from pyspark.sql import Window
from pyspark.sql import functions as f
from enum import Enum
+ from multiprocessing import cpu_count, Pool
from pyspark.mllib.linalg.distributed import CoordinateMatrix
from tempfile import TemporaryDirectory
import pyarrow
import pyarrow.dataset as ds
+ from sklearn.metrics import pairwise_distances
from scipy.sparse import csr_matrix, issparse
+ from sklearn.decomposition import TruncatedSVD
import pandas as pd
import numpy as np
import pathlib
MaxTF = 1
Norm05 = 2
- infile = "/gscratch/comdata/output/reddit_similarity/tfidf_weekly/comment_authors.parquet"
+ infile = "/gscratch/comdata/output/reddit_similarity/tfidf_weekly/comment_terms.parquet"
+ cache_file = "/gscratch/comdata/users/nathante/cdsc_reddit/similarities/term_tfidf_entries_bak.parquet"
- def reindex_tfidf_time_interval(infile, term_colname, min_df=None, max_df=None, included_subreddits=None, topN=500, exclude_phrases=False, from_date=None, to_date=None):
- term = term_colname
- term_id = term + '_id'
- term_id_new = term + '_id_new'
-
- spark = SparkSession.builder.getOrCreate()
- conf = spark.sparkContext.getConf()
- print(exclude_phrases)
- tfidf_weekly = spark.read.parquet(infile)
-
- # create the time interval
- if from_date is not None:
- if type(from_date) is str:
- from_date = datetime.fromisoformat(from_date)
-
- tfidf_weekly = tfidf_weekly.filter(tfidf_weekly.week >= from_date)
-
- if to_date is not None:
- if type(to_date) is str:
- to_date = datetime.fromisoformat(to_date)
- tfidf_weekly = tfidf_weekly.filter(tfidf_weekly.week < to_date)
-
- tfidf = tfidf_weekly.groupBy(["subreddit","week", term_id, term]).agg(f.sum("tf").alias("tf"))
- tfidf = _calc_tfidf(tfidf, term_colname, tf_weight.Norm05)
- tempdir = prep_tfidf_entries(tfidf, term_colname, min_df, max_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
- return(tempdir, subreddit_names)
-
- def reindex_tfidf(infile, term_colname, min_df=None, max_df=None, included_subreddits=None, topN=500, exclude_phrases=False):
- spark = SparkSession.builder.getOrCreate()
- conf = spark.sparkContext.getConf()
- print(exclude_phrases)
+ def termauthor_tfidf(term_tfidf_callable, author_tfidf_callable):
+
- tfidf = spark.read.parquet(infile)
+ # subreddits missing after this step don't have any terms that have a high enough idf
+ # try rewriting without merges
+ def reindex_tfidf(infile, term_colname, min_df=None, max_df=None, included_subreddits=None, topN=500, week=None, from_date=None, to_date=None, rescale_idf=True, tf_family=tf_weight.MaxTF):
+ print("loading tfidf", flush=True)
+ tfidf_ds = ds.dataset(infile)
if included_subreddits is None:
included_subreddits = select_topN_subreddits(topN)
else:
- included_subreddits = set(open(included_subreddits))
+ included_subreddits = set(map(str.strip,map(str.lower,open(included_subreddits))))
- if exclude_phrases == True:
- tfidf = tfidf.filter(~f.col(term_colname).contains("_"))
+ ds_filter = ds.field("subreddit").isin(included_subreddits)
+
+ if min_df is not None:
+ ds_filter &= ds.field("count") >= min_df
+
+ if max_df is not None:
+ ds_filter &= ds.field("count") <= max_df
