Update code for building simlarity matrices.

similarities_helper.py

@@ -2,11 +2,67 @@ from pyspark.sql import Window
 from pyspark.sql import functions as f
 from enum import Enum
 from pyspark.mllib.linalg.distributed import CoordinateMatrix
+from tempfile import TemporaryDirectory
+import pyarrow
+import pyarrow.dataset as ds
+from scipy.sparse import csr_matrix
+import pandas as pd
+import numpy as np
 
 class tf_weight(Enum):
     MaxTF = 1
     Norm05 = 2
 
+def read_tfidf_matrix(path,term_colname):
+    term = term_colname
+    term_id = term + '_id'
+    term_id_new = term + '_id_new'
+
+    dataset = ds.dataset(path,format='parquet')
+    entries = dataset.to_table(columns=['tf_idf','subreddit_id_new',term_id_new]).to_pandas()
+    return(csr_matrix((entries.tf_idf,(entries[term_id_new]-1, entries.subreddit_id_new-1))))
+    
+def column_similarities(mat):
+    norm = np.matrix(np.power(mat.power(2).sum(axis=0),0.5,dtype=np.float32))
+    mat = mat.multiply(1/norm)
+    sims = mat.T @ mat
+    return(sims)
+
+
+def prep_tfidf_entries(tfidf, term_colname, min_df, included_subreddits):
+    term = term_colname
+    term_id = term + '_id'
+    term_id_new = term + '_id_new'
+
+    if min_df is None:
+        min_df = 0.1 * len(included_subreddits)
+
+    tfidf = tfidf.filter(f.col("subreddit").isin(included_subreddits))
+
+    # reset the subreddit ids
+    sub_ids = tfidf.select('subreddit_id').distinct()
+    sub_ids = sub_ids.withColumn("subreddit_id_new",f.row_number().over(Window.orderBy("subreddit_id")))
+    tfidf = tfidf.join(sub_ids,'subreddit_id')
+
+    # only use terms in at least min_df included subreddits
+    new_count = tfidf.groupBy(term_id).agg(f.count(term_id).alias('new_count'))
+#    new_count = new_count.filter(f.col('new_count') >= min_df)
+    tfidf = tfidf.join(new_count,term_id,how='inner')
+    
+    # reset the term ids
+    term_ids = tfidf.select([term_id]).distinct()
+    term_ids = term_ids.withColumn(term_id_new,f.row_number().over(Window.orderBy(term_id)))
+    tfidf = tfidf.join(term_ids,term_id)
+
+    tfidf = tfidf.withColumnRenamed("tf_idf","tf_idf_old")
+    # tfidf = tfidf.withColumnRenamed("idf","idf_old")
+    # tfidf = tfidf.withColumn("idf",f.log(25000/f.col("count")))
+    tfidf = tfidf.withColumn("tf_idf", (tfidf.relative_tf * tfidf.idf).cast('float'))
+    
+    tempdir =TemporaryDirectory(suffix='.parquet',prefix='term_tfidf_entries',dir='.')
+    
+    tfidf.write.parquet(tempdir.name,mode='overwrite',compression='snappy')
+    return tempdir
 
 def cosine_similarities(tfidf, term_colname, min_df, included_subreddits, similarity_threshold):
     term = term_colname

term_cosine_similarity.py

@@ -8,38 +8,23 @@ import pandas as pd
 import fire
 from itertools import islice
 from pathlib import Path
-from similarities_helper import cosine_similarities
+from similarities_helper import cosine_similarities, prep_tfidf_entries, read_tfidf_matrix, column_similarities
-
+import scipy
-spark = SparkSession.builder.getOrCreate()
+# outfile='test_similarities_500.feather';
-conf = spark.sparkContext.getConf()
+# min_df = None;
-
+# included_subreddits=None; topN=100; exclude_phrases=True;
-# outfile = '/gscratch/comdata/users/nathante/test_similarities_500.feather'; min_df = None; included_subreddits=None; similarity_threshold=0;
-def term_cosine_similarities(outfile, min_df = None, included_subreddits=None, similarity_threshold=0, topN=500, exclude_phrases=True):
-    '''
-    Compute similarities between subreddits based on tfi-idf vectors of comment texts 
-    
-    included_subreddits : string
-        Text file containing a list of subreddits to include (one per line) if included_subreddits is None then do the top 500 subreddits
-
-    similarity_threshold : double (default = 0)
-        set > 0 for large numbers of subreddits to get an approximate solution using the DIMSUM algorithm
-https://stanford.edu/~rezab/papers/dimsum.pdf. If similarity_threshold=0 we get an exact solution using an O(N^2) algorithm.
-
-    min_df : int (default = 0.1 * (number of included_subreddits)
-         exclude terms that appear in fewer than this number of documents.
-
-    outfile: string
-         where to output csv and feather outputs
-'''
 
