> m_backoff;
+};
+
+#endif // PYP_TOPICS_HH
diff --git a/gi/pyp-topics/src/pyp.hh b/gi/pyp-topics/src/pyp.hh
new file mode 100644
index 00000000..b06c6021
--- /dev/null
+++ b/gi/pyp-topics/src/pyp.hh
@@ -0,0 +1,477 @@
+#ifndef _pyp_hh
+#define _pyp_hh
+
+#include <math.h>
+#include <map>
+#include <tr1/unordered_map>
+
+#include "log_add.h"
+#include "gammadist.h"
+#include "slice-sampler.h"
+#include "mt19937ar.h"
+
+//
+// Pitman-Yor process with customer and table tracking
+//
+
+template <typename Dish, typename Hash=std::tr1::hash<Dish> >
+class PYP : protected std::tr1::unordered_map<Dish, int, Hash>
+{
+public:
+ using std::tr1::unordered_map<Dish,int>::const_iterator;
+ using std::tr1::unordered_map<Dish,int>::iterator;
+ using std::tr1::unordered_map<Dish,int>::begin;
+ using std::tr1::unordered_map<Dish,int>::end;
+
+ PYP(long double a, long double b, Hash hash=Hash());
+
+ int increment(Dish d, long double p0);
+ int decrement(Dish d);
+
+ // lookup functions
+ int count(Dish d) const;
+ long double prob(Dish dish, long double p0) const;
+ long double prob(Dish dish, long double dcd, long double dca,
+ long double dtd, long double dta, long double p0) const;
+
+ int num_customers() const { return _total_customers; }
+ int num_types() const { return std::tr1::unordered_map<Dish,int>::size(); }
+ bool empty() const { return _total_customers == 0; }
+
+ long double log_prob(Dish dish, long double log_p0) const;
+ // nb. d* are NOT logs
+ long double log_prob(Dish dish, long double dcd, long double dca,
+ long double dtd, long double dta, long double log_p0) const;
+
+ int num_tables(Dish dish) const;
+ int num_tables() const;
+
+ long double a() const { return _a; }
+ void set_a(long double a) { _a = a; }
+
+ long double b() const { return _b; }
+ void set_b(long double b) { _b = b; }
+
+ void clear();
+ std::ostream& debug_info(std::ostream& os) const;
+
+ long double log_restaurant_prob() const;
+ long double log_prior() const;
+ static long double log_prior_a(long double a, long double beta_a, long double beta_b);
+ static long double log_prior_b(long double b, long double gamma_c, long double gamma_s);
+
+ void resample_prior();
+ void resample_prior_a();
+ void resample_prior_b();
+
+private:
+ long double _a, _b; // parameters of the Pitman-Yor distribution
+ long double _a_beta_a, _a_beta_b; // parameters of Beta prior on a
+ long double _b_gamma_s, _b_gamma_c; // parameters of Gamma prior on b
+
+ struct TableCounter
+ {
+ TableCounter() : tables(0) {};
+ int tables;
+ std::map<int, int> table_histogram; // num customers at table -> number tables
+ };
+ typedef std::tr1::unordered_map<Dish, TableCounter, Hash> DishTableType;
+ DishTableType _dish_tables;
+ int _total_customers, _total_tables;
+
+ // Function objects for calculating the parts of the log_prob for
+ // the parameters a and b
+ struct resample_a_type {
+ int n, m; long double b, a_beta_a, a_beta_b;
+ const DishTableType& dish_tables;
+ resample_a_type(int n, int m, long double b, long double a_beta_a,
+ long double a_beta_b, const DishTableType& dish_tables)
+ : n(n), m(m), b(b), a_beta_a(a_beta_a), a_beta_b(a_beta_b), dish_tables(dish_tables) {}
+
+ long double operator() (long double proposed_a) const {
+ long double log_prior = log_prior_a(proposed_a, a_beta_a, a_beta_b);
+ long double log_prob = 0.0;
+ long double lgamma1a = lgamma(1.0 - proposed_a);
+ for (typename DishTableType::const_iterator dish_it=dish_tables.begin(); dish_it != dish_tables.end(); ++dish_it)
+ for (std::map<int, int>::const_iterator table_it=dish_it->second.table_histogram.begin();
+ table_it !=dish_it->second.table_histogram.end(); ++table_it)
+ log_prob += (table_it->second * (lgamma(table_it->first - proposed_a) - lgamma1a));
+
+ log_prob += (proposed_a == 0.0 ? (m-1.0)*log(b)
+ : ((m-1.0)*log(proposed_a) + lgamma((m-1.0) + b/proposed_a) - lgamma(b/proposed_a)));
+ assert(std::isfinite(log_prob));
+ return log_prob + log_prior;
+ }
+ };
+
+ struct resample_b_type {
+ int n, m; long double a, b_gamma_c, b_gamma_s;
+ resample_b_type(int n, int m, long double a, long double b_gamma_c, long double b_gamma_s)
+ : n(n), m(m), a(a), b_gamma_c(b_gamma_c), b_gamma_s(b_gamma_s) {}
+
+ long double operator() (long double proposed_b) const {
+ long double log_prior = log_prior_b(proposed_b, b_gamma_c, b_gamma_s);
+ long double log_prob = 0.0;
+ log_prob += (a == 0.0 ? (m-1.0)*log(proposed_b)
+ : ((m-1.0)*log(a) + lgamma((m-1.0) + proposed_b/a) - lgamma(proposed_b/a)));
+ log_prob += (lgamma(1.0+proposed_b) - lgamma(n+proposed_b));
+ return log_prob + log_prior;
+ }
+ };
+};
+
+template <typename Dish, typename Hash>
+PYP<Dish,Hash>::PYP(long double a, long double b, Hash cmp)
+: std::tr1::unordered_map<Dish, int, Hash>(), _a(a), _b(b),
+ _a_beta_a(1), _a_beta_b(1), _b_gamma_s(1), _b_gamma_c(1),
+ //_a_beta_a(1), _a_beta_b(1), _b_gamma_s(10), _b_gamma_c(0.1),
+ _total_customers(0), _total_tables(0)
+{
+// std::cerr << "\t##PYP<Dish,Hash>::PYP(a=" << _a << ",b=" << _b << ")" << std::endl;
+}
+
+template <typename Dish, typename Hash>
+long double
+PYP<Dish,Hash>::prob(Dish dish, long double p0) const
+{
+ int c = count(dish), t = num_tables(dish);
+ long double r = num_tables() * _a + _b;
+ //std::cerr << "\t\t\t\tPYP<Dish,Hash>::prob(" << dish << "," << p0 << ") c=" << c << " r=" << r << std::endl;
+ if (c > 0)
+ return (c - _a * t + r * p0) / (num_customers() + _b);
+ else
+ return r * p0 / (num_customers() + _b);
+}
+
+template <typename Dish, typename Hash>
+long double
+PYP<Dish,Hash>::prob(Dish dish, long double dcd, long double dca,
+ long double dtd, long double dta, long double p0)
+const
+{
+ int c = count(dish) + dcd, t = num_tables(dish) + dtd;
+ long double r = (num_tables() + dta) * _a + _b;
+ if (c > 0)
+ return (c - _a * t + r * p0) / (num_customers() + dca + _b);
+ else
+ return r * p0 / (num_customers() + dca + _b);
+}
+
+template <typename Dish, typename Hash>
+long double
+PYP<Dish,Hash>::log_prob(Dish dish, long double log_p0) const
+{
+ using std::log;
+ int c = count(dish), t = num_tables(dish);
+ long double r = log(num_tables() * _a + b);
+ if (c > 0)
+ return Log<double>::add(log(c - _a * t), r + log_p0)
+ - log(num_customers() + _b);
+ else
+ return r + log_p0 - log(num_customers() + b);
+}
+
+template <typename Dish, typename Hash>
+long double
+PYP<Dish,Hash>::log_prob(Dish dish, long double dcd, long double dca,
+ long double dtd, long double dta, long double log_p0)
+const
+{
+ using std::log;
+ int c = count(dish) + dcd, t = num_tables(dish) + dtd;
+ long double r = log((num_tables() + dta) * _a + b);
+ if (c > 0)
+ return Log<double>::add(log(c - _a * t), r + log_p0)
+ - log(num_customers() + dca + _b);
+ else
+ return r + log_p0 - log(num_customers() + dca + b);
+}
+
+template <typename Dish, typename Hash>
+int
+PYP<Dish,Hash>::increment(Dish dish, long double p0) {
+ int delta = 0;
+ TableCounter &tc = _dish_tables[dish];
+
+ // seated on a new or existing table?
