add 2 more umap parameters

clustering/Makefile

@@ -1,8 +1,11 @@
 #srun_cdsc='srun -p comdata-int -A comdata --time=300:00:00 --time-min=00:15:00 --mem=100G --ntasks=1 --cpus-per-task=28'
-srun_singularity=source /gscratch/comdata/users/nathante/cdsc_reddit/bin/activate && srun_singularity.sh
+srun_singularity=srun -p compute-bigmem -A comdata --time=48:00:00 --mem=362G -c 40
 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]
+
+umap_hdbscan_selection_grid=--min_cluster_sizes=[2] --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] --n_neighbors=[5,15,25,50,75,100] --learning_rate=[1] --min_dist=[0,0.1,0.25,0.5,0.75,0.9,0.99] --local_connectivity=[1] --densmap=[True,False] --n_components=[2,5,10]
+
 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]
 
@@ -91,12 +94,28 @@ ${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)
 
+${authors_tf_10k_output_lsi}/umap_hdbscan/selection_data.csv:umap_hdbscan_clustering_lsi.py
+	$(srun_singularity) python3 umap_hdbscan_clustering_lsi.py --inpath=${authors_tf_10k_input_lsi} --outpath=${authors_tf_10k_output_lsi}/umap_hdbscan --savefile=${authors_tf_10k_output_lsi}/umap_hdbscan/selection_data.csv $(umap_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
 
+${authors_tf_10k_output_lsi}/best_umap_hdbscan_2.feather:${authors_tf_10k_output_lsi}/umap_hdbscan/selection_data.csv pick_best_clustering.py
+	$(srun_singularity) python3 pick_best_clustering.py $< $@ --min_clusters=50 --max_isolates=5000 --min_cluster_size=2
+
+best_umap_hdbscan.feather:${authors_tf_10k_output_lsi}/best_umap_hdbscan_2.feather
+
+# {'lsi_dimensions': 700, 'outpath': '/gscratch/comdata/output/reddit_clustering/subreddit_comment_authors-tf_10k_LSI/umap_hdbscan', 'silhouette_score': 0.27616957, 'name': 'mcs-2_ms-5_cse-0.05_csm-leaf_nn-15_lr-1.0_md-0.1_lc-1_lsi-700', 'n_clusters': 547, 'n_isolates': 2093, 'silhouette_samples': '/gscratch/comdata/output/reddit_clustering/subreddit_comment_authors-tf_10k_LSI/umap_hdbscan/silhouette_samples-mcs-2_ms-5_cse-0.05_csm-leaf_nn-15_lr-1.0_md-0.1_lc-1_lsi-700.feather', 'min_cluster_size': 2, 'min_samples': 5, 'cluster_selection_epsilon': 0.05, 'cluster_selection_method': 'leaf', 'n_neighbors': 15, 'learning_rate': 1.0, 'min_dist': 0.1, 'local_connectivity': 1, 'n_isolates_str': '2093', 'n_isolates_0': False}
+
+best_umap_grid=--min_cluster_sizes=[2] --min_samples=[5] --cluster_selection_epsilons=[0.05] --cluster_selection_methods=[leaf] --n_neighbors=[15] --learning_rate=[1] --min_dist=[0.1] --local_connectivity=[1] --save_step1=True
+
+umap_hdbscan_coords:
+	python3 umap_hdbscan_clustering_lsi.py --inpath=${authors_tf_10k_input_lsi} --outpath=${authors_tf_10k_output_lsi}/umap_hdbscan --savefile=/dev/null ${best_umap_grid}
+
 clean_affinity:
 	rm -f ${authors_10k_output}/affinity/selection_data.csv
 	rm -f ${authors_tf_10k_output}/affinity/selection_data.csv
@@ -159,7 +178,7 @@ clean_lsi_terms:
 
 clean: clean_affinity clean_kmeans clean_hdbscan
 
-PHONY: clean clean_affinity clean_kmeans clean_hdbscan clean_authors clean_authors_tf clean_terms terms_10k authors_10k authors_tf_10k
+PHONY: clean clean_affinity clean_kmeans clean_hdbscan clean_authors clean_authors_tf clean_terms terms_10k authors_10k authors_tf_10k best_umap_hdbscan.feather umap_hdbscan_coords
 
 # $(clustering_data)/subreddit_comment_authors_30k.feather/SUCCESS:selection.py $(similarity_data)/subreddit_comment_authors_30k.feather clustering.py
 # 	$(srun_singularity) python3 selection.py $(similarity_data)/subreddit_comment_authors_30k.feather $(clustering_data)/subreddit_comment_authors_30k $(selection_grid) -J 10 && touch $(clustering_data)/subreddit_comment_authors_30k.feather/SUCCESS

clustering/clustering_base.py

@@ -1,3 +1,4 @@
+import pickle
 from pathlib import Path
 import numpy as np
 import pandas as pd
@@ -24,6 +25,13 @@ class clustering_job:
         self.outpath.mkdir(parents=True, exist_ok=True)
         self.cluster_data.to_feather(self.outpath/(self.name + ".feather"))
         self.hasrun = True
+        self.cleanup()
+
+    def cleanup(self):
+        self.cluster_data = None
+        self.mat = None
+        self.clustering=None
+        self.subreddits=None
         
     def get_info(self):
         if not self.hasrun:
@@ -57,6 +65,7 @@ class clustering_job:
         return score
 
     def read_distance_mat(self, similarities, use_threads=True):
+        print(similarities)
         df = pd.read_feather(similarities, use_threads=use_threads)
         mat = np.array(df.drop('_subreddit',1))
         n = mat.shape[0]
@@ -95,6 +104,38 @@ class clustering_job:
 
         return cluster_data
 
+class twoway_clustering_job(clustering_job):
+    def __init__(self, infile, outpath, name, call1, call2, args1, args2):
+        self.outpath = Path(outpath)
+        self.call1 = call1
+        self.args1 = args1
+        self.call2 = call2
+        self.args2 = args2
+        self.infile = Path(infile)
+        self.name = name
+        self.hasrun = False
+        self.args = args1|args2
+
+    def run(self):
+        self.subreddits, self.mat = self.read_distance_mat(self.infile)
+        self.step1 = self.call1(self.mat, **self.args1)
+        self.clustering = self.call2(self.mat, self.step1, **self.args2)
+        self.cluster_data = self.process_clustering(self.clustering, self.subreddits)
+        self.hasrun = True
+        self.after_run()
+        self.cleanup()
+
+    def after_run():
+        self.score = self.silhouette()
+        self.outpath.mkdir(parents=True, exist_ok=True)
+        print(self.outpath/(self.name+".feather"))
+        self.cluster_data.to_feather(self.outpath/(self.name + ".feather"))
+
+
+    def cleanup(self):
+        super().cleanup()
+        self.step1 = None
+
 @dataclass
 class clustering_result:
     outpath:Path

clustering/grid_sweep.py

@@ -31,3 +31,19 @@ class grid_sweep:
         outcsv = Path(outcsv)
         outcsv.parent.mkdir(parents=True, exist_ok=True)
         self.infos.to_csv(outcsv)
+
+
+class twoway_grid_sweep(grid_sweep):
+    def __init__(self, jobtype, inpath, outpath, namer, args1, args2, *args, **kwargs):
+        self.jobtype = jobtype
+        self.namer = namer
+        prod1 = product(* args1.values())
+        prod2 = product(* args2.values())
+        grid1 = [dict(zip(args1.keys(), pargs)) for pargs in prod1]
+        grid2 = [dict(zip(args2.keys(), pargs)) for pargs in prod2]
+        grid = product(grid1, grid2)
+        inpath = Path(inpath)
+        outpath = Path(outpath)
+        self.hasrun = False
+        self.grid = [(inpath,outpath,namer(**(g[0] | g[1])), g[0], g[1], *args) for g in grid]
+        self.jobs = [jobtype(*g) for g in self.grid]

clustering/lsi_base.py

@@ -1,5 +1,5 @@
 from clustering_base import clustering_job, clustering_result
-from grid_sweep import grid_sweep
+from grid_sweep import grid_sweep, twoway_grid_sweep
 from dataclasses import dataclass
 from itertools import chain
 from pathlib import Path
@@ -27,3 +27,18 @@ class lsi_grid_sweep(grid_sweep):
         self.hasrun = False
         self.subgrids = [self.subsweep(lsi_path, outpath,  lsi_dim, *args, **kwargs) for lsi_dim, lsi_path in zip(lsi_nums, lsi_paths)]
         self.jobs = list(chain(*map(lambda gs: gs.jobs, self.subgrids)))
+
+class twoway_lsi_grid_sweep(twoway_grid_sweep):
+    def __init__(self, jobtype, subsweep, inpath, lsi_dimensions, outpath, args1, args2):
+        self.jobtype = jobtype
+        self.subsweep = subsweep
+        inpath = Path(inpath)
+        if lsi_dimensions == 'all':
+            lsi_paths = list(inpath.glob("*.feather"))
+        else:
+            lsi_paths = [inpath / (str(dim) + '.feather') for dim in lsi_dimensions]
+
+        lsi_nums = [int(p.stem) for p in lsi_paths]
+        self.hasrun = False
+        self.subgrids = [self.subsweep(lsi_path, outpath, lsi_dim, args1, args2) for lsi_dim, lsi_path in zip(lsi_nums, lsi_paths)]
+        self.jobs = list(chain(*map(lambda gs: gs.jobs, self.subgrids)))

