Merge pull request #64 from bab2min/dev

preparing 0.8.2

.github/workflows/deploy.yml

@@ -24,6 +24,11 @@ jobs:
         mkdir include
         mv eigen-git-mirror/Eigen/ include/
         rm -rf eigen-git-mirror/
+        git clone https://github.com/bab2min/EigenRand
+        cd EigenRand
+        git checkout tags/v0.2.1
+        cd ..
+        mv EigenRand/EigenRand include/
     - name: Deploy
       continue-on-error: True
       env:
@@ -61,6 +66,9 @@ jobs:
         wget https://github.com/eigenteam/eigen-git-mirror/archive/3.3.7.tar.gz
         tar -zxvf 3.3.7.tar.gz
         mv eigen-git-mirror-3.3.7 include
+        wget https://github.com/bab2min/EigenRand/archive/v0.2.1.tar.gz
+        tar -zxvf v0.2.1.tar.gz
+        mv EigenRand-0.2.1/EigenRand include/
     - name: Deploy
       continue-on-error: True
       env:
@@ -94,6 +102,9 @@ jobs:
         Invoke-WebRequest -OutFile 3.3.7.tar.gz https://github.com/eigenteam/eigen-git-mirror/archive/3.3.7.tar.gz
         tar -zxvf 3.3.7.tar.gz
         mv eigen-git-mirror-3.3.7 include
+        Invoke-WebRequest -OutFile v0.2.1.tar.gz https://github.com/bab2min/EigenRand/archive/v0.2.1.tar.gz
+        tar -zxvf v0.2.1.tar.gz
+        mv EigenRand-0.2.1/EigenRand include/
     - name: Deploy
       continue-on-error: True
       env:

.github/workflows/deploy_test.yml

@@ -23,6 +23,11 @@ jobs:
         mkdir include
         mv eigen-git-mirror/Eigen/ include/
         rm -rf eigen-git-mirror/
+        git clone https://github.com/bab2min/EigenRand
+        cd EigenRand
+        git checkout tags/v0.2.1
+        cd ..
+        mv EigenRand/EigenRand include/
     - name: Deploy
       continue-on-error: True
       env:
@@ -60,6 +65,9 @@ jobs:
         wget https://github.com/eigenteam/eigen-git-mirror/archive/3.3.7.tar.gz
         tar -zxvf 3.3.7.tar.gz
         mv eigen-git-mirror-3.3.7 include
+        wget https://github.com/bab2min/EigenRand/archive/v0.2.1.tar.gz
+        tar -zxvf v0.2.1.tar.gz
+        mv EigenRand-0.2.1/EigenRand include/
     - name: Deploy
       continue-on-error: True
       env:
@@ -93,6 +101,9 @@ jobs:
         Invoke-WebRequest -OutFile 3.3.7.tar.gz https://github.com/eigenteam/eigen-git-mirror/archive/3.3.7.tar.gz
         tar -zxvf 3.3.7.tar.gz
         mv eigen-git-mirror-3.3.7 include
+        Invoke-WebRequest -OutFile v0.2.1.tar.gz https://github.com/bab2min/EigenRand/archive/v0.2.1.tar.gz
+        tar -zxvf v0.2.1.tar.gz
+        mv EigenRand-0.2.1/EigenRand include/
     - name: Deploy
       continue-on-error: True
       env:

.github/workflows/generate_documentation.yml

@@ -27,6 +27,11 @@ jobs:
         wget https://github.com/eigenteam/eigen-git-mirror/archive/3.3.7.tar.gz
         tar -zxvf 3.3.7.tar.gz
         mv eigen-git-mirror-3.3.7 include
+        git clone https://github.com/bab2min/EigenRand
+        cd EigenRand
+        git checkout tags/v0.2.1
+        cd ..
+        mv EigenRand/EigenRand include/
     - name: build
       run: |
         python3 -m pip install pdoc3 numpy

