srun_singularity=source /gscratch/comdata/users/nathante/cdsc_reddit/bin/activate && srun_singularity.sh
similarity_data=/gscratch/comdata/output/reddit_similarity
clustering_data=/gscratch/comdata/output/reddit_clustering
-selection_grid="--max_iter=10000 --convergence_iter=15,30,100 --preference_quantile=0.85 --damping=0.5,0.6,0.7,0.8,0.85,0.9,0.95,0.97,0.99, --preference_quantile=0.1,0.3,0.5,0.7,0.9"
-all:$(clustering_data)/subreddit_comment_authors_30k.feather $(clustering_data)/subreddit_authors-tf_similarities_30k.feather $(clustering_data)/subreddit_comment_authors_10k.feather $(clustering_data)/subreddit_authors-tf_similarities_10k.feather $(clustering_data)/subreddit_comment_terms_30k.feather $(clustering_data)/subreddit_comment_terms_10k.feather
+kmeans_selection_grid=--max_iters=[3000] --n_inits=[10] --n_clusters=[100,500,1000,1250,1500,1750,2000]
+hdbscan_selection_grid=--min_cluster_sizes=[2,3,4,5] --min_samples=[2,3,4,5] --cluster_selection_epsilons=[0,0.01,0.05,0.1,0.15,0.2] --cluster_selection_methods=[eom,leaf]
+affinity_selection_grid=--dampings=[0.5,0.6,0.7,0.8,0.95,0.97,0.99] --preference_quantiles=[0.1,0.3,0.5,0.7,0.9] --convergence_iters=[15]
-$(clustering_data)/subreddit_comment_authors_10k.feather:selection.py $(similarity_data)/subreddit_comment_authors_10k.feather clustering.py
- $(srun_singularity) python3 selection.py $(similarity_data)/subreddit_comment_authors_10k.feather $(clustering_data)/subreddit_comment_authors_10k $(selection_grid) -J 20
+authors_10k_input=$(similarity_data)/subreddit_comment_authors_10k.feather
+authors_10k_input_lsi=$(similarity_data)/subreddit_comment_authors_10k_LSI
+authors_10k_output=$(clustering_data)/subreddit_comment_authors_10k
+authors_10k_output_lsi=$(clustering_data)/subreddit_comment_authors_10k_LSI
-$(clustering_data)/subreddit_comment_terms_10k.feather:selection.py $(similarity_data)/subreddit_comment_terms_10k.feather clustering.py
- $(srun_singularity) python3 selection.py $(similarity_data)/subreddit_comment_terms_10k.feather $(clustering_data)/subreddit_comment_terms_10k $(selection_grid) -J 20
+authors_tf_10k_input=$(similarity_data)/subreddit_comment_authors-tf_10k.feather
+authors_tf_10k_input_lsi=$(similarity_data)/subreddit_comment_authors-tf_10k_LSI
+authors_tf_10k_output=$(clustering_data)/subreddit_comment_authors-tf_10k
+authors_tf_10k_output_lsi=$(clustering_data)/subreddit_comment_authors-tf_10k_LSI
-$(clustering_data)/subreddit_authors-tf_similarities_10k.feather:clustering.py $(similarity_data)/subreddit_comment_authors-tf_10k.feather
- $(srun_singularity) python3 selection.py $(similarity_data)/subreddit_comment_authors-tf_10k.feather $(clustering_data)/subreddit_comment_authors-tf_10k $(selection_grid) -J 20
+terms_10k_input=$(similarity_data)/subreddit_comment_terms_10k.feather
+terms_10k_input_lsi=$(similarity_data)/subreddit_comment_terms_10k_LSI
+terms_10k_output=$(clustering_data)/subreddit_comment_terms_10k
+terms_10k_output_lsi=$(clustering_data)/subreddit_comment_terms_10k_LSI
-$(clustering_data)/subreddit_comment_authors_30k.feather: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 $(selection_grid) -J 10
+all:terms_10k authors_10k authors_tf_10k terms_10k_lsi authors_10k_lsi authors_tf_10k_lsi
-$(clustering_data)/subreddit_comment_terms_30k.feather:selection.py $(similarity_data)/subreddit_comment_terms_30k.feather clustering.py
- $(srun_singularity) python3 selection.py $(similarity_data)/subreddit_comment_terms_30k.feather $(clustering_data)/subreddit_comment_terms_30k $(selection_grid) -J 10
+terms_10k:${terms_10k_output}/kmeans/selection_data.csv ${terms_10k_output}/affinity/selection_data.csv ${terms_10k_output}/hdbscan/selection_data.csv
-$(clustering_data)/subreddit_authors-tf_similarities_30k.feather:clustering.py $(similarity_data)/subreddit_comment_authors-tf_30k.feather
