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[MRG] Lda training visualization in visdom #1399

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merged 36 commits into from
Aug 30, 2017
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[MRG] Lda training visualization in visdom #1399

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bb65439
save log params in a dict
parulsethi Jun 7, 2017
9d2e78d
remove redundant line
parulsethi Jun 7, 2017
33818ec
add diff log
parulsethi Jun 7, 2017
281222c
remove diff log
parulsethi Jun 8, 2017
c507bbb
write params to log directory
parulsethi Jun 8, 2017
6f75ccc
add convergence, remove alpha
parulsethi Jun 9, 2017
d9db4e2
calculate perplexity/diff instead of using log function
parulsethi Jun 9, 2017
cd5f822
add docstrings and comments
parulsethi Jun 9, 2017
f4728e0
add coherence/diff labels in graphs
parulsethi Jun 12, 2017
40cf092
Merge branch 'develop' of https://github.com/RaRe-Technologies/gensim…
parulsethi Jun 16, 2017
d4f69f5
optional measures for viz
parulsethi Jun 16, 2017
fde7d4d
add coherence params to lda init
parulsethi Jun 16, 2017
3f18076
added Lda Visom viz notebook
parulsethi Jun 26, 2017
546908e
add option to specify env
parulsethi Jun 26, 2017
651a61a
made requested changes
parulsethi Jun 28, 2017
13dfddc
Merge branch 'develop' of https://github.com/RaRe-Technologies/gensim…
parulsethi Jul 8, 2017
1376d90
add generic callback API
parulsethi Jul 8, 2017
44c8e58
modified Notebook for new API
parulsethi Jul 8, 2017
92949a3
fix flake8
parulsethi Jul 8, 2017
5b22e4d
correct lee corpus division
parulsethi Jul 12, 2017
c369fc5
added docstrings
parulsethi Jul 17, 2017
a32960d
fix flake8
parulsethi Jul 18, 2017
48526d9
add shell example
parulsethi Jul 18, 2017
adf2a60
fix queue import for both py2/py3
parulsethi Jul 19, 2017
a272090
store metrics in model instance
parulsethi Aug 2, 2017
d3389bb
add nb example for getting metrics after train
parulsethi Aug 3, 2017
96949f7
merge develop
parulsethi Aug 8, 2017
7d0f0ec
made rquested changes
parulsethi Aug 8, 2017
dcc64a1
use dict for saving metrics
parulsethi Aug 9, 2017
47434f9
use str method for metric classes
parulsethi Aug 10, 2017
30c9b64
correct a notebook description
parulsethi Aug 10, 2017
e55af47
remove child-classes str method
parulsethi Aug 10, 2017
df5e01f
made requested changes
parulsethi Aug 23, 2017
b334c50
Merge branch 'develop' into tensorboard_logs
parulsethi Aug 24, 2017
c54e6bf
add visdom screenshot
parulsethi Aug 24, 2017
5f3d902
Merge branch 'tensorboard_logs' of https://github.com/parulsethi/gens…
parulsethi Aug 24, 2017
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281 changes: 281 additions & 0 deletions docs/notebooks/Training_visualizations.ipynb
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{
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Please add an example with logger="shell" in notebook (and show logging output in notebook)

"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Setup Visdom\n",
"\n",
"Install it with:\n",
"\n",
"`pip install visdom`\n",
"\n",
"Start the server:\n",
"\n",
"`python -m visdom.server`\n",
"\n",
"Visdom now can be accessed at http://localhost:8097 in the browser.\n",
"\n",
"\n",
"# LDA Training Visualization\n",
"\n",
"To monitor the LDA training, a list of Metrics can be passed to the LDA function call for plotting their values live as the training progresses. \n",
"\n",
"Let's plot the training stats for an LDA model being trained on Lee corpus. We will use the four evaluation metrics available for topic models in gensim: Coherence, Perplexity, Topic diff and Convergence. (using separate hold_out and test corpus for evaluating the perplexity)"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"Using TensorFlow backend.\n"
]
}
],
"source": [
"import os\n",
"import re\n",
"import gensim\n",
"from gensim.models import ldamodel\n",
"from gensim.corpora.dictionary import Dictionary\n",
"\n",
"# Set file names for train data\n",
"test_data_dir = '{}'.format(os.sep).join([gensim.__path__[0], 'test', 'test_data'])\n",
"lee_corpus = test_data_dir + os.sep + 'lee.cor'\n",
"\n",
"def read_corpus(fname):\n",
" texts = []\n",
" with open(fname, encoding=\"ISO-8859-1\") as f:\n",
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Don't work for python2 (because encoding isn't supported in python2), replace it to smart_open.

" for line in f:\n",
" # lower case all words\n",
" lowered = line.lower()\n",
" # remove punctuation and split into seperate words\n",
" words = re.compile('\\w+').findall(lowered)\n",
" texts.append(words)\n",
" return texts\n",
"\n",
"texts = read_corpus(lee_corpus)\n",
"\n",
"# Split test data into hold_out and test corpus\n",
"training_texts = texts[:25]\n",
"holdout_texts = texts[25:40]\n",
"test_texts = texts[40:50]\n",
"\n",
"training_dictionary = Dictionary(training_texts)\n",
"holdout_dictionary = Dictionary(holdout_texts)\n",
"test_dictionary = Dictionary(test_texts)\n",
"\n",
"training_corpus = [training_dictionary.doc2bow(text) for text in training_texts]\n",
"holdout_corpus = [holdout_dictionary.doc2bow(text) for text in holdout_texts]\n",
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It's 3 different mappings, mistake.