.github/workflows/pull_request_test.yml

@@ -28,6 +28,11 @@ jobs:
         git checkout tags/3.3.7
         cd ..
         mv eigen-git-mirror include
+        git clone https://github.com/bab2min/EigenRand
+        cd EigenRand
+        git checkout tags/v0.2.1
+        cd ..
+        mv EigenRand/EigenRand include/
     - name: Build
       run: |
         /opt/python/${{ matrix.cp }}/bin/python -m pip install numpy
@@ -58,6 +63,9 @@ jobs:
         wget https://github.com/eigenteam/eigen-git-mirror/archive/3.3.7.tar.gz
         tar -zxvf 3.3.7.tar.gz
         mv eigen-git-mirror-3.3.7 include
+        wget https://github.com/bab2min/EigenRand/archive/v0.2.1.tar.gz
+        tar -zxvf v0.2.1.tar.gz
+        mv EigenRand-0.2.1/EigenRand include/
     - name: Build
       run: |
         python -m pip install numpy
@@ -91,6 +99,9 @@ jobs:
         Invoke-WebRequest -OutFile 3.3.7.tar.gz https://github.com/eigenteam/eigen-git-mirror/archive/3.3.7.tar.gz
         tar -zxvf 3.3.7.tar.gz
         mv eigen-git-mirror-3.3.7 include
+        Invoke-WebRequest -OutFile v0.2.1.tar.gz https://github.com/bab2min/EigenRand/archive/v0.2.1.tar.gz
+        tar -zxvf v0.2.1.tar.gz
+        mv EigenRand-0.2.1/EigenRand include/
     - name: Build
       run: |
         python -m pip install numpy

README.kr.rst

@@ -35,7 +35,7 @@ tomotopy 란?
 
 더 자세한 정보는 https://bab2min.github.io/tomotopy/index.kr.html 에서 확인하시길 바랍니다.
 
-tomotopy의 가장 최신버전은 0.8.1 입니다.
+tomotopy의 가장 최신버전은 0.8.2 입니다.
 
 시작하기
 ---------------
@@ -240,6 +240,10 @@ tomotopy의 Python3 예제 코드는 https://github.com/bab2min/tomotopy/blob/ma
 
 역사
 -------
+* 0.8.2 (2020-07-14)
+    * `tomotopy.DTModel.num_timepoints`와 `tomotopy.DTModel.num_docs_by_timepoint` 프로퍼티가 추가되었습니다.
+    * `seed`가 동일해서 플랫폼이 다르면 다른 결과를 내던 문제가 일부 해결되었습니다. 이로 인해 32bit 버전의 모델 학습 결과가 이전 버전과는 달라졌습니다.
+
 * 0.8.1 (2020-06-08)
     * `tomotopy.LDAModel.used_vocabs`가 잘못된 값을 반환하는 버그가 수정되었습니다.
     * 이제 `tomotopy.CTModel.prior_cov`가 `[k, k]` 모양의 공분산 행렬을 반환합니다.

README.rst

@@ -246,6 +246,11 @@ meaning you can use it for any reasonable purpose and remain in complete ownersh
 
 History
 -------
+* 0.8.2 (2020-07-14)
+    * New properties `tomotopy.DTModel.num_timepoints` and `tomotopy.DTModel.num_docs_by_timepoint` have been added.
+    * A bug which causes different results with the different platform even if `seeds` were the same was partially fixed. 
+      As a result of this fix, now `tomotopy` in 32 bit yields different training results from earlier version.
+
 * 0.8.1 (2020-06-08)
     * A bug where `tomotopy.LDAModel.used_vocabs` returned an incorrect value was fixed.
     * Now `tomotopy.CTModel.prior_cov` returns a covariance matrix with shape `[k, k]`.

examples/dtm_plot.py

@@ -0,0 +1,44 @@
+import tomotopy as tp
+import numpy as np
+import nltk
+
+def data_feeder(input_file):
+    for line in open(input_file, encoding='utf-8'):
+        fd = line.strip().split(maxsplit=1)
+        timepoint = int(fd[0])
+        yield fd[1], None, {'timepoint':timepoint}
+
+porter_stemmer = nltk.PorterStemmer().stem
+corpus = tp.utils.Corpus(
+    tokenizer=tp.utils.SimpleTokenizer(porter_stemmer)
+)
+corpus.process(data_feeder('../test/sample_tp.txt'))
+
+num_timepoints = 13
+
+mdl = tp.DTModel(min_cf=3, k=10, t=num_timepoints, phi_var=1e-2, corpus=corpus)
+mdl.train(0)
+
+print('Num docs:{}, Num Vocabs:{}, Total Words:{}'.format(
+    len(mdl.docs), len(mdl.used_vocabs), mdl.num_words
+))
+print('Removed Top words: ', *mdl.removed_top_words)
+
+# Let's train the model
+for i in range(0, 1000, 20):
+    print('Iteration: {:04}, LL per word: {:.4}'.format(i, mdl.ll_per_word))
+    mdl.train(20)
+print('Iteration: {:04}, LL per word: {:.4}'.format(1000, mdl.ll_per_word))
+
+topic_dist_by_time = np.zeros(shape=[num_timepoints, mdl.k], dtype=np.float)
+doc_counts_by_time = np.zeros(shape=[num_timepoints], dtype=np.int32)
+for doc in mdl.docs:
+    doc_counts_by_time[doc.timepoint] += 1
+    topic_dist_by_time[doc.timepoint] += doc.get_topic_dist()
+
+topic_dist_by_time /= doc_counts_by_time[:, np.newaxis]
+
+for k in range(mdl.k):
+    print('Topic #{}'.format(k), *(w for w, _ in mdl.get_topic_words(k, 0, top_n=5)))
+    print(topic_dist_by_time[:, k])
+