+def term_cosine_similarities(outfile, min_df = None, included_subreddits=None, topN=500, exclude_phrases=False):
+    spark = SparkSession.builder.getOrCreate()
+    conf = spark.sparkContext.getConf()
     print(outfile)
     print(exclude_phrases)
 
     tfidf = spark.read.parquet('/gscratch/comdata/users/nathante/subreddit_tfidf.parquet')
 
     if included_subreddits is None:
-        included_subreddits = list(islice(open("/gscratch/comdata/users/nathante/cdsc-reddit/top_25000_subs_by_comments.txt"),topN))
+        rankdf = pd.read_csv("/gscratch/comdata/users/nathante/cdsc-reddit/subreddits_by_num_comments.csv")
-        included_subreddits = {s.strip('\n') for s in included_subreddits}
+        included_subreddits = set(rankdf.loc[rankdf.comments_rank <= topN,'subreddit'].values)
 
     else:
         included_subreddits = set(open(included_subreddits))
@@ -47,7 +32,23 @@ https://stanford.edu/~rezab/papers/dimsum.pdf. If similarity_threshold=0 we get
     if exclude_phrases == True:
         tfidf = tfidf.filter(~f.col(term).contains("_"))
 
-    sim_dist, tfidf = cosine_similarities(tfidf, 'term', min_df, included_subreddits, similarity_threshold)
+    print("creating temporary parquet with matrix indicies")
+    tempdir = prep_tfidf_entries(tfidf, 'term', min_df, included_subreddits)
+    tfidf = spark.read.parquet(tempdir.name)
+    subreddit_names = tfidf.select(['subreddit','subreddit_id_new']).distinct().toPandas()
+    subreddit_names = subreddit_names.sort_values("subreddit_id_new")
+    subreddit_names['subreddit_id_new'] = subreddit_names['subreddit_id_new'] - 1
+    spark.stop()
+
+    print("loading matrix")
+    mat = read_tfidf_matrix(tempdir.name,'term')
+    print('computing similarities')
+    sims = column_similarities(mat)
+    del mat
+    
+    sims = pd.DataFrame(sims.todense())
+    sims = sims.rename({i:sr for i, sr in enumerate(subreddit_names.subreddit.values)},axis=1)
+    sims['subreddit'] = subreddit_names.subreddit.values
 
     p = Path(outfile)
 
@@ -55,25 +56,72 @@ https://stanford.edu/~rezab/papers/dimsum.pdf. If similarity_threshold=0 we get
     output_csv =  Path(str(p).replace("".join(p.suffixes), ".csv"))
     output_parquet =  Path(str(p).replace("".join(p.suffixes), ".parquet"))
 
-    sim_dist.entries.toDF().write.parquet(str(output_parquet),mode='overwrite',compression='snappy')
+    sims.to_feather(outfile)
+    tempdir.cleanup()
+    path = "term_tfidf_entriesaukjy5gv.parquet"
     
-    #instead of toLocalMatrix() why not read as entries and put strait into numpy
-    sim_entries = pd.read_parquet(output_parquet)
 
-    df = tfidf.select('subreddit','subreddit_id_new').distinct().toPandas()
+# outfile = '/gscratch/comdata/users/nathante/test_similarities_500.feather'; min_df = None; included_subreddits=None; similarity_threshold=0;
-    spark.stop()
+# def term_cosine_similarities(outfile, min_df = None, included_subreddits=None, similarity_threshold=0, topN=500, exclude_phrases=True):
-    df['subreddit_id_new'] = df['subreddit_id_new'] - 1
+#     '''
-    df = df.sort_values('subreddit_id_new').reset_index(drop=True)
+#     Compute similarities between subreddits based on tfi-idf vectors of comment texts 
-    df = df.set_index('subreddit_id_new')
+    
+#     included_subreddits : string
+#         Text file containing a list of subreddits to include (one per line) if included_subreddits is None then do the top 500 subreddits
 