- $(srun_singularity) python3 selection.py $(similarity_data)/subreddit_comment_authors-tf_30k.feather $(clustering_data)/subreddit_comment_authors-tf_30k $(selection_grid) -J 8
+authors_10k:${authors_10k_output}/kmeans/selection_data.csv ${authors_10k_output}/hdbscan/selection_data.csv ${authors_10k_output}/affinity/selection_data.csv
+
+authors_tf_10k:${authors_tf_10k_output}/kmeans/selection_data.csv ${authors_tf_10k_output}/hdbscan/selection_data.csv ${authors_tf_10k_output}/affinity/selection_data.csv
+
+terms_10k_lsi:${terms_10k_output_lsi}/kmeans/selection_data.csv ${terms_10k_output_lsi}/affinity/selection_data.csv ${terms_10k_output_lsi}/hdbscan/selection_data.csv
+
+authors_10k_lsi:${authors_10k_output_lsi}/kmeans/selection_data.csv ${authors_10k_output_lsi}/hdbscan/selection_data.csv ${authors_10k_output_lsi}/affinity/selection_data.csv
+
+authors_tf_10k_lsi:${authors_tf_10k_output_lsi}/kmeans/selection_data.csv ${authors_tf_10k_output_lsi}/hdbscan/selection_data.csv ${authors_tf_10k_output_lsi}/affinity/selection_data.csv
+
+${authors_10k_output}/kmeans/selection_data.csv:selection.py ${authors_10k_input} clustering_base.py kmeans_clustering.py
+ $(srun_singularity) python3 kmeans_clustering.py --inpath=${authors_10k_input} --outpath=${authors_10k_output}/kmeans --savefile=${authors_10k_output}/kmeans/selection_data.csv $(kmeans_selection_grid)
+
+${terms_10k_output}/kmeans/selection_data.csv:selection.py ${terms_10k_input} clustering_base.py kmeans_clustering.py
+ $(srun_singularity) python3 kmeans_clustering.py --inpath=${terms_10k_input} --outpath=${terms_10k_output}/kmeans --savefile=${terms_10k_output}/kmeans/selection_data.csv $(kmeans_selection_grid)
+
+${authors_tf_10k_output}/kmeans/selection_data.csv:clustering.py ${authors_tf_10k_input} clustering_base.py kmeans_clustering.py
+ $(srun_singularity) python3 kmeans_clustering.py --inpath=${authors_tf_10k_input} --outpath=${authors_tf_10k_output}/kmeans --savefile=${authors_tf_10k_output}/kmeans/selection_data.csv $(kmeans_selection_grid)
+
+${authors_10k_output}/affinity/selection_data.csv:selection.py ${authors_10k_input} clustering_base.py affinity_clustering.py
+ $(srun_singularity) python3 affinity_clustering.py --inpath=${authors_10k_input} --outpath=${authors_10k_output}/affinity --savefile=${authors_10k_output}/affinity/selection_data.csv $(affinity_selection_grid)
+
+${terms_10k_output}/affinity/selection_data.csv:selection.py ${terms_10k_input} clustering_base.py affinity_clustering.py
+ $(srun_singularity) python3 affinity_clustering.py --inpath=${terms_10k_input} --outpath=${terms_10k_output}/affinity --savefile=${terms_10k_output}/affinity/selection_data.csv $(affinity_selection_grid)
+
+${authors_tf_10k_output}/affinity/selection_data.csv:clustering.py ${authors_tf_10k_input} clustering_base.py affinity_clustering.py
+ $(srun_singularity) python3 affinity_clustering.py --inpath=${authors_tf_10k_input} --outpath=${authors_tf_10k_output}/affinity --savefile=${authors_tf_10k_output}/affinity/selection_data.csv $(affinity_selection_grid)
+
+${authors_10k_output}/hdbscan/selection_data.csv:selection.py ${authors_10k_input} clustering_base.py hdbscan_clustering.py
+ $(srun_singularity) python3 hdbscan_clustering.py --inpath=${authors_10k_input} --outpath=${authors_10k_output}/hdbscan --savefile=${authors_10k_output}/hdbscan/selection_data.csv $(hdbscan_selection_grid)
+
+${terms_10k_output}/hdbscan/selection_data.csv:selection.py ${terms_10k_input} clustering_base.py hdbscan_clustering.py
+ $(srun_singularity) python3 hdbscan_clustering.py --inpath=${terms_10k_input} --outpath=${terms_10k_output}/hdbscan --savefile=${terms_10k_output}/hdbscan/selection_data.csv $(hdbscan_selection_grid)