examples/gdmr_plot.py

@@ -51,7 +51,7 @@ def __call__(self, value, clip=None):
 '''
 
 corpus = tp.utils.Corpus()
-for line in open('examples/dataset2.txt', encoding='utf-8'):
+for line in open('dataset2.txt', encoding='utf-8'):
     fd = line.strip().split()
     corpus.add_doc(fd[2:], metadata=list(map(float, fd[:2])))
 

src/Labeling/FoRelevance.cpp

@@ -138,7 +138,7 @@ std::vector<Candidate> PMIExtractor::extract(const tomoto::ITopicModel * tm) con
 		trieNodes[0].traverse_with_keys([&](const TrieEx<Vid, size_t>* node, const std::vector<Vid>& rkeys)
 		{
 			if (rkeys.size() <= 2 || node->val < candMinCnt) return;
-			float n = tm->getN();
+			float n = (float)tm->getN();
 			auto pmi = node->val / n;
 			for (auto k : rkeys)
 			{

src/TopicModel/CT.h

@@ -3,11 +3,11 @@
 
 namespace tomoto
 {
-    template<TermWeight _tw, size_t _Flags = 0>
-	struct DocumentCTM : public DocumentLDA<_tw, _Flags>
+    template<TermWeight _tw>
+	struct DocumentCTM : public DocumentLDA<_tw>
 	{
-		using BaseDocument = DocumentLDA<_tw, _Flags>;
-		using DocumentLDA<_tw, _Flags>::DocumentLDA;
+		using BaseDocument = DocumentLDA<_tw>;
+		using DocumentLDA<_tw>::DocumentLDA;
 		Eigen::Matrix<Float, -1, -1> beta; // Dim: (K, betaSample)
 		Eigen::Matrix<Float, -1, 1> smBeta; // Dim: K
 
@@ -21,7 +21,8 @@ namespace tomoto
 		using DefaultDocType = DocumentCTM<TermWeight::one>;
 		static ICTModel* create(TermWeight _weight, size_t _K = 1,
 			Float smoothingAlpha = 0.1,  Float _eta = 0.01,
-			const RandGen& _rg = RandGen{ std::random_device{}() });
+			size_t seed = std::random_device{}(),
+			bool scalarRng = false);
 
 		virtual void setNumBetaSample(size_t numSample) = 0;
 		virtual size_t getNumBetaSample() const = 0;

src/TopicModel/CTModel.cpp

@@ -2,12 +2,12 @@
 
 namespace tomoto
 {
-	template class CTModel<TermWeight::one>;
+	/*template class CTModel<TermWeight::one>;
 	template class CTModel<TermWeight::idf>;
-	template class CTModel<TermWeight::pmi>;
+	template class CTModel<TermWeight::pmi>;*/
 
-	ICTModel* ICTModel::create(TermWeight _weight, size_t _K, Float smoothingAlpha, Float _eta, const RandGen& _rg)
+	ICTModel* ICTModel::create(TermWeight _weight, size_t _K, Float smoothingAlpha, Float _eta, size_t seed, bool scalarRng)
 	{
-		SWITCH_TW(_weight, CTModel, _K, smoothingAlpha, _eta, _rg);
+		TMT_SWITCH_TW(_weight, scalarRng, CTModel, _K, smoothingAlpha, _eta, seed);
 	}
 }

src/TopicModel/CTModel.hpp

@@ -16,18 +16,19 @@ namespace tomoto
 	{
 	};
 