+ int c = count(dish), t = num_tables(dish), T = num_tables();
+ long double pshare = (c > 0) ? (c - _a*t) : 0.0;
+ long double pnew = (_b + _a*T) * p0;
+ assert (pshare >= 0.0);
+ //assert (pnew > 0.0);
+
+ if (mt_genrand_res53() < pnew / (pshare + pnew)) {
+ // assign to a new table
+ tc.tables += 1;
+ tc.table_histogram[1] += 1;
+ _total_tables += 1;
+ delta = 1;
+ }
+ else {
+ // randomly assign to an existing table
+ // remove constant denominator from inner loop
+ long double r = mt_genrand_res53() * (c - _a*t);
+ for (std::map<int,int>::iterator
+ hit = tc.table_histogram.begin();
+ hit != tc.table_histogram.end(); ++hit) {
+ r -= ((hit->first - _a) * hit->second);
+ if (r <= 0) {
+ tc.table_histogram[hit->first+1] += 1;
+ hit->second -= 1;
+ if (hit->second == 0)
+ tc.table_histogram.erase(hit);
+ break;
+ }
+ }
+ if (r > 0) {
+ std::cerr << r << " " << c << " " << _a << " " << t << std::endl;
+ assert(false);
+ }
+ delta = 0;
+ }
+
+ std::tr1::unordered_map<Dish,int,Hash>::operator[](dish) += 1;
+ _total_customers += 1;
+
+ return delta;
+}
+
+template <typename Dish, typename Hash>
+int
+PYP<Dish,Hash>::count(Dish dish) const
+{
+ typename std::tr1::unordered_map<Dish, int>::const_iterator
+ dcit = find(dish);
+ if (dcit != end())
+ return dcit->second;
+ else
+ return 0;
+}
+
+template <typename Dish, typename Hash>
+int
+PYP<Dish,Hash>::decrement(Dish dish)
+{
+ typename std::tr1::unordered_map<Dish, int>::iterator dcit = find(dish);
+ if (dcit == end()) {
+ std::cerr << dish << std::endl;
+ assert(false);
+ }
+
+ int delta = 0;
+
+ typename std::tr1::unordered_map<Dish, TableCounter>::iterator dtit = _dish_tables.find(dish);
+ if (dtit == _dish_tables.end()) {
+ std::cerr << dish << std::endl;
+ assert(false);
+ }
+ TableCounter &tc = dtit->second;
+
+ //std::cerr << "\tdecrement for " << dish << "\n";
+ //std::cerr << "\tBEFORE histogram: " << tc.table_histogram << " ";
+ //std::cerr << "count: " << count(dish) << " ";
+ //std::cerr << "tables: " << tc.tables << "\n";
+
+ long double r = mt_genrand_res53() * count(dish);
+ for (std::map<int,int>::iterator hit = tc.table_histogram.begin();
+ hit != tc.table_histogram.end(); ++hit)
+ {
+ //r -= (hit->first - _a) * hit->second;
+ r -= (hit->first) * hit->second;
+ if (r <= 0)
+ {
+ if (hit->first > 1)
+ tc.table_histogram[hit->first-1] += 1;
+ else
+ {
+ delta = -1;
+ tc.tables -= 1;
+ _total_tables -= 1;
+ }
+
+ hit->second -= 1;
+ if (hit->second == 0) tc.table_histogram.erase(hit);
+ break;
+ }
+ }
+ if (r > 0) {
+ std::cerr << r << " " << count(dish) << " " << _a << " " << num_tables(dish) << std::endl;
+ assert(false);
+ }
+
+ // remove the customer
+ dcit->second -= 1;
+ _total_customers -= 1;
+ assert(dcit->second >= 0);
+ if (dcit->second == 0) {
+ erase(dcit);
+ _dish_tables.erase(dtit);
+ //std::cerr << "\tAFTER histogram: Empty\n";
+ }
+ else {
+ //std::cerr << "\tAFTER histogram: " << _dish_tables[dish].table_histogram << " ";
+ //std::cerr << "count: " << count(dish) << " ";
+ //std::cerr << "tables: " << _dish_tables[dish].tables << "\n";
+ }
+
+ return delta;
+}
+
+template <typename Dish, typename Hash>
+int
+PYP<Dish,Hash>::num_tables(Dish dish) const
+{
+ typename std::tr1::unordered_map<Dish, TableCounter, Hash>::const_iterator
+ dtit = _dish_tables.find(dish);
+
+ //assert(dtit != _dish_tables.end());
+ if (dtit == _dish_tables.end())
+ return 0;
+
+ return dtit->second.tables;
+}
+
+template <typename Dish, typename Hash>
+int
+PYP<Dish,Hash>::num_tables() const
+{
+ return _total_tables;
+}
+
+template <typename Dish, typename Hash>
+std::ostream&
+PYP<Dish,Hash>::debug_info(std::ostream& os) const
+{
+ int hists = 0, tables = 0;
+ for (typename std::tr1::unordered_map<Dish, TableCounter, Hash>::const_iterator
+ dtit = _dish_tables.begin(); dtit != _dish_tables.end(); ++dtit)
+ {
+ hists += dtit->second.table_histogram.size();
+ tables += dtit->second.tables;
+
+ assert(dtit->second.tables > 0);
+ assert(!dtit->second.table_histogram.empty());
+
+ for (std::map<int,int>::const_iterator
+ hit = dtit->second.table_histogram.begin();
+ hit != dtit->second.table_histogram.end(); ++hit)
+ assert(hit->second > 0);
+ }
+
+ os << "restaurant has "
+ << _total_customers << " customers; "
+ << _total_tables << " tables; "
+ << tables << " tables'; "
+ << num_types() << " dishes; "
+ << _dish_tables.size() << " dishes'; and "
+ << hists << " histogram entries\n";
+
+ return os;
+}
+
+template <typename Dish, typename Hash>
+void
+PYP<Dish,Hash>::clear()
+{
+ this->std::tr1::unordered_map<Dish,int,Hash>::clear();
+ _dish_tables.clear();
+ _total_tables = _total_customers = 0;
+}
+
+// log_restaurant_prob returns the log probability of the PYP table configuration.
+// Excludes Hierarchical P0 term which must be calculated separately.