+
+${authors_tf_10k_output}/hdbscan/selection_data.csv:clustering.py ${authors_tf_10k_input} clustering_base.py hdbscan_clustering.py
+ $(srun_singularity) python3 hdbscan_clustering.py --inpath=${authors_tf_10k_input} --outpath=${authors_tf_10k_output}/hdbscan --savefile=${authors_tf_10k_output}/hdbscan/selection_data.csv $(hdbscan_selection_grid)
+
+
+## LSI Models
+${authors_10k_output_lsi}/kmeans/selection_data.csv:selection.py ${authors_10k_input_lsi} clustering_base.py kmeans_clustering.py
+ $(srun_singularity) python3 kmeans_clustering_lsi.py --inpath=${authors_10k_input_lsi} --outpath=${authors_10k_output_lsi}/kmeans --savefile=${authors_10k_output_lsi}/kmeans/selection_data.csv $(kmeans_selection_grid)
+
+${terms_10k_output_lsi}/kmeans/selection_data.csv:selection.py ${terms_10k_input_lsi} clustering_base.py kmeans_clustering.py
+ $(srun_singularity) python3 kmeans_clustering_lsi.py --inpath=${terms_10k_input_lsi} --outpath=${terms_10k_output_lsi}/kmeans --savefile=${terms_10k_output_lsi}/kmeans/selection_data.csv $(kmeans_selection_grid)
+
+${authors_tf_10k_output_lsi}/kmeans/selection_data.csv:clustering.py ${authors_tf_10k_input_lsi} clustering_base.py kmeans_clustering.py
+ $(srun_singularity) python3 kmeans_clustering_lsi.py --inpath=${authors_tf_10k_input_lsi} --outpath=${authors_tf_10k_output_lsi}/kmeans --savefile=${authors_tf_10k_output_lsi}/kmeans/selection_data.csv $(kmeans_selection_grid)
+
+${authors_10k_output_lsi}/affinity/selection_data.csv:selection.py ${authors_10k_input_lsi} clustering_base.py affinity_clustering.py
+ $(srun_singularity) python3 affinity_clustering_lsi.py --inpath=${authors_10k_input_lsi} --outpath=${authors_10k_output_lsi}/affinity --savefile=${authors_10k_output_lsi}/affinity/selection_data.csv $(affinity_selection_grid)
+
+${terms_10k_output_lsi}/affinity/selection_data.csv:selection.py ${terms_10k_input_lsi} clustering_base.py affinity_clustering.py
+ $(srun_singularity) python3 affinity_clustering_lsi.py --inpath=${terms_10k_input_lsi} --outpath=${terms_10k_output_lsi}/affinity --savefile=${terms_10k_output_lsi}/affinity/selection_data.csv $(affinity_selection_grid)
+
+${authors_tf_10k_output_lsi}/affinity/selection_data.csv:clustering.py ${authors_tf_10k_input_lsi} clustering_base.py affinity_clustering.py
+ $(srun_singularity) python3 affinity_clustering_lsi.py --inpath=${authors_tf_10k_input_lsi} --outpath=${authors_tf_10k_output_lsi}/affinity --savefile=${authors_tf_10k_output_lsi}/affinity/selection_data.csv $(affinity_selection_grid)
+
+${authors_10k_output_lsi}/hdbscan/selection_data.csv:selection.py ${authors_10k_input_lsi} clustering_base.py hdbscan_clustering.py
+ $(srun_singularity) python3 hdbscan_clustering_lsi.py --inpath=${authors_10k_input_lsi} --outpath=${authors_10k_output_lsi}/hdbscan --savefile=${authors_10k_output_lsi}/hdbscan/selection_data.csv $(hdbscan_selection_grid)
+
+${terms_10k_output_lsi}/hdbscan/selection_data.csv:selection.py ${terms_10k_input_lsi} clustering_base.py hdbscan_clustering.py
+ $(srun_singularity) python3 hdbscan_clustering_lsi.py --inpath=${terms_10k_input_lsi} --outpath=${terms_10k_output_lsi}/hdbscan --savefile=${terms_10k_output_lsi}/hdbscan/selection_data.csv $(hdbscan_selection_grid)
+
+${authors_tf_10k_output_lsi}/hdbscan/selection_data.csv:clustering.py ${authors_tf_10k_input_lsi} clustering_base.py hdbscan_clustering.py
+ $(srun_singularity) python3 hdbscan_clustering_lsi.py --inpath=${authors_tf_10k_input_lsi} --outpath=${authors_tf_10k_output_lsi}/hdbscan --savefile=${authors_tf_10k_output_lsi}/hdbscan/selection_data.csv $(hdbscan_selection_grid)
+
+${terms_10k_output_lsi}/best_hdbscan.feather:${terms_10k_output_lsi}/hdbscan/selection_data.csv pick_best_clustering.py