clustering/umap_hdbscan_clustering.py

@@ -0,0 +1,230 @@
+from clustering_base import clustering_result, clustering_job, twoway_clustering_job
+from hdbscan_clustering import hdbscan_clustering_result
+import umap
+from grid_sweep import twoway_grid_sweep
+from dataclasses import dataclass
+import hdbscan
+from sklearn.neighbors import NearestNeighbors
+import plotnine as pn
+import numpy as np
+from itertools import product, starmap, chain
+import pandas as pd
+from multiprocessing import cpu_count
+import fire
+
+def test_select_hdbscan_clustering():
+    # select_hdbscan_clustering("/gscratch/comdata/output/reddit_similarity/subreddit_comment_authors-tf_30k_LSI",
+    #                           "test_hdbscan_author30k",
+    #                           min_cluster_sizes=[2],
+    #                           min_samples=[1,2],
+    #                           cluster_selection_epsilons=[0,0.05,0.1,0.15],
+    #                           cluster_selection_methods=['eom','leaf'],
+    #                           lsi_dimensions='all')
+    inpath = "/gscratch/comdata/output/reddit_similarity/subreddit_comment_authors-tf_10k_LSI"
+    outpath = "test_umap_hdbscan_lsi"
+    min_cluster_sizes=[2,3,4]
+    min_samples=[1,2,3]
+    cluster_selection_epsilons=[0,0.1,0.3,0.5]
+    cluster_selection_methods=[1]
+    lsi_dimensions='all'
+    n_neighbors = [5,10,15,25,35,70,100]
+    learning_rate = [0.1,0.5,1,2]
+    min_dist = [0.5,1,1.5,2]
+    local_connectivity = [1,2,3,4,5]
+
+    hdbscan_params = {"min_cluster_sizes":min_cluster_sizes, "min_samples":min_samples, "cluster_selection_epsilons":cluster_selection_epsilons, "cluster_selection_methods":cluster_selection_methods}
+    umap_params = {"n_neighbors":n_neighbors, "learning_rate":learning_rate, "min_dist":min_dist, "local_connectivity":local_connectivity}
+    gs = umap_hdbscan_grid_sweep(inpath, "all", outpath, hdbscan_params,umap_params)
+
+    # gs.run(20)
+    # gs.save("test_hdbscan/lsi_sweep.csv")
+
+
+    # job1 = hdbscan_lsi_job(infile=inpath, outpath=outpath, name="test", lsi_dims=500, min_cluster_size=2, min_samples=1,cluster_selection_epsilon=0,cluster_selection_method='eom')
+    # job1.run()
+    # print(job1.get_info())
+
+    # df = pd.read_csv("test_hdbscan/selection_data.csv")
+    # test_select_hdbscan_clustering()
+    # check_clusters = pd.read_feather("test_hdbscan/500_2_2_0.1_eom.feather")
+    # silscores = pd.read_feather("test_hdbscan/silhouette_samples500_2_2_0.1_eom.feather")
+    # c = check_clusters.merge(silscores,on='subreddit')#    fire.Fire(select_hdbscan_clustering)
+class umap_hdbscan_grid_sweep(twoway_grid_sweep):
+    def __init__(self,
+                 inpath,
+                 outpath,
+                 umap_params,
+                 hdbscan_params):
+
+        super().__init__(umap_hdbscan_job, inpath, outpath, self.namer, umap_params, hdbscan_params)
+
+    def namer(self,
+              min_cluster_size,
+              min_samples,
+              cluster_selection_epsilon,
+              cluster_selection_method,
+              n_components,
+              n_neighbors,
+              learning_rate,
+              min_dist,
+              local_connectivity,
+              densmap
+              ):
+        return f"mcs-{min_cluster_size}_ms-{min_samples}_cse-{cluster_selection_epsilon}_csm-{cluster_selection_method}_nc-{n_components}_nn-{n_neighbors}_lr-{learning_rate}_md-{min_dist}_lc-{local_connectivity}_dm-{densmap}"
+
+@dataclass
+class umap_hdbscan_clustering_result(hdbscan_clustering_result):
+    n_components:int
+    n_neighbors:int
+    learning_rate:float
+    min_dist:float
+    local_connectivity:int
+    densmap:bool
+
+class umap_hdbscan_job(twoway_clustering_job):
+    def __init__(self, infile, outpath, name,
+                 umap_args = {"n_components":2,"n_neighbors":15, "learning_rate":1, "min_dist":1, "local_connectivity":1,'densmap':False},
+                 hdbscan_args = {"min_cluster_size":2, "min_samples":1, "cluster_selection_epsilon":0, "cluster_selection_method":'eom'},
+                 *args,
+                 **kwargs):
+        super().__init__(infile,
+                         outpath,
+                         name,
+                         call1=umap_hdbscan_job._umap_embedding,
+                         call2=umap_hdbscan_job._hdbscan_clustering,
+                         args1=umap_args,
+                         args2=hdbscan_args,
+                         *args,
+                         **kwargs
+                         )
+
+        self.n_components = umap_args['n_components']
+        self.n_neighbors = umap_args['n_neighbors']
+        self.learning_rate = umap_args['learning_rate']
+        self.min_dist = umap_args['min_dist']
+        self.local_connectivity = umap_args['local_connectivity']
+        self.densmap = umap_args['densmap']
+        self.min_cluster_size = hdbscan_args['min_cluster_size']
+        self.min_samples = hdbscan_args['min_samples']
+        self.cluster_selection_epsilon = hdbscan_args['cluster_selection_epsilon']
+        self.cluster_selection_method = hdbscan_args['cluster_selection_method']
+
+    def after_run(self):
+        coords = self.step1.emedding_
+        self.cluster_data['x'] = coords[:,0]
+        self.cluster_data['y'] = coords[:,1]
+        super().after_run()
+
+
+    def _umap_embedding(mat, **umap_args):
+        print(f"running umap embedding. umap_args:{umap_args}")
+        umapmodel = umap.UMAP(metric='precomputed', **umap_args)
+        umapmodel = umapmodel.fit(mat)
+        return umapmodel
+
+    def _hdbscan_clustering(mat, umapmodel, **hdbscan_args):
+        print(f"running hdbascan clustering. hdbscan_args:{hdbscan_args}")
+        
+        umap_coords = umapmodel.transform(mat)
+
+        clusterer = hdbscan.HDBSCAN(metric='euclidean',
+                                    core_dist_n_jobs=cpu_count(),
+                                    **hdbscan_args
+                                    )
+    
+        clustering = clusterer.fit(umap_coords)
+    
+        return(clustering)
+
+    def get_info(self):
+        result = super().get_info()
+        self.result = umap_hdbscan_clustering_result(**result.__dict__,
+                                                     min_cluster_size=self.min_cluster_size,
+                                                     min_samples=self.min_samples,
+                                                     cluster_selection_epsilon=self.cluster_selection_epsilon,
+                                                     cluster_selection_method=self.cluster_selection_method,
+                                                     n_components = self.n_components,
+                                                     n_neighbors = self.n_neighbors,
+                                                     learning_rate = self.learning_rate,
+                                                     min_dist = self.min_dist,
+                                                     local_connectivity=self.local_connectivity,
+                                                     densmap=self.densmap
+                                                     )
+        return self.result
+
+def run_umap_hdbscan_grid_sweep(savefile, inpath, outpath, n_neighbors = [15], n_components=[2], learning_rate=[1], min_dist=[1], local_connectivity=[1],
+                                densmap=[False],
+                                min_cluster_sizes=[2], min_samples=[1], cluster_selection_epsilons=[0], cluster_selection_methods=['eom']):
+    """Run umap + hdbscan clustering once or more with different parameters.
+    
+    Usage:
+    umap_hdbscan_clustering.py --savefile=SAVEFILE --inpath=INPATH --outpath=OUTPATH --n_neighbors=<csv> --learning_rate=<csv> --min_dist=<csv> --local_connectivity=<csv> --min_cluster_sizes=<csv> --min_samples=<csv> --cluster_selection_epsilons=<csv> --cluster_selection_methods=<csv "eom"|"leaf">
+
+    Keword arguments:
+    savefile: path to save the metadata and diagnostics 
+    inpath: path to feather data containing a labeled matrix of subreddit similarities.
+    outpath: path to output fit kmeans clusterings.
+    n_neighbors: umap parameter takes integers greater than 1
+    learning_rate: umap parameter takes positive real values
+    min_dist: umap parameter takes positive real values
+    local_connectivity: umap parameter takes positive integers
+    min_cluster_sizes: one or more integers indicating the minumum cluster size
+    min_samples: one ore more integers indicating the minimum number of samples used in the algorithm
+    cluster_selection_epsilon: one or more similarity thresholds for transition from dbscan to hdbscan
+    cluster_selection_method: "eom" or "leaf" eom gives larger clusters. 
+    """    
+    
+    umap_args = {'n_neighbors':list(map(int, n_neighbors)),
+                 'learning_rate':list(map(float,learning_rate)),
+                 'min_dist':list(map(float,min_dist)),
+                 'local_connectivity':list(map(int,local_connectivity)),
+                 'n_components':list(map(int, n_components)),
+                 'densmap':list(map(bool,densmap))
+                 }
+
+    hdbscan_args = {'min_cluster_size':list(map(int,min_cluster_sizes)),
+                    'min_samples':list(map(int,min_samples)),
+                    'cluster_selection_epsilon':list(map(float,cluster_selection_epsilons)),
+                    'cluster_selection_method':cluster_selection_methods}
+
+    obj = umap_hdbscan_grid_sweep(inpath,
+                                  outpath,
+                                  umap_args,
+                                  hdbscan_args)
+    obj.run(cores=10)
+    obj.save(savefile)
+
+    
+def KNN_distances_plot(mat,outname,k=2):
+    nbrs = NearestNeighbors(n_neighbors=k,algorithm='auto',metric='precomputed').fit(mat)
+    distances, indices = nbrs.kneighbors(mat)
+    d2 = distances[:,-1]
+    df = pd.DataFrame({'dist':d2})
+    df = df.sort_values("dist",ascending=False)
+    df['idx'] = np.arange(0,d2.shape[0]) + 1
+    p = pn.qplot(x='idx',y='dist',data=df,geom='line') + pn.scales.scale_y_continuous(minor_breaks = np.arange(0,50)/50,
+                                                                                      breaks = np.arange(0,10)/10)
+    p.save(outname,width=16,height=10)
+    
+def make_KNN_plots():
+    similarities = "/gscratch/comdata/output/reddit_similarity/subreddit_comment_terms_10k.feather"
+    subreddits, mat = read_similarity_mat(similarities)
+    mat = sim_to_dist(mat)
+
+    KNN_distances_plot(mat,k=2,outname='terms_knn_dist2.png')
+
+    similarities = "/gscratch/comdata/output/reddit_similarity/subreddit_comment_authors_10k.feather"
+    subreddits, mat = read_similarity_mat(similarities)
+    mat = sim_to_dist(mat)
+    KNN_distances_plot(mat,k=2,outname='authors_knn_dist2.png')
+
+    similarities = "/gscratch/comdata/output/reddit_similarity/subreddit_comment_authors-tf_10k.feather"
+    subreddits, mat = read_similarity_mat(similarities)
+    mat = sim_to_dist(mat)
+    KNN_distances_plot(mat,k=2,outname='authors-tf_knn_dist2.png')
+
+if __name__ == "__main__":
+    fire.Fire(run_umap_hdbscan_grid_sweep)
+    
+#    test_select_hdbscan_clustering()
+    #fire.Fire(select_hdbscan_clustering)  

clustering/umap_hdbscan_clustering_lsi.py

@@ -0,0 +1,113 @@
+from umap_hdbscan_clustering import umap_hdbscan_job, umap_hdbscan_grid_sweep, umap_hdbscan_clustering_result
+from lsi_base import twoway_lsi_grid_sweep, lsi_mixin, lsi_result_mixin
+from grid_sweep import twoway_grid_sweep
+import fire
+from dataclasses import dataclass
+
+@dataclass
+class umap_hdbscan_clustering_result_lsi(umap_hdbscan_clustering_result, lsi_result_mixin):
+    pass 
+
+class umap_hdbscan_lsi_job(umap_hdbscan_job, lsi_mixin):
+    def __init__(self, infile, outpath, name, umap_args, hdbscan_args, lsi_dims):
+        super().__init__(
+            infile,
+            outpath,
+            name,
+            umap_args,
+            hdbscan_args
+        )
+        super().set_lsi_dims(lsi_dims)
+
+    def get_info(self):
+        partial_result = super().get_info()
+        self.result = umap_hdbscan_clustering_result_lsi(**partial_result.__dict__,
+                                                         lsi_dimensions=self.lsi_dims)
+        return self.result
+
+class umap_hdbscan_lsi_grid_sweep(twoway_lsi_grid_sweep):
+    def __init__(self,
+                 inpath,
+                 lsi_dims,
+                 outpath,
+                 umap_args,
+                 hdbscan_args
+                 ):
+
+        super().__init__(umap_hdbscan_lsi_job,
+                         _umap_hdbscan_lsi_grid_sweep,
+                         inpath,
+                         lsi_dims,
+                         outpath,
+                         umap_args,
+                         hdbscan_args
+                         )
+        
+
+
+class _umap_hdbscan_lsi_grid_sweep(twoway_grid_sweep):
+    def __init__(self,
+                 inpath,
+                 outpath,
+                 lsi_dim,
+                 umap_args,
+                 hdbscan_args,
+                 ):
+
+        self.lsi_dim = lsi_dim
+        self.jobtype = umap_hdbscan_lsi_job
+        super().__init__(self.jobtype, inpath, outpath, self.namer, umap_args, hdbscan_args, lsi_dim)
+
+
+    def namer(self, *args, **kwargs):
+        s = umap_hdbscan_grid_sweep.namer(self, *args, **kwargs)
+        s += f"_lsi-{self.lsi_dim}"
+        return s
+
+def run_umap_hdbscan_lsi_grid_sweep(savefile, inpath, outpath, n_neighbors = [15], n_components=[2], learning_rate=[1], min_dist=[1], local_connectivity=[1], 
+                                densmap=[False],
+                                    min_cluster_sizes=[2], min_samples=[1], cluster_selection_epsilons=[0], cluster_selection_methods=['eom'], lsi_dimensions='all'):
+    """Run hdbscan clustering once or more with different parameters.
+    
+    Usage:
+    hdbscan_clustering_lsi --savefile=SAVEFILE --inpath=INPATH --outpath=OUTPATH --min_cluster_sizes=<csv> --min_samples=<csv> --cluster_selection_epsilons=<csv> --cluster_selection_methods=[eom]> --lsi_dimensions: either "all" or one or more available lsi similarity dimensions at INPATH.
+
+    Keword arguments:
+    savefile: path to save the metadata and diagnostics 
+    inpath: path to folder containing feather files with LSI similarity labeled matrices of subreddit similarities.
+    outpath: path to output fit clusterings.
+    min_cluster_sizes: one or more integers indicating the minumum cluster size
+    min_samples: one ore more integers indicating the minimum number of samples used in the algorithm
+    cluster_selection_epsilons: one or more similarity thresholds for transition from dbscan to hdbscan
+    cluster_selection_methods: one or more of "eom" or "leaf" eom gives larger clusters. 
+    lsi_dimensions: either "all" or one or more available lsi similarity dimensions at INPATH.
+    """    
+
+
+    umap_args = {'n_neighbors':list(map(int, n_neighbors)),
+                 'learning_rate':list(map(float,learning_rate)),
+                 'min_dist':list(map(float,min_dist)),
+                 'local_connectivity':list(map(int,local_connectivity)),
+                 'n_components':list(map(int, n_components)),
+                 'densmap':list(map(bool,densmap))
+                 }
+
+    hdbscan_args = {'min_cluster_size':list(map(int,min_cluster_sizes)),
+                    'min_samples':list(map(int,min_samples)),
+                    'cluster_selection_epsilon':list(map(float,cluster_selection_epsilons)),
+                    'cluster_selection_method':cluster_selection_methods}
+
+    obj = umap_hdbscan_lsi_grid_sweep(inpath,
+                                      lsi_dimensions,
+                                      outpath,
+                                      umap_args,
+                                      hdbscan_args
+                                      )
+                                 
+
+    obj.run(10)
+    obj.save(savefile)
+
+
+if __name__ == "__main__":
+    fire.Fire(run_umap_hdbscan_lsi_grid_sweep)