+template <typename Dish, typename Hash>
+long double
+PYP<Dish,Hash>::log_restaurant_prob() const {
+ if (_total_customers < 1)
+ return (long double)0.0;
+
+ long double log_prob = 0.0;
+ long double lgamma1a = lgamma(1.0-_a);
+
+ //std::cerr << "-------------------\n" << std::endl;
+ for (typename DishTableType::const_iterator dish_it=_dish_tables.begin();
+ dish_it != _dish_tables.end(); ++dish_it) {
+ for (std::map<int, int>::const_iterator table_it=dish_it->second.table_histogram.begin();
+ table_it !=dish_it->second.table_histogram.end(); ++table_it) {
+ log_prob += (table_it->second * (lgamma(table_it->first - _a) - lgamma1a));
+ //std::cerr << "|" << dish_it->first->parent << " --> " << dish_it->first->rhs << " " << table_it->first << " " << table_it->second << " " << log_prob;
+ }
+ }
+ //std::cerr << std::endl;
+
+ log_prob += (_a == (long double)0.0 ? (_total_tables-1.0)*log(_b) : (_total_tables-1.0)*log(_a) + lgamma((_total_tables-1.0) + _b/_a) - lgamma(_b/_a));
+ //std::cerr << "\t\t" << log_prob << std::endl;
+ log_prob += (lgamma(1.0 + _b) - lgamma(_total_customers + _b));
+
+ //std::cerr << _total_customers << " " << _total_tables << " " << log_prob << " " << log_prior() << std::endl;
+ //std::cerr << _a << " " << _b << std::endl;
+ if (!std::isfinite(log_prob)) {
+ assert(false);
+ }
+ //return log_prob;
+ return log_prob + log_prior();
+}
+
+template <typename Dish, typename Hash>
+long double
+PYP<Dish,Hash>::log_prior() const {
+ long double prior = 0.0;
+ if (_a_beta_a > 0.0 && _a_beta_b > 0.0 && _a > 0.0)
+ prior += log_prior_a(_a, _a_beta_a, _a_beta_b);
+ if (_b_gamma_s > 0.0 && _b_gamma_c > 0.0)
+ prior += log_prior_b(_b, _b_gamma_c, _b_gamma_s);
+
+ return prior;
+}
+
+template <typename Dish, typename Hash>
+long double
+PYP<Dish,Hash>::log_prior_a(long double a, long double beta_a, long double beta_b) {
+ return lbetadist(a, beta_a, beta_b);
+}
+
+template <typename Dish, typename Hash>
+long double
+PYP<Dish,Hash>::log_prior_b(long double b, long double gamma_c, long double gamma_s) {
+ return lgammadist(b, gamma_c, gamma_s);
+}
+
+template <typename Dish, typename Hash>
+void
+PYP<Dish,Hash>::resample_prior() {
+ for (int num_its=5; num_its >= 0; --num_its) {
+ resample_prior_b();
+ resample_prior_a();
+ }
+ resample_prior_b();
+}
+
+template <typename Dish, typename Hash>
+void
+PYP<Dish,Hash>::resample_prior_b() {
+ if (_total_tables == 0)
+ return;
+
+ int niterations = 10; // number of resampling iterations
+ //std::cerr << "\n## resample_prior_b(), initial a = " << _a << ", b = " << _b << std::endl;
+ resample_b_type b_log_prob(_total_customers, _total_tables, _a, _b_gamma_c, _b_gamma_s);
+ _b = slice_sampler1d(b_log_prob, _b, mt_genrand_res53, (long double) 0.0, std::numeric_limits<long double>::infinity(),
+ (long double) 0.0, niterations, 100*niterations);
+ //std::cerr << "\n## resample_prior_b(), final a = " << _a << ", b = " << _b << std::endl;
+}
+
+template <typename Dish, typename Hash>
+void
+PYP<Dish,Hash>::resample_prior_a() {
+ if (_total_tables == 0)
+ return;
+
+ int niterations = 10;
+ //std::cerr << "\n## Initial a = " << _a << ", b = " << _b << std::endl;
+ resample_a_type a_log_prob(_total_customers, _total_tables, _b, _a_beta_a, _a_beta_b, _dish_tables);
+ _a = slice_sampler1d(a_log_prob, _a, mt_genrand_res53, std::numeric_limits<long double>::min(),
+ (long double) 1.0, (long double) 0.0, niterations, 100*niterations);
+}
+
+#endif
diff --git a/gi/pyp-topics/src/slice-sampler.h b/gi/pyp-topics/src/slice-sampler.h
new file mode 100644
index 00000000..3108a0f7
--- /dev/null
+++ b/gi/pyp-topics/src/slice-sampler.h
@@ -0,0 +1,192 @@
+//! slice-sampler.h is an MCMC slice sampler
+//!
+//! Mark Johnson, 1st August 2008
+
+#ifndef SLICE_SAMPLER_H
+#define SLICE_SAMPLER_H
+
+#include <algorithm>
+#include <cassert>
+#include <cmath>
+#include <iostream>
+#include <limits>
+
+//! slice_sampler_rfc_type{} returns the value of a user-specified
+//! function if the argument is within range, or - infinity otherwise
+//
+template <typename F, typename Fn, typename U>
+struct slice_sampler_rfc_type {
+ F min_x, max_x;
+ const Fn& f;
+ U max_nfeval, nfeval;
+ slice_sampler_rfc_type(F min_x, F max_x, const Fn& f, U max_nfeval)
+ : min_x(min_x), max_x(max_x), f(f), max_nfeval(max_nfeval), nfeval(0) { }
+
+ F operator() (F x) {
+ if (min_x < x && x < max_x) {
+ assert(++nfeval <= max_nfeval);
+ F fx = f(x);
+ assert(std::isfinite(fx));
+ return fx;
+ }
+ else
+ return -std::numeric_limits<F>::infinity();
+ }
+}; // slice_sampler_rfc_type{}
+
+//! slice_sampler1d() implements the univariate "range doubling" slice sampler
+//! described in Neal (2003) "Slice Sampling", The Annals of Statistics 31(3), 705-767.
+//
+template <typename F, typename LogF, typename Uniform01>
+F slice_sampler1d(const LogF& logF0, //!< log of function to sample
+ F x, //!< starting point
+ Uniform01& u01, //!< uniform [0,1) random number generator
+ F min_x = -std::numeric_limits<F>::infinity(), //!< minimum value of support
+ F max_x = std::numeric_limits<F>::infinity(), //!< maximum value of support
+ F w = 0.0, //!< guess at initial width
+ unsigned nsamples=1, //!< number of samples to draw
+ unsigned max_nfeval=200) //!< max number of function evaluations
+{
+ typedef unsigned U;
+ slice_sampler_rfc_type<F,LogF,U> logF(min_x, max_x, logF0, max_nfeval);
+
+ assert(std::isfinite(x));
+
+ if (w <= 0.0) { // set w to a default width
+ if (min_x > -std::numeric_limits<F>::infinity() && max_x < std::numeric_limits<F>::infinity())
+ w = (max_x - min_x)/4;
+ else
+ w = std::max(((x < 0.0) ? -x : x)/4, (F) 0.1);
+ }
+ assert(std::isfinite(w));
+
+ F logFx = logF(x);
+ for (U sample = 0; sample < nsamples; ++sample) {
+ F logY = logFx + log(u01()+1e-100); //! slice logFx at this value
+ assert(std::isfinite(logY));
+
+ F xl = x - w*u01(); //! lower bound on slice interval
+ F logFxl = logF(xl);
+ F xr = xl + w; //! upper bound on slice interval
+ F logFxr = logF(xr);
+
+ while (logY < logFxl || logY < logFxr) // doubling procedure
+ if (u01() < 0.5)
+ logFxl = logF(xl -= xr - xl);
+ else
+ logFxr = logF(xr += xr - xl);
+
+ F xl1 = xl;
+ F xr1 = xr;
+ while (true) { // shrinking procedure
+ F x1 = xl1 + u01()*(xr1 - xl1);
+ if (logY < logF(x1)) {
+ F xl2 = xl; // acceptance procedure
+ F xr2 = xr;
+ bool d = false;
+ while (xr2 - xl2 > 1.1*w) {
+ F xm = (xl2 + xr2)/2;
+ if ((x < xm && x1 >= xm) || (x >= xm && x1 < xm))
+ d = true;
+ if (x1 < xm)
+ xr2 = xm;
+ else
+ xl2 = xm;
+ if (d && logY >= logF(xl2) && logY >= logF(xr2))
+ goto unacceptable;
+ }
+ x = x1;
+ goto acceptable;
+ }
+ goto acceptable;
+ unacceptable:
+ if (x1 < x) // rest of shrinking procedure
+ xl1 = x1;
+ else
+ xr1 = x1;
+ }
+ acceptable:
+ w = (4*w + (xr1 - xl1))/5; // update width estimate
+ }
+ return x;
+}
+
+/*
+//! slice_sampler1d() implements a 1-d MCMC slice sampler.
