fixed pca and tlda tests and added demo scripts

examples/large_scale_demo.py

@@ -0,0 +1,344 @@
+# basic imports
+import numpy as np
+import os
+from pathlib import Path
+import gc
+import pandas as pd
+import time
+import pickle
+
+
+# Import stopwords
+import nltk
+nltk.download('stopwords')
+from nltk.corpus import stopwords
+
+# Cuda imports
+import cupy as cp
+import cudf
+from cudf import Series
+from cuml.feature_extraction.text import CountVectorizer
+from cuml.preprocessing.text.stem import PorterStemmer
+
+# Import TensorLy
+import tensorly as tl
+
+# Import utility functions from other files
+from tlda.tlda_wrapper import TLDA
+from tlda.file_operations import get_files_in_dir
+
+# Root Filepath -- can modify
+ROOT_DIR = "/tlda/data"
+
+# Data Relative Paths -- can modify
+INDIR = "MeTooMonthCleaned/"
+
+# Output Relative paths -- do not change
+X_MAT_FILEPATH_PREFIX = "x_mat/"
+X_FILEPATH = "X_full.obj"
+X_DF_FILEPATH = "X_df.obj"
+X_LST_FILEPATH = "X_lst.obj"
+CORPUS_FILEPATH_PREFIX = "corpus/"
+GENSIM_CORPUS_FILEPATH = "corpus.obj"
+COUNTVECTOR_FILEPATH = "countvec.obj"
+TLDA_FILEPATH = "tlda.obj"
+VOCAB_FILEPATH = "vocab.csv"
+EXISTING_VOCAB_FILEPATH = "vocab.obj"
+TOPIC_FILEPATH_PREFIX   = 'predicted_topics/'
+DOCUMENT_TOPIC_FILEPATH = 'dtm.csv'
+COHERENCE_FILEPATH = 'coherence.obj'
+DOCUMENT_TOPIC_FILEPATH_TOT = 'dtm_df.csv'
+OUT_ID_DATA_PREFIX = 'ids/'
+TOP_WORDS_FILEPATH ='top_words.csv'
+
+# Device settings
+backend="cupy"
+tl.set_backend(backend)
+device = 'cuda'
+porter = PorterStemmer()
+
+
+def basic_clean(df):
+    df['tweets'] = df['tweets'].astype('str')
+    df = df.drop_duplicates(keep="first")
+    return df
+
+
+def partial_fit(self , data):
+    if(hasattr(self , 'vocabulary_')):
+        vocab = self.vocabulary_ # series
+    else:
+        vocab = Series()
+    self.fit(data)
+    vocab = vocab.append(self.vocabulary_)
+    self.vocabulary_ = vocab.unique()
+
+
+# declare the stop words
+# potentially add extra stop words depending on the application dataset
+stop_words = (stopwords.words('english'))
+added_words = []
+
+# set stop words and countvectorizer method
+stop_words= list(np.append(stop_words,added_words))
+CountVectorizer.partial_fit = partial_fit
+
+# define function with no preprocessing
+def custom_preprocessor(doc):
+    return doc
+
+
+def fit_topics(num_tops, curr_dir, alpha_0 = 0.01, learning_rate = 0.0004, theta_param = 5.005, ortho_loss_param = 1000, smoothing = 1e-5, initialize_first_docs = False, n_eigenvec = None):
+
+    # make final directories for outputs
+    save_dir = os.path.join(ROOT_DIR, curr_dir)
+    if not os.path.exists(save_dir):
+        os.makedirs(save_dir)
+
+    # initialize RAPIDS CountVectorizer
+    countvec = CountVectorizer( stop_words = stop_words,
+                                lowercase = True,
+                                ngram_range = (1, 2),
+                                preprocessor = custom_preprocessor,
+                                max_df = 0.5,
+                                min_df = 0.00125)
+
+    # set directory for saving CountVectorizer and TLDA
+    eigenvec_str = "_n_eigenvec_" + (str(n_eigenvec) if n_eigenvec is not None else "None")
+    exp_save_dir = os.path.join(save_dir, "num_tops_" + str(num_tops) + "_alpha0_" + str(alpha_0) + "_learning_rate_" + str(learning_rate) + "_theta_" + str(theta_param) + "_orthogonality_" + str(ortho_loss_param) + "_initialize_first_docs_" + str(initialize_first_docs) + eigenvec_str + "/")
+    if not os.path.exists(exp_save_dir):
+        os.makedirs(exp_save_dir)
+
+    # DEFAULT PARAMS -- Grid search according to dataset
+    batch_size_pca  = 100000
+    batch_size_grad = 80000
+    n_iter_train = 200
+    n_iter_test = 10
+
+    #SET SEED
+    seed = 57
+
+    # Program controls -- decide which portions to run
+    if os.path.exists(save_dir + "/" + COUNTVECTOR_FILEPATH):
+        first_run = 1
+    vocab_build    = first_run
+    save_files     = first_run
+    stgd           = 1
+    recover_top_words = 1
+
+    # Start
+    print("\n\nSTART...")