datasets/checkpoint_parallelsql.sbatch

@@ -1,26 +0,0 @@
-#!/bin/bash
-## parallel_sql_job.sh
-#SBATCH --job-name=tf_subreddit_comments
-## Allocation Definition
-#SBATCH --account=comdata-ckpt
-#SBATCH --partition=ckpt
-## Resources
-## Nodes. This should always be 1 for parallel-sql.
-#SBATCH --nodes=1    
-## Walltime (12 hours)
-#SBATCH --time=12:00:00
-## Memory per node
-#SBATCH --mem=32G
-#SBATCH --cpus-per-task=4
-#SBATCH --ntasks=1
-#SBATCH -D /gscratch/comdata/users/nathante/cdsc-reddit
-source ./bin/activate
-module load parallel_sql
-echo $(which perl)
-conda list pyarrow
-which python3
-#Put here commands to load other modules (e.g. matlab etc.)
-#Below command means that parallel_sql will get tasks from the database
-#and run them on the node (in parallel). So a 16 core node will have
-#16 tasks running at one time.
-parallel-sql --sql -a parallel --exit-on-term --jobs 4

datasets/comments_2_parquet.sh

@@ -1,10 +1,10 @@
+#!/usr/bin/env bash
 ## needs to be run by hand since i don't have a nice way of waiting on a parallel-sql job to complete 
 
-#!/usr/bin/env bash
 echo "#!/usr/bin/bash" > job_script.sh
 #echo "source $(pwd)/../bin/activate" >> job_script.sh
 echo "python3 $(pwd)/comments_2_parquet_part1.py" >> job_script.sh
 
-srun -p comdata -A comdata --nodes=1 --mem=120G --time=48:00:00 --pty job_script.sh
+srun -p compute-bigmem -A comdata --nodes=1 --mem-per-cpu=9g -c 40 --time=120:00:00 --pty job_script.sh
 
 start_spark_and_run.sh 1 $(pwd)/comments_2_parquet_part2.py

datasets/comments_2_parquet_part1.py

@@ -1,12 +1,15 @@
 #!/usr/bin/env python3
+import os
 import json
 from datetime import datetime
 from multiprocessing import Pool
 from itertools import islice
-from helper import find_dumps, open_fileset
+from helper import open_input_file, find_dumps
 import pandas as pd
 import pyarrow as pa
 import pyarrow.parquet as pq
+from pathlib import Path
+import fire
 
 def parse_comment(comment, names= None):
     if names is None:
@@ -46,17 +49,12 @@ def parse_comment(comment, names= None):
 
 #    conf = sc._conf.setAll([('spark.executor.memory', '20g'), ('spark.app.name', 'extract_reddit_timeline'), ('spark.executor.cores', '26'), ('spark.cores.max', '26'), ('spark.driver.memory','84g'),('spark.driver.maxResultSize','0'),('spark.local.dir','/gscratch/comdata/spark_tmp')])
 
-dumpdir = "/gscratch/comdata/raw_data/reddit_dumps/comments/"
+def parse_dump(partition):
 
-files = list(find_dumps(dumpdir, base_pattern="RC_20*"))
+    dumpdir = f"/gscratch/comdata/raw_data/reddit_dumps/comments/{partition}"
 
-pool = Pool(28)
-
-stream = open_fileset(files)
-
-N = int(1e4)
-
-rows = pool.imap_unordered(parse_comment, stream, chunksize=int(N/28))
+    stream = open_input_file(dumpdir)
+    rows = map(parse_comment, stream)
 
     schema = pa.schema([
         pa.field('id', pa.string(), nullable=True),
@@ -78,33 +76,16 @@ schema = pa.schema([
         pa.field('error', pa.string(), nullable=True),
     ])
 
-from pathlib import Path
-p = Path("/gscratch/comdata/output/reddit_comments.parquet_temp2")
+    p = Path("/gscratch/comdata/output/temp/reddit_comments.parquet")
+    p.mkdir(exist_ok=True,parents=True)
 
-if not p.is_dir():
-    if p.exists():
-        p.unlink()
-    p.mkdir()
-
-else:
-    list(map(Path.unlink,p.glob('*')))
-
-part_size = int(1e7)
-part = 1
-n_output = 0
-writer = pq.ParquetWriter(f"/gscratch/comdata/output/reddit_comments.parquet_temp2/part_{part}.parquet",schema=schema,compression='snappy',flavor='spark')
+    N=10000
+    with pq.ParquetWriter(f"/gscratch/comdata/output/temp/reddit_comments.parquet/{partition}.parquet",
+                          schema=schema,
+                          compression='snappy',
+                          flavor='spark') as writer:
 
         while True:
-    if n_output > part_size:
-        if part > 1:
-            writer.close()
-
-        part = part + 1
-        n_output = 0
-    
-        writer = pq.ParquetWriter(f"/gscratch/comdata/output/reddit_comments.parquet_temp2/part_{part}.parquet",schema=schema,compression='snappy',flavor='spark')
-
-    n_output += N
             chunk = islice(rows,N)
             pddf = pd.DataFrame(chunk, columns=schema.names)
             table = pa.Table.from_pandas(pddf,schema=schema)
@@ -112,4 +93,19 @@ while True:
                 break
             writer.write_table(table)
 
+        writer.close()
+
+
+def gen_task_list(dumpdir="/gscratch/comdata/raw_data/reddit_dumps/comments", overwrite=True):
+    files = list(find_dumps(dumpdir,base_pattern="RC_20*.*"))
+    with open("comments_task_list.sh",'w') as of:
+        for fpath in files:
+            partition = os.path.split(fpath)[1]
+            if (not Path(f"/gscratch/comdata/output/temp/reddit_comments.parquet/{partition}.parquet").exists()) or (overwrite is True):
+                of.write(f'python3 comments_2_parquet_part1.py parse_dump {partition}\n')
+
+
+if __name__ == '__main__':
+    fire.Fire({'parse_dump':parse_dump,
+              'gen_task_list':gen_task_list})
 

datasets/comments_2_parquet_part2.py

@@ -2,12 +2,19 @@
 
 # spark script to make sorted, and partitioned parquet files 
 
+import pyspark
 from pyspark.sql import functions as f
 from pyspark.sql import SparkSession
 
 spark = SparkSession.builder.getOrCreate()
 
-df = spark.read.parquet("/gscratch/comdata/output/reddit_comments.parquet_temp2",compression='snappy')
+conf = pyspark.SparkConf().setAppName("Reddit submissions to parquet")
+conf = conf.set("spark.sql.shuffle.partitions",2000)
+conf = conf.set('spark.sql.crossJoin.enabled',"true")
+conf = conf.set('spark.debug.maxToStringFields',200)
+sc = spark.sparkContext
+
+df = spark.read.parquet("/gscratch/comdata/output/temp/reddit_comments.parquet",compression='snappy')
 
 df = df.withColumn("subreddit_2", f.lower(f.col('subreddit')))
 df = df.drop('subreddit')
@@ -21,9 +28,9 @@ df = df.withColumn("Day",f.dayofmonth(f.col("CreatedAt")))
 df = df.repartition('subreddit')
 df2 = df.sort(["subreddit","CreatedAt","link_id","parent_id","Year","Month","Day"],ascending=True)
 df2 = df2.sortWithinPartitions(["subreddit","CreatedAt","link_id","parent_id","Year","Month","Day"],ascending=True)
-df2.write.parquet("/gscratch/comdata/users/nathante/reddit_comments_by_subreddit.parquet_new", mode='overwrite', compression='snappy')
+df2.write.parquet("/gscratch/scrubbed/comdata/output/reddit_comments_by_subreddit.parquet", mode='overwrite', compression='snappy')
 
 df = df.repartition('author')
 df3 = df.sort(["author","CreatedAt","subreddit","link_id","parent_id","Year","Month","Day"],ascending=True)
 df3 = df3.sortWithinPartitions(["author","CreatedAt","subreddit","link_id","parent_id","Year","Month","Day"],ascending=True)
-df3.write.parquet("/gscratch/comdata/users/nathante/reddit_comments_by_author.parquet_new", mode='overwrite',compression='snappy')
+df3.write.parquet("/gscratch/scrubbed/comdata/output/reddit_comments_by_author.parquet", mode='overwrite',compression='snappy')

datasets/helper.py

@@ -24,8 +24,7 @@ def open_fileset(files):
     for fh in files:
         print(fh)
         lines = open_input_file(fh)
-        for line in lines:
-            yield line
+        yield from lines
 
 def open_input_file(input_filename):
     if re.match(r'.*\.7z$', input_filename):
@@ -39,7 +38,7 @@ def open_input_file(input_filename):
     elif re.match(r'.*\.xz', input_filename):
         cmd = ["xzcat",'-dk', '-T 20',input_filename]
     elif re.match(r'.*\.zst',input_filename):
-        cmd = ['zstd','-dck', input_filename]
+        cmd = ['/kloneusr/bin/zstd','-dck', input_filename,  '--memory=2048MB --stdout']
     elif re.match(r'.*\.gz',input_filename):
         cmd = ['gzip','-dc', input_filename]
     try:

datasets/job_script.sh

@@ -1,4 +1,4 @@
 #!/usr/bin/bash
 start_spark_cluster.sh
-spark-submit --master spark://$(hostname):18899 weekly_cosine_similarities.py term --outfile=/gscratch/comdata/users/nathante/subreddit_term_similarity_weekly_5000.parquet --topN=5000
-stop-all.sh
+singularity exec  /gscratch/comdata/users/nathante/containers/nathante.sif spark-submit --master spark://$(hostname):7077 comments_2_parquet_part2.py 
+singularity exec /gscratch/comdata/users/nathante/containers/nathante.sif stop-all.sh

datasets/submissions_2_parquet.sh

@@ -1,8 +1,8 @@
+#!/usr/bin/env bash
 ## this should be run manually since we don't have a nice way to wait on parallel_sql jobs
 