+
+ if week is not None:
+ ds_filter &= ds.field("week") == week
+
+ if from_date is not None:
+ ds_filter &= ds.field("week") >= from_date
- print("creating temporary parquet with matrix indicies")
- tempdir = prep_tfidf_entries(tfidf, term_colname, min_df, max_df, included_subreddits)
+ if to_date is not None:
+ ds_filter &= ds.field("week") <= to_date
- tfidf = spark.read.parquet(tempdir.name)
- subreddit_names = tfidf.select(['subreddit','subreddit_id_new']).distinct().toPandas()
+ term = term_colname
+ term_id = term + '_id'
+ term_id_new = term + '_id_new'
+
+ projection = {
+ 'subreddit_id':ds.field('subreddit_id'),
+ term_id:ds.field(term_id),
+ 'relative_tf':ds.field("relative_tf").cast('float32')
+ }
+
+ if not rescale_idf:
+ projection = {
+ 'subreddit_id':ds.field('subreddit_id'),
+ term_id:ds.field(term_id),
+ 'relative_tf':ds.field('relative_tf').cast('float32'),
+ 'tf_idf':ds.field('tf_idf').cast('float32')}
+
+ tfidf_ds = ds.dataset(infile)
+
+ df = tfidf_ds.to_table(filter=ds_filter,columns=projection)
+
+ df = df.to_pandas(split_blocks=True,self_destruct=True)
+ print("assigning indexes",flush=True)
+ df['subreddit_id_new'] = df.groupby("subreddit_id").ngroup()
+ grouped = df.groupby(term_id)
+ df[term_id_new] = grouped.ngroup()
+
+ if rescale_idf:
+ print("computing idf", flush=True)
+ df['new_count'] = grouped[term_id].transform('count')
+ N_docs = df.subreddit_id_new.max() + 1
+ df['idf'] = np.log(N_docs/(1+df.new_count),dtype='float32') + 1
+ if tf_family == tf_weight.MaxTF:
+ df["tf_idf"] = df.relative_tf * df.idf
+ else: # tf_fam = tf_weight.Norm05
+ df["tf_idf"] = (0.5 + 0.5 * df.relative_tf) * df.idf
+
+ print("assigning names")
+ subreddit_names = tfidf_ds.to_table(filter=ds_filter,columns=['subreddit','subreddit_id'])
+ batches = subreddit_names.to_batches()
+
+ with Pool(cpu_count()) as pool:
+ chunks = pool.imap_unordered(pull_names,batches)
+ subreddit_names = pd.concat(chunks,copy=False).drop_duplicates()
+
+ subreddit_names = subreddit_names.set_index("subreddit_id")
+ new_ids = df.loc[:,['subreddit_id','subreddit_id_new']].drop_duplicates()
+ new_ids = new_ids.set_index('subreddit_id')
+ subreddit_names = subreddit_names.join(new_ids,on='subreddit_id').reset_index()
+ subreddit_names = subreddit_names.drop("subreddit_id",1)
subreddit_names = subreddit_names.sort_values("subreddit_id_new")
- subreddit_names['subreddit_id_new'] = subreddit_names['subreddit_id_new'] - 1
- spark.stop()
- return (tempdir, subreddit_names)
+ return(df, subreddit_names)
+ def pull_names(batch):
+ return(batch.to_pandas().drop_duplicates())
- def similarities(infile, simfunc, term_colname, outfile, min_df=None, max_df=None, included_subreddits=None, topN=500, exclude_phrases=False, from_date=None, to_date=None, tfidf_colname='tf_idf'):
+ def similarities(infile, simfunc, term_colname, outfile, min_df=None, max_df=None, included_subreddits=None, topN=500, from_date=None, to_date=None, tfidf_colname='tf_idf'):
'''
tfidf_colname: set to 'relative_tf' to use normalized term frequency instead of tf-idf, which can be useful for author-based similarities.
