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Merge branch 'excise_reindex' of code:cdsc_reddit into excise_reindex

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Nathan TeBlunthuis 2021-08-03 15:13:21 -07:00
commit ce549c6c97
15 changed files with 103 additions and 44 deletions
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10
clustering/Makefile
View File

@ -2,9 +2,9 @@
srun_singularity=source /gscratch/comdata/users/nathante/cdsc_reddit/bin/activate && srun_singularity.sh
similarity_data=/gscratch/comdata/output/reddit_similarity
clustering_data=/gscratch/comdata/output/reddit_clustering
kmeans_selection_grid="--max_iters=[3000] --n_inits=[10] --n_clusters=[100,500,1000,1250,1500,1750,2000]"
hdbscan_selection_grid="--min_cluster_sizes=[2,3,4,5] --min_samples=[2,3,4,5] --cluster_selection_epsilons=[0,0.01,0.05,0.1,0.15,0.2] --cluster_selection_methods=eom,leaf"
affinity_selection_grid="--dampings=[0.5,0.6,0.7,0.8,0.95,0.97,0.99] --preference_quantiles=[0.1,0.3,0.5,0.7,0.9] --convergence_iters=[15]"
kmeans_selection_grid=--max_iters=[3000] --n_inits=[10] --n_clusters=[100,500,1000,1250,1500,1750,2000]
hdbscan_selection_grid=--min_cluster_sizes=[2,3,4,5] --min_samples=[2,3,4,5] --cluster_selection_epsilons=[0,0.01,0.05,0.1,0.15,0.2] --cluster_selection_methods=[eom,leaf]
affinity_selection_grid=--dampings=[0.5,0.6,0.7,0.8,0.95,0.97,0.99] --preference_quantiles=[0.1,0.3,0.5,0.7,0.9] --convergence_iters=[15]
authors_10k_input=$(similarity_data)/subreddit_comment_authors_10k.feather
authors_10k_input_lsi=$(similarity_data)/subreddit_comment_authors_10k_LSI
@ -91,7 +91,11 @@ ${terms_10k_output_lsi}/hdbscan/selection_data.csv:selection.py ${terms_10k_inpu
${authors_tf_10k_output_lsi}/hdbscan/selection_data.csv:clustering.py ${authors_tf_10k_input_lsi} clustering_base.py hdbscan_clustering.py
$(srun_singularity) python3 hdbscan_clustering_lsi.py --inpath=${authors_tf_10k_input_lsi} --outpath=${authors_tf_10k_output_lsi}/hdbscan --savefile=${authors_tf_10k_output_lsi}/hdbscan/selection_data.csv $(hdbscan_selection_grid)
${terms_10k_output_lsi}/best_hdbscan.feather:${terms_10k_output_lsi}/hdbscan/selection_data.csv pick_best_clustering.py
$(srun_singularity) python3 pick_best_clustering.py $< $@ --min_clusters=50 --max_isolates=5000 --min_cluster_size=2
${authors_tf_10k_output_lsi}/best_hdbscan.feather:${authors_tf_10k_output_lsi}/hdbscan/selection_data.csv pick_best_clustering.py
$(srun_singularity) python3 pick_best_clustering.py $< $@ --min_clusters=50 --max_isolates=5000 --min_cluster_size=2
clean_affinity:
rm -f ${authors_10k_output}/affinity/selection_data.csv

1
clustering/grid_sweep.py
View File

@ -7,6 +7,7 @@ class grid_sweep:
def __init__(self, jobtype, inpath, outpath, namer, *args):
self.jobtype = jobtype
self.namer = namer
print(*args)
grid = list(product(*args))
inpath = Path(inpath)
outpath = Path(outpath)

8
clustering/hdbscan_clustering_lsi.py
View File

@ -59,7 +59,7 @@ class _hdbscan_lsi_grid_sweep(grid_sweep):
self.lsi_dim = lsi_dim
self.jobtype = hdbscan_lsi_job
super().__init__(self.jobtype, inpath, outpath, self.namer, self.lsi_dim, *args, **kwargs)
super().__init__(self.jobtype, inpath, outpath, self.namer, [self.lsi_dim], *args, **kwargs)
def namer(self, *args, **kwargs):
@ -87,9 +87,9 @@ def run_hdbscan_lsi_grid_sweep(savefile, inpath, outpath, min_cluster_sizes=[2]
obj = hdbscan_lsi_grid_sweep(inpath,
lsi_dimensions,
outpath,
map(int,min_cluster_sizes),
map(int,min_samples),
map(float,cluster_selection_epsilons),
list(map(int,min_cluster_sizes)),
list(map(int,min_samples)),
list(map(float,cluster_selection_epsilons)),
cluster_selection_methods
)

