Cythonized Python code for sslm and LdaPost classes

Author: Sharganov

.gitignore

@@ -89,5 +89,7 @@ gensim/models/fasttext_inner.c
 gensim/models/nmf_pgd.c
 gensim/models/word2vec_corpusfile.cpp
 gensim/models/word2vec_inner.c
+gensim/models/ldaseq_sslm_inner.c
+gensim/models/ldaseq_posterior_inner.c
 
 .ipynb_checkpoints

gensim/models/__init__.py

@@ -22,6 +22,7 @@
 from .fasttext import FastText  # noqa:F401
 from .translation_matrix import TranslationMatrix, BackMappingTranslationMatrix  # noqa:F401
 from .nmf import Nmf  # noqa:F401
+from .ldaseqmodel_optimized import LdaSeqModel_V4
 
 from gensim import interfaces, utils
 

gensim/models/ldaseq_posterior_inner.pyx

@@ -0,0 +1,317 @@
+from scipy.special.cython_special cimport gammaln
+from scipy.special.cython_special cimport psi
+
+from libc.math cimport exp, log, abs
+from libc.string cimport memcpy
+from libc.stdlib cimport malloc, free
+
+cimport numpy as np
+
+import numpy as np
+
+ctypedef np.float64_t REAL_t
+
+
+cdef update_phi(REAL_t * gamma, REAL_t *phi, REAL_t * log_phi,
+               int * word_ids, REAL_t * lda_topics, const int num_topics,
+               const int doc_length):
+
+    """Update variational multinomial parameters, based on a document and a time-slice.
+
+    This is done based on the original Blei-LDA paper, where:
+    log_phi := beta * exp(Ψ(gamma)), over every topic for every word.
+
+    TODO: incorporate lee-sueng trick used in
+    **Lee, Seung: Algorithms for non-negative matrix factorization, NIPS 2001**.
+
+    Parameters
+    ----------
+    gamma : size of num_topics. in-parameter
+
+    phi : size of (max_doc_len, num_topics). int/out-parameter
+
+    log_phi: size of (max_doc_len, num_topics). in/out-parameter
+
+    word_ids: size of doc_length. in-parameter
+
+    lda_topics: size of (vocab_len, num_topics). in-parameter
+
+    num_topics: number of topics in the model. in-parameter
+
+    doc_length: length of the document (number of words in the document). in-parameter
+
+    """
+
+    cdef int k, i
+
+    # digamma values
+    cdef REAL_t * dig = <REAL_t *> malloc(num_topics * sizeof(REAL_t))
+    if dig == NULL:
+        raise
+    if dig == NULL:
+        print("NULL pointer")
+
+    for k in range(num_topics):
+        dig[k] = psi(gamma[k])
+
+    cdef REAL_t *log_phi_row = NULL
+    cdef REAL_t *phi_row = NULL
+
+    for i in range(doc_length):
+        for k in range(num_topics):
+            # TODO check if proper indexing
+            log_phi[i * num_topics + k] = \
+                dig[k] + lda_topics[word_ids[i] * num_topics + k]
+
+        log_phi_row = log_phi + i * num_topics
+
+        phi_row = phi + i * num_topics
+
+        # log normalize
+        v = log_phi_row[0]
+        for i in range(1, num_topics):
+            v = log(exp(v) + exp(log_phi_row[i]))
+
+        # subtract every element by v
+        # TODO blas
+        for i in range(num_topics):
+            log_phi_row[i] = log_phi_row[i] - v
+
+        for i in range(num_topics):
+            phi_row[i] = exp(log_phi_row[i])
+
+    free(dig)
+
+
+cdef update_phi_fixed():
+    return
+
+
+cdef update_gamma(REAL_t * gamma, const REAL_t * phi, const REAL_t *lda_alpha,
+                  const int *word_counts, const int num_topics, const int doc_length):
+    """Update variational dirichlet parameters.
+
+    This operations is described in the original Blei LDA paper:
+    gamma = alpha + sum(phi), over every topic for every word.
+
+    Parameters
+    ----------
+    gamma: size of num_topics. int/out-parameter
+    
+    phi: size of (max_doc_len, num_topics). in-parameter
+    
+    lda_alpha: size of num_topics. in-parameter
+    