+
+    # Set files to read
+    inDir = os.path.join(ROOT_DIR, INDIR)
+    dl = sorted(get_files_in_dir(inDir))
+
+    # Build the vocabulary
+    if vocab_build == 1:
+        if not os.path.exists(save_dir + "/" + EXISTING_VOCAB_FILEPATH):
+            for i, f in enumerate(dl):
+                print("Beginning vocabulary build: " + f)
+                path_in      = os.path.join(inDir,f)
+
+                mempool = cp.get_default_memory_pool()
+                mempool.free_all_blocks()
+                pinned_mempool = cp.get_default_pinned_memory_pool()
+                pinned_mempool.free_all_blocks()
+
+                # read in dataframe
+                df = pd.read_csv(path_in, names = ['tweets'])
+
+                # basic preprocessing
+                mask = df['tweets'].str.len() > 10
+                df   = df.loc[mask]
+                df   = cudf.from_pandas(df)
+                df   = basic_clean(df)
+
+                mempool = cp.get_default_memory_pool()
+                mempool.free_all_blocks()
+                pinned_mempool = cp.get_default_pinned_memory_pool()
+                pinned_mempool.free_all_blocks()
+                gc.collect()
+
+                # add vocabulary from current file to CountVectorizer vocabulary
+                countvec.partial_fit(df['tweets'])
+                print("End " + f)
+
+                # count rows of data
+                num_data_rows += len(df.index)
+                print(num_data_rows)
+                print(len(df.index))
+        else:
+            countvec.vocabulary_ = countvec.vocabulary
+            vocab = len(countvec.vocabulary_)
+
+        # Save fitted CountVectorizer and vocabulary
+        pickle.dump(countvec, open(os.path.join(save_dir, COUNTVECTOR_FILEPATH), 'wb'))
+        vocab = len(countvec.vocabulary_)
+        df_voc = cudf.DataFrame({'words':countvec.vocabulary_})
+        df_voc.to_csv(save_dir + "/" + VOCAB_FILEPATH)
+        print("right after countvec partial fit vocab\n\n\n: ", vocab)
+
+        # make directories to save:
+        #  - X matrices
+        #  - corpus (only needed if computing coherence)
+        x_mat_dir = os.path.join(save_dir, X_MAT_FILEPATH_PREFIX)
+        if not os.path.exists(x_mat_dir):
+            os.makedirs(x_mat_dir)
+        corpus_dir = os.path.join(save_dir, CORPUS_FILEPATH_PREFIX)
+        if not os.path.exists(corpus_dir):
+            os.makedirs(corpus_dir)
+
+
+        # transform X matrices with fitted CountVectorizer and save to disk
+        transform_time = 0.0
+        if save_files == 1:
+            for f in dl:
+                print("Beginning CountVectorizer transform: " + f)
+                path_in  = os.path.join(inDir,f)
+
+                mempool = cp.get_default_memory_pool()
+                mempool.free_all_blocks()
+                pinned_mempool = cp.get_default_pinned_memory_pool()
+                pinned_mempool.free_all_blocks()
+
+                # read in dataframe
+                df = pd.read_csv(path_in, names = ['tweets'])
+
+                # basic preprocessing
+                mask = df['tweets'].str.len() > 10
+                df   = df.loc[mask]
+                df   = cudf.from_pandas(df)
+                df   = basic_clean(df)
+
+                mempool = cp.get_default_memory_pool()
+                mempool.free_all_blocks()
+                gc.collect()
+
+                # transform data from current file
+                t1 = time.time()
+                corpus = countvec.transform(df['tweets'])
+                t2 = time.time()
+                transform_time += t2 - t1
+                X_batch = tl.tensor(corpus.toarray())
+
+                # save current X matrix and corpus to disk
