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Learning DP Mixtures on Toy Bars Data with Birth and Merge moves

Goal

This demo walks you through using bnpy from within python to train a Dirichlet process (DP) mixture model on bag-of-words data. We'll use memoized variational inference with birth and merge moves.

We can use the following import statements to load bnpy.

import bnpy

from matplotlib import pylab
%pylab inline

imshowArgs = dict(interpolation='nearest',
                  cmap='bone_r',
                  vmin=0.0,
                  vmax=10./900,
                  )

Populating the interactive namespace from numpy and matplotlib

Toy dataset : MixBarsK10V900

We'll use a simple "toy bars" dataset generated from a mixture model.

**Our task here is to assign exactly one cluster to every whole document. Be aware that this is different than assigning a cluster/topic to each word token, like in LDA or HDP topic models. **

import MixBarsK10V900
Data = MixBarsK10V900.get_data(nDocTotal=1000, nWordsPerDoc=100)
Data.name = 'MixBarsK10V900'

First, we can visualize the 10 "true" topics. Each one is a distribution over the same set of 900 vocabulary "words". We can show this distribution as an image with 30x30 pixels, where each pixel's intensity indicates the probability of the corresponding word.

bnpy.viz.BarsViz.showTopicsAsSquareImages(MixBarsK10V900.Defaults['topics'], **imshowArgs)
BarsToyData-DPMixtureModel-MemoizedWithBirthsAndMerges_files/BarsToyData-DPMixtureModel-MemoizedWithBirthsAndMerges_7_0.png BarsToyData-DPMixtureModel-MemoizedWithBirthsAndMerges_files/BarsToyData-DPMixtureModel-MemoizedWithBirthsAndMerges_7_1.png

Next, we can visualize some example documents.

bnpy.viz.BarsViz.plotExampleBarsDocs(Data, **imshowArgs)
BarsToyData-DPMixtureModel-MemoizedWithBirthsAndMerges_files/BarsToyData-DPMixtureModel-MemoizedWithBirthsAndMerges_9_0.png

Running inference with bnpy

We'll fit a DP mixture model with a multinomial likelihood, using birth and merge moves. We use the moves keyword argument to specify which moves to employ.

We'll look at several possible initial numbers of clusters, and show that the birth/merge moves consistently reach the ideal set of 8 clusters.

1 initial cluster, repeated for 2 trials

hmodel, RInfo = bnpy.run(Data, 'DPMixtureModel', 'Mult', 'moVB',
                         nLap=20, K=1, lam=0.1, moves='birth,merge',
                         nTask=2, jobname='demobirthmerge-Kinit=1')

