1. Mike Hughes Avatar Mike Hughes
  2. Untitled project
  3. bnpy-dev

Wiki

Clone wiki

bnpy-dev / demos / GaussianToyData-DPMixtureModel-MemoizedWithBirthsAndMerges

View History

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

Goal

This demo walks you through a "Hello World" example of using bnpy from within Python.

We'll train a Dirichlet process (DP) Gaussian mixture model using memoized variational inference.

We can use the following import statements to load bnpy.

import bnpy

Toy dataset : AsteriskK8

We'll use a simple dataset of 2D points, drawn from 8 well-separated Gaussian clusters.

Our goal will be to recover the true set of 8 clusters.

import AsteriskK8
Data = AsteriskK8.get_data()

We can visualize this dataset as follows:

from matplotlib import pylab
%pylab inline

Populating the interactive namespace from numpy and matplotlib

pylab.plot(Data.X[:,0], Data.X[:,1], 'k.');
pylab.gcf().set_size_inches(4, 4);
pylab.axis('image'); pylab.xlim([-1.75, 1.75]); pylab.ylim([-1.75, 1.75]);
GaussianToyData-DPMixtureModel-MemoizedWithBirthsAndMerges_files/GaussianToyData-DPMixtureModel-MemoizedWithBirthsAndMerges_8_0.png

Running inference with bnpy

We'll fit a DP Gaussian mixture model, 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('AsteriskK8', 'DPMixtureModel', 'Gauss', 'moVB',
                         nLap=20, K=1, moves='birth,merge',
                         nTask=2, jobname='demobirthmerge-Kinit=1')