+    word_counts: size of doc_length. in-parameter
+    
+    num_topics: number of topics in the model 
+    
+    doc_length: length of the document
+
+    """
+    memcpy(gamma, lda_alpha, num_topics * sizeof(REAL_t))
+
+    cdef int i, k
+    # TODO BLAS matrix*vector
+    for i in range(doc_length):
+        for k in range(num_topics):
+            gamma[k] += phi[i * num_topics + k] * word_counts[i]
+
+
+cdef REAL_t compute_lda_lhood(REAL_t * lhood, const REAL_t *gamma, const REAL_t * phi, const REAL_t *log_phi,
+                       const REAL_t * lda_alpha, const REAL_t *lda_topics,
+                       int *word_counts, int *word_ids,
+                       const int num_topics, const int doc_length):
+    """Compute the log likelihood bound.
+    Parameters
+    ----------
+    gamma: size of num_topics
+    
+    lhood: size of num_topics + 1
+    
+    phi: size of (max_doc_len, num_topics). in-parameter
+    
+    log_phi: size of (max_doc_len, num_topics). in-parameter
+    
+    lda_alpha: size of num_topics. in-parameter
+
+    lda_topics: size of (vocab_len, num_topics). in-parameter
+    
+    word_counts: size of doc_len
+    
+    word_ids: size of doc_len 
+    
+    num_topics: number of topics in the model 
+    
+    doc_length: length of the document 
+
+    Returns
+    -------
+    float
+        The optimal lower bound for the true posterior using the approximate distribution.
+
+    """
+    cdef int i
+
+    cdef REAL_t gamma_sum = 0.0
+
+    for i in range(num_topics):
+        gamma_sum += gamma[i]
+
+    cdef REAL_t alpha_sum = 0.0
+    for i in range(num_topics):
+        alpha_sum += lda_alpha[i]
+
+    cdef REAL_t lhood_v = gammaln(alpha_sum) - gammaln(gamma_sum)
+    lhood[num_topics] = lhood_v
+
+    cdef REAL_t digsum = psi(gamma_sum)
+    cdef REAL_t lhood_term, e_log_theta_k
+
+    for k in range(num_topics):
+
+        e_log_theta_k = psi(gamma[k]) - digsum
+
+        lhood_term = \
+            (lda_alpha[k] - gamma[k]) * e_log_theta_k + \
+            gammaln(gamma[k]) - gammaln(lda_alpha[k])
+
+        # TODO: check why there's an IF
+        for i in range(doc_length):
+            if phi[i * num_topics + k] > 0:
+                lhood_term += \
+                    word_counts[i] * phi[i * num_topics + k] \
+                    *  (e_log_theta_k + lda_topics[word_ids[i] * num_topics + k]
+                        - log_phi[i * num_topics + k])
+
+        lhood[k] = lhood_term
+        lhood_v += lhood_term
+
+    return lhood_v
+
+cdef init_lda_post(REAL_t *gamma, REAL_t * phi, const int *word_counts,
+                   const REAL_t *lda_alpha,
+                   const int doc_length, const int num_topics):
+
+    """Initialize variational posterior. """
+
+    cdef int i, j
+
+    cdef int total = 0
+
+    # BLAS sum of absolute numbers
+    for i in range(doc_length):
+        total += word_counts[i]
+
+    cdef REAL_t init_value = lda_alpha[0] + float(total) / num_topics
+
+    for i in range(num_topics):
+        gamma[i] = init_value
+
+    init_value = 1.0 / num_topics
+
+    for i in range(doc_length):
+        phi_doc = phi + i * num_topics
+        for j in range(num_topics):
+            phi_doc[j] = init_value
+
+
+def fit_lda_post(self, doc_number, time, ldaseq, LDA_INFERENCE_CONVERGED=1e-8,
+                lda_inference_max_iter=25, g=None, g3_matrix=None, g4_matrix=None, g5_matrix=None):
+    """Posterior inference for lda.
+
+    Parameters
+    ----------
+
+    Returns
+    -------
+    float
+        The optimal lower bound for the true posterior using the approximate distribution.
+    """
+
+    cdef int i
+
+    ###############
