176 lines
7.4 KiB
Python
176 lines
7.4 KiB
Python
from clustering_base import sim_to_dist, process_clustering_result, clustering_result, read_similarity_mat
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from dataclasses import dataclass
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import hdbscan
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from sklearn.neighbors import NearestNeighbors
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import plotnine as pn
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import numpy as np
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from itertools import product, starmap
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import pandas as pd
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from sklearn.metrics import silhouette_score, silhouette_samples
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from pathlib import Path
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from multiprocessing import Pool, cpu_count
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import fire
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from pyarrow.feather import write_feather
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def test_select_hdbscan_clustering():
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select_hdbscan_clustering("/gscratch/comdata/output/reddit_similarity/subreddit_comment_authors-tf_30k_LSI",
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"test_hdbscan_author30k",
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min_cluster_sizes=[2],
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min_samples=[1,2],
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cluster_selection_epsilons=[0,0.05,0.1,0.15],
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cluster_selection_methods=['eom','leaf'],
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lsi_dimensions='all')
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inpath = "/gscratch/comdata/output/reddit_similarity/subreddit_comment_authors-tf_30k_LSI"
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outpath = "test_hdbscan";
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min_cluster_sizes=[2,3,4];
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min_samples=[1,2,3];
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cluster_selection_epsilons=[0,0.1,0.3,0.5];
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cluster_selection_methods=['eom'];
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lsi_dimensions='all'
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df = pd.read_csv("test_hdbscan/selection_data.csv")
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test_select_hdbscan_clustering()
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check_clusters = pd.read_feather("test_hdbscan/500_2_2_0.1_eom.feather")
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silscores = pd.read_feather("test_hdbscan/silhouette_samples500_2_2_0.1_eom.feather")
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c = check_clusters.merge(silscores,on='subreddit')# fire.Fire(select_hdbscan_clustering)
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@dataclass
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class hdbscan_clustering_result(clustering_result):
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min_cluster_size:int
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min_samples:int
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cluster_selection_epsilon:float
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cluster_selection_method:str
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lsi_dimensions:int
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n_isolates:int
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silhouette_samples:str
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def select_hdbscan_clustering(inpath,
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outpath,
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outfile=None,
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min_cluster_sizes=[2],
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min_samples=[1],
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cluster_selection_epsilons=[0],
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cluster_selection_methods=['eom'],
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lsi_dimensions='all'
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):
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inpath = Path(inpath)
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outpath = Path(outpath)
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outpath.mkdir(exist_ok=True, parents=True)
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if lsi_dimensions == 'all':
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lsi_paths = list(inpath.glob("*"))
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else:
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lsi_paths = [inpath / (dim + '.feather') for dim in lsi_dimensions]
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lsi_nums = [p.stem for p in lsi_paths]
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grid = list(product(lsi_nums,
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min_cluster_sizes,
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min_samples,
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cluster_selection_epsilons,
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cluster_selection_methods))
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# fix the output file names
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names = list(map(lambda t:'_'.join(map(str,t)),grid))
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grid = [(inpath/(str(t[0])+'.feather'),outpath/(name + '.feather'), t[0], name) + t[1:] for t, name in zip(grid, names)]
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with Pool(int(cpu_count()/4)) as pool:
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mods = starmap(hdbscan_clustering, grid)
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res = pd.DataFrame(mods)
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if outfile is None:
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outfile = outpath / "selection_data.csv"
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res.to_csv(outfile)
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def hdbscan_clustering(similarities, output, lsi_dim, name, min_cluster_size=2, min_samples=1, cluster_selection_epsilon=0, cluster_selection_method='eom'):
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subreddits, mat = read_similarity_mat(similarities)
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mat = sim_to_dist(mat)
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clustering = _hdbscan_clustering(mat,
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min_cluster_size=min_cluster_size,
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min_samples=min_samples,
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cluster_selection_epsilon=cluster_selection_epsilon,
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cluster_selection_method=cluster_selection_method,
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metric='precomputed',
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core_dist_n_jobs=cpu_count()
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)
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cluster_data = process_clustering_result(clustering, subreddits)
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isolates = clustering.labels_ == -1
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scoremat = mat[~isolates][:,~isolates]
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score = silhouette_score(scoremat, clustering.labels_[~isolates], metric='precomputed')
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cluster_data.to_feather(output)
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silhouette_samp = silhouette_samples(mat, clustering.labels_, metric='precomputed')
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silhouette_samp = pd.DataFrame({'subreddit':subreddits,'score':silhouette_samp})
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silsampout = output.parent / ("silhouette_samples" + output.name)
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silhouette_samp.to_feather(silsampout)
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result = hdbscan_clustering_result(outpath=output,
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max_iter=None,
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silhouette_samples=silsampout,
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silhouette_score=score,
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alt_silhouette_score=score,
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name=name,
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min_cluster_size=min_cluster_size,
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min_samples=min_samples,
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cluster_selection_epsilon=cluster_selection_epsilon,
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cluster_selection_method=cluster_selection_method,
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lsi_dimensions=lsi_dim,
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n_isolates=isolates.sum(),
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n_clusters=len(set(clustering.labels_))
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)
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return(result)
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# for all runs we should try cluster_selection_epsilon = None
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# for terms we should try cluster_selection_epsilon around 0.56-0.66
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# for authors we should try cluster_selection_epsilon around 0.98-0.99
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def _hdbscan_clustering(mat, *args, **kwargs):
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print(f"running hdbscan clustering. args:{args}. kwargs:{kwargs}")
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print(mat)
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clusterer = hdbscan.HDBSCAN(*args,
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**kwargs,
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)
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clustering = clusterer.fit(mat.astype('double'))
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return(clustering)
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def KNN_distances_plot(mat,outname,k=2):
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nbrs = NearestNeighbors(n_neighbors=k,algorithm='auto',metric='precomputed').fit(mat)
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distances, indices = nbrs.kneighbors(mat)
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d2 = distances[:,-1]
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df = pd.DataFrame({'dist':d2})
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df = df.sort_values("dist",ascending=False)
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df['idx'] = np.arange(0,d2.shape[0]) + 1
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p = pn.qplot(x='idx',y='dist',data=df,geom='line') + pn.scales.scale_y_continuous(minor_breaks = np.arange(0,50)/50,
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breaks = np.arange(0,10)/10)
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p.save(outname,width=16,height=10)
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def make_KNN_plots():
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similarities = "/gscratch/comdata/output/reddit_similarity/subreddit_comment_terms_10k.feather"
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subreddits, mat = read_similarity_mat(similarities)
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mat = sim_to_dist(mat)
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KNN_distances_plot(mat,k=2,outname='terms_knn_dist2.png')
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similarities = "/gscratch/comdata/output/reddit_similarity/subreddit_comment_authors_10k.feather"
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subreddits, mat = read_similarity_mat(similarities)
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mat = sim_to_dist(mat)
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KNN_distances_plot(mat,k=2,outname='authors_knn_dist2.png')
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similarities = "/gscratch/comdata/output/reddit_similarity/subreddit_comment_authors-tf_10k.feather"
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subreddits, mat = read_similarity_mat(similarities)
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mat = sim_to_dist(mat)
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KNN_distances_plot(mat,k=2,outname='authors-tf_knn_dist2.png')
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if __name__ == "__main__":
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fire.Fire(select_hdbscan_clustering)
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