Asterisk Toy Data. 8 true clusters.
Entire Dataset Summary:
  total size: 25000 units
  batch size: 2500 units
  num. batches: 10
Data for Initialization:
  size: 25000 units (single observations)
  dimension: 2
Allocation Model:  DP mixture with K=1. Concentration gamma0= 1.00
Obs. Data  Model:  Gaussian with full covariance.
Obs. Data  Prior:  Gauss-Wishart on each mean/prec matrix pair: mu, Lam
  E[ mu[k] ]     = [ 0.  0.]
  E[ CovMat[k] ] =
  [[ 1.  0.]
   [ 0.  1.]]
Learn Alg: moVB
Trial  1/2 | alg. seed: 2497280 | data order seed: 8541952
savepath: /results/AsteriskK8/demobirthmerge-Kinit=1/1
    0.100/20 after      0 sec. | K    1 | ev -1.108127377e+00 |
    0.200/20 after      0 sec. | K    1 | ev -1.108663274e+00 |
    0.300/20 after      0 sec. | K    1 | ev -1.110766628e+00 |
    1.000/20 after      0 sec. | K    1 | ev -1.104282665e+00 |
BIRTH ACCEPTED. 4 fresh comps.
MERGE 0/3 accepted.
    2.000/20 after      0 sec. | K    5 | ev -1.016891994e+00 | Ndiff    545.066
BIRTH ACCEPTED. 3 fresh comps.
MERGE 0/5 accepted.
    3.000/20 after      1 sec. | K    8 | ev -7.642300722e-01 | Ndiff   1068.284
BIRTH ACCEPTED. 4 fresh comps.
MERGE 3/8 accepted. ev increased  1.9837e-03
    4.000/20 after      1 sec. | K    9 | ev -4.743017979e-01 | Ndiff   1032.489
BIRTH ACCEPTED. 5 fresh comps.
MERGE 2/9 accepted. ev increased  2.5825e-03
    5.000/20 after      2 sec. | K   12 | ev -3.074946741e-01 | Ndiff    412.162
BIRTH ACCEPTED. 4 fresh comps.
MERGE 4/5 accepted. ev increased  1.3074e-02
    6.000/20 after      2 sec. | K   12 | ev -1.276881407e-01 | Ndiff    277.107
BIRTH ACCEPTED. 4 fresh comps.
MERGE 5/7 accepted. ev increased  4.9037e-03
    7.000/20 after      3 sec. | K   11 | ev -2.572591276e-02 | Ndiff    216.745
MERGE 1/1 accepted. ev increased  4.6030e-04
    8.000/20 after      3 sec. | K   10 | ev -2.584905797e-03 | Ndiff     39.118
MERGE 1/1 accepted. ev increased  3.2250e-04
    9.000/20 after      3 sec. | K    9 | ev  1.109397198e-03 | Ndiff     12.643
MERGE 0/0 accepted.
   10.000/20 after      3 sec. | K    9 | ev  1.803132779e-03 | Ndiff      4.367
MERGE 0/0 accepted.
   11.000/20 after      3 sec. | K    9 | ev  1.996103141e-03 | Ndiff      0.794
MERGE 0/0 accepted.
   12.000/20 after      4 sec. | K    9 | ev  2.072616626e-03 | Ndiff      0.198
MERGE 1/1 accepted. ev increased  2.0252e-04
   13.000/20 after      4 sec. | K    8 | ev  2.408926998e-03 | Ndiff      0.017
MERGE 0/0 accepted.
   14.000/20 after      4 sec. | K    8 | ev  2.408927530e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   15.000/20 after      4 sec. | K    8 | ev  2.408927530e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   16.000/20 after      4 sec. | K    8 | ev  2.408927530e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   17.000/20 after      4 sec. | K    8 | ev  2.408927530e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   18.000/20 after      5 sec. | K    8 | ev  2.408927530e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   19.000/20 after      5 sec. | K    8 | ev  2.408927530e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   20.000/20 after      5 sec. | K    8 | ev  2.408927530e-03 | Ndiff      0.000
... done. converged.
Trial  2/2 | alg. seed: 1128064 | data order seed: 7673856
savepath: /results/AsteriskK8/demobirthmerge-Kinit=1/2
    0.100/20 after      0 sec. | K    1 | ev -1.106116048e+00 |
    0.200/20 after      0 sec. | K    1 | ev -1.106848843e+00 |
    0.300/20 after      0 sec. | K    1 | ev -1.107106005e+00 |
    1.000/20 after      0 sec. | K    1 | ev -1.104282665e+00 |
BIRTH ACCEPTED. 4 fresh comps.
MERGE 0/3 accepted.
    2.000/20 after      0 sec. | K    5 | ev -1.034087643e+00 | Ndiff    461.926
BIRTH ACCEPTED. 3 fresh comps.
MERGE 1/5 accepted. ev increased  8.4192e-05
    3.000/20 after      1 sec. | K    7 | ev -7.444108143e-01 | Ndiff   1080.763
BIRTH ACCEPTED. 3 fresh comps.
MERGE 2/6 accepted. ev increased  4.4727e-03
    4.000/20 after      1 sec. | K    8 | ev -4.684278566e-01 | Ndiff    632.104
BIRTH ACCEPTED. 3 fresh comps.
MERGE 1/6 accepted. ev increased  2.8012e-04
    5.000/20 after      1 sec. | K   10 | ev -3.695900973e-01 | Ndiff    352.647
BIRTH ACCEPTED. 4 fresh comps.
MERGE 4/7 accepted. ev increased  3.7992e-03
    6.000/20 after      2 sec. | K   10 | ev -1.409357981e-01 | Ndiff    284.190
BIRTH ACCEPTED. 3 fresh comps.
MERGE 3/5 accepted. ev increased  1.0351e-02
    7.000/20 after      2 sec. | K   10 | ev -2.126028050e-02 | Ndiff    130.023
MERGE 0/1 accepted.
    8.000/20 after      2 sec. | K   10 | ev -2.017934874e-03 | Ndiff     47.118
MERGE 1/1 accepted. ev increased  1.3809e-04
    9.000/20 after      2 sec. | K    9 | ev  1.113776726e-03 | Ndiff     16.418
MERGE 0/0 accepted.
   10.000/20 after      3 sec. | K    9 | ev  1.808072227e-03 | Ndiff      2.962
MERGE 0/0 accepted.
   11.000/20 after      3 sec. | K    9 | ev  1.993362590e-03 | Ndiff      0.700
MERGE 0/0 accepted.
   12.000/20 after      3 sec. | K    9 | ev  2.067939012e-03 | Ndiff      0.110
MERGE 1/1 accepted. ev increased  2.0341e-04
   13.000/20 after      3 sec. | K    8 | ev  2.409556966e-03 | Ndiff      0.007
MERGE 0/0 accepted.
   14.000/20 after      3 sec. | K    8 | ev  2.409564246e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   15.000/20 after      3 sec. | K    8 | ev  2.409564246e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   16.000/20 after      4 sec. | K    8 | ev  2.409564246e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   17.000/20 after      4 sec. | K    8 | ev  2.409564246e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   18.000/20 after      4 sec. | K    8 | ev  2.409564246e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   19.000/20 after      4 sec. | K    8 | ev  2.409564246e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   20.000/20 after      4 sec. | K    8 | ev  2.409564246e-03 | Ndiff      0.000
... done. converged.