-#!/usr/bin/env bash
 
-./parse_submissions.sh
+srun -p compute-bigmem -A comdata --nodes=1 --mem-per-cpu=9g -c 40 --time=120:00:00 python3 $(pwd)/submissions_2_parquet_part1.py gen_task_list
 
 start_spark_and_run.sh 1 $(pwd)/submissions_2_parquet_part2.py
 

datasets/submissions_2_parquet_part1.py

@@ -3,26 +3,23 @@
 # two stages:
 # 1. from gz to arrow parquet (this script) 
 # 2. from arrow parquet to spark parquet (submissions_2_parquet_part2.py)
-
 from datetime import datetime
-from multiprocessing import Pool
+from pathlib import Path
 from itertools import islice
 from helper import find_dumps, open_fileset
 import pandas as pd
 import pyarrow as pa
 import pyarrow.parquet as pq
-import simdjson
 import fire
 import os
-
-parser = simdjson.Parser()
+import json
 
 def parse_submission(post, names = None):
     if names is None:
         names = ['id','author','subreddit','title','created_utc','permalink','url','domain','score','ups','downs','over_18','has_media','selftext','retrieved_on','num_comments','gilded','edited','time_edited','subreddit_type','subreddit_id','subreddit_subscribers','name','is_self','stickied','quarantine','error']
 
     try:
-        post = parser.parse(post)
+        post = json.loads(post)
     except (ValueError) as e:
         #        print(e)
         #        print(post)
@@ -92,8 +89,7 @@ def parse_dump(partition):
         pa.field('quarantine',pa.bool_(),nullable=True),
         pa.field('error',pa.string(),nullable=True)])
 
-    if not os.path.exists("/gscratch/comdata/output/temp/reddit_submissions.parquet/"):
-        os.mkdir("/gscratch/comdata/output/temp/reddit_submissions.parquet/")
+    Path("/gscratch/comdata/output/temp/reddit_submissions.parquet/").mkdir(exist_ok=True,parents=True)
 
     with pq.ParquetWriter(f"/gscratch/comdata/output/temp/reddit_submissions.parquet/{partition}",schema=schema,compression='snappy',flavor='spark') as writer:
         while True:
@@ -108,7 +104,7 @@ def parse_dump(partition):
 
 def gen_task_list(dumpdir="/gscratch/comdata/raw_data/reddit_dumps/submissions"):
     files = list(find_dumps(dumpdir,base_pattern="RS_20*.*"))
-    with open("parse_submissions_task_list",'w') as of:
+    with open("submissions_task_list.sh",'w') as of:
         for fpath in files:
             partition = os.path.split(fpath)[1]
             of.write(f'python3 submissions_2_parquet_part1.py parse_dump {partition}\n')

density/overlap_density.py

@@ -4,9 +4,9 @@ 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
+# sys.path.append("..")
+# sys.path.append("../similarities")
+# from similarities.similarities_helper import pull_tfidf
 
 # this is the mean of the ratio of the overlap to the focal size.
 # mean shared membership per focal community member

dumps/check_comments_shas.py

@@ -8,7 +8,7 @@ import hashlib
 shasums1 = requests.get("https://files.pushshift.io/reddit/comments/sha256sum.txt").text
 #shasums2 = requests.get("https://files.pushshift.io/reddit/comments/daily/sha256sum.txt").text
 
-shasums = shasums1 + shasums2
+shasums = shasums1 
 dumpdir = "/gscratch/comdata/raw_data/reddit_dumps/comments"
 
 for l in shasums.strip().split('\n'):

ngrams/run_tf_jobs.sh

@@ -1,8 +1,6 @@
 #!/usr/bin/env bash
-module load parallel_sql
+
 source ./bin/activate
 python3 tf_comments.py gen_task_list
-psu --del --Y
-cat tf_task_list | psu --load
 
 for job in $(seq 1 50); do sbatch checkpoint_parallelsql.sbatch; done;

ngrams/sort_tf_comments.py

@@ -2,12 +2,17 @@
 
 from pyspark.sql import functions as f
 from pyspark.sql import SparkSession
+import fire
 
+def main(inparquet, outparquet, colname):
     spark = SparkSession.builder.getOrCreate()
-df = spark.read.parquet("/gscratch/comdata/users/nathante/reddit_tfidf_test.parquet_temp/")
+    df = spark.read.parquet(inparquet)
 
-df = df.repartition(2000,'term')
-df = df.sort(['term','week','subreddit'])
-df = df.sortWithinPartitions(['term','week','subreddit'])
+    df = df.repartition(2000,colname)
+    df = df.sort([colname,'week','subreddit'])
+    df = df.sortWithinPartitions([colname,'week','subreddit'])
 
-df.write.parquet("/gscratch/comdata/users/nathante/reddit_tfidf_test_sorted_tf.parquet_temp",mode='overwrite',compression='snappy')
+    df.write.parquet(outparquet,mode='overwrite',compression='snappy')
+
+if __name__ == '__main__':
+    fire.Fire(main)

ngrams/tf_comments.py

@@ -14,21 +14,29 @@ from nltk.util import ngrams
 import string
 from random import random
 from redditcleaner import clean
+from pathlib import Path
 
 # compute term frequencies for comments in each subreddit by week
-def weekly_tf(partition, mwe_pass = 'first'):
-    dataset = ds.dataset(f'/gscratch/comdata/output/reddit_comments_by_subreddit.parquet/{partition}', format='parquet')
-    if not os.path.exists("/gscratch/comdata/users/nathante/reddit_comment_ngrams_10p_sample/"):
-        os.mkdir("/gscratch/comdata/users/nathante/reddit_comment_ngrams_10p_sample/")
+def weekly_tf(partition, outputdir = '/gscratch/comdata/output/reddit_ngrams/', input_dir="/gscratch/comdata/output/reddit_comments_by_subreddit.parquet/", mwe_pass = 'first', excluded_users=None):
 
-    if not os.path.exists("/gscratch/comdata/users/nathante/reddit_tfidf_test_authors.parquet_temp/"):
-        os.mkdir("/gscratch/comdata/users/nathante/reddit_tfidf_test_authors.parquet_temp/")
+    dataset = ds.dataset(Path(input_dir)/partition, format='parquet')
+    outputdir = Path(outputdir)
+    samppath = outputdir / "reddit_comment_ngrams_10p_sample"
+
+    if not samppath.exists():
+        samppath.mkdir(parents=True, exist_ok=True)
 
     ngram_output = partition.replace("parquet","txt")
 
+    if excluded_users is not None:
+        excluded_users = set(map(str.strip,open(excluded_users)))
+        df = df.filter(~ (f.col("author").isin(excluded_users)))
+
+
+    ngram_path = samppath / ngram_output
     if mwe_pass == 'first':
-        if os.path.exists(f"/gscratch/comdata/output/reddit_ngrams/comment_ngrams_10p_sample/{ngram_output}"):
-            os.remove(f"/gscratch/comdata/output/reddit_ngrams/comment_ngrams_10p_sample/{ngram_output}")
+        if ngram_path.exists():
+            ngram_path.unlink()
     
     batches = dataset.to_batches(columns=['CreatedAt','subreddit','body','author'])
 
@@ -62,8 +70,10 @@ def weekly_tf(partition, mwe_pass = 'first'):
 
     subreddit_weeks = groupby(rows, lambda r: (r.subreddit, r.week))
 
+    mwe_path = outputdir / "multiword_expressions.feather"
+
     if mwe_pass != 'first':
-        mwe_dataset = pd.read_feather(f'/gscratch/comdata/output/reddit_ngrams/multiword_expressions.feather')
+        mwe_dataset = pd.read_feather(mwe_path)
         mwe_dataset = mwe_dataset.sort_values(['phrasePWMI'],ascending=False)
         mwe_phrases = list(mwe_dataset.phrase)
         mwe_phrases = [tuple(s.split(' ')) for s in mwe_phrases]
@@ -115,7 +125,7 @@ def weekly_tf(partition, mwe_pass = 'first'):
             for sentence in sentences:
                 if random() <= 0.1:
                     grams = list(chain(*map(lambda i : ngrams(sentence,i),range(4))))
-                    with open(f'/gscratch/comdata/output/reddit_ngrams/comment_ngrams_10p_sample/{ngram_output}','a') as gram_file:
+                    with open(ngram_path,'a') as gram_file:
                         for ng in grams:
                             gram_file.write(' '.join(ng) + '\n')
                 for token in sentence:
@@ -150,7 +160,14 @@ def weekly_tf(partition, mwe_pass = 'first'):
 
     outchunksize = 10000
     
-    with pq.ParquetWriter(f"/gscratch/comdata/output/reddit_ngrams/comment_terms.parquet/{partition}",schema=schema,compression='snappy',flavor='spark') as writer, pq.ParquetWriter(f"/gscratch/comdata/output/reddit_ngrams/comment_authors.parquet/{partition}",schema=author_schema,compression='snappy',flavor='spark') as author_writer:
+    termtf_outputdir = (outputdir / "comment_terms")
+    termtf_outputdir.mkdir(parents=True, exist_ok=True)
+    authortf_outputdir = (outputdir / "comment_authors")
+    authortf_outputdir.mkdir(parents=True, exist_ok=True)    
+    termtf_path = termtf_outputdir / partition
+    authortf_path = authortf_outputdir / partition
+    with pq.ParquetWriter(termtf_path, schema=schema, compression='snappy', flavor='spark') as writer, \
+         pq.ParquetWriter(authortf_path, schema=author_schema, compression='snappy', flavor='spark') as author_writer:
     
         while True:
 
@@ -179,12 +196,12 @@ def weekly_tf(partition, mwe_pass = 'first'):
         author_writer.close()
 
 
-def gen_task_list(mwe_pass='first'):
+def gen_task_list(mwe_pass='first', outputdir='/gscratch/comdata/output/reddit_ngrams/', tf_task_list='tf_task_list', excluded_users_file=None):
     files = os.listdir("/gscratch/comdata/output/reddit_comments_by_subreddit.parquet/")
-    with open("tf_task_list",'w') as outfile:
+    with open(tf_task_list,'w') as outfile:
         for f in files:
             if f.endswith(".parquet"):
-                outfile.write(f"./tf_comments.py weekly_tf --mwe-pass {mwe_pass} {f}\n")
+                outfile.write(f"./tf_comments.py weekly_tf --mwe-pass {mwe_pass} --outputdir {outputdir} --excluded_users {excluded_users_file} {f}\n")
 
 if __name__ == "__main__":
     fire.Fire({"gen_task_list":gen_task_list,

ngrams/top_comment_phrases.py

@@ -1,10 +1,17 @@
+#!/usr/bin/env python3
 from pyspark.sql import functions as f
 from pyspark.sql import Window
 from pyspark.sql import SparkSession
 import numpy as np
+import fire
+from pathlib import Path
 
+
+def main(ngram_dir="/gscratch/comdata/output/reddit_ngrams"):
     spark = SparkSession.builder.getOrCreate()
-df = spark.read.text("/gscratch/comdata/users/nathante/reddit_comment_ngrams_10p_sample/")
+    ngram_dir = Path(ngram_dir)
+    ngram_sample = ngram_dir / "reddit_comment_ngrams_10p_sample"
+    df = spark.read.text(str(ngram_sample))
 
     df = df.withColumnRenamed("value","phrase")
 
@@ -13,7 +20,6 @@ phrases = df.groupby('phrase').count()
     phrases = phrases.withColumnRenamed('count','phraseCount')
     phrases = phrases.filter(phrases.phraseCount > 10)
 
-
     # count overall
     N = phrases.select(f.sum(phrases.phraseCount).alias("phraseCount")).collect()[0].phraseCount
 
@@ -41,18 +47,23 @@ df = terms.select(['phrase','phraseCount','phraseLogProb','phrasePWMI'])
 
     df = df.sort(['phrasePWMI'],descending=True)
     df = df.sortWithinPartitions(['phrasePWMI'],descending=True)
-df.write.parquet("/gscratch/comdata/users/nathante/reddit_comment_ngrams_pwmi.parquet/",mode='overwrite',compression='snappy')
 
-df = spark.read.parquet("/gscratch/comdata/users/nathante/reddit_comment_ngrams_pwmi.parquet/")
+    pwmi_dir = ngram_dir / "reddit_comment_ngrams_pwmi.parquet/"
+    df.write.parquet(str(pwmi_dir), mode='overwrite', compression='snappy')
 
-df.write.csv("/gscratch/comdata/users/nathante/reddit_comment_ngrams_pwmi.csv/",mode='overwrite',compression='none')
+    df = spark.read.parquet(str(pwmi_dir))
 