2
clustering/kmeans_clustering_lsi.py
View File

@ -34,7 +34,7 @@ class _kmeans_lsi_grid_sweep(grid_sweep):
print(kwargs)
self.lsi_dim = lsi_dim
self.jobtype = kmeans_lsi_job
super().__init__(self.jobtype, inpath, outpath, self.namer, self.lsi_dim, *args, **kwargs)
super().__init__(self.jobtype, inpath, outpath, self.namer, [self.lsi_dim], *args, **kwargs)
def namer(self, *args, **kwargs):
s = kmeans_grid_sweep.namer(self, *args[1:], **kwargs)

11
clustering/pick_best_clustering.py
View File

@ -2,15 +2,15 @@ import fire
import pandas as pd
from pathlib import Path
import shutil
selection_data="/gscratch/comdata/output/reddit_clustering/subreddit_comment_authors-tf_10k_LSI/affinity/selection_data.csv"
selection_data="/gscratch/comdata/output/reddit_clustering/subreddit_comment_authors-tf_10k_LSI/hdbscan/selection_data.csv"
outpath = 'test_best.feather'
min_clusters=50; max_isolates=5000; min_cluster_size=2
# pick the best clustering according to silhouette score subject to contraints
def pick_best_clustering(selection_data, output, min_clusters, max_isolates):
def pick_best_clustering(selection_data, output, min_clusters, max_isolates, min_cluster_size):
df = pd.read_csv(selection_data,index_col=0)
df = df.sort_values("silhouette_score")
df = df.sort_values("silhouette_score",ascending=False)
# not sure I fixed the bug underlying this fully or not.
df['n_isolates_str'] = df.n_isolates.str.strip("[]")
@ -18,11 +18,10 @@ def pick_best_clustering(selection_data, output, min_clusters, max_isolates):
df.loc[df.n_isolates_0,'n_isolates'] = 0
df.loc[~df.n_isolates_0,'n_isolates'] = df.loc[~df.n_isolates_0].n_isolates_str.apply(lambda l: int(l))
best_cluster = df[(df.n_isolates <= max_isolates)&(df.n_clusters >= min_clusters)].iloc[df.shape[1]]
best_cluster = df[(df.n_isolates <= max_isolates)&(df.n_clusters >= min_clusters)&(df.min_cluster_size==min_cluster_size)].iloc[df.shape[1]]
print(best_cluster.to_dict())
best_path = Path(best_cluster.outpath) / (str(best_cluster['name']) + ".feather")
shutil.copy(best_path,output)
if __name__ == "__main__":

43
clustering/selection.py
View File

@ -1,7 +1,38 @@
import fire
from select_affinity import select_affinity_clustering
from select_kmeans import select_kmeans_clustering
import pandas as pd
import plotnine as pn
from pathlib import Path
from clustering.fit_tsne import fit_tsne
from visualization.tsne_vis import build_visualization
df = pd.read_csv("/gscratch/comdata/output/reddit_clustering/subreddit_comment_authors-tf_10k_LSI/hdbscan/selection_data.csv",index_col=0)
# plot silhouette_score as a function of isolates
df = df.sort_values("silhouette_score")
df['n_isolates'] = df.n_isolates.str.split("\n0").apply(lambda rg: int(rg[1]))
p = pn.ggplot(df,pn.aes(x='n_isolates',y='silhouette_score')) + pn.geom_point()
p.save("isolates_x_score.png")
p = pn.ggplot(df,pn.aes(y='n_clusters',x='n_isolates',color='silhouette_score')) + pn.geom_point()
p.save("clusters_x_isolates.png")
# the best result for hdbscan seems like this one: it has a decent number of
# i think I prefer the 'eom' clustering style because larger clusters are less likely to suffer from ommitted variables
best_eom = df[(df.n_isolates <5000)&(df.silhouette_score>0.4)&(df.cluster_selection_method=='eom')&(df.min_cluster_size==2)].iloc[df.shape[1]]
best_lsi = df[(df.n_isolates <5000)&(df.silhouette_score>0.4)&(df.cluster_selection_method=='leaf')&(df.min_cluster_size==2)].iloc[df.shape[1]]
tsne_data = Path("./clustering/authors-tf_lsi850_tsne.feather")
if not tnse_data.exists():
fit_tsne("/gscratch/comdata/output/reddit_similarity/subreddit_comment_authors-tf_10k_LSI/850.feather",
tnse_data)
build_visualization("./clustering/authors-tf_lsi850_tsne.feather",
Path(best_eom.outpath)/(best_eom['name']+'.feather'),
"./authors-tf_lsi850_best_eom.html")
build_visualization("./clustering/authors-tf_lsi850_tsne.feather",
Path(best_leaf.outpath)/(best_leaf['name']+'.feather'),
"./authors-tf_lsi850_best_leaf.html")
if __name__ == "__main__":
fire.Fire({"kmeans":select_kmeans_clustering,
"affinity":select_affinity_clustering})