4 initial clusters, repeated for 2 trials

hmodel, RInfo = bnpy.run('AsteriskK8', 'DPMixtureModel', 'Gauss', 'moVB',
                         nLap=20, K=4, moves='birth,merge',
                         nTask=2, jobname='demobirthmerge-Kinit=4')

Asterisk Toy Data. 8 true clusters.
Entire Dataset Summary:
  total size: 25000 units
  batch size: 2500 units
  num. batches: 10
Data for Initialization:
  size: 25000 units (single observations)
  dimension: 2
Allocation Model:  DP mixture with K=4. Concentration gamma0= 1.00
Obs. Data  Model:  Gaussian with full covariance.
Obs. Data  Prior:  Gauss-Wishart on each mean/prec matrix pair: mu, Lam
  E[ mu[k] ]     = [ 0.  0.]
  E[ CovMat[k] ] =
  [[ 1.  0.]
   [ 0.  1.]]
Learn Alg: moVB
Trial  1/2 | alg. seed: 2497280 | data order seed: 8541952
savepath: /results/AsteriskK8/demobirthmerge-Kinit=4/1
    0.100/20 after      0 sec. | K    4 | ev -1.047304800e+00 |
    0.200/20 after      0 sec. | K    4 | ev -1.036752818e+00 |
    0.300/20 after      0 sec. | K    4 | ev -1.034697291e+00 |
    1.000/20 after      0 sec. | K    4 | ev -1.021824496e+00 |
BIRTH ACCEPTED. 5 fresh comps.
MERGE 0/10 accepted.
    2.000/20 after      0 sec. | K    9 | ev -8.816303504e-01 | Ndiff    563.551
BIRTH ACCEPTED. 3 fresh comps.
MERGE 2/6 accepted. ev increased  2.6682e-03
    3.000/20 after      1 sec. | K   10 | ev -5.113303580e-01 | Ndiff    472.360
BIRTH ACCEPTED. 4 fresh comps.
MERGE 4/5 accepted. ev increased  2.1211e-03
    4.000/20 after      1 sec. | K   10 | ev -4.002681731e-01 | Ndiff    346.902
BIRTH ACCEPTED. 3 fresh comps.
MERGE 2/6 accepted. ev increased  7.8694e-04
    5.000/20 after      2 sec. | K   11 | ev -3.113172387e-01 | Ndiff    339.691
BIRTH ACCEPTED. 2 fresh comps.
MERGE 2/3 accepted. ev increased  3.7824e-03
    6.000/20 after      2 sec. | K   11 | ev -7.822969648e-02 | Ndiff    169.558
MERGE 1/1 accepted. ev increased  6.1792e-04
    7.000/20 after      2 sec. | K   10 | ev -1.036240544e-02 | Ndiff    112.482
MERGE 1/1 accepted. ev increased  4.2725e-04
    8.000/20 after      3 sec. | K    9 | ev  2.697950188e-04 | Ndiff     27.357
MERGE 0/0 accepted.
    9.000/20 after      3 sec. | K    9 | ev  1.646967412e-03 | Ndiff      5.863
MERGE 0/0 accepted.
   10.000/20 after      3 sec. | K    9 | ev  1.920246795e-03 | Ndiff      0.956
MERGE 0/0 accepted.
   11.000/20 after      3 sec. | K    9 | ev  2.001534235e-03 | Ndiff      0.188
MERGE 1/1 accepted. ev increased  2.2118e-04
   12.000/20 after      3 sec. | K    8 | ev  2.350332795e-03 | Ndiff      0.014
MERGE 0/0 accepted.
   13.000/20 after      4 sec. | K    8 | ev  2.350562004e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   14.000/20 after      4 sec. | K    8 | ev  2.350562004e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   15.000/20 after      4 sec. | K    8 | ev  2.350562004e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   16.000/20 after      4 sec. | K    8 | ev  2.350562004e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   17.000/20 after      4 sec. | K    8 | ev  2.350562004e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   18.000/20 after      4 sec. | K    8 | ev  2.350562004e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   19.000/20 after      5 sec. | K    8 | ev  2.350562004e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   20.000/20 after      5 sec. | K    8 | ev  2.350562004e-03 | Ndiff      0.000
