X-Git-Url: https://code.communitydata.science/cdsc_reddit.git/blobdiff_plain/e6294b5b90135a5163441c8dc62252dd6a188412..7b130a30af863dfa727d80d9fea23648dcc9d5d8:/similarities/similarities_helper.py?ds=sidebyside diff --git a/similarities/similarities_helper.py b/similarities/similarities_helper.py index 88c830c..202220c 100644 --- a/similarities/similarities_helper.py +++ b/similarities/similarities_helper.py @@ -1,173 +1,278 @@ +from pyspark.sql import SparkSession 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 scipy.sparse import csr_matrix +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 +from datetime import datetime +from pathlib import Path +import pickle class tf_weight(Enum): MaxTF = 1 Norm05 = 2 -def read_tfidf_matrix_weekly(path, term_colname, week): - term = term_colname - term_id = term + '_id' - term_id_new = term + '_id_new' +# 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" - dataset = ds.dataset(path,format='parquet') - entries = dataset.to_table(columns=['tf_idf','subreddit_id_new',term_id_new],filter=ds.field('week')==week).to_pandas() - return(csr_matrix((entries.tf_idf,(entries[term_id_new]-1, entries.subreddit_id_new-1)))) +# subreddits missing after this step don't have any terms that have a high enough idf +# try rewriting without merges -def write_weekly_similarities(path, sims, week, names): - sims['week'] = week - p = pathlib.Path(path) - if not p.is_dir(): - p.mkdir() - - # reformat as a pairwise list - sims = sims.melt(id_vars=['subreddit','week'],value_vars=names.subreddit.values) - sims.to_parquet(p / week.isoformat()) +# does reindex_tfidf, but without reindexing. +def reindex_tfidf(*args, **kwargs): + df, tfidf_ds, ds_filter = _pull_or_reindex_tfidf(*args, **kwargs, reindex=True) - - -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)))) + print("assigning names") + subreddit_names = tfidf_ds.to_table(filter=ds_filter,columns=['subreddit','subreddit_id']) + batches = subreddit_names.to_batches() -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, included_subreddits): - term = term_colname - term_id = term + '_id' - term_id_new = term + '_id_new' + 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",axis=1) + subreddit_names = subreddit_names.sort_values("subreddit_id_new") + return(df, subreddit_names) + +def pull_tfidf(*args, **kwargs): + df, _, _ = _pull_or_reindex_tfidf(*args, **kwargs, reindex=False) + return df - if min_df is None: - min_df = 0.1 * len(included_subreddits) +def _pull_or_reindex_tfidf(infile, term_colname, min_df=None, max_df=None, included_subreddits=None, topN=None, week=None, from_date=None, to_date=None, rescale_idf=True, tf_family=tf_weight.MaxTF, reindex=True): + print(f"loading tfidf {infile}, week {week}, min_df {min_df}, max_df {max_df}", flush=True) - tfidf = tfidf.filter(f.col("subreddit").isin(included_subreddits)) + if week is not None: + tfidf_ds = ds.dataset(infile, partitioning='hive') + else: + tfidf_ds = ds.dataset(infile) - # 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']) + if included_subreddits is None: + included_subreddits = select_topN_subreddits(topN) + else: + included_subreddits = set(map(str.strip,open(included_subreddits))) - # 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') + ds_filter = ds.field("subreddit").isin(included_subreddits) - # 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']) + if min_df is not None: + ds_filter &= ds.field("count") >= min_df - tfidf = tfidf.withColumnRenamed("tf_idf","tf_idf_old") - tfidf = tfidf.withColumn("tf_idf", (tfidf.relative_tf * tfidf.idf).cast('float')) + if max_df is not None: + ds_filter &= ds.field("count") <= max_df - tempdir =TemporaryDirectory(suffix='.parquet',prefix='term_tfidf_entries',dir='.') + if week is not None: + ds_filter &= ds.field("week") == week - tfidf = tfidf.repartition('week') + if from_date is not None: + ds_filter &= ds.field("week") >= from_date - tfidf.write.parquet(tempdir.name,mode='overwrite',compression='snappy') - return(tempdir) - + if to_date is not None: + ds_filter &= ds.field("week") <= to_date -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')) - 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) + 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), + 