+//! It should be correct for unimodal distributions, but
+//! not for multimodal ones.
+//
+template <typename F, typename LogP, typename Uniform01>
+F slice_sampler1d(const LogP& logP, //!< log of distribution to sample
+ F x, //!< initial sample
+ Uniform01& u01, //!< uniform random number generator
+ F min_x = -std::numeric_limits<F>::infinity(), //!< minimum value of support
+ F max_x = std::numeric_limits<F>::infinity(), //!< maximum value of support
+ F w = 0.0, //!< guess at initial width
+ unsigned nsamples=1, //!< number of samples to draw
+ unsigned max_nfeval=200) //!< max number of function evaluations
+{
+ typedef unsigned U;
+ assert(std::isfinite(x));
+ if (w <= 0.0) {
+ if (min_x > -std::numeric_limits<F>::infinity() && max_x < std::numeric_limits<F>::infinity())
+ w = (max_x - min_x)/4;
+ else
+ w = std::max(((x < 0.0) ? -x : x)/4, 0.1);
+ }
+ // TRACE4(x, min_x, max_x, w);
+ F logPx = logP(x);
+ assert(std::isfinite(logPx));
+ U nfeval = 1;
+ for (U sample = 0; sample < nsamples; ++sample) {
+ F x0 = x;
+ F logU = logPx + log(u01()+1e-100);
+ assert(std::isfinite(logU));
+ F r = u01();
+ F xl = std::max(min_x, x - r*w);
+ F xr = std::min(max_x, x + (1-r)*w);
+ // TRACE3(x, logPx, logU);
+ while (xl > min_x && logP(xl) > logU) {
+ xl -= w;
+ w *= 2;
+ ++nfeval;
+ if (nfeval >= max_nfeval)
+ std::cerr << "## Error: nfeval = " << nfeval << ", max_nfeval = " << max_nfeval << ", sample = " << sample << ", nsamples = " << nsamples << ", r = " << r << ", w = " << w << ", xl = " << xl << std::endl;
+ assert(nfeval < max_nfeval);
+ }
+ xl = std::max(xl, min_x);
+ while (xr < max_x && logP(xr) > logU) {
+ xr += w;
+ w *= 2;
+ ++nfeval;
+ if (nfeval >= max_nfeval)
+ std::cerr << "## Error: nfeval = " << nfeval << ", max_nfeval = " << max_nfeval << ", sample = " << sample << ", nsamples = " << nsamples << ", r = " << r << ", w = " << w << ", xr = " << xr << std::endl;
+ assert(nfeval < max_nfeval);
+ }
+ xr = std::min(xr, max_x);
+ while (true) {
+ r = u01();
+ x = r*xl + (1-r)*xr;
+ assert(std::isfinite(x));
+ logPx = logP(x);
+ // TRACE4(logPx, x, xl, xr);
+ assert(std::isfinite(logPx));
+ ++nfeval;
+ if (nfeval >= max_nfeval)
+ std::cerr << "## Error: nfeval = " << nfeval << ", max_nfeval = " << max_nfeval << ", sample = " << sample << ", nsamples = " << nsamples << ", r = " << r << ", w = " << w << ", xl = " << xl << ", xr = " << xr << ", x = " << x << std::endl;
+ assert(nfeval < max_nfeval);
+ if (logPx > logU)
+ break;
+ else if (x > x0)
+ xr = x;
+ else
+ xl = x;
+ }
+ // w = (4*w + (xr-xl))/5; // gradually adjust w
+ }
+ // TRACE2(logPx, x);
+ return x;
+} // slice_sampler1d()
+*/
+
+#endif // SLICE_SAMPLER_H
diff --git a/gi/pyp-topics/src/train.cc b/gi/pyp-topics/src/train.cc
new file mode 100644
index 00000000..0d107f11
--- /dev/null
+++ b/gi/pyp-topics/src/train.cc
@@ -0,0 +1,136 @@
+// STL
+#include <iostream>
+#include <fstream>
+
+// Boost
+#include <boost/program_options/parsers.hpp>
+#include <boost/program_options/variables_map.hpp>
+#include <boost/scoped_ptr.hpp>
+
+// Local
+#include "pyp-topics.hh"
+#include "corpus.hh"
+#include "gzstream.hh"
+#include "mt19937ar.h"
+
+static const char *REVISION = "$Revision: 0.1 $";
+
+// Namespaces
+using namespace boost;
+using namespace boost::program_options;
+using namespace std;
+
+int main(int argc, char **argv)
+{
+ std::cout << "Pitman Yor topic models: Copyright 2010 Phil Blunsom\n";
+ std::cout << REVISION << '\n' << std::endl;
+
+ ////////////////////////////////////////////////////////////////////////////////////////////
+ // Command line processing
+ variables_map vm;
+
+ // Command line processing
+ options_description cmdline_specific("Command line specific options");
+ cmdline_specific.add_options()
+ ("help,h", "print help message")
+ ("config,c", value<string>(), "config file specifying additional command line options")
+ ;
+ options_description generic("Allowed options");
+ generic.add_options()
+ ("documents,d", value<string>(), "file containing the documents")
+ ("topics,t", value<int>()->default_value(50), "number of topics")
+ ("document-topics-out,o", value<string>(), "file to write the document topics to")
+ ("topic-words-out,w", value<string>(), "file to write the topic word distribution to")
+ ("samples,s", value<int>()->default_value(10), "number of sampling passes through the data")
+ ("test-corpus", value<string>(), "file containing the test data")
+ ("backoff-paths", value<string>(), "file containing the term backoff paths")
+ ;
+ options_description config_options, cmdline_options;
+ config_options.add(generic);
+ cmdline_options.add(generic).add(cmdline_specific);
+
+ store(parse_command_line(argc, argv, cmdline_options), vm);
+ if (vm.count("config") > 0) {
+ ifstream config(vm["config"].as<string>().c_str());
+ store(parse_config_file(config, cmdline_options), vm);
+ }
+ notify(vm);
+ ////////////////////////////////////////////////////////////////////////////////////////////
+
+ if (vm.count("help")) {
+ cout << cmdline_options << "\n";
+ return 1;
+ }
+
+ if (vm.count("documents") == 0) {
+ cerr << "Please specify a file containing the documents." << endl;
+ cout << cmdline_options << "\n";
+ return 1;
+ }
+
+ // seed the random number generator
+ //mt_init_genrand(time(0));
+
+ // read the data
+ Corpus corpus;
+ corpus.read(vm["documents"].as<string>());
+
+ // run the sampler
+ PYPTopics model(vm["topics"].as<int>());
+
+ // read the backoff dictionary
+ if (vm.count("backoff-paths"))
+ model.set_backoff(vm["backoff-paths"].as<string>());
+
+ // train the sampler
+ model.sample(corpus, vm["samples"].as<int>());
+
+ if (vm.count("document-topics-out")) {
+ ogzstream documents_out(vm["document-topics-out"].as<string>().c_str());
+ //model.print_document_topics(documents_out);
+
+ int document_id=0;
+ for (Corpus::const_iterator corpusIt=corpus.begin();
+ corpusIt != corpus.end(); ++corpusIt, ++document_id) {
+ std::vector<int> unique_terms;
+ for (Document::const_iterator docIt=corpusIt->begin();