Toy Bars Data with 10 true topics. Each doc uses ONE topic.
Entire Dataset Summary:
  total size: 1000 units
  batch size: 100 units
  num. batches: 10
Data for Initialization:
  size: 1000 units (documents)
  vocab size: 900
  min    5%   50%   95%   max
   66    73    79    84    88  nUniqueTokensPerDoc
  100   100   100   100   100  nTotalTokensPerDoc
Hist of word_count across tokens
      1      2      3    <10   <100  >=100
   0.77   0.19   0.03    382      0      0
Hist of unique docs per word type
     <1    <10   <100  <0.20  <0.50 >=0.50
      0      0   0.93   0.07      0      0
Allocation Model:  DP mixture with K=1. Concentration gamma0= 1.00
Obs. Data  Model:  Multinomial over finite vocabulary.
Obs. Data  Prior:  Dirichlet over finite vocabulary
  lam = [ 0.1  0.1] ...
Learn Alg: moVB
Trial  1/2 | alg. seed: 2497280 | data order seed: 8541952
savepath: /results/MixBarsK10V900/demobirthmerge-Kinit=1/1
    0.100/20 after      0 sec. | K    1 | ev -6.969793109e+00 |
    0.200/20 after      0 sec. | K    1 | ev -6.910657011e+00 |
    0.300/20 after      0 sec. | K    1 | ev -6.885383576e+00 |
    1.000/20 after      0 sec. | K    1 | ev -6.833745697e+00 |
BIRTH ACCEPTED. 8 fresh comps.
MERGE 0/0 accepted.
    2.000/20 after      0 sec. | K    9 | ev -5.682738824e+00 | Ndiff     93.000
MERGE 0/0 accepted.
    3.000/20 after      0 sec. | K    9 | ev -5.671719201e+00 | Ndiff      0.000
BIRTH ACCEPTED. 2 fresh comps.
MERGE 0/0 accepted.
    4.000/20 after      0 sec. | K   11 | ev -5.580876852e+00 | Ndiff     93.000
MERGE 1/1 accepted. ev increased  1.3314e-03
    5.000/20 after      1 sec. | K   10 | ev -5.579190605e+00 | Ndiff      0.000
MERGE 0/0 accepted.
    6.000/20 after      1 sec. | K   10 | ev -5.579190605e+00 | Ndiff      0.000
MERGE 0/0 accepted.
    7.000/20 after      1 sec. | K   10 | ev -5.579190605e+00 | Ndiff      0.000
MERGE 0/0 accepted.
    8.000/20 after      1 sec. | K   10 | ev -5.579190605e+00 | Ndiff      0.000
MERGE 0/0 accepted.
    9.000/20 after      1 sec. | K   10 | ev -5.579190605e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   10.000/20 after      1 sec. | K   10 | ev -5.579190605e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   11.000/20 after      1 sec. | K   10 | ev -5.579190605e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   12.000/20 after      1 sec. | K   10 | ev -5.579190605e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   13.000/20 after      1 sec. | K   10 | ev -5.579190605e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   14.000/20 after      2 sec. | K   10 | ev -5.579190605e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   15.000/20 after      2 sec. | K   10 | ev -5.579190605e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   16.000/20 after      2 sec. | K   10 | ev -5.579190605e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   17.000/20 after      2 sec. | K   10 | ev -5.579190605e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   18.000/20 after      2 sec. | K   10 | ev -5.579190605e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   19.000/20 after      2 sec. | K   10 | ev -5.579190605e+00 | Ndiff      0.000
... done. converged.
Trial  2/2 | alg. seed: 1128064 | data order seed: 7673856
savepath: /results/MixBarsK10V900/demobirthmerge-Kinit=1/2
    0.100/20 after      0 sec. | K    1 | ev -6.981597526e+00 |
    0.200/20 after      0 sec. | K    1 | ev -6.916391582e+00 |
    0.300/20 after      0 sec. | K    1 | ev -6.880774941e+00 |
    1.000/20 after      0 sec. | K    1 | ev -6.833745697e+00 |
BIRTH ACCEPTED. 8 fresh comps.
MERGE 0/0 accepted.
    2.000/20 after      0 sec. | K    9 | ev -5.673084280e+00 | Ndiff     92.000
MERGE 0/0 accepted.
    3.000/20 after      0 sec. | K    9 | ev -5.668395610e+00 | Ndiff      0.000
BIRTH ACCEPTED. 2 fresh comps.
MERGE 0/0 accepted.
    4.000/20 after      1 sec. | K   11 | ev -5.579253419e+00 | Ndiff     89.000
MERGE 1/1 accepted. ev increased  6.5338e-05
    5.000/20 after      1 sec. | K   10 | ev -5.579188081e+00 | Ndiff      0.000
MERGE 0/0 accepted.
    6.000/20 after      1 sec. | K   10 | ev -5.579188081e+00 | Ndiff      0.000
MERGE 0/0 accepted.
    7.000/20 after      1 sec. | K   10 | ev -5.579188081e+00 | Ndiff      0.000
MERGE 0/0 accepted.
    8.000/20 after      1 sec. | K   10 | ev -5.579188081e+00 | Ndiff      0.000
MERGE 0/0 accepted.
    9.000/20 after      1 sec. | K   10 | ev -5.579188081e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   10.000/20 after      1 sec. | K   10 | ev -5.579188081e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   11.000/20 after      1 sec. | K   10 | ev -5.579188081e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   12.000/20 after      1 sec. | K   10 | ev -5.579188081e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   13.000/20 after      1 sec. | K   10 | ev -5.579188081e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   14.000/20 after      2 sec. | K   10 | ev -5.579188081e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   15.000/20 after      2 sec. | K   10 | ev -5.579188081e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   16.000/20 after      2 sec. | K   10 | ev -5.579188081e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   17.000/20 after      2 sec. | K   10 | ev -5.579188081e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   18.000/20 after      2 sec. | K   10 | ev -5.579188081e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   19.000/20 after      2 sec. | K   10 | ev -5.579188081e+00 | Ndiff      0.000
... done. converged.

