X-Git-Url: https://code.communitydata.science/cdsc_reddit.git/blobdiff_plain/56269deee3d33620550d67bdd3c1a7b64eb3f7e4..5a40465a629a1d7d95dbec9730d3950842bcb4f5:/clustering/Makefile?ds=sidebyside diff --git a/clustering/Makefile b/clustering/Makefile index c97cb0d..2ba9c0c 100644 --- a/clustering/Makefile +++ b/clustering/Makefile @@ -1,4 +1,218 @@ -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' -affinity/subreddit_comment_authors_10000.feather:clustering.py /gscratch/comdata/output/reddit_similarity/subreddit_comment_authors_10000.parquet -# $srun_cdsc python3 - clustering.py /gscratch/comdata/output/reddit_similarity/subreddit_comment_authors_10000.feather affinity/subreddit_comment_authors_10000.feather ---max_iter=400 --convergence_iter=15 --preference_quantile=0.85 --damping=0.85 +#srun_cdsc='srun -p comdata-int -A comdata --time=300:00:00 --time-min=00:15:00 --mem=100G --ntasks=1 --cpus-per-task=28' +srun_singularity=source /gscratch/comdata/users/nathante/cdsc_reddit/bin/activate && srun_singularity.sh +similarity_data=/gscratch/comdata/output/reddit_similarity +clustering_data=/gscratch/comdata/output/reddit_clustering +kmeans_selection_grid=--max_iters=[3000] --n_inits=[10] --n_clusters=[100,500,1000,1250,1500,1750,2000] + +umap_hdbscan_selection_grid=--min_cluster_sizes=[2] --min_samples=[2,3,4,5] --cluster_selection_epsilons=[0,0.01,0.05,0.1,0.15,0.2] --cluster_selection_methods=[eom,leaf] --n_neighbors=[5,15,25,50,75,100] --learning_rate=[1] --min_dist=[0,0.1,0.25,0.5,0.75,0.9,0.99] --local_connectivity=[1] + +hdbscan_selection_grid=--min_cluster_sizes=[2,3,4,5] --min_samples=[2,3,4,5] --cluster_selection_epsilons=[0,0.01,0.05,0.1,0.15,0.2] --cluster_selection_methods=[eom,leaf] +affinity_selection_grid=--dampings=[0.5,0.6,0.7,0.8,0.95,0.97,0.99] --preference_quantiles=[0.1,0.3,0.5,0.7,0.9] --convergence_iters=[15] + +authors_10k_input=$(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=$(clustering_data)/subreddit_comment_authors_10k_LSI + +authors_tf_10k_input=$(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=$(clustering_data)/subreddit_comment_authors-tf_10k_LSI + +terms_10k_input=$(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=$(clustering_data)/subreddit_comment_terms_10k_LSI + +all:terms_10k authors_10k authors_tf_10k terms_10k_lsi authors_10k_lsi authors_tf_10k_lsi + +terms_10k:${terms_10k_output}/kmeans/selection_data.csv ${terms_10k_output}/affinity/selection_data.csv ${terms_10k_output}/hdbscan/selection_data.csv + +authors_10k:${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 $(hdbscan_selection_grid) + +${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 + 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 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_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 +# $(srun_singularity) python3 clustering.py $(similarity_data)/subreddit_comment_authors_100k.feather $(clustering_data)/subreddit_comment_authors_100k.feather ---max_iter=400 --convergence_iter=15 --preference_quantile=0.85 --damping=0.85 + +# $(clustering_data)/comment_terms_100k.feather:clustering.py $(similarity_data)/subreddit_comment_terms_100k.feather +# $(srun_singularity) python3 clustering.py $(similarity_data)/comment_terms_10000.feather $(clustering_data)/comment_terms_10000.feather ---max_iter=1000 --convergence_iter=15 --preference_quantile=0.9 --damping=0.5 + +# $(clustering_data)/subreddit_comment_author-tf_100k.feather:clustering.py $(similarity_data)/subreddit_comment_author-tf_100k.feather +# $(srun_singularity) python3 clustering.py $(similarity_data)/subreddit_comment_author-tf_100k.parquet $(clustering_data)/subreddit_comment_author-tf_100k.feather ---max_iter=400 --convergence_iter=15 --preference_quantile=0.5 --damping=0.85 + + +# it's pretty difficult to get a result that isn't one huge megacluster. A sign that it's bullcrap +# /gscratch/comdata/output/reddit_clustering/wang_similarity_10000.feather:clustering.py /gscratch/comdata/output/reddit_similarity/wang_similarity_10000.feather +# ./clustering.py /gscratch/comdata/output/reddit_similarity/wang_similarity_10000.feather /gscratch/comdata/output/reddit_clustering/wang_similarity_10000.feather ---max_iter=400 --convergence_iter=15 --preference_quantile=0.9 --damping=0.85 + +# /gscratch/comdata/output/reddit_tsne/subreddit_author_tf_similarities_10000.feather:fit_tsne.py /gscratch/comdata/output/reddit_similarity/subreddit_author_tf_similarities_10000.parquet + +# start_spark_and_run.sh 1 fit_tsne.py --similarities=/gscratch/comdata/output/reddit_similarity/subreddit_author_tf_similarities_10000.parquet --output=/gscratch/comdata/output/reddit_tsne/subreddit_author_tf_similarities_10000.feather + + +# /gscratch/comdata/output/reddit_tsne/wang_similarity_10000.feather:fit_tsne.py /gscratch/comdata/output/reddit_similarity/wang_similarity_10000.feather + +# python3 fit_tsne.py --similarities=/gscratch/comdata/output/reddit_similarity/wang_similarity_10000.feather --output=/gscratch/comdata/output/reddit_tsne/wang_similarity_10000.feather + +# /gscratch/comdata/output/reddit_tsne/comment_authors_10000.feather:clustering.py /gscratch/comdata/output/reddit_similarity/comment_authors_10000.feather +# # $srun_cdsc python3 +# start_spark_and_run.sh 1 fit_tsne.py --similarities=/gscratch/comdata/output/reddit_similarity/comment_authors_10000.feather --output=/gscratch/comdata/output/reddit_tsne/comment_authors_10000.feather