... done. converged.
Trial  2/2 | alg. seed: 1128064 | data order seed: 7673856
savepath: /results/AsteriskK8/demobirthmerge-Kinit=4/2
    0.100/20 after      0 sec. | K    4 | ev -9.495577494e-01 |
    0.200/20 after      0 sec. | K    4 | ev -9.343023972e-01 |
    0.300/20 after      0 sec. | K    4 | ev -9.250155247e-01 |
    1.000/20 after      0 sec. | K    4 | ev -9.060052809e-01 |
BIRTH ACCEPTED. 3 fresh comps.
MERGE 0/5 accepted.
    2.000/20 after      0 sec. | K    7 | ev -8.527296815e-01 | Ndiff    327.295
BIRTH ACCEPTED. 3 fresh comps.
MERGE 3/6 accepted. ev increased  9.5830e-03
    3.000/20 after      1 sec. | K    7 | ev -6.718527761e-01 | Ndiff    494.004
BIRTH ACCEPTED. 3 fresh comps.
MERGE 1/5 accepted. ev increased  6.1158e-04
    4.000/20 after      1 sec. | K    9 | ev -4.378927182e-01 | Ndiff    386.498
BIRTH ACCEPTED. 2 fresh comps.
MERGE 2/3 accepted. ev increased  6.5918e-03
    5.000/20 after      1 sec. | K    9 | ev -2.584362805e-01 | Ndiff    162.352
BIRTH ACCEPTED. 2 fresh comps.
MERGE 0/2 accepted.
    6.000/20 after      1 sec. | K   11 | ev -1.643085956e-01 | Ndiff    465.042
BIRTH ACCEPTED. 2 fresh comps.
MERGE 3/3 accepted. ev increased  6.1574e-03
    7.000/20 after      2 sec. | K   10 | ev -2.531009200e-02 | Ndiff    195.879
MERGE 0/0 accepted.
    8.000/20 after      2 sec. | K   10 | ev -2.217996816e-03 | Ndiff     47.799
MERGE 1/1 accepted. ev increased  3.7208e-04
    9.000/20 after      2 sec. | K    9 | ev  1.343588569e-03 | Ndiff     13.117
MERGE 0/0 accepted.
   10.000/20 after      2 sec. | K    9 | ev  1.896451034e-03 | Ndiff      1.319
MERGE 0/0 accepted.
   11.000/20 after      3 sec. | K    9 | ev  2.011138803e-03 | Ndiff      0.291
MERGE 0/0 accepted.
   12.000/20 after      3 sec. | K    9 | ev  2.120211961e-03 | Ndiff      0.020
MERGE 1/1 accepted. ev increased  1.9889e-04
   13.000/20 after      3 sec. | K    8 | ev  2.369082970e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   14.000/20 after      3 sec. | K    8 | ev  2.369082970e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   15.000/20 after      4 sec. | K    8 | ev  2.369082970e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   16.000/20 after      4 sec. | K    8 | ev  2.369082970e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   17.000/20 after      4 sec. | K    8 | ev  2.369082970e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   18.000/20 after      4 sec. | K    8 | ev  2.369082970e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   19.000/20 after      4 sec. | K    8 | ev  2.369082970e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   20.000/20 after      5 sec. | K    8 | ev  2.369082970e-03 | Ndiff      0.000
... done. converged.