+ docIt != corpusIt->end(); ++docIt) {
+ if (unique_terms.empty() || *docIt != unique_terms.back())
+ unique_terms.push_back(*docIt);
+ }
+ documents_out << unique_terms.size();
+ for (std::vector<int>::const_iterator termIt=unique_terms.begin();
+ termIt != unique_terms.end(); ++termIt)
+ documents_out << " " << *termIt << ":" << model.max(document_id, *termIt);
+ documents_out << std::endl;
+ }
+ documents_out.close();
+ }
+
+ if (vm.count("topic-words-out")) {
+ ogzstream topics_out(vm["topic-words-out"].as<string>().c_str());
+ model.print_topic_terms(topics_out);
+ topics_out.close();
+ }
+
+ if (vm.count("test-corpus")) {
+ TestCorpus test_corpus;
+ test_corpus.read(vm["test-corpus"].as<string>());
+ ogzstream topics_out((vm["test-corpus"].as<string>() + ".topics.gz").c_str());
+
+ for (TestCorpus::const_iterator corpusIt=test_corpus.begin();
+ corpusIt != test_corpus.end(); ++corpusIt) {
+ int index=0;
+ for (DocumentTerms::const_iterator instanceIt=corpusIt->begin();
+ instanceIt != corpusIt->end(); ++instanceIt, ++index) {
+ int topic = model.max(instanceIt->doc, instanceIt->term);
+ if (index != 0) topics_out << " ";
+ topics_out << topic;
+ }
+ topics_out << std::endl;
+ }
+ topics_out.close();
+ }
+
+ return 0;
+}
diff --git a/gi/pyp-topics/src/utility.h b/gi/pyp-topics/src/utility.h
new file mode 100644
index 00000000..405a5b0a
--- /dev/null
+++ b/gi/pyp-topics/src/utility.h
@@ -0,0 +1,962 @@
+// utility.h
+//
+// (c) Mark Johnson, 24th January 2005
+//
+// modified 6th May 2002 to ensure write/read consistency, fixed 18th July 2002
+// modified 14th July 2002 to include insert() (generic inserter)
+// modified 26th September 2003 to use mapped_type instead of data_type
+// 25th August 2004 added istream >> const char*
+// 24th January 2005 added insert_newkey()
+//
+// Defines:
+// loop macros foreach, cforeach
+// dfind (default find function)
+// afind (find function that asserts key exists)
+// insert_newkey (inserts a new key into a map)
+// insert (generic inserter into standard data structures)
+// disjoint (set operation)
+// first_lessthan and second_lessthan (compares elements of pairs)
+//
+// Simplified interfaces to STL routines:
+//
+// includes (simplified interface)
+// set_intersection (simplified interface)
+// inserter (simplified interface)
+// max_element (simplified interface)
+// min_element (simplified interface)
+// hash functions for pairs, vectors, lists, slists and maps
+// input and output for pairs and vectors
+// resource_usage (interface improved)
+
+
+#ifndef UTILITY_H
+#define UTILITY_H
+
+#include <algorithm>
+// #include <boost/smart_ptr.hpp> // Comment out this line if boost is not used
+#include <cassert>
+#include <cmath>
+#include <cctype>
+#include <cstdio>
+#include <unordered_map>
+#include <unordered_set>
+#include <ext/slist>
+#include <iostream>
+#include <iterator>
+#include <list>
+#include <map>
+#include <set>
+#include <string>
+#include <utility>
+#include <vector>
+#include <memory>
+
+#if (__GNUC__ > 3) || (__GNUC__ >= 3 && __GNUC_MINOR__ >= 1)
+#define EXT_NAMESPACE __gnu_cxx
+#else
+#define EXT_NAMESPACE std
+#endif
+
+namespace ext = EXT_NAMESPACE;
+
+inline float power(float x, float y) { return powf(x, y); }
+inline double power(double x, double y) { return pow(x, y); }
+inline long double power(long double x, long double y) { return powl(x, y); }
+
+typedef unsigned U;
+typedef long double F; // slower than double, but underflows less
+
+///////////////////////////////////////////////////////////////////////////
+// //
+// Looping constructs //
+// //
+///////////////////////////////////////////////////////////////////////////
+
+// foreach is a simple loop construct
+//
+// STORE should be an STL container
+// TYPE is the typename of STORE
+// VAR will be defined as a local variable of type TYPE::iterator
+//
+#define foreach(TYPE, VAR, STORE) \
+ for (TYPE::iterator VAR = (STORE).begin(); VAR != (STORE).end(); ++VAR)
+
+// cforeach is just like foreach, except that VAR is a const_iterator
+//
+// STORE should be an STL container
+// TYPE is the typename of STORE
+// VAR will be defined as a local variable of type TYPE::const_iterator
+//
+#define cforeach(TYPE, VAR, STORE) \
+ for (TYPE::const_iterator VAR = (STORE).begin(); VAR != (STORE).end(); ++VAR)
+
+
+///////////////////////////////////////////////////////////////////////////
+// //
+// Map searching //
+// //
+// dfind(map, key) returns the key's value in map, or map's default //
+// value if no such key exists (the default value is not inserted) //
+// //
+// afind(map, key) returns a reference to the key's value in map, and //
+// asserts that this value exists //
+// //
+///////////////////////////////////////////////////////////////////////////
+
+// dfind(Map, Key) returns the value Map associates with Key, or the
+// Map's default value if no such Key exists
+//
+template <class Map, class Key>
+inline typename Map::mapped_type dfind(Map& m, const Key& k)
+{
+ typename Map::iterator i = m.find(k);
+ if (i == m.end())
+ return typename Map::mapped_type();
+ else
+ return i->second;
+}
+
+template <class Map, class Key>
+inline const typename Map::mapped_type dfind(const Map& m, const Key& k)
+{
+ typename Map::const_iterator i = m.find(k);
+ if (i == m.end())
+ return typename Map::mapped_type();
+ else
+ return i->second;
+}
+
+
+// afind(map, key) returns a reference to the value associated
+// with key in map. It uses assert to check that the key's value
+// is defined.
+//
+template <class Map, class Key>
+inline typename Map::mapped_type& afind(Map& m, const Key& k)
+{
+ typename Map::iterator i = m.find(k);
+ assert(i != m.end());
+ return i->second;
+}
+
+template <class Map, class Key>
+inline const typename Map::mapped_type& afind(const Map& m, const Key& k)
+{
+ typename Map::const_iterator i = m.find(k);
+ assert(i != m.end());
+ return i->second;
+}
+
+//! insert_newkey(map, key, value) checks that map does not contain
+//! key, and binds key to value.