-	template<TermWeight _tw, size_t _Flags = flags::partitioned_multisampling,
+	template<TermWeight _tw, typename _RandGen,
+		size_t _Flags = flags::partitioned_multisampling,
 		typename _Interface = ICTModel,
 		typename _Derived = void,
 		typename _DocType = DocumentCTM<_tw>,
 		typename _ModelState = ModelStateCTM<_tw>>
-	class CTModel : public LDAModel<_tw, _Flags, _Interface,
-		typename std::conditional<std::is_same<_Derived, void>::value, CTModel<_tw, _Flags>, _Derived>::type,
+	class CTModel : public LDAModel<_tw, _RandGen, _Flags, _Interface,
+		typename std::conditional<std::is_same<_Derived, void>::value, CTModel<_tw, _RandGen, _Flags>, _Derived>::type,
 		_DocType, _ModelState>
 	{
 	protected:
-		using DerivedClass = typename std::conditional<std::is_same<_Derived, void>::value, CTModel<_tw>, _Derived>::type;
-		using BaseClass = LDAModel<_tw, _Flags, _Interface, DerivedClass, _DocType, _ModelState>;
+		using DerivedClass = typename std::conditional<std::is_same<_Derived, void>::value, CTModel<_tw, _RandGen>, _Derived>::type;
+		using BaseClass = LDAModel<_tw, _RandGen, _Flags, _Interface, DerivedClass, _DocType, _ModelState>;
 		friend BaseClass;
 		friend typename BaseClass::BaseClass;
 		using WeightType = typename BaseClass::WeightType;
@@ -53,12 +54,11 @@ namespace tomoto
 			return &zLikelihood[0];
 		}
 
-		void updateBeta(_DocType& doc, RandGen& rg) const
+		void updateBeta(_DocType& doc, _RandGen& rg) const
 		{
 			Eigen::Matrix<Float, -1, 1> pbeta, lowerBound, upperBound;
 			constexpr Float epsilon = 1e-8;
 			constexpr size_t burnIn = 3;
-			sample::FastRealGenerator frg;
 
 			pbeta = lowerBound = upperBound = Eigen::Matrix<Float, -1, 1>::Zero(this->K);
 			for (size_t i = 0; i < numBetaSample + burnIn; ++i)
@@ -71,7 +71,7 @@ namespace tomoto
 				{
 					Float N_k = doc.numByTopic[k] + this->alpha;
 					Float N_nk = doc.getSumWordWeight() + this->alpha * (this->K + 1) - N_k;
-					Float u1 = frg(rg), u2 = frg(rg);
+					Float u1 = rg.uniform_real(), u2 = rg.uniform_real();
 					Float max_uk = epsilon + pow(u1, (Float)1 / N_k)  * (pbeta[k] - epsilon);
 					Float min_unk = (1 - pow(u2, (Float)1 / N_nk))
 						* (1 - pbeta[k]) + pbeta[k];
@@ -111,7 +111,7 @@ namespace tomoto
 		}
 
 		template<ParallelScheme _ps, bool _infer, typename _ExtraDocData>
-		void sampleDocument(_DocType& doc, const _ExtraDocData& edd, size_t docId, _ModelState& ld, RandGen& rgs, size_t iterationCnt, size_t partitionId = 0) const
+		void sampleDocument(_DocType& doc, const _ExtraDocData& edd, size_t docId, _ModelState& ld, _RandGen& rgs, size_t iterationCnt, size_t partitionId = 0) const
 		{
 			BaseClass::template sampleDocument<_ps, _infer>(doc, edd, docId, ld, rgs, iterationCnt, partitionId);
 			/*if (iterationCnt >= this->burnIn && this->optimInterval && (iterationCnt + 1) % this->optimInterval == 0)
@@ -121,7 +121,7 @@ namespace tomoto
 		}
 
 		template<typename _DocIter>
-		void sampleGlobalLevel(ThreadPool* pool, _ModelState* localData, RandGen* rgs, _DocIter first, _DocIter last) const
+		void sampleGlobalLevel(ThreadPool* pool, _ModelState* localData, _RandGen* rgs, _DocIter first, _DocIter last) const
 		{
 			if (this->iterated < this->burnIn || !this->optimInterval || (this->iterated + 1) % this->optimInterval != 0) return;
 