16 initial clusters, repeated for 2 trials

hmodel, RInfo = bnpy.run('AsteriskK8', 'DPMixtureModel', 'Gauss', 'moVB',
                         nLap=20, K=16, moves='birth,merge',
                         nTask=2, jobname='demobirthmerge-Kinit=16')

Asterisk Toy Data. 8 true clusters.
Entire Dataset Summary:
  total size: 25000 units
  batch size: 2500 units
  num. batches: 10
Data for Initialization:
  size: 25000 units (single observations)
  dimension: 2
Allocation Model:  DP mixture with K=16. Concentration gamma0= 1.00
Obs. Data  Model:  Gaussian with full covariance.
Obs. Data  Prior:  Gauss-Wishart on each mean/prec matrix pair: mu, Lam
  E[ mu[k] ]     = [ 0.  0.]
  E[ CovMat[k] ] =
  [[ 1.  0.]
   [ 0.  1.]]
Learn Alg: moVB
Trial  1/2 | alg. seed: 2497280 | data order seed: 8541952
savepath: /results/AsteriskK8/demobirthmerge-Kinit=16/1
    0.100/20 after      0 sec. | K   16 | ev -1.027305690e+00 |
    0.200/20 after      0 sec. | K   16 | ev -9.753695193e-01 |
    0.300/20 after      0 sec. | K   16 | ev -9.560752456e-01 |
    1.000/20 after      0 sec. | K   16 | ev -8.879254976e-01 |
BIRTH ACCEPTED. 2 fresh comps.
MERGE 4/16 accepted. ev increased  2.9864e-03
    2.000/20 after      1 sec. | K   14 | ev -6.570084469e-01 | Ndiff    209.941
BIRTH ACCEPTED. 2 fresh comps.
MERGE 4/8 accepted. ev increased  6.6230e-03
    3.000/20 after      1 sec. | K   12 | ev -3.465047823e-01 | Ndiff    207.696
MERGE 1/4 accepted. ev increased  5.9019e-04
    4.000/20 after      2 sec. | K   11 | ev -1.522618031e-01 | Ndiff    240.370
MERGE 1/2 accepted. ev increased  2.5773e-03
    5.000/20 after      2 sec. | K   10 | ev -3.498169425e-02 | Ndiff     31.836
MERGE 0/0 accepted.
    6.000/20 after      2 sec. | K   10 | ev  2.837920014e-04 | Ndiff     20.621
MERGE 1/1 accepted. ev increased  3.5597e-04
    7.000/20 after      2 sec. | K    9 | ev  1.688624507e-03 | Ndiff      3.199
MERGE 0/0 accepted.
    8.000/20 after      2 sec. | K    9 | ev  1.926058924e-03 | Ndiff      1.694
MERGE 0/0 accepted.
    9.000/20 after      3 sec. | K    9 | ev  2.006017744e-03 | Ndiff      0.184
MERGE 1/1 accepted. ev increased  2.1958e-04
   10.000/20 after      3 sec. | K    8 | ev  2.353395676e-03 | Ndiff      0.010
MERGE 0/0 accepted.
   11.000/20 after      3 sec. | K    8 | ev  2.353688739e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   12.000/20 after      3 sec. | K    8 | ev  2.353688739e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   13.000/20 after      3 sec. | K    8 | ev  2.353688739e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   14.000/20 after      4 sec. | K    8 | ev  2.353688739e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   15.000/20 after      4 sec. | K    8 | ev  2.353688739e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   16.000/20 after      4 sec. | K    8 | ev  2.353688739e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   17.000/20 after      4 sec. | K    8 | ev  2.353688739e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   18.000/20 after      4 sec. | K    8 | ev  2.353688739e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   19.000/20 after      4 sec. | K    8 | ev  2.353688739e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   20.000/20 after      5 sec. | K    8 | ev  2.353688739e-03 | Ndiff      0.000
... done. converged.
Trial  2/2 | alg. seed: 1128064 | data order seed: 7673856
savepath: /results/AsteriskK8/demobirthmerge-Kinit=16/2
    0.100/20 after      0 sec. | K   16 | ev -1.006223491e+00 |
    0.200/20 after      0 sec. | K   16 | ev -9.547728942e-01 |
    0.300/20 after      0 sec. | K   16 | ev -9.252499010e-01 |
    1.000/20 after      0 sec. | K   16 | ev -8.145731669e-01 |
BIRTH ACCEPTED. 3 fresh comps.
MERGE 2/18 accepted. ev increased  6.9098e-04
    2.000/20 after      1 sec. | K   17 | ev -3.607285169e-01 | Ndiff    103.212
MERGE 3/10 accepted. ev increased  9.3908e-03
    3.000/20 after      1 sec. | K   14 | ev -1.012415763e-01 | Ndiff    230.897
MERGE 2/2 accepted. ev increased  7.2418e-04
    4.000/20 after      1 sec. | K   12 | ev -1.275171392e-02 | Ndiff    110.627
MERGE 2/2 accepted. ev increased  6.9119e-04
    5.000/20 after      2 sec. | K   10 | ev -7.502210663e-04 | Ndiff     14.396
MERGE 1/1 accepted. ev increased  3.8190e-04
    6.000/20 after      2 sec. | K    9 | ev  1.473841203e-03 | Ndiff      2.657
MERGE 0/0 accepted.
    7.000/20 after      2 sec. | K    9 | ev  1.928947628e-03 | Ndiff      1.077
MERGE 0/0 accepted.
    8.000/20 after      2 sec. | K    9 | ev  2.035183484e-03 | Ndiff      0.215
MERGE 0/0 accepted.
    9.000/20 after      3 sec. | K    9 | ev  2.117391812e-03 | Ndiff      0.046
MERGE 1/1 accepted. ev increased  1.9677e-04
   10.000/20 after      3 sec. | K    8 | ev  2.399714286e-03 | Ndiff      0.001
MERGE 0/0 accepted.
   11.000/20 after      3 sec. | K    8 | ev  2.399714286e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   12.000/20 after      3 sec. | K    8 | ev  2.399714286e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   13.000/20 after      3 sec. | K    8 | ev  2.399714286e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   14.000/20 after      4 sec. | K    8 | ev  2.399714286e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   15.000/20 after      4 sec. | K    8 | ev  2.399714286e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   16.000/20 after      4 sec. | K    8 | ev  2.399714286e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   17.000/20 after      4 sec. | K    8 | ev  2.399714286e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   18.000/20 after      4 sec. | K    8 | ev  2.399714286e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   19.000/20 after      5 sec. | K    8 | ev  2.399714286e-03 | Ndiff      0.000
MERGE 0/0 accepted.
   20.000/20 after      5 sec. | K    8 | ev  2.399714286e-03 | 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('AsteriskK8/demobirthmerge-*');
pylab.legend(loc='lower right');