+//
+template <class Map, class Key, class Value>
+inline typename Map::value_type&
+insert_newkey(Map& m, const Key& k,const Value& v)
+{
+ std::pair<typename Map::iterator, bool> itb
+ = m.insert(Map::value_type(k, v));
+ assert(itb.second);
+ return *(itb.first);
+} // insert_newkey()
+
+
+///////////////////////////////////////////////////////////////////////////
+// //
+// Insert operations //
+// //
+///////////////////////////////////////////////////////////////////////////
+
+
+template <typename T>
+void insert(std::list<T>& xs, const T& x) {
+ xs.push_back(x);
+}
+
+template <typename T>
+void insert(std::set<T>& xs, const T& x) {
+ xs.insert(x);
+}
+
+template <typename T>
+void insert(std::vector<T>& xs, const T& x) {
+ xs.push_back(x);
+}
+
+
+///////////////////////////////////////////////////////////////////////////
+// //
+// Additional versions of standard algorithms //
+// //
+///////////////////////////////////////////////////////////////////////////
+
+template <typename Set1, typename Set2>
+inline bool includes(const Set1& set1, const Set2& set2)
+{
+ return std::includes(set1.begin(), set1.end(), set2.begin(), set2.end());
+}
+
+template <typename Set1, typename Set2, typename Compare>
+inline bool includes(const Set1& set1, const Set2& set2, Compare comp)
+{
+ return std::includes(set1.begin(), set1.end(), set2.begin(), set2.end(), comp);
+}
+
+
+template <typename InputIter1, typename InputIter2>
+bool disjoint(InputIter1 first1, InputIter1 last1,
+ InputIter2 first2, InputIter2 last2)
+{
+ while (first1 != last1 && first2 != last2)
+ if (*first1 < *first2)
+ ++first1;
+ else if (*first2 < *first1)
+ ++first2;
+ else // *first1 == *first2
+ return false;
+ return true;
+}
+
+template <typename InputIter1, typename InputIter2, typename Compare>
+bool disjoint(InputIter1 first1, InputIter1 last1,
+ InputIter2 first2, InputIter2 last2, Compare comp)
+{
+ while (first1 != last1 && first2 != last2)
+ if (comp(*first1, *first2))
+ ++first1;
+ else if (comp(*first2, *first1))
+ ++first2;
+ else // *first1 == *first2
+ return false;
+ return true;
+}
+
+template <typename Set1, typename Set2>
+inline bool disjoint(const Set1& set1, const Set2& set2)
+{
+ return disjoint(set1.begin(), set1.end(), set2.begin(), set2.end());
+}
+
+template <typename Set1, typename Set2, typename Compare>
+inline bool disjoint(const Set1& set1, const Set2& set2, Compare comp)
+{
+ return disjoint(set1.begin(), set1.end(), set2.begin(), set2.end(), comp);
+}
+
+
+template <typename Set1, typename Set2, typename OutputIterator>
+inline OutputIterator set_intersection(const Set1& set1, const Set2& set2,
+ OutputIterator result)
+{
+ return set_intersection(set1.begin(), set1.end(), set2.begin(), set2.end(), result);
+}
+
+template <typename Set1, typename Set2, typename OutputIterator, typename Compare>
+inline OutputIterator set_intersection(const Set1& set1, const Set2& set2,
+ OutputIterator result, Compare comp)
+{
+ return set_intersection(set1.begin(), set1.end(), set2.begin(), set2.end(), result, comp);
+}
+
+
+template <typename Container>
+inline std::insert_iterator<Container> inserter(Container& container)
+{
+ return std::inserter(container, container.begin());
+}
+
+// max_element
+//
+template <class Es> inline typename Es::iterator max_element(Es& es)
+{
+ return std::max_element(es.begin(), es.end());
+}
+
+template <class Es> inline typename Es::const_iterator max_element(const Es& es)
+{
+ return std::max_element(es.begin(), es.end());
+}
+
+template <class Es, class BinaryPredicate>
+inline typename Es::iterator max_element(Es& es, BinaryPredicate comp)
+{
+ return std::max_element(es.begin(), es.end(), comp);
+}
+
+template <class Es, class BinaryPredicate>
+inline typename Es::const_iterator max_element(const Es& es, BinaryPredicate comp)
+{
+ return std::max_element(es.begin(), es.end(), comp);
+}
+
+// min_element
+//
+template <class Es> inline typename Es::iterator min_element(Es& es)
+{
+ return std::min_element(es.begin(), es.end());
+}
+
+template <class Es> inline typename Es::const_iterator min_element(const Es& es)
+{
+ return std::min_element(es.begin(), es.end());
+}
+
+template <class Es, class BinaryPredicate>
+inline typename Es::iterator min_element(Es& es, BinaryPredicate comp)
+{
+ return std::min_element(es.begin(), es.end(), comp);
+}
+
+template <class Es, class BinaryPredicate>
+inline typename Es::const_iterator min_element(const Es& es, BinaryPredicate comp)
+{
+ return std::min_element(es.begin(), es.end(), comp);
+}
+
+// first_lessthan and second_lessthan
+//
+struct first_lessthan {
+ template <typename T1, typename T2>
+ bool operator() (const T1& e1, const T2& e2) {
+ return e1.first < e2.first;
+ }
+};
+
+struct second_lessthan {
+ template <typename T1, typename T2>
+ bool operator() (const T1& e1, const T2& e2) {
+ return e1.second < e2.second;
+ }
+};
+
+// first_greaterthan and second_greaterthan
+//
+struct first_greaterthan {
+ template <typename T1, typename T2>
+ bool operator() (const T1& e1, const T2& e2) {
+ return e1.first > e2.first;
+ }
+};
+
+struct second_greaterthan {
+ template <typename T1, typename T2>
+ bool operator() (const T1& e1, const T2& e2) {
+ return e1.second > e2.second;
+ }
+};
+
+
+///////////////////////////////////////////////////////////////////////////
+// //
+// hash<> specializations //
+// //
+// These must be in namespace std. They permit the corresponding STL //
+// container to be used as a key in an STL hash table. //
+// //
+///////////////////////////////////////////////////////////////////////////
+
+//namespace EXT_NAMESPACE {
+namespace std {
+ /*
+ // hash function for bool
+ //
+ template <> struct hash<bool>
+ {
+ size_t operator() (bool b) const
+ {
+ return b;
+ } // operator()
+ }; // hash<bool>{}
+
+ // hash function for double
+ //
+ template <> struct hash<double>
+ {
+ size_t operator() (double d) const
+ {
+ int exponent;
+ double fraction = frexp(d, &exponent);
+ return size_t(exponent) ^ size_t(1000000.0*(fabs(fraction-0.5)));
+ } // operator()
+ }; // hash<double>{}
+
+ // hash function for strings
+ //
+ template <> struct hash<std::string>
+ {
+ size_t operator()(const std::string& s) const
+ {
+ typedef std::string::const_iterator CI;
+
+ unsigned long h = 0;
+ unsigned long g;
+ CI p = s.begin();
+ CI end = s.end();
+
+ while (p!=end) {
+ h = (h << 4) + (*p++);
+ if ((g = h&0xf0000000)) {
+ h = h ^ (g >> 24);
+ h = h ^ g;
+ }}
+ return size_t(h);
+ } // operator()
+ }; // hash<string>{}
+
+*/
+ // hash function for arbitrary pairs
+ //
+ template<class T1, class T2> struct hash<std::pair<T1,T2> > {
+ size_t operator()(const std::pair<T1,T2>& p) const
+ {
+ size_t h1 = hash<T1>()(p.first);
+ size_t h2 = hash<T2>()(p.second);
+ return h1 ^ (h1 >> 1) ^ h2 ^ (h2 << 1);
+ }
+ };
+
+
+ // hash function for vectors
+ //
+ template<class T> struct hash<std::vector<T> >
+ { // This is the fn hashpjw of Aho, Sethi and Ullman, p 436.
+ size_t operator()(const std::vector<T>& s) const
+ {
+ typedef typename std::vector<T>::const_iterator CI;
+
+ unsigned long h = 0;
+ unsigned long g;
+ CI p = s.begin();
+ CI end = s.end();
+
+ while (p!=end) {
+ h = (h << 5) + hash<T>()(*p++);
+ if ((g = h&0xff000000)) {
+ h = h ^ (g >> 23);
+ h = h ^ g;
+ }}
+ return size_t(h);
+ }
+ };
+
+ // hash function for slists
+ //
+ template<class T> struct hash<ext::slist<T> >
+ { // This is the fn hashpjw of Aho, Sethi and Ullman, p 436.