-df = spark.read.parquet("/gscratch/comdata/users/nathante/reddit_comment_ngrams_pwmi.parquet")
+    df.write.csv(str(ngram_dir / "reddit_comment_ngrams_pwmi.csv/"),mode='overwrite',compression='none')
+
+    df = spark.read.parquet(str(pwmi_dir))
     df = df.select('phrase','phraseCount','phraseLogProb','phrasePWMI')
 
     # choosing phrases occurring at least 3500 times in the 10% sample (35000 times) and then with a PWMI of at least 3 yeids about 65000 expressions.
     #
     df = df.filter(f.col('phraseCount') > 3500).filter(f.col("phrasePWMI")>3)
     df = df.toPandas()
-df.to_feather("/gscratch/comdata/users/nathante/reddit_multiword_expressions.feather")
-df.to_csv("/gscratch/comdata/users/nathante/reddit_multiword_expressions.csv")
+    df.to_feather(ngram_dir / "multiword_expressions.feather")
+    df.to_csv(ngram_dir / "multiword_expressions.csv")
+
+if __name__ == '__main__':
+    fire.Fire(main)

similarities/Makefile

@@ -1,8 +1,10 @@
+
 #all: /gscratch/comdata/output/reddit_similarity/tfidf/comment_terms_130k.parquet /gscratch/comdata/output/reddit_similarity/tfidf/comment_authors_130k.parquet /gscratch/comdata/output/reddit_similarity/tfidf_weekly/comment_terms_130k.parquet /gscratch/comdata/output/reddit_similarity/tfidf_weekly/comment_authors_130k.parquet
-srun_singularity=source /gscratch/comdata/users/nathante/cdsc_reddit/bin/activate && srun_singularity.sh
-srun_singularity_huge=source /gscratch/comdata/users/nathante/cdsc_reddit/bin/activate && srun_singularity_huge.sh
-base_data=/gscratch/comdata/output
-similarity_data=${base_data}/reddit_similarity
+# srun_singularity=source /gscratch/comdata/users/nathante/cdsc_reddit/bin/activate && srun_singularity.sh
+# srun_singularity_huge=source /gscratch/comdata/users/nathante/cdsc_reddit/bin/activate && srun_singularity_huge.sh
+srun=srun -p compute-bigmem -A comdata --mem-per-cpu=9g --time=200:00:00 -c 40 
+srun_huge=srun -p compute-hugemem -A comdata --mem-per-cpu=9g --time=200:00:00 -c 40 
+similarity_data=/gscratch/scrubbed/comdata/reddit_similarity
 tfidf_data=${similarity_data}/tfidf
 tfidf_weekly_data=${similarity_data}/tfidf_weekly
 similarity_weekly_data=${similarity_data}/weekly
@@ -10,7 +12,10 @@ lsi_components=[10,50,100,200,300,400,500,600,700,850,1000,1500]
 
 lsi_similarities: ${similarity_data}/subreddit_comment_terms_10k_LSI ${similarity_data}/subreddit_comment_authors-tf_10k_LSI ${similarity_data}/subreddit_comment_authors_10k_LSI ${similarity_data}/subreddit_comment_terms_30k_LSI ${similarity_data}/subreddit_comment_authors-tf_30k_LSI ${similarity_data}/subreddit_comment_authors_30k_LSI
 
-all: ${tfidf_data}/comment_terms_100k.parquet ${tfidf_data}/comment_terms_30k.parquet ${tfidf_data}/comment_terms_10k.parquet ${tfidf_data}/comment_authors_100k.parquet ${tfidf_data}/comment_authors_30k.parquet ${tfidf_data}/comment_authors_10k.parquet ${similarity_data}/subreddit_comment_authors_30k.feather ${similarity_data}/subreddit_comment_authors_10k.feather  ${similarity_data}/subreddit_comment_terms_10k.feather ${similarity_data}/subreddit_comment_terms_30k.feather ${similarity_data}/subreddit_comment_authors-tf_30k.feather ${similarity_data}/subreddit_comment_authors-tf_10k.feather ${similarity_data}/subreddit_comment_terms_100k.feather ${similarity_data}/subreddit_comment_authors_100k.feather ${similarity_data}/subreddit_comment_authors-tf_100k.feather ${similarity_weekly_data}/comment_terms.parquet
+
+all: ${tfidf_data}/comment_terms_30k.parquet ${tfidf_data}/comment_terms_10k.parquet ${tfidf_data}/comment_authors_30k.parquet ${tfidf_data}/comment_authors_10k.parquet ${similarity_data}/subreddit_comment_authors_30k.feather ${similarity_data}/subreddit_comment_authors_10k.feather  ${similarity_data}/subreddit_comment_terms_10k.feather ${similarity_data}/subreddit_comment_terms_30k.feather ${similarity_data}/subreddit_comment_authors-tf_30k.feather ${similarity_data}/subreddit_comment_authors-tf_10k.feather
+
+#all: ${tfidf_data}/comment_terms_100k.parquet ${tfidf_data}/comment_terms_30k.parquet ${tfidf_data}/comment_terms_10k.parquet ${tfidf_data}/comment_authors_100k.parquet ${tfidf_data}/comment_authors_30k.parquet ${tfidf_data}/comment_authors_10k.parquet ${similarity_data}/subreddit_comment_authors_30k.feather ${similarity_data}/subreddit_comment_authors_10k.feather  ${similarity_data}/subreddit_comment_terms_10k.feather ${similarity_data}/subreddit_comment_terms_30k.feather ${similarity_data}/subreddit_comment_authors-tf_30k.feather ${similarity_data}/subreddit_comment_authors-tf_10k.feather ${similarity_data}/subreddit_comment_terms_100k.feather ${similarity_data}/subreddit_comment_authors_100k.feather ${similarity_data}/subreddit_comment_authors-tf_100k.feather ${similarity_weekly_data}/comment_terms.parquet
 
 #${tfidf_weekly_data}/comment_terms_100k.parquet ${tfidf_weekly_data}/comment_authors_100k.parquet ${tfidf_weekly_data}/comment_terms_30k.parquet ${tfidf_weekly_data}/comment_authors_30k.parquet ${similarity_weekly_data}/comment_terms_100k.parquet ${similarity_weekly_data}/comment_authors_100k.parquet  ${similarity_weekly_data}/comment_terms_30k.parquet ${similarity_weekly_data}/comment_authors_30k.parquet
 
@@ -18,103 +23,106 @@ all: ${tfidf_data}/comment_terms_100k.parquet ${tfidf_data}/comment_terms_30k.pa
 
 # all: /gscratch/comdata/output/reddit_similarity/subreddit_comment_terms_25000.parquet /gscratch/comdata/output/reddit_similarity/subreddit_comment_authors_25000.parquet /gscratch/comdata/output/reddit_similarity/subreddit_comment_authors_10000.parquet /gscratch/comdata/output/reddit_similarity/comment_terms_10000_weekly.parquet
 
-${similarity_weekly_data}/comment_terms.parquet: weekly_cosine_similarities.py similarities_helper.py /gscratch/comdata/output/reddit_ngrams/comment_terms.parquet ${similarity_data}/subreddits_by_num_comments.csv ${tfidf_weekly_data}/comment_terms.parquet
-	${srun_singularity} python3 weekly_cosine_similarities.py terms --topN=10000 --outfile=${similarity_weekly_data}/comment_terms.parquet
+${similarity_weekly_data}/comment_terms.parquet: weekly_cosine_similarities.py similarities_helper.py /gscratch/comdata/output/reddit_ngrams/comment_terms.parquet ${similarity_data}/subreddits_by_num_comments_nonsfw.csv ${tfidf_weekly_data}/comment_terms.parquet
+	 ${srun} python3 weekly_cosine_similarities.py terms --topN=10000 --outfile=${similarity_weekly_data}/comment_terms.parquet
 
 ${similarity_data}/subreddit_comment_terms_10k.feather: ${tfidf_data}/comment_terms_100k.parquet similarities_helper.py
-	${srun_singularity} python3 cosine_similarities.py term --outfile=${similarity_data}/subreddit_comment_terms_10k.feather --topN=10000
+	 ${srun} python3 cosine_similarities.py term --outfile=${similarity_data}/subreddit_comment_terms_10k.feather --topN=10000
 
 ${similarity_data}/subreddit_comment_terms_10k_LSI: ${tfidf_data}/comment_terms_100k.parquet similarities_helper.py
-	${srun_singularity} python3 lsi_similarities.py term --outfile=${similarity_data}/subreddit_comment_terms_10k_LSI --topN=10000 --n_components=${lsi_components} --min_df=200
+	 ${srun_huge} python3 lsi_similarities.py term --outfile=${similarity_data}/subreddit_comment_terms_10k_LSI --topN=10000 --n_components=${lsi_components} --min_df=200
 
 ${similarity_data}/subreddit_comment_terms_30k_LSI: ${tfidf_data}/comment_terms_100k.parquet similarities_helper.py
-	${srun_singularity} python3 lsi_similarities.py term --outfile=${similarity_data}/subreddit_comment_terms_30k_LSI --topN=30000 --n_components=${lsi_components} --min_df=200
+	 ${srun_huge} python3 lsi_similarities.py term --outfile=${similarity_data}/subreddit_comment_terms_30k_LSI --topN=30000 --n_components=${lsi_components} --min_df=200 --inpath=$<
 
 ${similarity_data}/subreddit_comment_terms_30k.feather: ${tfidf_data}/comment_terms_30k.parquet similarities_helper.py
-	${srun_singularity} python3 cosine_similarities.py term --outfile=${similarity_data}/subreddit_comment_terms_30k.feather --topN=30000
+	 ${srun_huge} python3 cosine_similarities.py term --outfile=${similarity_data}/subreddit_comment_terms_30k.feather --topN=30000 --inpath=$<
 
 ${similarity_data}/subreddit_comment_authors_30k.feather: ${tfidf_data}/comment_authors_30k.parquet similarities_helper.py
-	${srun_singularity} python3 cosine_similarities.py author --outfile=${similarity_data}/subreddit_comment_authors_30k.feather --topN=30000
+	 ${srun_huge} python3 cosine_similarities.py author --outfile=${similarity_data}/subreddit_comment_authors_30k.feather --topN=30000 --inpath=$<
 
 ${similarity_data}/subreddit_comment_authors_10k.feather: ${tfidf_data}/comment_authors_10k.parquet similarities_helper.py
-	${srun_singularity} python3 cosine_similarities.py author --outfile=${similarity_data}/subreddit_comment_authors_10k.feather --topN=10000
+	 ${srun_huge} python3 cosine_similarities.py author --outfile=${similarity_data}/subreddit_comment_authors_10k.feather --topN=10000 --inpath=$<
 
 ${similarity_data}/subreddit_comment_authors_10k_LSI: ${tfidf_data}/comment_authors_100k.parquet similarities_helper.py
-	${srun_singularity} python3 lsi_similarities.py author --outfile=${similarity_data}/subreddit_comment_authors_10k_LSI --topN=10000 --n_components=${lsi_components} --min_df=2
+	 ${srun_huge} python3 lsi_similarities.py author --outfile=${similarity_data}/subreddit_comment_authors_10k_LSI --topN=10000 --n_components=${lsi_components} --min_df=10 --inpath=$<
 
 ${similarity_data}/subreddit_comment_authors_30k_LSI: ${tfidf_data}/comment_authors_100k.parquet similarities_helper.py
-	${srun_singularity} python3 lsi_similarities.py author --outfile=${similarity_data}/subreddit_comment_authors_30k_LSI --topN=30000 --n_components=${lsi_components} --min_df=2
+	 ${srun_huge} python3 lsi_similarities.py author --outfile=${similarity_data}/subreddit_comment_authors_30k_LSI --topN=30000 --n_components=${lsi_components} --min_df=10 --inpath=$<
 
-${similarity_data}/subreddit_comment_authors-tf_30k.feather: ${tfidf_data}/comment_authors_30k.parquet similarities_helper.py
-	${srun_singularity} python3 cosine_similarities.py author-tf --outfile=${similarity_data}/subreddit_comment_authors-tf_30k.feather --topN=30000
+${similarity_data}/subreddit_comment_authors-tf_30k.feather: ${tfidf_data}/comment_authors_100k.parquet similarities_helper.py
+	 ${srun} python3 cosine_similarities.py author-tf --outfile=${similarity_data}/subreddit_comment_authors-tf_30k.feather --topN=30000 --inpath=$<
 