'''
- if from_date is not None or to_date is not None:
- tempdir, subreddit_names = reindex_tfidf_time_interval(infile, term_colname=term_colname, min_df=min_df, max_df=max_df, included_subreddits=included_subreddits, topN=topN, exclude_phrases=False, from_date=from_date, to_date=to_date)
-
- else:
- tempdir, subreddit_names = reindex_tfidf(infile, term_colname=term_colname, min_df=min_df, max_df=max_df, included_subreddits=included_subreddits, topN=topN, exclude_phrases=False)
-
- print("loading matrix")
- # mat = read_tfidf_matrix("term_tfidf_entries7ejhvnvl.parquet", term_colname)
- mat = read_tfidf_matrix(tempdir.name, term_colname, tfidf_colname)
- print(f'computing similarities on mat. mat.shape:{mat.shape}')
- print(f"size of mat is:{mat.data.nbytes}")
- sims = simfunc(mat)
- del mat
- if issparse(sims):
- sims = sims.todense()
+ def proc_sims(sims, outfile):
+ if issparse(sims):
+ sims = sims.todense()
- print(f"shape of sims:{sims.shape}")
- print(f"len(subreddit_names.subreddit.values):{len(subreddit_names.subreddit.values)}")
- sims = pd.DataFrame(sims)
- sims = sims.rename({i:sr for i, sr in enumerate(subreddit_names.subreddit.values)}, axis=1)
- sims['subreddit'] = subreddit_names.subreddit.values
+ print(f"shape of sims:{sims.shape}")
+ print(f"len(subreddit_names.subreddit.values):{len(subreddit_names.subreddit.values)}",flush=True)
+ sims = pd.DataFrame(sims)
+ 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)
+ 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"))
+ 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"))
+ outfile.parent.mkdir(exist_ok=True, parents=True)
- sims.to_feather(outfile)
- tempdir.cleanup()
+ sims.to_feather(outfile)
- def read_tfidf_matrix_weekly(path, term_colname, week, tfidf_colname='tf_idf'):
term = term_colname
term_id = term + '_id'
term_id_new = term + '_id_new'
- dataset = ds.dataset(path,format='parquet')
- entries = dataset.to_table(columns=[tfidf_colname,'subreddit_id_new', term_id_new],filter=ds.field('week')==week).to_pandas()
- return(csr_matrix((entries[tfidf_colname], (entries[term_id_new]-1, entries.subreddit_id_new-1))))
+ entries, subreddit_names = reindex_tfidf(infile, term_colname=term_colname, min_df=min_df, max_df=max_df, included_subreddits=included_subreddits, topN=topN,from_date=from_date,to_date=to_date)
+ mat = csr_matrix((entries[tfidf_colname],(entries[term_id_new], entries.subreddit_id_new)))
- def read_tfidf_matrix(path, term_colname, tfidf_colname='tf_idf'):
- term = term_colname
- term_id = term + '_id'
- term_id_new = term + '_id_new'
- dataset = ds.dataset(path,format='parquet')
- print(f"tfidf_colname:{tfidf_colname}")
- entries = dataset.to_table(columns=[tfidf_colname, 'subreddit_id_new',term_id_new]).to_pandas()
- return(csr_matrix((entries[tfidf_colname],(entries[term_id_new]-1, entries.subreddit_id_new-1))))
-
+ print("loading matrix")
+
+ # mat = read_tfidf_matrix("term_tfidf_entries7ejhvnvl.parquet", term_colname)
+
+ print(f'computing similarities on mat. mat.shape:{mat.shape}')
+ print(f"size of mat is:{mat.data.nbytes}",flush=True)
+ sims = simfunc(mat)
+ del mat
+
+ if hasattr(sims,'__next__'):
+ for simmat, name in sims:
+ proc_sims(simmat, Path(outfile)/(str(name) + ".feather"))
+ else:
+ proc_sims(simmat, outfile)
def write_weekly_similarities(path, sims, week, names):
sims['week'] = week
p = pathlib.Path(path)
if not p.is_dir():
- p.mkdir()
+ p.mkdir(exist_ok=True,parents=True)
# reformat as a pairwise list
- sims = sims.melt(id_vars=['subreddit','week'],value_vars=names.subreddit.values)
+ sims = sims.melt(id_vars=['_subreddit','week'],value_vars=names.subreddit.values)
sims.to_parquet(p / week.isoformat())
def column_overlaps(mat):
return intersection / den
- 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_weekly(tfidf, term_colname, min_df, max_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('count') >= min_df)
- if max_df is not None:
- tfidf = tfidf.filter(f.col('count') <= max_df)
-
- tfidf = tfidf.filter(f.col("subreddit").isin(included_subreddits))
-
- # we might not have the same terms or subreddits each week, so we need to make unique ids for each week.