6
density/Makefile
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@ -8,3 +8,9 @@ all: /gscratch/comdata/output/reddit_density/comment_terms_10000.feather /gscrat
/gscratch/comdata/output/reddit_density/subreddit_author_tf_similarities_10000.feather: overlap_density.py /gscratch/comdata/output/reddit_similarity/subreddit_author_tf_similarities_10000.parquet
start_spark_and_run.sh 1 overlap_density.py authors --inpath="/gscratch/comdata/output/reddit_similarity/subreddit_author_tf_similarities_10000.parquet" --outpath="/gscratch/comdata/output/reddit_density/subreddit_author_tf_similarities_10000.feather" --agg=pd.DataFrame.sum
/gscratch/comdata/output/reddit_density/subreddit_author_tf_similarities_10K_LSI/850.feather: overlap_density.py /gscratch/comdata/output/reddit_similarity/subreddit_comment_authors-tf_10k_LSI/850.feather
start_spark_and_run.sh 1 overlap_density.py authors --inpath="/gscratch/comdata/output/reddit_similarity/subreddit_comment_authors-tf_10k_LSI/850.feather" --outpath="/gscratch/comdata/output/reddit_density/subreddit_author_tf_similarities_10K_LSI/850.feather" --agg=pd.DataFrame.sum
/gscratch/comdata/output/reddit_density/subreddit_author_tf_similarities_10K_LSI/600.feather: overlap_density.py /gscratch/comdata/output/reddit_similarity/subreddit_comment_authors-tf_10k_LSI/600.feather
start_spark_and_run.sh 1 overlap_density.py authors --inpath="/gscratch/comdata/output/reddit_similarity/subreddit_comment_authors-tf_10k_LSI/600.feather" --outpath="/gscratch/comdata/output/reddit_density/subreddit_author_tf_similarities_10K_LSI/600.feather" --agg=pd.DataFrame.sum

4
density/job_script.sh
View File

@ -1,4 +1,4 @@
#!/usr/bin/bash
start_spark_cluster.sh
spark-submit --master spark://$(hostname):18899 overlap_density.py authors --inpath=/gscratch/comdata/output/reddit_similarity/comment_authors_10000.feather --outpath=/gscratch/comdata/output/reddit_density/comment_authors_10000.feather --agg=pd.DataFrame.sum
stop-all.sh
singularity exec /gscratch/comdata/users/nathante/cdsc_base.sif spark-submit --master spark://$(hostname).hyak.local:7077 overlap_density.py authors --inpath=/gscratch/comdata/output/reddit_similarity/subreddit_comment_authors-tf_10k_LSI/600.feather --outpath=/gscratch/comdata/output/reddit_density/subreddit_author_tf_similarities_10K_LSI/600.feather --agg=pd.DataFrame.sum
singularity exec /gscratch/comdata/users/nathante/cdsc_base.sif stop-all.sh

9
density/overlap_density.py
View File

@ -1,11 +1,12 @@
import pandas as pd
from pandas.core.groupby import DataFrameGroupBy as GroupBy
from pathlib import Path
import fire
import numpy as np
import sys
sys.path.append("..")
sys.path.append("../similarities")
from similarities.similarities_helper import reindex_tfidf, reindex_tfidf_time_interval
from similarities.similarities_helper import reindex_tfidf
# this is the mean of the ratio of the overlap to the focal size.
# mean shared membership per focal community member
@ -13,10 +14,12 @@ from similarities.similarities_helper import reindex_tfidf, reindex_tfidf_time_i
def overlap_density(inpath, outpath, agg = pd.DataFrame.sum):
df = pd.read_feather(inpath)
df = df.drop('subreddit',1)
df = df.drop('_subreddit',1)
np.fill_diagonal(df.values,0)
df = agg(df, 0).reset_index()
df = df.rename({0:'overlap_density'},axis='columns')
outpath = Path(outpath)
outpath.parent.mkdir(parents=True, exist_ok = True)
df.to_feather(outpath)
return df
@ -25,6 +28,8 @@ def overlap_density_weekly(inpath, outpath, agg = GroupBy.sum):
# exclude the diagonal
df = df.loc[df.subreddit != df.variable]
res = agg(df.groupby(['subreddit','week'])).reset_index()
outpath = Path(outpath)
outpath.parent.mkdir(parents=True, exist_ok = True)
res.to_feather(outpath)
return res