4 initial clusters, repeated for 2 trials

hmodel, RInfo = bnpy.run(Data, 'DPMixtureModel', 'Mult', 'moVB',
                         nLap=20, K=4, lam=0.1, moves='birth,merge',
                         nTask=2, jobname='demobirthmerge-Kinit=4')

Toy Bars Data with 10 true topics. Each doc uses ONE topic.
Entire Dataset Summary:
  total size: 1000 units
  batch size: 100 units
  num. batches: 10
Data for Initialization:
  size: 1000 units (documents)
  vocab size: 900
  min    5%   50%   95%   max
   66    73    79    84    88  nUniqueTokensPerDoc
  100   100   100   100   100  nTotalTokensPerDoc
Hist of word_count across tokens
      1      2      3    <10   <100  >=100
   0.77   0.19   0.03    382      0      0
Hist of unique docs per word type
     <1    <10   <100  <0.20  <0.50 >=0.50
      0      0   0.93   0.07      0      0
Allocation Model:  DP mixture with K=4. Concentration gamma0= 1.00
Obs. Data  Model:  Multinomial over finite vocabulary.
Obs. Data  Prior:  Dirichlet over finite vocabulary
  lam = [ 0.1  0.1] ...
Learn Alg: moVB
Trial  1/2 | alg. seed: 2497280 | data order seed: 8541952
savepath: /results/MixBarsK10V900/demobirthmerge-Kinit=4/1
    0.100/20 after      0 sec. | K    4 | ev -6.740510449e+00 |
    0.200/20 after      0 sec. | K    4 | ev -6.571153609e+00 |
    0.300/20 after      0 sec. | K    4 | ev -6.492200573e+00 |
    1.000/20 after      0 sec. | K    4 | ev -6.312338396e+00 |
BIRTH ACCEPTED. 4 fresh comps.
MERGE 0/0 accepted.
    2.000/20 after      0 sec. | K    8 | ev -5.896559293e+00 | Ndiff     48.000
MERGE 1/1 accepted. ev increased  1.0139e-03
    3.000/20 after      0 sec. | K    7 | ev -5.895542786e+00 | Ndiff      0.000
BIRTH ACCEPTED. 3 fresh comps.
MERGE 0/0 accepted.
    4.000/20 after      0 sec. | K   10 | ev -5.670595821e+00 | Ndiff     62.000
MERGE 1/1 accepted. ev increased  2.9988e-03
    5.000/20 after      1 sec. | K    9 | ev -5.667199827e+00 | Ndiff      0.000
BIRTH ACCEPTED. 2 fresh comps.
MERGE 0/0 accepted.
    6.000/20 after      1 sec. | K   11 | ev -5.579252348e+00 | Ndiff     88.000
MERGE 1/1 accepted. ev increased  6.5468e-05
    7.000/20 after      1 sec. | K   10 | ev -5.579186880e+00 | Ndiff      0.000
MERGE 0/0 accepted.
    8.000/20 after      1 sec. | K   10 | ev -5.579186880e+00 | Ndiff      0.000
MERGE 0/0 accepted.
    9.000/20 after      1 sec. | K   10 | ev -5.579186880e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   10.000/20 after      1 sec. | K   10 | ev -5.579186880e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   11.000/20 after      1 sec. | K   10 | ev -5.579186880e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   12.000/20 after      1 sec. | K   10 | ev -5.579186880e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   13.000/20 after      1 sec. | K   10 | ev -5.579186880e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   14.000/20 after      1 sec. | K   10 | ev -5.579186880e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   15.000/20 after      2 sec. | K   10 | ev -5.579186880e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   16.000/20 after      2 sec. | K   10 | ev -5.579186880e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   17.000/20 after      2 sec. | K   10 | ev -5.579186880e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   18.000/20 after      2 sec. | K   10 | ev -5.579186880e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   19.000/20 after      2 sec. | K   10 | ev -5.579186880e+00 | Ndiff      0.000