+ size_t operator()(const ext::slist<T>& s) const
+ {
+ typedef typename ext::slist<T>::const_iterator CI;
+
+ unsigned long h = 0;
+ unsigned long g;
+ CI p = s.begin();
+ CI end = s.end();
+
+ while (p!=end) {
+ h = (h << 7) + hash<T>()(*p++);
+ if ((g = h&0xff000000)) {
+ h = h ^ (g >> 23);
+ h = h ^ g;
+ }}
+ return size_t(h);
+ }
+ };
+
+ // hash function for maps
+ //
+ template<typename T1, typename T2> struct hash<std::map<T1,T2> >
+ {
+ size_t operator()(const std::map<T1,T2>& m) const
+ {
+ typedef typename std::map<T1,T2> M;
+ typedef typename M::const_iterator CI;
+
+ unsigned long h = 0;
+ unsigned long g;
+ CI p = m.begin();
+ CI end = m.end();
+
+ while (p != end) {
+ h = (h << 11) + hash<typename M::value_type>()(*p++);
+ if ((g = h&0xff000000)) {
+ h = h ^ (g >> 23);
+ h = h ^ g;
+ }}
+ return size_t(h);
+ }
+ };
+
+} // namespace EXT_NAMESPACE
+
+
+
+///////////////////////////////////////////////////////////////////////////
+// //
+// Write/Read code //
+// //
+// These routines should possess write/read invariance IF their elements //
+// also have write-read invariance. Whitespace, '(' and ')' are used as //
+// delimiters. //
+// //
+///////////////////////////////////////////////////////////////////////////
+
+
+// Define istream >> const char* so that it consumes the characters from the
+// istream. Just as in scanf, a space consumes an arbitrary amount of whitespace.
+//
+inline std::istream& operator>> (std::istream& is, const char* cp)
+{
+ if (*cp == '\0')
+ return is;
+ else if (*cp == ' ') {
+ char c;
+ if (is.get(c)) {
+ if (isspace(c))
+ return is >> cp;
+ else {
+ is.unget();
+ return is >> (cp+1);
+ }
+ }
+ else {
+ is.clear(is.rdstate() & ~std::ios::failbit); // clear failbit
+ return is >> (cp+1);
+ }
+ }
+ else {
+ char c;
+ if (is.get(c)) {
+ if (c == *cp)
+ return is >> (cp+1);
+ else {
+ is.unget();
+ is.setstate(std::ios::failbit);
+ }
+ }
+ return is;
+ }
+}
+
+
+// Write out an auto_ptr object just as you would write out the pointer object
+//
+template <typename T>
+inline std::ostream& operator<<(std::ostream& os, const std::auto_ptr<T>& sp)
+{
+ return os << sp.get();
+}
+
+
+// Pairs
+//
+template <class T1, class T2>
+std::ostream& operator<< (std::ostream& os, const std::pair<T1,T2>& p)
+{
+ return os << '(' << p.first << ' ' << p.second << ')';
+}
+
+template <class T1, class T2>
+std::istream& operator>> (std::istream& is, std::pair<T1,T2>& p)
+{
+ char c;
+ if (is >> c) {
+ if (c == '(') {
+ if (is >> p.first >> p.second >> c && c == ')')
+ return is;
+ else
+ is.setstate(std::ios::badbit);
+ }
+ else
+ is.putback(c);
+ }
+ is.setstate(std::ios::failbit);
+ return is;
+}
+
+// Lists
+//
+template <class T>
+std::ostream& operator<< (std::ostream& os, const std::list<T>& xs)
+{
+ os << '(';
+ for (typename std::list<T>::const_iterator xi = xs.begin(); xi != xs.end(); ++xi) {
+ if (xi != xs.begin())
+ os << ' ';
+ os << *xi;
+ }
+ return os << ')';
+}
+
+template <class T>
+std::istream& operator>> (std::istream& is, std::list<T>& xs)
+{
+ char c; // This code avoids unnecessary copy
+ if (is >> c) { // read the initial '('
+ if (c == '(') {
+ xs.clear(); // clear the list
+ do {
+ xs.push_back(T()); // create a new elt in list
+ is >> xs.back(); // read element
+ }
+ while (is.good()); // read as long as possible
+ xs.pop_back(); // last read failed; pop last elt
+ is.clear(is.rdstate() & ~std::ios::failbit); // clear failbit
+ if (is >> c && c == ')') // read terminating ')'
+ return is; // successful return
+ else
+ is.setstate(std::ios::badbit); // something went wrong, set badbit
+ }
+ else // c is not '('
+ is.putback(c); // put c back into input
+ }
+ is.setstate(std::ios::failbit); // read failed, set failbit
+ return is;
+}
+
+// Vectors
+//
+template <class T>
+std::ostream& operator<< (std::ostream& os, const std::vector<T>& xs)
+{
+ os << '(';
+ for (typename std::vector<T>::const_iterator xi = xs.begin(); xi != xs.end(); ++xi) {
+ if (xi != xs.begin())
+ os << ' ';
+ os << *xi;
+ }
+ return os << ')';
+}
+
+template <class T>
+std::istream& operator>> (std::istream& is, std::vector<T>& xs)
+{
+ char c; // This code avoids unnecessary copy
+ if (is >> c) { // read the initial '('
+ if (c == '(') {
+ xs.clear(); // clear the list
+ do {
+ xs.push_back(T()); // create a new elt in list
+ is >> xs.back(); // read element
+ }
+ while (is.good()); // read as long as possible
+ xs.pop_back(); // last read failed; pop last elt
+ is.clear(is.rdstate() & ~std::ios::failbit); // clear failbit
+ if (is >> c && c == ')') // read terminating ')'
+ return is; // successful return
+ else
+ is.setstate(std::ios::badbit); // something went wrong, set badbit
+ }
+ else // c is not '('
+ is.putback(c); // put c back into input
+ }
+ is.setstate(std::ios::failbit); // read failed, set failbit
+ return is;
+}
+
+// Slists
+//
+template <class T>
+std::ostream& operator<< (std::ostream& os, const ext::slist<T>& xs)
+{
+ os << '(';
+ for (typename ext::slist<T>::const_iterator xi = xs.begin(); xi != xs.end(); ++xi) {
+ if (xi != xs.begin())
+ os << ' ';
+ os << *xi;
+ }
+ return os << ')';
+}
+
+template <class T>
+std::istream& operator>> (std::istream& is, ext::slist<T>& xs)
+{
+ char c;
+ if (is >> c) {
+ if (c == '(') {
+ xs.clear();
+ T e;
+ if (is >> e) {
+ xs.push_front(e);
+ typename ext::slist<T>::iterator xi = xs.begin();
+ while (is >> e)
+ xi = xs.insert_after(xi, e);
+ is.clear(is.rdstate() & ~std::ios::failbit);
+ if (is >> c && c == ')')
+ return is;
+ else
+ is.setstate(std::ios::badbit);
+ }
+ else { // empty list
+ is.clear(is.rdstate() & ~std::ios::failbit);
+ if (is >> c && c == ')')
+ return is;
+ else // didn't see closing ')'
+ is.setstate(std::ios::badbit);
+ }
+ }
+ else // didn't read '('
+ is.putback(c);
+ }
+ is.setstate(std::ios::failbit);
+ return is;
+}
+
+// Sets
+//
+template <class T>
+std::ostream& operator<< (std::ostream& os, const std::set<T>& s)
+{
+ os << '(';
+ for (typename std::set<T>::const_iterator i = s.begin(); i != s.end(); ++i) {
+ if (i != s.begin())
+ os << ' ';
+ os << *i;