2
dumps/pull_pushshift_comments.sh
View File

@ -8,7 +8,5 @@ wget -r --no-parent -A 'RC_201*.bz2' -U $user_agent -P $output_dir -nd -nc $base
wget -r --no-parent -A 'RC_201*.xz' -U $user_agent -P $output_dir -nd -nc $base_url
wget -r --no-parent -A 'RC_201*.zst' -U $user_agent -P $output_dir -nd -nc $base_url
# starting in 2020 we use daily dumps not monthly dumps
wget -r --no-parent -A 'RC_202*.gz' -U $user_agent -P $output_dir -nd -nc $base_url/daily/
./check_comments_shas.py

19
similarities/cosine_similarities.py
View File

@ -4,44 +4,49 @@ from pathlib import Path
from similarities_helper import similarities, column_similarities
from functools import partial
def cosine_similarities(infile, term_colname, outfile, min_df=None, max_df=None, included_subreddits=None, topN=500, from_date=None, to_date=None, tfidf_colname='tf_idf'):
def cosine_similarities(infile, 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'):
return similarities(inpath=infile, simfunc=column_similarities, term_colname=term_colname, outfile=outfile, min_df=min_df, max_df=max_df, included_subreddits=included_subreddits, topN=topN, from_date=from_date, to_date=to_date, tfidf_colname=tfidf_colname)
return similarities(infile=infile, simfunc=column_similarities, term_colname=term_colname, outfile=outfile, min_df=min_df, max_df=max_df, included_subreddits=included_subreddits, topN=topN, exclude_phrases=exclude_phrases,from_date=from_date, to_date=to_date, tfidf_colname=tfidf_colname)
# change so that these take in an input as an optional argument (for speed, but also for idf).
def term_cosine_similarities(outfile, min_df=None, max_df=None, included_subreddits=None, topN=500, exclude_phrases=False, from_date=None, to_date=None):
return cosine_similarities('/gscratch/comdata/output/reddit_similarity/tfidf/comment_terms_100k.parquet',
def term_cosine_similarities(outfile, infile='/gscratch/comdata/output/reddit_similarity/tfidf/comment_terms_100k.parquet', min_df=None, max_df=None, included_subreddits=None, topN=500, exclude_phrases=False, from_date=None, to_date=None):
return cosine_similarities(infile,
'term',
outfile,
min_df,
max_df,
included_subreddits,
topN,
exclude_phrases,
from_date,
to_date
)
def author_cosine_similarities(outfile, min_df=2, max_df=None, included_subreddits=None, topN=10000, from_date=None, to_date=None):
return cosine_similarities('/gscratch/comdata/output/reddit_similarity/tfidf/comment_authors_100k.parquet',
def author_cosine_similarities(outfile, infile='/gscratch/comdata/output/reddit_similarity/tfidf/comment_authors_100k.parquet', min_df=2, max_df=None, included_subreddits=None, topN=10000, from_date=None, to_date=None):
return cosine_similarities(infile,
'author',
outfile,
min_df,
max_df,
included_subreddits,
topN,
exclude_phrases=False,
from_date=from_date,
to_date=to_date
)
def author_tf_similarities(outfile, min_df=2, max_df=None, included_subreddits=None, topN=10000, from_date=None, to_date=None):
return cosine_similarities('/gscratch/comdata/output/reddit_similarity/tfidf/comment_authors_100k.parquet',
def author_tf_similarities(outfile, infile='/gscratch/comdata/output/reddit_similarity/tfidf/comment_authors_100k.parquet', min_df=2, max_df=None, included_subreddits=None, topN=10000, from_date=None, to_date=None):
return cosine_similarities(infile,
'author',
outfile,
min_df,
max_df,
included_subreddits,
topN,
exclude_phrases=False,
from_date=from_date,
to_date=to_date,
tfidf_colname='relative_tf'