+ $(srun_singularity) python3 pick_best_clustering.py $< $@ --min_clusters=50 --max_isolates=5000 --min_cluster_size=2
+
+${authors_tf_10k_output_lsi}/best_hdbscan.feather:${authors_tf_10k_output_lsi}/hdbscan/selection_data.csv pick_best_clustering.py
+ $(srun_singularity) python3 pick_best_clustering.py $< $@ --min_clusters=50 --max_isolates=5000 --min_cluster_size=2
+
+clean_affinity:
+ rm -f ${authors_10k_output}/affinity/selection_data.csv
+ rm -f ${authors_tf_10k_output}/affinity/selection_data.csv
+ rm -f ${terms_10k_output}/affinity/selection_data.csv
+
+clean_kmeans:
+ rm -f ${authors_10k_output}/kmeans/selection_data.csv
+ rm -f ${authors_tf_10k_output}/kmeans/selection_data.csv
+ rm -f ${terms_10k_output}/kmeans/selection_data.csv
+
+clean_hdbscan:
+ rm -f ${authors_10k_output}/hdbscan/selection_data.csv
+ rm -f ${authors_tf_10k_output}/hdbscan/selection_data.csv
+ rm -f ${terms_10k_output}/hdbscan/selection_data.csv
+
+clean_authors:
+ rm -f ${authors_10k_output}/affinity/selection_data.csv
+ rm -f ${authors_10k_output}/kmeans/selection_data.csv
+ rm -f ${authors_10k_output}/hdbscan/selection_data.csv
+
+clean_authors_tf:
+ rm -f ${authors_tf_10k_output}/affinity/selection_data.csv
+ rm -f ${authors_tf_10k_output}/kmeans/selection_data.csv
+ rm -f ${authors_tf_10k_output}/hdbscan/selection_data.csv
+
+clean_terms:
+ rm -f ${terms_10k_output}/affinity/selection_data.csv
+ rm -f ${terms_10k_output}/kmeans/selection_data.csv
+ rm -f ${terms_10k_output}/hdbscan/selection_data.csv
+
+clean_lsi_affinity:
+ rm -f ${authors_10k_output_lsi}/affinity/selection_data.csv
+ rm -f ${authors_tf_10k_output_lsi}/affinity/selection_data.csv
+ rm -f ${terms_10k_output_lsi}/affinity/selection_data.csv
+
+clean_lsi_kmeans:
+ rm -f ${authors_10k_output_lsi}/kmeans/selection_data.csv
+ rm -f ${authors_tf_10k_output_lsi}/kmeans/selection_data.csv
+ rm -f ${terms_10k_output_lsi}/kmeans/selection_data.csv
+
+clean_lsi_hdbscan:
+ rm -f ${authors_10k_output_lsi}/hdbscan/selection_data.csv
+ rm -f ${authors_tf_10k_output_lsi}/hdbscan/selection_data.csv
+ rm -f ${terms_10k_output_lsi}/hdbscan/selection_data.csv
+
+clean_lsi_authors:
+ rm -f ${authors_10k_output_lsi}/affinity/selection_data.csv
+ rm -f ${authors_10k_output_lsi}/kmeans/selection_data.csv
+ rm -f ${authors_10k_output_lsi}/hdbscan/selection_data.csv
+
+clean_lsi_authors_tf:
+ rm -f ${authors_tf_10k_output_lsi}/affinity/selection_data.csv
+ rm -f ${authors_tf_10k_output_lsi}/kmeans/selection_data.csv
+ rm -f ${authors_tf_10k_output_lsi}/hdbscan/selection_data.csv
+
+clean_lsi_terms:
+ rm -f ${terms_10k_output_lsi}/affinity/selection_data.csv
+ rm -f ${terms_10k_output_lsi}/kmeans/selection_data.csv
+ rm -f ${terms_10k_output_lsi}/hdbscan/selection_data.csv
+
+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
+
+# $(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_data)/subreddit_comment_terms_30k.feather/SUCCESS:selection.py $(similarity_data)/subreddit_comment_terms_30k.feather clustering.py
+# $(srun_singularity) python3 selection.py $(similarity_data)/subreddit_comment_terms_30k.feather $(clustering_data)/subreddit_comment_terms_30k $(selection_grid) -J 10 && touch $(clustering_data)/subreddit_comment_terms_30k.feather/SUCCESS
+
+# $(clustering_data)/subreddit_authors-tf_similarities_30k.feather/SUCCESS:clustering.py $(similarity_data)/subreddit_comment_authors-tf_30k.feather
+# $(srun_singularity) python3 selection.py $(similarity_data)/subreddit_comment_authors-tf_30k.feather $(clustering_data)/subreddit_comment_authors-tf_30k $(selection_grid) -J 8 && touch $(clustering_data)/subreddit_authors-tf_similarities_30k.feather/SUCCESS
# $(clustering_data)/subreddit_comment_authors_100k.feather:clustering.py $(similarity_data)/subreddit_comment_authors_100k.feather
projects / cdsc_reddit.git / blobdiff