From: Nate E TeBlunthuis Date: Wed, 18 Nov 2020 00:31:48 +0000 (-0800) Subject: git-annex in nathante@mox2.hyak.local:/gscratch/comdata/users/nathante/cdsc-reddit X-Git-Url: https://code.communitydata.science/cdsc_reddit.git/commitdiff_plain/1bf206d219a38ffb0290dde83cd061d4a848f1c7 git-annex in nathante@mox2.hyak.local:/gscratch/comdata/users/nathante/cdsc-reddit --- diff --git a/fit_tsne.py b/fit_tsne.py index 7de2ac0..28b0fd3 100644 --- a/fit_tsne.py +++ b/fit_tsne.py @@ -1,35 +1,34 @@ +import fire import pyarrow import pandas as pd from numpy import random import numpy as np from sklearn.manifold import TSNE -df = pd.read_feather("reddit_term_similarity_3000.feather") -df = df.sort_values(['i','j']) +similarities = "term_similarities_10000.feather" -n = max(df.i.max(),df.j.max()) +def fit_tsne(similarities, output, learning_rate=750, perplexity=50, n_iter=10000, early_exaggeration=20): + ''' + similarities: feather file with a dataframe of similarity scores + learning_rate: parameter controlling how fast the model converges. Too low and you get outliers. Too high and you get a ball. + perplexity: number of neighbors to use. the default of 50 is often good. -def zero_pad(grp): - p = grp.shape[0] - grp = grp.sort_values('j') - return np.concatenate([np.zeros(n-p),np.ones(1),np.array(grp.value)]) + ''' + df = pd.read_feather(similarities) -col_names = df.sort_values('j').loc[:,['subreddit_j']].drop_duplicates() -first_name = list(set(df.subreddit_i) - set(df.subreddit_j))[0] -col_names = [first_name] + list(col_names.subreddit_j) -mat = df.groupby('i').apply(zero_pad) -mat.loc[n] = np.concatenate([np.zeros(n),np.ones(1)]) -mat = np.stack(mat) + n = df.shape[0] + mat = np.array(df.drop('subreddit',1),dtype=np.float64) + mat[range(n),range(n)] = 1 + mat[mat > 1] = 1 + dist = 2*np.arccos(mat)/np.pi + tsne_model = TSNE(2,learning_rate=750,perplexity=50,n_iter=10000,metric='precomputed',early_exaggeration=20,n_jobs=-1) + tsne_fit_model = tsne_model.fit(dist) -mat = mat + np.tril(mat.transpose(),k=-1) -dist = 2*np.arccos(mat)/np.pi + tsne_fit_whole = tsne_fit_model.fit_transform(dist) -tsne_model = TSNE(2,learning_rate=750,perplexity=50,n_iter=10000,metric='precomputed',early_exaggeration=20,n_jobs=-1) + plot_data = pd.DataFrame({'x':tsne_fit_whole[:,0],'y':tsne_fit_whole[:,1], 'subreddit':df.subreddit}) -tsne_fit_model = tsne_model.fit(dist) + plot_data.to_feather(output) -tsne_fit_whole = tsne_fit_model.fit_transform(dist) - -plot_data = pd.DataFrame({'x':tsne_fit_whole[:,0],'y':tsne_fit_whole[:,1], 'subreddit':col_names}) - -plot_data.to_feather("tsne_subreddit_fit.feather") +if __name__ == "__main__": + fire.Fire(fit_tsne) diff --git a/visualization/data/term_affinityprop_10000.feather b/visualization/data/term_affinityprop_10000.feather new file mode 120000 index 0000000..188939f --- /dev/null +++ b/visualization/data/term_affinityprop_10000.feather @@ -0,0 +1 @@ +../../.git/annex/objects/Qk/wG/SHA256E-s145210--14a2ad6660d1e4015437eff556ec349dd10a115a4f96594152a29e83d00aa784/SHA256E-s145210--14a2ad6660d1e4015437eff556ec349dd10a115a4f96594152a29e83d00aa784 \ No newline at end of file diff --git a/visualization/data/term_affinityprop_3000.feather b/visualization/data/term_affinityprop_3000.feather new file mode 120000 index 0000000..c9b4233 --- /dev/null +++ b/visualization/data/term_affinityprop_3000.feather @@ -0,0 +1 @@ +../../.git/annex/objects/w7/2f/SHA256E-s44458--f1c5247775ecf06514a0ff9e523e944bc8fcd9d0fdb6f214cc1329b759d4354e/SHA256E-s44458--f1c5247775ecf06514a0ff9e523e944bc8fcd9d0fdb6f214cc1329b759d4354e \ No newline at end of file diff --git a/visualization/data/term_tsne_10000.feather b/visualization/data/term_tsne_10000.feather new file mode 120000 index 0000000..764f2e0 --- /dev/null +++ b/visualization/data/term_tsne_10000.feather @@ -0,0 +1 @@ +../../.git/annex/objects/WX/v3/SHA256E-s190874--c2aea719f989dde297ca5f13371e156693c574e44acd9a0e313e5e3a3ad4b543/SHA256E-s190874--c2aea719f989dde297ca5f13371e156693c574e44acd9a0e313e5e3a3ad4b543 \ No newline at end of file diff --git a/visualization/data/term_tsne_3000.feather b/visualization/data/term_tsne_3000.feather new file mode 120000 index 0000000..21f156f --- /dev/null +++ b/visualization/data/term_tsne_3000.feather @@ -0,0 +1 @@ +../../.git/annex/objects/mq/2z/SHA256E-s58834--2e7b3ee11f47011fd9b34bddf8f1e788d35ab9c9e0bb6a1301b0b916135400cf/SHA256E-s58834--2e7b3ee11f47011fd9b34bddf8f1e788d35ab9c9e0bb6a1301b0b916135400cf \ No newline at end of file