'tf_idf':ds.field('tf_idf').cast('float32')} + + print(projection, flush=True) + print(ds_filter, flush=True) + df = tfidf_ds.to_table(filter=ds_filter,columns=projection) + + df = df.to_pandas(split_blocks=True,self_destruct=True) + + if reindex: + print("assigning indexes",flush=True) + df['subreddit_id_new'] = df.groupby("subreddit_id").ngroup() + 1 + else: + df['subreddit_id_new'] = df['subreddit_id'] + + if reindex: + grouped = df.groupby(term_id) + df[term_id_new] = grouped.ngroup() + 1 + else: + df[term_id_new] = df[term_id] + + 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 + + return (df, tfidf_ds, ds_filter) + + # 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") + # return(df, subreddit_names) + +def pull_names(batch): + return(batch.to_pandas().drop_duplicates()) + +def similarities(inpath, 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. + ''' + + 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)}",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) + + 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")) + p.parent.mkdir(exist_ok=True, parents=True) + + sims.to_feather(outfile) - 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.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) + entries, subreddit_names = reindex_tfidf(inpath, 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]-1, entries.subreddit_id_new-1))) - tfidf = tfidf.filter(f.col("subreddit").isin(included_subreddits)) - tfidf = tfidf.cache() + print("loading matrix") - # 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) + # mat = read_tfidf_matrix("term_tfidf_entries7ejhvnvl.parquet", term_colname) - tfidf = tfidf.withColumnRenamed("tf_idf","tf_idf_old") - tfidf = tfidf.withColumn("tf_idf", tfidf.relative_tf * tfidf.idf) + 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 - # step 1 make an rdd of entires - # sorted by (dense) spark subreddit id - n_partitions = int(len(included_subreddits)*2 / 5) + if hasattr(sims,'__next__'): + for simmat, name in sims: + proc_sims(simmat, Path(outfile)/(str(name) + ".feather")) + else: + proc_sims(sims, outfile) - 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 +def write_weekly_similarities(path, sims, week, names): + sims['week'] = week + p = pathlib.Path(path) + if not p.is_dir(): + 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.to_parquet(p / week.isoformat()) - # step 2 make it into a distributed.RowMatrix - coordMat = CoordinateMatrix(entries) +def column_overlaps(mat): + non_zeros = (mat != 0).astype('double') + + intersection = non_zeros.T @ non_zeros + card1 = non_zeros.sum(axis=0) + den = np.add.outer(card1,card1) - intersection - coordMat = CoordinateMatrix(coordMat.entries.repartition(n_partitions)) + return intersection / den + +def test_lsi_sims(): + term = "term" + term_id = term + '_id' + term_id_new = term + '_id_new' - # this needs to be an IndexedRowMatrix() - mat = coordMat.toRowMatrix() + 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 +# lsi_model_load = "/gscratch/comdata/users/nathante/competitive_exclusion_reddit/data/similarity/comment_terms_compex_LSI/1000_term_LSIMOD.pkl" +def lsi_column_similarities(tfidfmat,n_components=300,n_iter=10,random_state=1968,algorithm='randomized',lsi_model_save=None,lsi_model=None): + # first compute the lsi of the matrix + # then take the column similarities + + if type(n_components) is int: + n_components = [n_components] + + n_components = sorted(n_components,reverse=True) + + svd_components = n_components[0] + + if lsi_model is None: + print("running LSI",flush=True) + svd = TruncatedSVD(n_components=svd_components,random_state=random_state,algorithm=algorithm,n_iter=n_iter) + mod = svd.fit(tfidfmat.T) + else: + mod = lsi_model + + lsimat = mod.transform(tfidfmat.T) + if lsi_model_save is not None: + Path(lsi_model_save).parent.mkdir(exist_ok=True,parents=True) + pickle.dump(mod, open(lsi_model_save,'wb')) + + print(n_components) + for n_dims in n_components: + print("computing similarities") + sims = column_similarities(lsimat[:,np.arange(n_dims)]) + yield (sims, n_dims) - #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): @@ -194,20 +299,20 @@ def build_weekly_tfidf_dataset(df, include_subs, term_colname, tf_family=tf_weig