-    similarities = sim_entries.join(df, on='i')
+#     similarity_threshold : double (default = 0)
-    similarities = similarities.rename(columns={'subreddit':"subreddit_i"})
+#         set > 0 for large numbers of subreddits to get an approximate solution using the DIMSUM algorithm
-    similarities = similarities.join(df, on='j')
+# https://stanford.edu/~rezab/papers/dimsum.pdf. If similarity_threshold=0 we get an exact solution using an O(N^2) algorithm.
-    similarities = similarities.rename(columns={'subreddit':"subreddit_j"})
 
-    similarities.to_feather(output_feather)
+#     min_df : int (default = 0.1 * (number of included_subreddits)
-    similarities.to_csv(output_csv)
+#          exclude terms that appear in fewer than this number of documents.
-    return similarities
+
+#     outfile: string
+#          where to output csv and feather outputs
+# '''
+
+#     print(outfile)
+#     print(exclude_phrases)
+
+#     tfidf = spark.read.parquet('/gscratch/comdata/users/nathante/subreddit_tfidf.parquet')
+
+#     if included_subreddits is None:
+#         included_subreddits = list(islice(open("/gscratch/comdata/users/nathante/cdsc-reddit/top_25000_subs_by_comments.txt"),topN))
+#         included_subreddits = {s.strip('\n') for s in included_subreddits}
+
+#     else:
+#         included_subreddits = set(open(included_subreddits))
+
+#     if exclude_phrases == True:
+#         tfidf = tfidf.filter(~f.col(term).contains("_"))
+
+#     sim_dist, tfidf = cosine_similarities(tfidf, 'term', min_df, included_subreddits, similarity_threshold)
+
+#     p = Path(outfile)
+
+#     output_feather =  Path(str(p).replace("".join(p.suffixes), ".feather"))
+#     output_csv =  Path(str(p).replace("".join(p.suffixes), ".csv"))
+#     output_parquet =  Path(str(p).replace("".join(p.suffixes), ".parquet"))
+
+#     sim_dist.entries.toDF().write.parquet(str(output_parquet),mode='overwrite',compression='snappy')
+    
+#     #instead of toLocalMatrix() why not read as entries and put strait into numpy
+#     sim_entries = pd.read_parquet(output_parquet)
+
+#     df = tfidf.select('subreddit','subreddit_id_new').distinct().toPandas()
+#     spark.stop()
+#     df['subreddit_id_new'] = df['subreddit_id_new'] - 1
+#     df = df.sort_values('subreddit_id_new').reset_index(drop=True)
+#     df = df.set_index('subreddit_id_new')
+
+#     similarities = sim_entries.join(df, on='i')
+#     similarities = similarities.rename(columns={'subreddit':"subreddit_i"})
+#     similarities = similarities.join(df, on='j')
+#     similarities = similarities.rename(columns={'subreddit':"subreddit_j"})
+
+#     similarities.to_feather(output_feather)
+#     similarities.to_csv(output_csv)
+#     return similarities
     
 if __name__ == '__main__':
     fire.Fire(term_cosine_similarities)

top_subreddits_by_comments.py

@@ -0,0 +1,30 @@
+from pyspark.sql import functions as f
+from pyspark.sql import SparkSession
+from pyspark.sql import Window
+from pyspark.mllib.linalg.distributed import RowMatrix, CoordinateMatrix
+import numpy as np
+import pyarrow
+import pandas as pd
+import fire
+from itertools import islice
+from pathlib import Path
+from similarities_helper import cosine_similarities
+
+spark = SparkSession.builder.getOrCreate()
+conf = spark.sparkContext.getConf()
+
+df = spark.read.parquet("/gscratch/comdata/output/reddit_comments_by_subreddit.parquet")
+
+# remove /u/ pages
+df = df.filter(~df.subreddit.like("u_%"))
+
+df = df.groupBy('subreddit').agg(f.count('id').alias("n_comments"))
+
+win = Window.orderBy(f.col('n_comments').desc())
+df = df.withColumn('comments_rank',f.rank().over(win))
+
+df = df.toPandas()
+
+df = df.sort_values("n_comments")
+
+df.to_csv('/gscratch/comdata/users/nathante/cdsc-reddit/subreddits_by_num_comments.csv',index=False)