Populating the interactive namespace from numpy and matplotlib
GaussianToyData-DPMixtureModel-MemoizedWithBirthsAndMerges_files/GaussianToyData-DPMixtureModel-MemoizedWithBirthsAndMerges_17_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('AsteriskK8/demobirthmerge-*', yvar='K');
GaussianToyData-DPMixtureModel-MemoizedWithBirthsAndMerges_files/GaussianToyData-DPMixtureModel-MemoizedWithBirthsAndMerges_20_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('AsteriskK8/demobirthmerge-Kinit=16/1/')
GaussianToyData-DPMixtureModel-MemoizedWithBirthsAndMerges_files/GaussianToyData-DPMixtureModel-MemoizedWithBirthsAndMerges_23_0.png

** Conclusion:** This run discovers the 8 ideal clusters.

How do I plot the initial clusters?

bnpy.viz.PlotComps.plotCompsForTask('AsteriskK8/demobirthmerge-Kinit=16/1/', lap=0)
GaussianToyData-DPMixtureModel-MemoizedWithBirthsAndMerges_files/GaussianToyData-DPMixtureModel-MemoizedWithBirthsAndMerges_26_0.png

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

bnpy.viz.PlotComps.plotCompsForTask('AsteriskK8/demobirthmerge-Kinit=16/1/', lap=2)
GaussianToyData-DPMixtureModel-MemoizedWithBirthsAndMerges_files/GaussianToyData-DPMixtureModel-MemoizedWithBirthsAndMerges_28_0.png

Updated