+++ /dev/null
-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)
projects / cdsc_reddit.git / blobdiff