idf = idf.withColumn('idf',f.log(idf.subreddits_in_week) / (1+f.col('count'))+1) # collect the dictionary to make a pydict of terms to indexes - terms = idf.select([term,'week']).distinct() # terms are distinct + terms = idf.select([term]).distinct() # terms are distinct - terms = terms.withColumn(term_id,f.row_number().over(Window.partitionBy('week').orderBy(term))) # term ids are distinct + terms = terms.withColumn(term_id,f.row_number().over(Window.orderBy(term))) # term ids are distinct # make subreddit ids - subreddits = df.select(['subreddit','week']).distinct() - subreddits = subreddits.withColumn('subreddit_id',f.row_number().over(Window.partitionBy("week").orderBy("subreddit"))) + subreddits = df.select(['subreddit']).distinct() + subreddits = subreddits.withColumn('subreddit_id',f.row_number().over(Window.orderBy("subreddit"))) - df = df.join(subreddits,on=['subreddit','week']) + df = df.join(subreddits,on=['subreddit']) # map terms to indexes in the tfs and the idfs - df = df.join(terms,on=[term,'week']) # subreddit-term-id is unique + df = df.join(terms,on=[term]) # subreddit-term-id is unique - idf = idf.join(terms,on=[term,'week']) + idf = idf.join(terms,on=[term]) # join on subreddit/term to create tf/dfs indexed by term df = df.join(idf, on=[term_id, term,'week']) @@ -219,35 +324,35 @@ def build_weekly_tfidf_dataset(df, include_subs, term_colname, tf_family=tf_weig else: # tf_fam = tf_weight.Norm05 df = df.withColumn("tf_idf", (0.5 + 0.5 * df.relative_tf) * df.idf) - return df - - - -def build_tfidf_dataset(df, include_subs, term_colname, tf_family=tf_weight.Norm05): + df = df.repartition('week') + dfwriter = df.write.partitionBy("week") + return dfwriter +def _calc_tfidf(df, term_colname, tf_family, min_df=None, max_df=None): term = term_colname term_id = term + '_id' - # aggregate counts by week. now subreddit-term is distinct - df = df.filter(df.subreddit.isin(include_subs)) - df = df.groupBy(['subreddit',term]).agg(f.sum('tf').alias('tf')) max_subreddit_terms = df.groupby(['subreddit']).max('tf') # subreddits are unique max_subreddit_terms = max_subreddit_terms.withColumnRenamed('max(tf)','sr_max_tf') 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() - N_docs = df.select('subreddit').distinct().count() - # add a little smoothing to the idf idf = idf.withColumn('idf',f.log(N_docs/(1+f.col('count')))+1) # collect the dictionary to make a pydict of terms to indexes - terms = idf.select(term).distinct() # terms are distinct + terms = idf + if min_df is not None: + terms = terms.filter(f.col('count')>=min_df) + if max_df is not None: + terms = terms.filter(f.col('count')<=max_df) + + terms = terms.select(term).distinct() # terms are distinct terms = terms.withColumn(term_id,f.row_number().over(Window.orderBy(term))) # term ids are distinct # make subreddit ids @@ -257,12 +362,12 @@ def build_tfidf_dataset(df, include_subs, term_colname, tf_family=tf_weight.Norm df = df.join(subreddits,on='subreddit') # map terms to indexes in the tfs and the idfs - df = df.join(terms,on=term) # subreddit-term-id is unique + df = df.join(terms,on=term,how='inner') # subreddit-term-id is unique - idf = idf.join(terms,on=term) + idf = idf.join(terms,on=term,how='inner') # join on subreddit/term to create tf/dfs indexed by term - df = df.join(idf, on=[term_id, term]) + df = df.join(idf, on=[term_id, term],how='inner') # agg terms by subreddit to make sparse tf/df vectors if tf_family == tf_weight.MaxTF: @@ -271,8 +376,38 @@ def build_tfidf_dataset(df, include_subs, term_colname, tf_family=tf_weight.Norm df = df.withColumn("tf_idf", (0.5 + 0.5 * df.relative_tf) * df.idf) return df + -def select_topN_subreddits(topN, path="/gscratch/comdata/output/reddit_similarity/subreddits_by_num_comments.csv"): +def tfidf_dataset(df, include_subs, term_colname, tf_family=tf_weight.Norm05, min_df=None, max_df=None): + term = term_colname + term_id = term + '_id' + + df = df.filter(df.subreddit.isin(include_subs)) + df = df.groupBy(['subreddit',term]).agg(f.sum('tf').alias('tf')) + + df = _calc_tfidf(df, term_colname, tf_family, min_df, max_df) + df = df.repartition('subreddit') + dfwriter = df.write + 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')