... done. converged.
Trial  2/2 | alg. seed: 1128064 | data order seed: 7673856
savepath: /results/MixBarsK10V900/demobirthmerge-Kinit=4/2
    0.100/20 after      0 sec. | K    4 | ev -6.731800712e+00 |
    0.200/20 after      0 sec. | K    4 | ev -6.518718345e+00 |
    0.300/20 after      0 sec. | K    4 | ev -6.427244547e+00 |
    1.000/20 after      0 sec. | K    4 | ev -6.252611666e+00 |
BIRTH ACCEPTED. 3 fresh comps.
MERGE 0/0 accepted.
    2.000/20 after      0 sec. | K    7 | ev -5.987733905e+00 | Ndiff     61.000
BIRTH ACCEPTED. 3 fresh comps.
MERGE 0/0 accepted.
    3.000/20 after      0 sec. | K   10 | ev -5.762998351e+00 | Ndiff     61.000
MERGE 2/2 accepted. ev increased  2.0063e-03
    4.000/20 after      0 sec. | K    8 | ev -5.760988104e+00 | Ndiff      0.000
BIRTH ACCEPTED. 2 fresh comps.
MERGE 0/0 accepted.
    5.000/20 after      1 sec. | K   10 | ev -5.667997831e+00 | Ndiff     88.000
MERGE 1/1 accepted. ev increased  7.2433e-04
    6.000/20 after      1 sec. | K    9 | ev -5.667010822e+00 | Ndiff      0.000
BIRTH ACCEPTED. 2 fresh comps.
MERGE 0/0 accepted.
    7.000/20 after      1 sec. | K   11 | ev -5.579250413e+00 | Ndiff     87.000
MERGE 1/1 accepted. ev increased  6.5294e-05
    8.000/20 after      1 sec. | K   10 | ev -5.579185119e+00 | Ndiff      0.000
MERGE 0/0 accepted.
    9.000/20 after      1 sec. | K   10 | ev -5.579185119e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   10.000/20 after      1 sec. | K   10 | ev -5.579185119e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   11.000/20 after      1 sec. | K   10 | ev -5.579185119e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   12.000/20 after      1 sec. | K   10 | ev -5.579185119e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   13.000/20 after      1 sec. | K   10 | ev -5.579185119e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   14.000/20 after      2 sec. | K   10 | ev -5.579185119e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   15.000/20 after      2 sec. | K   10 | ev -5.579185119e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   16.000/20 after      2 sec. | K   10 | ev -5.579185119e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   17.000/20 after      2 sec. | K   10 | ev -5.579185119e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   18.000/20 after      2 sec. | K   10 | ev -5.579185119e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   19.000/20 after      2 sec. | K   10 | ev -5.579185119e+00 | Ndiff      0.000
... done. converged.

16 initial clusters, repeated for 2 trials

hmodel, RInfo = bnpy.run(Data, 'DPMixtureModel', 'Mult', 'moVB',
                         nLap=20, K=16, lam=0.1, moves='birth,merge',
                         nTask=2, jobname='demobirthmerge-Kinit=16')