+                pickle.dump(
+                    (X_batch),
+                    open(x_mat_dir + Path(f).stem + '.obj','wb')
+                )
+                pickle.dump(
+                    (corpus),
+                    open(corpus_dir + Path(f).stem + '.obj','wb')
+                )
+                del X_batch
+                del corpus
+                print("End " + f)
+                del df
+                del mask
+
+        gc.collect()
+
+    print("Transform Time:" + str(transform_time))
+
+
+    # initialize TLDA using parameters from above
+    tlda = TLDA(
+        num_tops, alpha_0, n_iter_train, n_iter_test,learning_rate,
+        pca_batch_size = batch_size_pca, third_order_cumulant_batch = batch_size_grad,
+        gamma_shape = 1.0, smoothing = smoothing, theta=theta_param, ortho_loss_criterion = ortho_loss_param, random_seed = seed,
+        n_eigenvec = n_eigenvec,
+    )
+
+    tot_tlda_time = 0.0
+    if stgd == 1:
+        # keep track of iterations
+        i = 0
+
+        t1 = time.time()
+        for f in dl:
+            mempool = cp.get_default_memory_pool()
+            mempool.free_all_blocks()
+            pinned_mempool = cp.get_default_pinned_memory_pool()
+            pinned_mempool.free_all_blocks()
+
+            print("Beginning TLDA: " + f)
+
+            # load saved X matrix batch from disk
+            X_batch = pickle.load(
+                        open(save_dir + X_MAT_FILEPATH_PREFIX + Path(f).stem + '.obj','rb')
+                    )
+
+            mempool = cp.get_default_memory_pool()
+            mempool.free_all_blocks()
+            pinned_mempool = cp.get_default_pinned_memory_pool()
+            pinned_mempool.free_all_blocks()
+            gc.collect()
+
+
+            t3 = time.time()
+            # fit tensor LDA fully online
+            if initialize_first_docs and i == 0:
+                # fully fit tensor LDA on first batch
+                tlda.fit(X_batch)
+            else:
+                # partial fit tensor LDA on remaining batches
+                tlda.partial_fit_online(X_batch)
+
+        t4 = time.time()
+        print("New fit time" + str(t4-t3))
+        tot_tlda_time += t4-t3
+
+        del X_batch
+        gc.collect()
+        mempool = cp.get_default_memory_pool()
+        mempool.free_all_blocks()
+        pinned_mempool = cp.get_default_pinned_memory_pool()
+        pinned_mempool.free_all_blocks()
+
+        i += 1
+    else:
+        tlda = pickle.load(open(exp_save_dir + TLDA_FILEPATH,'rb'))
+
+
+    # save top words in each topic
+    if recover_top_words == 1:
+        n_top_words = 100
+
+        top_words_df = cudf.DataFrame({})
+        for k in range(0,num_tops):
+            t_n_indices   =  tlda.unwhitened_factors_[:,k].argsort()[:-n_top_words - 1:-1]
+            top_words_LDA = countvec.vocabulary_[t_n_indices]
+            top_words_df['words_'+str(k)] = top_words_LDA.reset_index(drop=True)
+
+
+        top_words_df.to_csv(exp_save_dir + TOP_WORDS_FILEPATH)
+        del top_words_df
+
+    gc.collect()
+    mempool = cp.get_default_memory_pool()
+    mempool.free_all_blocks()
+    pinned_mempool = cp.get_default_pinned_memory_pool()
+    pinned_mempool.free_all_blocks()
+
+
+def main():
+    curr_dir = "metoo_evaluation_initialized_paper_exps/"
+
+    # set parameters
+    num_tops = 10
+    alpha_0  = 0.01
+    lr = 0.0001
+    pca_dim = 40
+
+    # run method to fit topics and save top words in each topic
+    fit_topics(
+        num_tops = num_tops,
+        curr_dir = curr_dir,
+        alpha_0 = alpha_0,
+        learning_rate = lr,
+        n_eigenvec = pca_dim
+    )
+
+if __name__ == "__main__":
+    main()