-${similarity_data}/subreddit_comment_authors-tf_10k.feather: ${tfidf_data}/comment_authors_10k.parquet similarities_helper.py
-	${srun_singularity} python3 cosine_similarities.py author-tf --outfile=${similarity_data}/subreddit_comment_authors-tf_10k.feather --topN=10000
+${similarity_data}/subreddit_comment_authors-tf_10k.feather: ${tfidf_data}/comment_authors_100k.parquet similarities_helper.py
+	 ${srun} python3 cosine_similarities.py author-tf --outfile=${similarity_data}/subreddit_comment_authors-tf_10k.feather --topN=10000
 
 ${similarity_data}/subreddit_comment_authors-tf_10k_LSI: ${tfidf_data}/comment_authors_100k.parquet similarities_helper.py
-	${srun_singularity} python3 lsi_similarities.py author-tf --outfile=${similarity_data}/subreddit_comment_authors-tf_10k_LSI --topN=10000 --n_components=${lsi_components} --min_df=2
+	 ${srun_huge} python3 lsi_similarities.py author-tf --outfile=${similarity_data}/subreddit_comment_authors-tf_10k_LSI --topN=10000 --n_components=${lsi_components} --min_df=10 --inpath=$<
 
 ${similarity_data}/subreddit_comment_authors-tf_30k_LSI: ${tfidf_data}/comment_authors_100k.parquet similarities_helper.py
-	${srun_singularity} python3 lsi_similarities.py author-tf --outfile=${similarity_data}/subreddit_comment_authors-tf_30k_LSI --topN=30000 --n_components=${lsi_components} --min_df=2
+	 ${srun_huge} python3 lsi_similarities.py author-tf --outfile=${similarity_data}/subreddit_comment_authors-tf_30k_LSI --topN=30000 --n_components=${lsi_components} --min_df=10 --inpath=$<
 
 ${similarity_data}/subreddit_comment_terms_100k.feather: ${tfidf_data}/comment_terms_100k.parquet similarities_helper.py
-	${srun_singularity} python3 cosine_similarities.py term --outfile=${similarity_data}/subreddit_comment_terms_100k.feather --topN=100000
+	 ${srun} python3 cosine_similarities.py term --outfile=${similarity_data}/subreddit_comment_terms_100k.feather --topN=100000
 
 ${similarity_data}/subreddit_comment_authors_100k.feather: ${tfidf_data}/comment_authors_100k.parquet similarities_helper.py
-	${srun_singularity} python3 cosine_similarities.py author --outfile=${similarity_data}/subreddit_comment_authors_100k.feather --topN=100000
+	 ${srun} python3 cosine_similarities.py author --outfile=${similarity_data}/subreddit_comment_authors_100k.feather --topN=100000
 
 ${similarity_data}/subreddit_comment_authors-tf_100k.feather: ${tfidf_data}/comment_authors_100k.parquet similarities_helper.py
-	${srun_singularity} python3 cosine_similarities.py author-tf --outfile=${similarity_data}/subreddit_comment_authors-tf_100k.feather --topN=100000
+	 ${srun} python3 cosine_similarities.py author-tf --outfile=${similarity_data}/subreddit_comment_authors-tf_100k.feather --topN=100000
 
-${tfidf_data}/comment_terms_100k.feather/: /gscratch/comdata/output/reddit_ngrams/comment_terms.parquet ${similarity_data}/subreddits_by_num_comments.csv
-	mkdir -p ${tfidf_data}/
-	start_spark_and_run.sh 4 tfidf.py terms --topN=100000 --outpath=${tfidf_data}/comment_terms_100k.feather 
+${similarity_data}/subreddits_by_num_comments_nonsfw.csv:
+	start_spark_and_run.sh 3 top_subreddits_by_comments.py
 
-${tfidf_data}/comment_terms_30k.feather: /gscratch/comdata/output/reddit_ngrams/comment_terms.parquet ${similarity_data}/subreddits_by_num_comments.csv
-	mkdir -p ${tfidf_data}/
-	start_spark_and_run.sh 4 tfidf.py terms --topN=30000 --outpath=${tfidf_data}/comment_terms_30k.feather
+${tfidf_data}/comment_terms_100k.parquet: /gscratch/comdata/output/reddit_ngrams/comment_terms.parquet ${similarity_data}/subreddits_by_num_comments_nonsfw.csv
+#	mkdir -p ${tfidf_data}/
+	start_spark_and_run.sh 3 tfidf.py terms --topN=100000 --inpath=$< --outpath=${tfidf_data}/comment_terms_100k.parquet
 
-${tfidf_data}/comment_terms_10k.feather: /gscratch/comdata/output/reddit_ngrams/comment_terms.parquet ${similarity_data}/subreddits_by_num_comments.csv
-	mkdir -p ${tfidf_data}/
-	start_spark_and_run.sh 4 tfidf.py terms --topN=10000 --outpath=${tfidf_data}/comment_terms_10k.feather
+${tfidf_data}/comment_terms_30k.feather: /gscratch/comdata/output/reddit_ngrams/comment_terms.parquet ${similarity_data}/subreddits_by_num_comments_nonsfw.csv
+#	mkdir -p ${tfidf_data}/
+	start_spark_and_run.sh 3 tfidf.py terms --topN=30000 --inpath=$< --outpath=${tfidf_data}/comment_terms_30k.feather
 
-${tfidf_data}/comment_authors_100k.feather: /gscratch/comdata/output/reddit_ngrams/comment_authors.parquet ${similarity_data}/subreddits_by_num_comments.csv
-	mkdir -p ${tfidf_data}/
-	start_spark_and_run.sh 4 tfidf.py authors --topN=100000 --outpath=${tfidf_data}/comment_authors_100k.feather
+${tfidf_data}/comment_terms_10k.feather: /gscratch/comdata/output/reddit_ngrams/comment_terms.parquet ${similarity_data}/subreddits_by_num_comments_nonsfw.csv
+#	mkdir -p ${tfidf_data}/
+	start_spark_and_run.sh 3 tfidf.py terms --topN=10000 --inpath=$< --outpath=${tfidf_data}/comment_terms_10k.feather
 
-${tfidf_data}/comment_authors_10k.parquet: /gscratch/comdata/output/reddit_ngrams/comment_authors.parquet ${similarity_data}/subreddits_by_num_comments.csv
-	mkdir -p ${tfidf_data}/
-	start_spark_and_run.sh 4 tfidf.py authors --topN=10000 --outpath=${tfidf_data}/comment_authors_10k.parquet
+${tfidf_data}/comment_authors_100k.parquet: /gscratch/comdata/output/reddit_ngrams/comment_authors.parquet ${similarity_data}/subreddits_by_num_comments_nonsfw.csv
+#	mkdir -p ${tfidf_data}/
+	start_spark_and_run.sh 3 tfidf.py authors --topN=100000 --inpath=$< --outpath=${tfidf_data}/comment_authors_100k.parquet
 
-${tfidf_data}/comment_authors_30k.parquet: /gscratch/comdata/output/reddit_ngrams/comment_authors.parquet ${similarity_data}/subreddits_by_num_comments.csv
-	mkdir -p ${tfidf_data}/
-	start_spark_and_run.sh 4 tfidf.py authors --topN=30000 --outpath=${tfidf_data}/comment_authors_30k.parquet
+${tfidf_data}/comment_authors_10k.parquet: /gscratch/comdata/output/reddit_ngrams/comment_authors.parquet ${similarity_data}/subreddits_by_num_comments_nonsfw.csv
+#	mkdir -p ${tfidf_data}/
+	start_spark_and_run.sh 3 tfidf.py authors --topN=10000 --inpath=$< --outpath=${tfidf_data}/comment_authors_10k.parquet
 
-${tfidf_data}/tfidf_weekly/comment_terms_100k.parquet: /gscratch/comdata/output/reddit_ngrams/comment_terms.parquet ${similarity_data}/subreddits_by_num_comments.csv
-	start_spark_and_run.sh 4 tfidf.py terms_weekly --topN=100000 --outpath=${similarity_data}/tfidf_weekly/comment_authors_100k.parquet
+${tfidf_data}/comment_authors_30k.parquet: /gscratch/comdata/output/reddit_ngrams/comment_authors.parquet ${similarity_data}/subreddits_by_num_comments_nonsfw.csv
+#	mkdir -p ${tfidf_data}/
+	start_spark_and_run.sh 3 tfidf.py authors --topN=30000 --inpath=$< --outpath=${tfidf_data}/comment_authors_30k.parquet
+
+${tfidf_data}/tfidf_weekly/comment_terms_100k.parquet: /gscratch/comdata/output/reddit_ngrams/comment_terms.parquet ${similarity_data}/subreddits_by_num_comments_nonsfw.csv
+	start_spark_and_run.sh 3 tfidf.py terms_weekly --topN=100000 --outpath=${similarity_data}/tfidf_weekly/comment_authors_100k.parquet
 
 ${tfidf_data}/tfidf_weekly/comment_authors_100k.parquet: /gscratch/comdata/output/reddit_ngrams/comment_terms.parquet ${similarity_data}/subreddits_by_ppnum_comments.csv
-	start_spark_and_run.sh 4 tfidf.py authors_weekly --topN=100000 --outpath=${tfidf_weekly_data}/comment_authors_100k.parquet
+	start_spark_and_run.sh 3 tfidf.py authors_weekly --topN=100000 --inpath=$< --outpath=${tfidf_weekly_data}/comment_authors_100k.parquet
 
-${tfidf_weekly_data}/comment_terms_30k.parquet:  /gscratch/comdata/output/reddit_ngrams/comment_terms.parquet ${similarity_data}/subreddits_by_num_comments.csv
-	start_spark_and_run.sh 2 tfidf.py terms_weekly --topN=30000 --outpath=${tfidf_weekly_data}/comment_authors_30k.parquet
+${tfidf_weekly_data}/comment_terms_30k.parquet:  /gscratch/comdata/output/reddit_ngrams/comment_terms.parquet ${similarity_data}/subreddits_by_num_comments_nonsfw.csv
+	start_spark_and_run.sh 2 tfidf.py terms_weekly --topN=30000 --inpath=$< --outpath=${tfidf_weekly_data}/comment_authors_30k.parquet
 
-${tfidf_weekly_data}/comment_authors_30k.parquet: /gscratch/comdata/output/reddit_ngrams/comment_terms.parquet ${similarity_data}/subreddits_by_num_comments.csv
-	start_spark_and_run.sh 4 tfidf.py authors_weekly --topN=30000 --outpath=${tfidf_weekly_data}/comment_authors_30k.parquet
+${tfidf_weekly_data}/comment_authors_30k.parquet: /gscratch/comdata/output/reddit_ngrams/comment_terms.parquet ${similarity_data}/subreddits_by_num_comments_nonsfw.csv
+	start_spark_and_run.sh 3 tfidf.py authors_weekly --topN=30000 --inpath=$< --outpath=${tfidf_weekly_data}/comment_authors_30k.parquet
 
 ${similarity_weekly_data}/comment_terms_100k.parquet: weekly_cosine_similarities.py similarities_helper.py ${tfidf_weekly_data}/comment_terms_100k.parquet
-	${srun_singularity} python3 weekly_cosine_similarities.py terms --topN=100000 --outfile=${similarity_weekly_data}/comment_authors_100k.parquet
+	 ${srun} python3 weekly_cosine_similarities.py terms --topN=100000 --outfile=${similarity_weekly_data}/comment_terms_100k.parquet
 
-${similarity_weekly_data}/comment_authors_100k.parquet: weekly_cosine_similarities.py similarities_helper.py /gscratch/comdata/output/reddit_ngrams/comment_terms.parquet ${similarity_data}/subreddits_by_num_comments.csv ${tfidf_weekly_data}/comment_authors_100k.parquet
-	${srun_singularity} python3 weekly_cosine_similarities.py authors --topN=100000 --outfile=${similarity_weekly_data}/comment_authors_100k.parquet
+${similarity_weekly_data}/comment_authors_100k.parquet: weekly_cosine_similarities.py similarities_helper.py /gscratch/comdata/output/reddit_ngrams/comment_terms.parquet ${similarity_data}/subreddits_by_num_comments_nonsfw.csv ${tfidf_weekly_data}/comment_authors_100k.parquet
+	 ${srun} python3 weekly_cosine_similarities.py authors --topN=100000 --outfile=${similarity_weekly_data}/comment_authors_100k.parquet
 