- sub_ids = tfidf.select(['subreddit_id','week']).distinct()
- sub_ids = sub_ids.withColumn("subreddit_id_new",f.row_number().over(Window.partitionBy('week').orderBy("subreddit_id")))
- tfidf = tfidf.join(sub_ids,['subreddit_id','week'])
-
- # only use terms in at least min_df included subreddits in a given week
- new_count = tfidf.groupBy([term_id,'week']).agg(f.count(term_id).alias('new_count'))
- tfidf = tfidf.join(new_count,[term_id,'week'],how='inner')
-
- # reset the term ids
- term_ids = tfidf.select([term_id,'week']).distinct()
- term_ids = term_ids.withColumn(term_id_new,f.row_number().over(Window.partitionBy('week').orderBy(term_id)))
- tfidf = tfidf.join(term_ids,[term_id,'week'])
-
- tfidf = tfidf.withColumnRenamed("tf_idf","tf_idf_old")
- tfidf = tfidf.withColumn("tf_idf", (tfidf.relative_tf * tfidf.idf).cast('float'))
-
- tempdir =TemporaryDirectory(suffix='.parquet',prefix='term_tfidf_entries',dir='.')
-
- tfidf = tfidf.repartition('week')
-
- tfidf.write.parquet(tempdir.name,mode='overwrite',compression='snappy')
- return(tempdir)
-
-
- def prep_tfidf_entries(tfidf, term_colname, min_df, max_df, included_subreddits):
- term = term_colname
+ def test_lsi_sims():
+ term = "term"
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('count') >= min_df)
- if max_df is not None:
- tfidf = tfidf.filter(f.col('count') <= max_df)
-
- 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'))
- 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.withColumn("tf_idf", (tfidf.relative_tf * tfidf.idf).cast('float'))
+ t1 = time.perf_counter()
+ entries, subreddit_names = reindex_tfidf("/gscratch/comdata/output/reddit_similarity/tfidf/comment_terms_100k_repartitioned.parquet",
+ term_colname='term',
+ min_df=2000,
+ topN=10000
+ )
+ t2 = time.perf_counter()
+ print(f"first load took:{t2 - t1}s")
+
+ entries, subreddit_names = reindex_tfidf("/gscratch/comdata/output/reddit_similarity/tfidf/comment_terms_100k.parquet",
+ term_colname='term',
+ min_df=2000,
+ topN=10000
+ )
+ t3=time.perf_counter()
+
+ print(f"second load took:{t3 - t2}s")
+
+ mat = csr_matrix((entries['tf_idf'],(entries[term_id_new], entries.subreddit_id_new)))
+ sims = list(lsi_column_similarities(mat, [10,50]))
+ sims_og = sims
+ sims_test = list(lsi_column_similarities(mat,[10,50],algorithm='randomized',n_iter=10))
+
+ # n_components is the latent dimensionality. sklearn recommends 100. More might be better
+ # if n_components is a list we'll return a list of similarities with different latent dimensionalities
+ # if algorithm is 'randomized' instead of 'arpack' then n_iter gives the number of iterations.
+ # this function takes the svd and then the column similarities of it
+ def lsi_column_similarities(tfidfmat,n_components=300,n_iter=10,random_state=1968,algorithm='randomized'):
+ # first compute the lsi of the matrix
+ # then take the column similarities
+ print("running LSI",flush=True)
+
+ if type(n_components) is int:
+ n_components = [n_components]
+
+ n_components = sorted(n_components,reverse=True)
- tempdir =TemporaryDirectory(suffix='.parquet',prefix='term_tfidf_entries',dir='.')