+    # Setup C structures
+    ###############
+
+    cdef int num_topics = self.lda.num_topics
+    cdef int vocab_len = len(self.lda.id2word)
+
+    cdef int doc_length = len(self.doc)
+    cdef int max_doc_len = doc_length
+
+    # TODO adopt implementation to avoid memory allocation for every document.
+    #  E.g. create numpy array field of Python class. Be careful with the array size, it should be at least
+    #  the length of the longest document
+    cdef int * word_ids = <int *> malloc(doc_length * sizeof(int))
+    if word_ids == NULL:
+        raise
+    cdef int * word_counts = <int *> malloc(doc_length * sizeof(int))
+    if word_counts == NULL:
+        raise
+    # TODO Would it be better to create numpy array first?
+    for i in range(doc_length):
+        word_ids[i] = self.doc[i][0]
+        word_counts[i] = self.doc[i][0]
+
+    cdef REAL_t * gamma = <REAL_t *> (np.PyArray_DATA(self.gamma))
+    cdef REAL_t * phi = <REAL_t *> (np.PyArray_DATA(self.phi))
+    cdef REAL_t * log_phi = <REAL_t *> (np.PyArray_DATA(self.log_phi))
+    cdef REAL_t * lhood  = <REAL_t *> (np.PyArray_DATA(self.lhood))
+
+    cdef REAL_t * lda_topics = <REAL_t *> (np.PyArray_DATA(self.lda.topics))
+    cdef REAL_t * lda_alpha = <REAL_t *> (np.PyArray_DATA(self.lda.alpha))
+
+    ###############
+    # Finished setup of c structures here
+    ###############
+
+    init_lda_post(gamma, phi, word_counts, lda_alpha, doc_length, num_topics)
+
+    # sum of counts in a doc
+    cdef REAL_t total = sum(count for word_id, count in self.doc)
+
+    cdef REAL_t lhood_v = compute_lda_lhood(lhood, gamma, phi, log_phi,
+                                          lda_alpha, lda_topics, word_counts, word_ids,
+                                          num_topics, doc_length)
+
+    cdef REAL_t lhood_old = 0.0
+    cdef REAL_t converged = 0.0
+    cdef int iter_ = 0
+
+    # TODO Why first iteration starts here is done outside of the loop?
+    iter_ += 1
+    lhood_old = lhood_v
+    update_gamma(gamma, phi, lda_alpha, word_counts, num_topics, doc_length)
+
+    model = "DTM"
+
+    # if model == "DTM" or sslm is None:
+    update_phi(gamma, phi, log_phi, word_ids, lda_topics, num_topics, doc_length)
+
+    lhood_v = compute_lda_lhood(lhood, gamma, phi, log_phi,
+                              lda_alpha, lda_topics, word_counts, word_ids,
+                              num_topics, doc_length)
+
+    converged = abs((lhood_old - lhood_v) / (lhood_old * total))
+
+    while converged > LDA_INFERENCE_CONVERGED and iter_ <= lda_inference_max_iter:
+
+        iter_ += 1
+        lhood_old = lhood_v
+        update_gamma(gamma, phi, lda_alpha, word_counts, num_topics, doc_length)
+        model = "DTM"
+
+        update_phi(gamma, phi, log_phi, word_ids, lda_topics, num_topics, doc_length)
+
+        lhood_v = compute_lda_lhood(lhood, gamma, phi, log_phi,
+                              lda_alpha, lda_topics, word_counts, word_ids,
+                              num_topics, doc_length)
+
+        converged = np.fabs((lhood_old - lhood_v) / (lhood_old * total))
+
+    free(word_ids)
+    free(word_counts)
+
+    return lhood_v

gensim/models/ldaseq_sslm_inner.pxd

@@ -0,0 +1,27 @@
+cimport numpy as np
+ctypedef np.float64_t REAL_t
+
+
+
+cdef struct StateSpaceLanguageModelConfig:
+    int num_time_slices, vocab_len
+    REAL_t chain_variance, obs_variance
+
+    REAL_t * obs
+    REAL_t * mean
+    REAL_t * variance
+
+    REAL_t * fwd_mean
+    REAL_t * fwd_variance
+    REAL_t * zeta
+    REAL_t * e_log_prob
+    # T
+    REAL_t * word_counts
+    # T
+    REAL_t * totals
+
+    REAL_t * deriv
+    # T * (T+1)
+    REAL_t * mean_deriv_mtx
+    int word
+