2
similarities/job_script.sh
View File

@ -1,4 +1,4 @@
#!/usr/bin/bash
start_spark_cluster.sh
singularity exec /gscratch/comdata/users/nathante/cdsc_base.sif spark-submit --master spark://$(hostname).hyak.local:7077 lsi_similarities.py author --outfile=/gscratch/comdata/output//reddit_similarity/subreddit_comment_authors_10k_LSI.feather --topN=10000
singularity exec /gscratch/comdata/users/nathante/cdsc_base.sif spark-submit --master spark://$(hostname):7077 top_subreddits_by_comments.py
singularity exec /gscratch/comdata/users/nathante/cdsc_base.sif stop-all.sh

19
similarities/similarities_helper.py
View File

@ -97,6 +97,7 @@ def _pull_or_reindex_tfidf(infile, term_colname, min_df=None, max_df=None, inclu
'relative_tf':ds.field('relative_tf').cast('float32'),
'tf_idf':ds.field('tf_idf').cast('float32')}
df = tfidf_ds.to_table(filter=ds_filter,columns=projection)
df = df.to_pandas(split_blocks=True,self_destruct=True)
@ -124,6 +125,17 @@ def _pull_or_reindex_tfidf(infile, term_colname, min_df=None, max_df=None, inclu
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())
@ -165,7 +177,6 @@ def similarities(inpath, simfunc, term_colname, outfile, min_df=None, max_df=Non
print(f'computing similarities on mat. mat.shape:{mat.shape}')
print(f"size of mat is:{mat.data.nbytes}",flush=True)
# transform this to debug term tfidf
sims = simfunc(mat)
del mat
@ -257,12 +268,11 @@ def lsi_column_similarities(tfidfmat,n_components=300,n_iter=10,random_state=196
else:
return sims
def column_similarities(mat):
return 1 - pairwise_distances(mat,metric='cosine')
# need to rewrite this so that subreddit ids and term ids are fixed over the whole thing.
# this affords taking the LSI similarities.
# fill all 0s if we don't have it.
def build_weekly_tfidf_dataset(df, include_subs, term_colname, tf_family=tf_weight.Norm05):
term = term_colname
term_id = term + '_id'
@ -295,7 +305,6 @@ def build_weekly_tfidf_dataset(df, include_subs, term_colname, tf_family=tf_weig
subreddits = df.select(['subreddit']).distinct()
subreddits = subreddits.withColumn('subreddit_id',f.row_number().over(Window.orderBy("subreddit")))
# df = df.cache()
df = df.join(subreddits,on=['subreddit'])
# map terms to indexes in the tfs and the idfs

7
similarities/tfidf.py
View File

@ -52,7 +52,7 @@ def tfidf_terms(outpath='/gscratch/comdata/output/reddit_similarity/tfidf/commen
def tfidf_authors_weekly(outpath='/gscratch/comdata/output/reddit_similarity/tfidf_weekly/comment_authors.parquet',
topN=None,
include_subreddits=None):
included_subreddits=None):
return tfidf_weekly("/gscratch/comdata/output/reddit_ngrams/comment_authors.parquet",
outpath,
@ -63,7 +63,8 @@ def tfidf_authors_weekly(outpath='/gscratch/comdata/output/reddit_similarity/tfi
)
def tfidf_terms_weekly(outpath='/gscratch/comdata/output/reddit_similarity/tfidf_weekly/comment_terms.parquet',
topN=25000):
topN=None,
included_subreddits=None):
return tfidf_weekly("/gscratch/comdata/output/reddit_ngrams/comment_terms.parquet",
@ -71,7 +72,7 @@ def tfidf_terms_weekly(outpath='/gscratch/comdata/output/reddit_similarity/tfidf
topN,
'term',
[],
included_subreddits=None
included_subreddits=included_subreddits
)

4
similarities/top_subreddits_by_comments.py
View File

@ -17,7 +17,7 @@ df = df.filter(~df.subreddit.like("u_%"))
df = df.groupBy('subreddit').agg(f.count('id').alias("n_comments"))
df = df.join(prop_nsfw,on='subreddit')
df = df.filter(df.prop_nsfw < 0.5)
#df = df.filter(df.prop_nsfw < 0.5)
win = Window.orderBy(f.col('n_comments').desc())
df = df.withColumn('comments_rank', f.rank().over(win))
@ -26,4 +26,4 @@ df = df.toPandas()
df = df.sort_values("n_comments")
df.to_csv('/gscratch/comdata/output/reddit_similarity/subreddits_by_num_comments.csv', index=False)
df.to_csv('/gscratch/comdata/output/reddit_similarity/subreddits_by_num_comments_nsfw.csv', index=False)