+ svd_components = n_components[0]
+ svd = TruncatedSVD(n_components=svd_components,random_state=random_state,algorithm=algorithm,n_iter=n_iter)
+ mod = svd.fit(tfidfmat.T)
+ lsimat = mod.transform(tfidfmat.T)
+ for n_dims in n_components:
+ sims = column_similarities(lsimat[:,np.arange(n_dims)])
+ if len(n_components) > 1:
+ yield (sims, n_dims)
+ else:
+ return sims
- tfidf.write.parquet(tempdir.name,mode='overwrite',compression='snappy')
- return tempdir
-
-
- # try computing cosine similarities using spark
- def spark_cosine_similarities(tfidf, term_colname, min_df, included_subreddits, similarity_threshold):
- 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))
- tfidf = tfidf.cache()
-
- # 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'))
- 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.withColumn("tf_idf", tfidf.relative_tf * tfidf.idf)
-
- # step 1 make an rdd of entires
- # sorted by (dense) spark subreddit id
- n_partitions = int(len(included_subreddits)*2 / 5)
-
- entries = tfidf.select(f.col(term_id_new)-1,f.col("subreddit_id_new")-1,"tf_idf").rdd.repartition(n_partitions)
-
- # put like 10 subredis in each partition
-
- # step 2 make it into a distributed.RowMatrix
- coordMat = CoordinateMatrix(entries)
-
- coordMat = CoordinateMatrix(coordMat.entries.repartition(n_partitions))
-
- # this needs to be an IndexedRowMatrix()
- mat = coordMat.toRowMatrix()
-
- #goal: build a matrix of subreddit columns and tf-idfs rows
- sim_dist = mat.columnSimilarities(threshold=similarity_threshold)
-
- return (sim_dist, tfidf)
+ def column_similarities(mat):
+ return 1 - pairwise_distances(mat,metric='cosine')
def build_weekly_tfidf_dataset(df, include_subs, term_colname, tf_family=tf_weight.Norm05):
else: # tf_fam = tf_weight.Norm05
df = df.withColumn("tf_idf", (0.5 + 0.5 * df.relative_tf) * df.idf)
- return df
+ df = df.repartition(400,'subreddit','week')
+ dfwriter = df.write.partitionBy("week").sortBy("subreddit")
+ return dfwriter
def _calc_tfidf(df, term_colname, tf_family):
term = term_colname
df = df.join(max_subreddit_terms, on='subreddit')
- df = df.withColumn("relative_tf", df.tf / df.sr_max_tf)
+ df = df.withColumn("relative_tf", (df.tf / df.sr_max_tf))
# group by term. term is unique
idf = df.groupby([term]).count()
df = df.groupBy(['subreddit',term]).agg(f.sum('tf').alias('tf'))
df = _calc_tfidf(df, term_colname, tf_family)
-
- return df
+ df = df.repartition('subreddit')
+ dfwriter = df.write.sortBy("subreddit","tf")
+ return dfwriter
def select_topN_subreddits(topN, path="/gscratch/comdata/output/reddit_similarity/subreddits_by_num_comments_nonsfw.csv"):
rankdf = pd.read_csv(path)
included_subreddits = set(rankdf.loc[rankdf.comments_rank <= topN,'subreddit'].values)
return included_subreddits
+
+
+ def repartition_tfidf(inpath="/gscratch/comdata/output/reddit_similarity/tfidf/comment_terms_100k.parquet",
+ outpath="/gscratch/comdata/output/reddit_similarity/tfidf/comment_terms_100k_repartitioned.parquet"):
+ spark = SparkSession.builder.getOrCreate()
+ df = spark.read.parquet(inpath)
+ df = df.repartition(400,'subreddit')
+ df.write.parquet(outpath,mode='overwrite')
+
+
+ def repartition_tfidf_weekly(inpath="/gscratch/comdata/output/reddit_similarity/tfidf_weekly/comment_terms.parquet",
+ outpath="/gscratch/comdata/output/reddit_similarity/tfidf/comment_terms_repartitioned.parquet"):
+ spark = SparkSession.builder.getOrCreate()
+ df = spark.read.parquet(inpath)
+ df = df.repartition(400,'subreddit','week')
+ dfwriter = df.write.partitionBy("week")
+ dfwriter.parquet(outpath,mode='overwrite')
projects / cdsc_reddit.git / commitdiff