Toy Bars Data with 10 true topics. Each doc uses ONE topic.
Entire Dataset Summary:
  total size: 1000 units
  batch size: 100 units
  num. batches: 10
Data for Initialization:
  size: 1000 units (documents)
  vocab size: 900
  min    5%   50%   95%   max
   66    73    79    84    88  nUniqueTokensPerDoc
  100   100   100   100   100  nTotalTokensPerDoc
Hist of word_count across tokens
      1      2      3    <10   <100  >=100
   0.77   0.19   0.03    382      0      0
Hist of unique docs per word type
     <1    <10   <100  <0.20  <0.50 >=0.50
      0      0   0.93   0.07      0      0
Allocation Model:  DP mixture with K=16. Concentration gamma0= 1.00
Obs. Data  Model:  Multinomial over finite vocabulary.
Obs. Data  Prior:  Dirichlet over finite vocabulary
  lam = [ 0.1  0.1] ...
Learn Alg: moVB
Trial  1/2 | alg. seed: 2497280 | data order seed: 8541952
savepath: /results/MixBarsK10V900/demobirthmerge-Kinit=16/1
    0.100/20 after      0 sec. | K   16 | ev -6.419219019e+00 |
    0.200/20 after      0 sec. | K   16 | ev -6.094286752e+00 |
    0.300/20 after      0 sec. | K   16 | ev -5.940957526e+00 |
    1.000/20 after      0 sec. | K   16 | ev -5.664293326e+00 |
MERGE 5/5 accepted. ev increased  1.2310e-02
    2.000/20 after      0 sec. | K   11 | ev -5.581792852e+00 | Ndiff      0.000
MERGE 1/1 accepted. ev increased  1.6549e-03
    3.000/20 after      0 sec. | K   10 | ev -5.579189293e+00 | Ndiff      0.000
MERGE 0/0 accepted.
    4.000/20 after      1 sec. | K   10 | ev -5.579189293e+00 | Ndiff      0.000
MERGE 0/0 accepted.
    5.000/20 after      1 sec. | K   10 | ev -5.579189293e+00 | Ndiff      0.000
MERGE 0/0 accepted.
    6.000/20 after      1 sec. | K   10 | ev -5.579189293e+00 | Ndiff      0.000
MERGE 0/0 accepted.
    7.000/20 after      1 sec. | K   10 | ev -5.579189293e+00 | Ndiff      0.000
MERGE 0/0 accepted.
    8.000/20 after      1 sec. | K   10 | ev -5.579189293e+00 | Ndiff      0.000
MERGE 0/0 accepted.
    9.000/20 after      1 sec. | K   10 | ev -5.579189293e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   10.000/20 after      1 sec. | K   10 | ev -5.579189293e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   11.000/20 after      1 sec. | K   10 | ev -5.579189293e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   12.000/20 after      1 sec. | K   10 | ev -5.579189293e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   13.000/20 after      1 sec. | K   10 | ev -5.579189293e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   14.000/20 after      2 sec. | K   10 | ev -5.579189293e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   15.000/20 after      2 sec. | K   10 | ev -5.579189293e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   16.000/20 after      2 sec. | K   10 | ev -5.579189293e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   17.000/20 after      2 sec. | K   10 | ev -5.579189293e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   18.000/20 after      2 sec. | K   10 | ev -5.579189293e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   19.000/20 after      2 sec. | K   10 | ev -5.579189293e+00 | Ndiff      0.000
... done. converged.
Trial  2/2 | alg. seed: 1128064 | data order seed: 7673856
savepath: /results/MixBarsK10V900/demobirthmerge-Kinit=16/2
    0.100/20 after      0 sec. | K   16 | ev -6.372100577e+00 |
    0.200/20 after      0 sec. | K   16 | ev -6.068842570e+00 |
    0.300/20 after      0 sec. | K   16 | ev -5.930562281e+00 |
    1.000/20 after      0 sec. | K   16 | ev -5.719622612e+00 |
MERGE 6/6 accepted. ev increased  1.6625e-02
    2.000/20 after      0 sec. | K   10 | ev -5.675899603e+00 | Ndiff      0.000
BIRTH ACCEPTED. 2 fresh comps.
MERGE 1/1 accepted. ev increased  2.0633e-03
    3.000/20 after      1 sec. | K   11 | ev -5.579254286e+00 | Ndiff     21.000
MERGE 1/1 accepted. ev increased  6.6657e-05
    4.000/20 after      1 sec. | K   10 | ev -5.579187626e+00 | Ndiff      0.000
MERGE 0/0 accepted.
    5.000/20 after      1 sec. | K   10 | ev -5.579187626e+00 | Ndiff      0.000
MERGE 0/0 accepted.
    6.000/20 after      1 sec. | K   10 | ev -5.579187626e+00 | Ndiff      0.000
MERGE 0/0 accepted.
    7.000/20 after      1 sec. | K   10 | ev -5.579187626e+00 | Ndiff      0.000
MERGE 0/0 accepted.
    8.000/20 after      1 sec. | K   10 | ev -5.579187626e+00 | Ndiff      0.000
MERGE 0/0 accepted.
    9.000/20 after      1 sec. | K   10 | ev -5.579187626e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   10.000/20 after      1 sec. | K   10 | ev -5.579187626e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   11.000/20 after      1 sec. | K   10 | ev -5.579187626e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   12.000/20 after      1 sec. | K   10 | ev -5.579187626e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   13.000/20 after      2 sec. | K   10 | ev -5.579187626e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   14.000/20 after      2 sec. | K   10 | ev -5.579187626e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   15.000/20 after      2 sec. | K   10 | ev -5.579187626e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   16.000/20 after      2 sec. | K   10 | ev -5.579187626e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   17.000/20 after      2 sec. | K   10 | ev -5.579187626e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   18.000/20 after      2 sec. | K   10 | ev -5.579187626e+00 | Ndiff      0.000
MERGE 0/0 accepted.
   19.000/20 after      2 sec. | K   10 | ev -5.579187626e+00 | Ndiff      0.000
... done. converged.