-${similarity_weekly_data}/comment_terms_30k.parquet: weekly_cosine_similarities.py similarities_helper.py /gscratch/comdata/output/reddit_ngrams/comment_terms.parquet ${similarity_data}/subreddits_by_num_comments.csv ${tfidf_weekly_data}/comment_terms_30k.parquet
-	${srun_singularity} python3 weekly_cosine_similarities.py terms --topN=30000 --outfile=${similarity_weekly_data}/comment_authors_30k.parquet
+${similarity_weekly_data}/comment_terms_30k.parquet: weekly_cosine_similarities.py similarities_helper.py /gscratch/comdata/output/reddit_ngrams/comment_terms.parquet ${similarity_data}/subreddits_by_num_comments_nonsfw.csv ${tfidf_weekly_data}/comment_terms_30k.parquet
+	 ${srun} python3 weekly_cosine_similarities.py terms --topN=30000 --outfile=${similarity_weekly_data}/comment_authors_30k.parquet
 
-${similarity_weekly_data}/comment_authors_30k.parquet: weekly_cosine_similarities.py similarities_helper.py /gscratch/comdata/output/reddit_ngrams/comment_terms.parquet ${similarity_data}/subreddits_by_num_comments.csv ${tfidf_weekly_data}/comment_authors_30k.parquet
-	${srun_singularity} python3 weekly_cosine_similarities.py authors --topN=30000 --outfile=${similarity_weekly_data}/comment_authors_30k.parquet
+,${similarity_weekly_data}/comment_authors_30k.parquet: weekly_cosine_similarities.py similarities_helper.py /gscratch/comdata/output/reddit_ngrams/comment_terms.parquet ${similarity_data}/subreddits_by_num_comments_nonsfw.csv ${tfidf_weekly_data}/comment_authors_30k.parquet
+	 ${srun} python3 weekly_cosine_similarities.py authors --topN=30000 --outfile=${similarity_weekly_data}/comment_authors_30k.parquet
 
-# ${tfidf_weekly_data}/comment_authors_130k.parquet: tfidf.py similarities_helper.py /gscratch/comdata/output/reddit_ngrams/comment_authors.parquet /gscratch/comdata/output/reddit_similarity/subreddits_by_num_comments.csv
+# ${tfidf_weekly_data}/comment_authors_130k.parquet: tfidf.py similarities_helper.py /gscratch/comdata/output/reddit_ngrams/comment_authors.parquet /gscratch/comdata/output/reddit_similarity/subreddits_by_num_comments_nonsfw.csv
 # 	start_spark_and_run.sh 1 tfidf.py authors_weekly --topN=130000
 
 # /gscratch/comdata/output/reddit_similarity/comment_authors_10000.parquet: cosine_similarities.py similarities_helper.py /gscratch/comdata/output/reddit_similarity/tfidf/comment_authors.parquet /gscratch/comdata/output/reddit_similarity/tfidf/comment_authors.parquet 

similarities/job_script.sh

@@ -1,4 +1,4 @@
 #!/usr/bin/bash
 start_spark_cluster.sh
-singularity exec  /gscratch/comdata/users/nathante/cdsc_base.sif spark-submit --master spark://$(hostname):7077 top_subreddits_by_comments.py 
-singularity exec /gscratch/comdata/users/nathante/cdsc_base.sif stop-all.sh
+singularity exec  /gscratch/comdata/users/nathante/containers/nathante.sif spark-submit --master spark://$(hostname):7077 tfidf.py authors --topN=100000 --inpath=/gscratch/comdata/output/reddit_ngrams/comment_authors.parquet --outpath=/gscratch/scrubbed/comdata/reddit_similarity/tfidf/comment_authors_100k.parquet
+singularity exec /gscratch/comdata/users/nathante/containers/nathante.sif stop-all.sh

similarities/lsi_similarities.py

@@ -5,19 +5,20 @@ from similarities_helper import *
 #from similarities_helper import similarities, lsi_column_similarities
 from functools import partial
 
-inpath = "/gscratch/comdata/users/nathante/competitive_exclusion_reddit/data/tfidf/comment_terms_compex.parquet/"
-term_colname='term'
-outfile='/gscratch/comdata/users/nathante/competitive_exclusion_reddit/data/similarity/comment_terms_compex_LSI'
-n_components=[10,50,100]
-included_subreddits="/gscratch/comdata/users/nathante/competitive_exclusion_reddit/data/included_subreddits.txt"
-n_iter=5
-random_state=1968
-algorithm='arpack'
-topN = None
-from_date=None
-to_date=None
-min_df=None
-max_df=None
+# inpath = "/gscratch/comdata/users/nathante/competitive_exclusion_reddit/data/tfidf/comment_authors_compex.parquet"
+# term_colname='authors'
+# outfile='/gscratch/comdata/users/nathante/competitive_exclusion_reddit/data/similarity/comment_test_compex_LSI'
+# n_components=[10,50,100]
+# included_subreddits="/gscratch/comdata/users/nathante/competitive_exclusion_reddit/data/included_subreddits.txt"
+# n_iter=5
+# random_state=1968
+# algorithm='randomized'
+# topN = None
+# from_date=None
+# to_date=None
+# min_df=None
+# max_df=None
+
 def lsi_similarities(inpath, term_colname, outfile, min_df=None, max_df=None, included_subreddits=None, topN=None, from_date=None, to_date=None, tfidf_colname='tf_idf',n_components=100,n_iter=5,random_state=1968,algorithm='arpack',lsi_model=None):
     print(n_components,flush=True)
 
@@ -62,7 +63,7 @@ def author_lsi_similarities(inpath='/gscratch/comdata/output/reddit_similarity/t
                             n_components=n_components
                                )
 
-def author_tf_similarities(inpath='/gscratch/comdata/output/reddit_similarity/tfidf/comment_authors_100k.parquet',outfile=None, min_df=2, max_df=None, included_subreddits=None, topN=None, from_date=None, to_date=None,n_components=300,n_iter=5,random_state=1968):
+def author_tf_similarities(inpath='/gscratch/comdata/output/reddit_similarity/tfidf/comment_authors_100k.parquet',outfile=None, min_df=2, max_df=None, included_subreddits=None, topN=None, from_date=None, to_date=None,algorithm='arpack',n_components=300,n_iter=5,random_state=1968):
     return lsi_similarities(inpath,
                             'author',
                             outfile,

similarities/similarities_helper.py

@@ -262,6 +262,7 @@ def lsi_column_similarities(tfidfmat,n_components=300,n_iter=10,random_state=196
 
     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'))
 
     sims_list = []

similarities/tfidf.py

@@ -2,9 +2,12 @@ import fire
 from pyspark.sql import SparkSession
 from pyspark.sql import functions as f
 from similarities_helper import tfidf_dataset, build_weekly_tfidf_dataset, select_topN_subreddits
+from functools import partial
 
-def _tfidf_wrapper(func, inpath, outpath, topN, term_colname, exclude, included_subreddits):
-    spark = SparkSession.builder.getOrCreate()y
+inpath = '/gscratch/comdata/users/nathante/competitive_exclusion_reddit/data/tfidf/comment_authors_compex.parquet'
+# include_terms is a path to a parquet file that contains a column of term_colname + '_id' to include.
+def _tfidf_wrapper(func, inpath, outpath, topN, term_colname, exclude, included_subreddits, included_terms=None, min_df=None, max_df=None):
+    spark = SparkSession.builder.getOrCreate()
 
     df = spark.read.parquet(inpath)
 
@@ -15,50 +18,71 @@ def _tfidf_wrapper(func, inpath, outpath, topN, term_colname, exclude, included_
     else:
         include_subs = select_topN_subreddits(topN)
 
-    dfwriter = func(df, include_subs, term_colname)
+    include_subs = spark.sparkContext.broadcast(include_subs)
+
+    #    term_id = term_colname + "_id"
+
+    if included_terms is not None:
+        terms_df = spark.read.parquet(included_terms)
+        terms_df = terms_df.select(term_colname).distinct()
+        df = df.join(terms_df, on=term_colname, how='left_semi')
+
+    dfwriter = func(df, include_subs.value, term_colname)
 
     dfwriter.parquet(outpath,mode='overwrite',compression='snappy')
     spark.stop()
 
-def tfidf(inpath, outpath, topN, term_colname, exclude, included_subreddits):
-    return _tfidf_wrapper(tfidf_dataset, inpath, outpath, topN, term_colname, exclude, included_subreddits)
+def tfidf(inpath, outpath, topN, term_colname, exclude, included_subreddits, min_df, max_df):
+    tfidf_func = partial(tfidf_dataset, max_df=max_df, min_df=min_df)
+    return _tfidf_wrapper(tfidf_func, inpath, outpath, topN, term_colname, exclude, included_subreddits)
+
+def tfidf_weekly(inpath, outpath, static_tfidf_path, topN, term_colname, exclude, included_subreddits):
+    return _tfidf_wrapper(build_weekly_tfidf_dataset, inpath, outpath, topN, term_colname, exclude, included_subreddits, included_terms=static_tfidf_path)
 
-def tfidf_weekly(inpath, outpath, topN, term_colname, exclude, included_subreddits):
-    return _tfidf_wrapper(build_weekly_tfidf_dataset, inpath, outpath, topN, term_colname, exclude, included_subreddits)
 
 def tfidf_authors(inpath="/gscratch/comdata/output/reddit_ngrams/comment_authors.parquet",
                   outpath='/gscratch/comdata/output/reddit_similarity/tfidf/comment_authors.parquet',
                   topN=None,
-                  included_subreddits=None):
+                  included_subreddits=None,
+                  min_df=None,
+                  max_df=None):
 
     return tfidf(inpath,
                  outpath,
                  topN,
                  'author',
                  ['[deleted]','AutoModerator'],
-                 included_subreddits=included_subreddits
+                 included_subreddits=included_subreddits,
+                 min_df=min_df,
+                 max_df=max_df
                  )
 
 def tfidf_terms(inpath="/gscratch/comdata/output/reddit_ngrams/comment_terms.parquet",
                 outpath='/gscratch/comdata/output/reddit_similarity/tfidf/comment_terms.parquet',
                 topN=None,
-                included_subreddits=None):
+                included_subreddits=None,
+                min_df=None,
+                max_df=None):
 
     return tfidf(inpath,
                  outpath,
                  topN,
                  'term',
                  [],
-                 included_subreddits=included_subreddits
+                 included_subreddits=included_subreddits,
+                 min_df=min_df,
+                 max_df=max_df
                  )
 
 def tfidf_authors_weekly(inpath="/gscratch/comdata/output/reddit_ngrams/comment_authors.parquet",
+                         static_tfidf_path="/gscratch/comdata/output/reddit_similarity/tfidf/comment_authors.parquet",
                          outpath='/gscratch/comdata/output/reddit_similarity/tfidf_weekly/comment_authors.parquet',
                          topN=None,
                          included_subreddits=None):
 
     return tfidf_weekly(inpath,
                         outpath,
+                        static_tfidf_path,
                         topN,
                         'author',
                         ['[deleted]','AutoModerator'],
@@ -66,6 +90,7 @@ def tfidf_authors_weekly(inpath="/gscratch/comdata/output/reddit_ngrams/comment_
                         )
 
 def tfidf_terms_weekly(inpath="/gscratch/comdata/output/reddit_ngrams/comment_terms.parquet",
+                       static_tfidf_path="/gscratch/comdata/output/reddit_similarity/tfidf/comment_terms.parquet",
                        outpath='/gscratch/comdata/output/reddit_similarity/tfidf_weekly/comment_terms.parquet',
                        topN=None,
                        included_subreddits=None):
@@ -73,6 +98,7 @@ def tfidf_terms_weekly(inpath="/gscratch/comdata/output/reddit_ngrams/comment_te
 
     return tfidf_weekly(inpath,
                         outpath,
+                        static_tfidf_path,
                         topN,
                         'term',
                         [],

similarities/top_subreddits_by_comments.py

@@ -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_nsfw.csv', index=False)
+df.to_csv('/gscratch/scrubbed/comdata/reddit_similarity/subreddits_by_num_comments_nonsfw.csv', index=False)

similarities/weekly_cosine_similarities.py

@@ -13,18 +13,23 @@ from similarities_helper import pull_tfidf, column_similarities, write_weekly_si
 from scipy.sparse import csr_matrix
 from multiprocessing import Pool, cpu_count
 from functools import partial
+import pickle
 
