65 lines
2.6 KiB
Python
Executable File
65 lines
2.6 KiB
Python
Executable File
#!/usr/bin/env python3
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# TODO: replace prints with logging.
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import sys
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import pandas as pd
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import numpy as np
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from sklearn.cluster import AffinityPropagation
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import fire
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from pathlib import Path
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def read_similarity_mat(similarities, use_threads=True):
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df = pd.read_feather(similarities, use_threads=use_threads)
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mat = np.array(df.drop('_subreddit',1))
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n = mat.shape[0]
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mat[range(n),range(n)] = 1
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return (df._subreddit,mat)
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def affinity_clustering(similarities, *args, **kwargs):
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subreddits, mat = read_similarity_mat(similarities)
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return _affinity_clustering(mat, subreddits, *args, **kwargs)
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def _affinity_clustering(mat, subreddits, output, damping=0.9, max_iter=100000, convergence_iter=30, preference_quantile=0.5, random_state=1968, verbose=True):
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'''
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similarities: feather file with a dataframe of similarity scores
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preference_quantile: parameter controlling how many clusters to make. higher values = more clusters. 0.85 is a good value with 3000 subreddits.
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damping: parameter controlling how iterations are merged. Higher values make convergence faster and more dependable. 0.85 is a good value for the 10000 subreddits by author.
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'''
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print(f"damping:{damping}; convergenceIter:{convergence_iter}; preferenceQuantile:{preference_quantile}")
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preference = np.quantile(mat,preference_quantile)
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print(f"preference is {preference}")
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print("data loaded")
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sys.stdout.flush()
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clustering = AffinityPropagation(damping=damping,
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max_iter=max_iter,
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convergence_iter=convergence_iter,
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copy=False,
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preference=preference,
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affinity='precomputed',
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verbose=verbose,
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random_state=random_state).fit(mat)
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print(f"clustering took {clustering.n_iter_} iterations")
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clusters = clustering.labels_
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print(f"found {len(set(clusters))} clusters")
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cluster_data = pd.DataFrame({'subreddit': subreddits,'cluster':clustering.labels_})
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cluster_sizes = cluster_data.groupby("cluster").count()
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print(f"the largest cluster has {cluster_sizes.subreddit.max()} members")
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print(f"the median cluster has {cluster_sizes.subreddit.median()} members")
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print(f"{(cluster_sizes.subreddit==1).sum()} clusters have 1 member")
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sys.stdout.flush()
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cluster_data.to_feather(output)
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print(f"saved {output}")
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return clustering
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if __name__ == "__main__":
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fire.Fire(affinity_clustering)
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