Frequently asked questions

How do I plot the objective function over time?

Here, we plot the log evidence (sometimes called the evidence lower bound or ELBO). Here, larger objective scores indicate better model quality.

from matplotlib import pylab
%pylab inline

bnpy.viz.PlotELBO.plotJobsThatMatchKeywords('MixBarsK10V900/demobirthmerge-*');
pylab.legend(loc='lower right');

Populating the interactive namespace from numpy and matplotlib
BarsToyData-DPMixtureModel-MemoizedWithBirthsAndMerges_files/BarsToyData-DPMixtureModel-MemoizedWithBirthsAndMerges_18_1.png

Conclusion: All the different initial conditions quickly converge to similar scores of high quality.

How do I plot the number of clusters over time?

bnpy.viz.PlotELBO.plotJobsThatMatchKeywords('MixBarsK10V900/demobirthmerge-*', yvar='K');
BarsToyData-DPMixtureModel-MemoizedWithBirthsAndMerges_files/BarsToyData-DPMixtureModel-MemoizedWithBirthsAndMerges_21_0.png

** Conclusion:** Across very different initial conditions, we consistently reach exactly 8 learned clusters.

How do I plot the final learned clusters?

bnpy.viz.PlotComps.plotCompsForTask('MixBarsK10V900/demobirthmerge-Kinit=16/1/', **imshowArgs)
BarsToyData-DPMixtureModel-MemoizedWithBirthsAndMerges_files/BarsToyData-DPMixtureModel-MemoizedWithBirthsAndMerges_24_0.png

** Conclusion:** This run discovers the 10 ideal bars topics.

How do I plot the initial clusters?

bnpy.viz.PlotComps.plotCompsForTask('MixBarsK10V900/demobirthmerge-Kinit=16/1/', lap=0, **imshowArgs)
BarsToyData-DPMixtureModel-MemoizedWithBirthsAndMerges_files/BarsToyData-DPMixtureModel-MemoizedWithBirthsAndMerges_27_0.png

How do I plot the clusters after 2 passes through the data?

bnpy.viz.PlotComps.plotCompsForTask('MixBarsK10V900/demobirthmerge-Kinit=16/1/', lap=2, **imshowArgs)
BarsToyData-DPMixtureModel-MemoizedWithBirthsAndMerges_files/BarsToyData-DPMixtureModel-MemoizedWithBirthsAndMerges_29_0.png

Updated