-infile = "/gscratch/comdata/output/reddit_similarity/tfidf_weekly/comment_authors_10k.parquet"
-tfidf_path = "/gscratch/comdata/users/nathante/competitive_exclusion_reddit/data/tfidf/comment_authors_compex.parquet"
-min_df=None
-included_subreddits="/gscratch/comdata/users/nathante/competitive_exclusion_reddit/data/included_subreddits.txt"
-max_df = None
-topN=100
-term_colname='author'
-# outfile = '/gscratch/comdata/output/reddit_similarity/weekly/comment_authors_test.parquet'
-# included_subreddits=None
+# tfidf_path = "/gscratch/comdata/users/nathante/competitive_exclusion_reddit/data/similarity_weekly/comment_authors_tfidf.parquet"
+# #tfidf_path = "/gscratch/comdata/users/nathante/competitive_exclusion_reddit/data//comment_authors_compex.parquet"
+# min_df=2
+# included_subreddits="/gscratch/comdata/users/nathante/competitive_exclusion_reddit/data/included_subreddits.txt"
+# max_df = None
+# topN=100
+# term_colname='author'
+# # outfile = '/gscratch/comdata/output/reddit_similarity/weekly/comment_authors_test.parquet'
+# # included_subreddits=None
+outfile="/gscratch/comdata/users/nathante/competitive_exclusion_reddit/data/similarity_weekly/comment_authors.parquet"; infile="/gscratch/comdata/users/nathante/competitive_exclusion_reddit/data/tfidf_weekly/comment_authors_tfidf.parquet"; included_subreddits="/gscratch/comdata/users/nathante/competitive_exclusion_reddit/data/included_subreddits.txt"; lsi_model="/gscratch/comdata/users/nathante/competitive_exclusion_reddit/data/similarity/comment_authors_compex_LSI/2000_authors_LSIMOD.pkl"; n_components=1500; algorithm="randomized"; term_colname='author'; tfidf_path=infile; random_state=1968;
 
-def _week_similarities(week, simfunc, tfidf_path, term_colname, min_df, max_df, included_subreddits, topN, outdir:Path, subreddit_names, nterms):
+# static_tfidf = "/gscratch/comdata/users/nathante/competitive_exclusion_reddit/data/tfidf/comment_authors_compex.parquet"
+# dftest = spark.read.parquet(static_tfidf)
+
+def _week_similarities(week, simfunc, tfidf_path, term_colname, included_subreddits, outdir:Path, subreddit_names, nterms, topN=None, min_df=None, max_df=None):
     term = term_colname
     term_id = term + '_id'
     term_id_new = term + '_id_new'
@@ -32,20 +37,19 @@ def _week_similarities(week, simfunc, tfidf_path, term_colname, min_df, max_df,
 
     entries = pull_tfidf(infile = tfidf_path,
                          term_colname=term_colname,
-                         min_df=min_df,
-                         max_df=max_df,
                          included_subreddits=included_subreddits,
                          topN=topN,
-                         week=week,
+                         week=week.isoformat(),
                          rescale_idf=False)
     
     tfidf_colname='tf_idf'
     # if the max subreddit id we found is less than the number of subreddit names then we have to fill in 0s
     mat = csr_matrix((entries[tfidf_colname],(entries[term_id_new]-1, entries.subreddit_id_new-1)),shape=(nterms,subreddit_names.shape[0]))
-
     print('computing similarities')
+    print(simfunc)
     sims = simfunc(mat)
     del mat
+    sims = next(sims)[0]
     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
@@ -56,18 +60,20 @@ def pull_weeks(batch):
     return set(batch.to_pandas()['week'])
 
 # This requires a prefit LSI model, since we shouldn't fit different LSI models for every week. 
-def cosine_similarities_weekly_lsi(n_components=100, lsi_model=None, *args, **kwargs):
+def cosine_similarities_weekly_lsi(*args, n_components=100, lsi_model=None, **kwargs):
+    print(args)
+    print(kwargs)
     term_colname= kwargs.get('term_colname')
-    #lsi_model = "/gscratch/comdata/users/nathante/competitive_exclusion_reddit/data/similarity/comment_terms_compex_LSI/1000_term_LSIMOD.pkl"
+    # lsi_model = "/gscratch/comdata/users/nathante/competitive_exclusion_reddit/data/similarity/comment_authors_compex_LSI/1000_author_LSIMOD.pkl"
 
-    # simfunc = partial(lsi_column_similarities,n_components=n_components,n_iter=n_iter,random_state=random_state,algorithm='randomized',lsi_model_load=lsi_model)
-
-    simfunc = partial(lsi_column_similarities,n_components=n_components,n_iter=kwargs.get('n_iter'),random_state=kwargs.get('random_state'),algorithm=kwargs.get('algorithm'),lsi_model_load=lsi_model)
+    lsi_model = pickle.load(open(lsi_model,'rb'))
+    #simfunc = partial(lsi_column_similarities,n_components=n_components,random_state=random_state,algorithm='randomized',lsi_model=lsi_model)
+    simfunc = partial(lsi_column_similarities,n_components=n_components,random_state=kwargs.get('random_state'),lsi_model=lsi_model)
 
     return cosine_similarities_weekly(*args, simfunc=simfunc, **kwargs)
 
 #tfidf = spark.read.parquet('/gscratch/comdata/users/nathante/subreddit_tfidf_weekly.parquet')
-def cosine_similarities_weekly(tfidf_path, outfile, term_colname, min_df = None, max_df=None, included_subreddits = None, topN = 500, simfunc=column_similarities):
+def cosine_similarities_weekly(tfidf_path, outfile, term_colname, included_subreddits = None, topN = None, simfunc=column_similarities, min_df=None,max_df=None):
     print(outfile)
     # do this step in parallel if we have the memory for it.
     # should be doable with pool.map
@@ -84,12 +90,14 @@ def cosine_similarities_weekly(tfidf_path, outfile, term_colname, min_df = None,
     spark.stop()
 
     print(f"computing weekly similarities")
-    week_similarities_helper = partial(_week_similarities,simfunc=simfunc, tfidf_path=tfidf_path, term_colname=term_colname, outdir=outfile, min_df=min_df,max_df=max_df,included_subreddits=included_subreddits,topN=topN, subreddit_names=subreddit_names,nterms=nterms)
+    week_similarities_helper = partial(_week_similarities,simfunc=simfunc, tfidf_path=tfidf_path, term_colname=term_colname, outdir=outfile, min_df=min_df, max_df=max_df, included_subreddits=included_subreddits, topN=None, subreddit_names=subreddit_names,nterms=nterms)
 
-    pool = Pool(cpu_count())
+    for week in weeks:
+        week_similarities_helper(week)
+    # pool = Pool(cpu_count())
         
-    list(pool.imap(week_similarities_helper,weeks))
-    pool.close()
+    # list(pool.imap(week_similarities_helper, weeks))
+    # pool.close()
     #    with Pool(cpu_count()) as pool: # maybe it can be done with 40 cores on the huge machine?
 
 
@@ -97,10 +105,11 @@ def author_cosine_similarities_weekly(outfile, infile='/gscratch/comdata/output/
     return cosine_similarities_weekly(infile,
                                       outfile,
                                       'author',
-                                      min_df,
                                       max_df,
                                       included_subreddits,
-                                      topN)
+                                      topN,
+                                      min_df=2
+)
 
 def term_cosine_similarities_weekly(outfile, infile='/gscratch/comdata/output/reddit_similarity/tfidf_weekly/comment_terms.parquet', min_df=None, max_df=None, included_subreddits=None, topN=None):
         return cosine_similarities_weekly(infile,
@@ -112,32 +121,29 @@ def term_cosine_similarities_weekly(outfile, infile='/gscratch/comdata/output/re
                                           topN)
 
 
-def author_cosine_similarities_weekly_lsi(outfile, infile = '/gscratch/comdata/output/reddit_similarity/tfidf_weekly/comment_authors_test.parquet', min_df=2, max_df=None, included_subreddits=None, topN=None,n_components=100,lsi_model=None):
+def author_cosine_similarities_weekly_lsi(outfile, infile = '/gscratch/comdata/output/reddit_similarity/tfidf_weekly/comment_authors_test.parquet', included_subreddits=None, n_components=100,lsi_model=None):
     return cosine_similarities_weekly_lsi(infile,
                                           outfile,
                                           'author',
-                                          min_df,
-                                          max_df,
-                                          included_subreddits,
-                                          topN,
+                                          included_subreddits=included_subreddits,
                                           n_components=n_components,
-                                          lsi_model=lsi_model)
+                                          lsi_model=lsi_model
+                                          )
 
 
-def term_cosine_similarities_weekly_lsi(outfile, infile = '/gscratch/comdata/output/reddit_similarity/tfidf_weekly/comment_terms.parquet', min_df=None, max_df=None, included_subreddits=None, topN=500,n_components=100,lsi_model=None):
+def term_cosine_similarities_weekly_lsi(outfile, infile = '/gscratch/comdata/output/reddit_similarity/tfidf_weekly/comment_terms.parquet', included_subreddits=None, n_components=100,lsi_model=None):
         return cosine_similarities_weekly_lsi(infile,
                                               outfile,
                                               'term',
-                                              min_df,
-                                              max_df,
-                                              included_subreddits,
-                                              topN,
+                                              included_subreddits=included_subreddits,
                                               n_components=n_components,
-                                              lsi_model=lsi_model)
+                                              lsi_model=lsi_model,
+                                              )
 
 if __name__ == "__main__":
     fire.Fire({'authors':author_cosine_similarities_weekly,
                'terms':term_cosine_similarities_weekly,
                'authors-lsi':author_cosine_similarities_weekly_lsi,
-               'terms-lsi':term_cosine_similarities_weekly
+               'terms-lsi':term_cosine_similarities_weekly_lsi
                })
+

timeseries/cluster_timeseries.py

@@ -12,10 +12,6 @@ def build_cluster_timeseries(term_clusters_path="/gscratch/comdata/output/reddit
          author_densities_path="/gscratch/comdata/output/reddit_density/comment_authors_10000.feather",
          output="data/subreddit_timeseries.parquet"):
 
-
-    clusters = load_clusters(term_clusters_path, author_clusters_path)
-    densities = load_densities(term_densities_path, author_densities_path)
-    
     spark = SparkSession.builder.getOrCreate()
     
     df = spark.read.parquet("/gscratch/comdata/output/reddit_comments_by_subreddit.parquet")
@@ -26,11 +22,15 @@ def build_cluster_timeseries(term_clusters_path="/gscratch/comdata/output/reddit
     ts = df.select(['subreddit','week','author']).distinct().groupby(['subreddit','week']).count()
     
     ts = ts.repartition('subreddit')
-    spk_clusters = spark.createDataFrame(clusters)
 
-    ts = ts.join(spk_clusters, on='subreddit', how='inner')
+    if term_densities_path is not None and author_densities_path is not None:
+        densities = load_densities(term_densities_path, author_densities_path)
         spk_densities = spark.createDataFrame(densities)
         ts = ts.join(spk_densities, on='subreddit', how='inner')
+    
+    clusters = load_clusters(term_clusters_path, author_clusters_path)
+    spk_clusters = spark.createDataFrame(clusters)
+    ts = ts.join(spk_clusters, on='subreddit', how='inner')
     ts.write.parquet(output, mode='overwrite')
 
 if __name__ == "__main__":