+ }
+ return os << ')';
+}
+
+template <class T>
+std::istream& operator>> (std::istream& is, std::set<T>& s)
+{
+ char c;
+ if (is >> c) {
+ if (c == '(') {
+ s.clear();
+ T e;
+ while (is >> e)
+ s.insert(e);
+ is.clear(is.rdstate() & ~std::ios::failbit);
+ if (is >> c && c == ')')
+ return is;
+ else
+ is.setstate(std::ios::badbit);
+ }
+ else
+ is.putback(c);
+ }
+ is.setstate(std::ios::failbit);
+ return is;
+}
+
+// Hash_sets
+//
+template <class T>
+std::ostream& operator<< (std::ostream& os, const std::unordered_set<T>& s)
+{
+ os << '(';
+ for (typename std::unordered_set<T>::const_iterator i = s.begin(); i != s.end(); ++i) {
+ if (i != s.begin())
+ os << ' ';
+ os << *i;
+ }
+ return os << ')';
+}
+
+template <class T>
+std::istream& operator>> (std::istream& is, std::unordered_set<T>& s)
+{
+ char c;
+ if (is >> c) {
+ if (c == '(') {
+ s.clear();
+ T e;
+ while (is >> e)
+ s.insert(e);
+ is.clear(is.rdstate() & ~std::ios::failbit);
+ if (is >> c && c == ')')
+ return is;
+ else
+ is.setstate(std::ios::badbit);
+ }
+ else
+ is.putback(c);
+ }
+ is.setstate(std::ios::failbit);
+ return is;
+}
+
+
+// Maps
+//
+template <class Key, class Value>
+std::ostream& operator<< (std::ostream& os, const std::map<Key,Value>& m)
+{
+ typedef std::map<Key,Value> M;
+ os << '(';
+ for (typename M::const_iterator it = m.begin(); it != m.end(); ++it) {
+ if (it != m.begin())
+ os << ' ';
+ os << *it;
+ }
+ return os << ")";
+}
+
+template <class Key, class Value>
+std::istream& operator>> (std::istream& is, std::map<Key,Value>& m)
+{
+ char c;
+ if (is >> c) {
+ if (c == '(') {
+ m.clear();
+ std::pair<Key,Value> e;
+ while (is >> e)
+ m.insert(e);
+ is.clear(is.rdstate() & ~std::ios::failbit);
+ if (is >> c && c == ')')
+ return is;
+ else
+ is.setstate(std::ios::badbit);
+ }
+ else
+ is.putback(c);
+ }
+ is.setstate(std::ios::failbit);
+ return is;
+}
+
+// Hash_maps
+//
+template <class Key, class Value>
+std::ostream& operator<< (std::ostream& os, const std::unordered_map<Key,Value>& m)
+{
+ typedef std::unordered_map<Key,Value> M;
+ os << '(';
+ for (typename M::const_iterator it = m.begin(); it != m.end(); ++it) {
+ if (it != m.begin())
+ os << ' ';
+ os << *it;
+ }
+ return os << ")";
+}
+
+template <class Key, class Value>
+std::istream& operator>> (std::istream& is, std::unordered_map<Key,Value>& m)
+{
+ char c;
+ if (is >> c) {
+ if (c == '(') {
+ m.clear();
+ std::pair<Key,Value> e;
+ while (is >> e)
+ m.insert(e);
+ is.clear(is.rdstate() & ~std::ios::failbit);
+ if (is >> c && c == ')')
+ return is;
+ else
+ is.setstate(std::ios::badbit);
+ }
+ else
+ is.putback(c);
+ }
+ is.setstate(std::ios::failbit);
+ return is;
+}
+
+
+///////////////////////////////////////////////////////////////////////////
+// //
+// Boost library additions //
+// //
+///////////////////////////////////////////////////////////////////////////
+
+#ifdef BOOST_SHARED_PTR_HPP_INCLUDED
+
+// enhancements to boost::shared_ptr so it can be used with hash
+//
+namespace std {
+ template <typename T> struct equal_to<boost::shared_ptr<T> >
+ : public binary_function<boost::shared_ptr<T>, boost::shared_ptr<T>, bool> {
+ bool operator() (const boost::shared_ptr<T>& p1, const boost::shared_ptr<T>& p2) const {
+ return equal_to<T*>()(p1.get(), p2.get());
+ }
+ };
+} // namespace std
+
+//namespace EXT_NAMESPACE {
+namespace std {
+ template <typename T> struct hash<boost::shared_ptr<T> > {
+ size_t operator() (const boost::shared_ptr<T>& a) const {
+ return hash<T*>()(a.get());
+ }
+ };
+} // namespace ext
+
+template <typename T>
+inline std::ostream& operator<< (std::ostream& os, const boost::shared_ptr<T>& sp)
+{
+ return os << sp.get();
+}
+
+#endif // BOOST_SHARED_PTR_HPP_INCLUDED
+
+struct resource_usage { };
+
+#ifndef __i386
+inline std::ostream& operator<< (std::ostream& os, resource_usage r)
+{
+ return os;
+}
+#else // Assume we are on a 586 linux
+inline std::ostream& operator<< (std::ostream& os, resource_usage r)
+{
+ FILE* fp = fopen("/proc/self/stat", "r");
+ assert(fp);
+ int utime;
+ int stime;
+ unsigned int vsize;
+ unsigned int rss;
+ int result =
+ fscanf(fp, "%*d %*s %*c %*d %*d %*d %*d %*d %*u %*u %*u %*u %*u %d %d %*d %*d %*d %*d"
+ "%*u %*u %*d %u %u", &utime, &stime, &vsize, &rss);
+ assert(result == 4);
+ fclose(fp);
+ // s << "utime = " << utime << ", stime = " << stime << ", vsize = " << vsize << ", rss = " << rss
+ ;
+ // return s << "utime = " << utime << ", vsize = " << vsize;
+ return os << "utime " << float(utime)/1.0e2 << "s, vsize "
+ << float(vsize)/1048576.0 << " Mb.";
+}
+#endif
+
+//! A default_value_type{} object is used to read an object from a stream,
+//! assigning a default value if the read fails. Users should not need to
+//! construct such objects, but should use default_value() instead.
+//
+template <typename object_type, typename default_type>
+struct default_value_type {
+ object_type& object;
+ const default_type defaultvalue;
+ default_value_type(object_type& object, const default_type defaultvalue)
+ : object(object), defaultvalue(defaultvalue) { }
+};
+
+//! default_value() is used to read an object from a stream, assigning a
+//! default value if the read fails. It returns a default_value_type{}
+//! object, which does the actual reading.
+//
+template <typename object_type, typename default_type>
+default_value_type<object_type,default_type>
+default_value(object_type& object, const default_type defaultvalue=default_type()) {
+ return default_value_type<object_type,default_type>(object, defaultvalue);
+}
+
+//! This version of operator>>() reads default_value_type{} from an input stream.
+//
+template <typename object_type, typename default_type>
+std::istream& operator>> (std::istream& is,
+ default_value_type<object_type, default_type> dv) {
+ if (is) {
+ if (is >> dv.object)
+ ;
+ else {
+ is.clear(is.rdstate() & ~std::ios::failbit); // clear failbit
+ dv.object = dv.defaultvalue;
+ }
+ }
+ return is;
+}
+
+// inline F random1() { return rand()/(RAND_MAX+1.0); }
+inline F random1() { return mt_genrand_res53(); }
+
+#endif // UTILITY_H