@@ -154,7 +154,7 @@ namespace tomoto
 			}
 		}
 
-		int restoreFromTrainingError(const exception::TrainingError& e, ThreadPool& pool, _ModelState* localData, RandGen* rgs)
+		int restoreFromTrainingError(const exception::TrainingError& e, ThreadPool& pool, _ModelState* localData, _RandGen* rgs)
 		{
 			std::cerr << "Failed to sample! Reset prior and retry!" << std::endl;
 			const size_t chStride = std::min(pool.getNumWorkers() * 8, this->docs.size());
@@ -175,7 +175,7 @@ namespace tomoto
 			return 0;
 		}
 
-		void optimizeParameters(ThreadPool& pool, _ModelState* localData, RandGen* rgs)
+		void optimizeParameters(ThreadPool& pool, _ModelState* localData, _RandGen* rgs)
 		{
 			std::vector<std::future<void>> res;
 			topicPrior = math::MultiNormalDistribution<Float>::estimate([this](size_t i)
@@ -239,7 +239,7 @@ namespace tomoto
 		DEFINE_SERIALIZER_AFTER_BASE_WITH_VERSION(BaseClass, 0, numBetaSample, numTMNSample, topicPrior);
 		DEFINE_TAGGED_SERIALIZER_AFTER_BASE_WITH_VERSION(BaseClass, 1, 0x00010001, numBetaSample, numTMNSample, topicPrior);
 
-		CTModel(size_t _K = 1, Float smoothingAlpha = 0.1, Float _eta = 0.01, const RandGen& _rg = RandGen{ std::random_device{}() })
+		CTModel(size_t _K = 1, Float smoothingAlpha = 0.1, Float _eta = 0.01, const _RandGen& _rg = _RandGen{ std::random_device{}() })
 			: BaseClass(_K, smoothingAlpha, _eta, _rg)
 		{
 			this->optimInterval = 2;

src/TopicModel/DMR.h

@@ -3,11 +3,11 @@
 
 namespace tomoto
 {
-	template<TermWeight _tw, size_t _Flags = 0>
-	struct DocumentDMR : public DocumentLDA<_tw, _Flags>
+	template<TermWeight _tw>
+	struct DocumentDMR : public DocumentLDA<_tw>
 	{
-		using BaseDocument = DocumentLDA<_tw, _Flags>;
-		using DocumentLDA<_tw, _Flags>::DocumentLDA;
+		using BaseDocument = DocumentLDA<_tw>;
+		using DocumentLDA<_tw>::DocumentLDA;
 		size_t metadata = 0;
 
 		DEFINE_SERIALIZER_AFTER_BASE_WITH_VERSION(BaseDocument, 0, metadata);
@@ -20,7 +20,8 @@ namespace tomoto
 		using DefaultDocType = DocumentDMR<TermWeight::one>;
 		static IDMRModel* create(TermWeight _weight, size_t _K = 1,
 			Float defaultAlpha = 1.0, Float _sigma = 1.0, Float _eta = 0.01, Float _alphaEps = 1e-10,
-			const RandGen& _rg = RandGen{ std::random_device{}() });
+			size_t seed = std::random_device{}(),
+			bool scalarRng = false);
 
 		virtual size_t addDoc(const std::vector<std::string>& words, const std::vector<std::string>& metadata) = 0;
 		virtual std::unique_ptr<DocumentBase> makeDoc(const std::vector<std::string>& words, const std::vector<std::string>& metadata) const = 0;

src/TopicModel/DMRModel.cpp

@@ -2,12 +2,12 @@
 
 namespace tomoto
 {
-	template class DMRModel<TermWeight::one>;
+	/*template class DMRModel<TermWeight::one>;
 	template class DMRModel<TermWeight::idf>;
-	template class DMRModel<TermWeight::pmi>;
+	template class DMRModel<TermWeight::pmi>;*/
 
-	IDMRModel* IDMRModel::create(TermWeight _weight, size_t _K, Float _defaultAlpha, Float _sigma, Float _eta, Float _alphaEps, const RandGen& _rg)
+	IDMRModel* IDMRModel::create(TermWeight _weight, size_t _K, Float _defaultAlpha, Float _sigma, Float _eta, Float _alphaEps, size_t seed, bool scalarRng)
 	{
-		SWITCH_TW(_weight, DMRModel, _K, _defaultAlpha, _sigma, _eta, _alphaEps, _rg);
+		TMT_SWITCH_TW(_weight, scalarRng, DMRModel, _K, _defaultAlpha, _sigma, _eta, _alphaEps, seed);
 	}
 }