You should fit your Dictionary on training_texts and use it for all conversions (for holdout/test too)

"test_corpus = [test_dictionary.doc2bow(text) for text in test_texts]"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"from gensim.models.callbacks import CoherenceMetric, DiffMetric, PerplexityMetric, ConvergenceMetric\n",
"\n",
"# define perplexity callback for hold_out and test corpus\n",
"pl_holdout = PerplexityMetric(corpus=holdout_corpus, logger=\"visdom\", viz_env=\"LdaModel\", title=\"Perplexity (hold_out)\")\n",
"pl_test = PerplexityMetric(corpus=test_corpus, logger=\"visdom\", viz_env=\"LdaModel\", title=\"Perplexity (test)\")\n",
"\n",
"# define other remaining metrics available\n",
"ch_umass = CoherenceMetric(corpus=training_corpus, coherence=\"u_mass\", logger=\"visdom\", viz_env=\"LdaModel\", title=\"Coherence (u_mass)\")\n",
"diff_kl = DiffMetric(distance=\"kullback_leibler\", logger=\"visdom\", viz_env=\"LdaModel\", title=\"Diff (kullback_leibler)\")\n",
"convergence_jc = ConvergenceMetric(distance=\"hellinger\", logger=\"visdom\", viz_env=\"LdaModel\", title=\"Convergence (jaccard)\")\n",
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Docs say jaccard, but distance is hellinger.

"\n",
"callbacks = [pl_holdout, pl_test, ch_umass, diff_kl, convergence_jc]\n",
"\n",
"# training LDA model\n",
"model = ldamodel.LdaModel(corpus=training_corpus, id2word=training_dictionary, passes=5, num_topics=5, callbacks=callbacks)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"When the model is set for training, you can open http://localhost:8097 to see the training progress."
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"-22.4298221364\n"
]
}
],
"source": [
"# to get a metric value on a trained model\n",
"print(CoherenceMetric(corpus=training_corpus, coherence=\"u_mass\").get_value(model=model))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"The four types of graphs which are plotted for LDA:\n",
"\n",
"**Coherence**\n",
"\n",
"Coherence is a measure used to evaluate topic models. A good model will generate coherent topics, i.e., topics with high topic coherence scores. Good topics are topics that can be described by a short label based on the topic terms they spit out. \n",
"\n",
"<img src=\"Coherence.gif\">\n",
"\n",
"Now, this graph along with the others explained below, can be used to decide if it's time to stop the training. We can see if the value stops changing after some epochs and that we are able to get the highest possible coherence of our model. \n",
"\n",
"\n",
"**Perplexity**\n",
"\n",
"Perplexity is a measurement of how well a probability distribution or probability model predicts a sample. In LDA, topics are described by a probability distribution over vocabulary words. So, perplexity can be used to compare probabilistic models like LDA.\n",
"\n",
"<img src=\"Perplexity.gif\">\n",
"\n",
"For a good model, perplexity should be as low as possible.\n",
"\n",
"\n",
"**Topic Difference**\n",
"\n",
"Topic Diff calculates the distance between two LDA models. This distance is calculated based on the topics, by either using their probability distribution over vocabulary words (kullback_leibler, hellinger) or by simply using the common vocabulary words between the topics from both model.\n",
"\n",
"<img src=\"Diff.gif\">\n",
"\n",
"In the heatmap, X-axis define the Epoch no. and Y-axis define the distance between the identical topic from consecutive epochs. For ex. a particular cell in the heatmap with values (x=3, y=5, z=0.4) represent the distance(=0.4) between the topic 5 from 3rd epoch and topic 5 from 2nd epoch. With increasing epochs, the distance between the identical topics should decrease.\n",
" \n",
" \n",
"**Convergence**\n",
"\n",
"Convergence is the sum of the difference between all the identical topics from two consecutive epochs. It is basically the sum of column values in the heatmap above.\n",
"\n",
"<img src=\"Convergence.gif\">\n",
"\n",
"The model is said to be converged when the convergence value stops descending with increasing epochs."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Training Logs\n",
"\n",
"We can also log the metric values after every epoch to the shell apart from visualizing them in Visdom. The only change is to define `logger=\"shell\"` instead of `\"visdom\"` in the input callbacks."
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Can you add an example on how to get the values out programatically (no logging or plotting, using them from arbitrary Python code instead)?

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It can be done by using a loop to manually iterate over model and call metric classes at the end to store value:

model=LdaModel(passes=1)
perplexity=[]
for epoch in range(epochs):
    model.update(passes=1)
    pl = PerplexityMetric().get_value(model)
    perplexity.append(pl)

and sure, I'll add an example for this in notebook.

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@piskvorky piskvorky Jul 27, 2017 •
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Thanks. Is there a way to use the callbacks in a way that they collect this info?

I'm thinking a type of "logger" that instead of logging, appends the value to some internal list. Which other parts of the app can read from.

The idea is the interface would be the same as for logger=visdom/shell, without a need for an explicit outer loop like in your example.

Is that possible?

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Yes we can store them just after they are calculated in this step.

Maybe in a dict which could be an attribute of LdaModel? Structure could be:

metrics = {'PerplexityMetric':[val1, val2, ...], 'DiffMetric':[val1, val2, ...] }

on_epoch_end() can be made to return the metric values from current epoch which could then be appended in metrics dict after this step.

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Used metrics dict to save values as described above

]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"scrolled": false
},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"INFO:gensim.models.ldamodel:using symmetric alpha at 0.2\n",
"INFO:gensim.models.ldamodel:using symmetric eta at 0.0009950248756218905\n",
"INFO:gensim.models.ldamodel:using serial LDA version on this node\n",
"INFO:gensim.models.ldamodel:running online (multi-pass) LDA training, 5 topics, 3 passes over the supplied corpus of 25 documents, updating model once every 25 documents, evaluating perplexity every 25 documents, iterating 50x with a convergence threshold of 0.001000\n",
"WARNING:gensim.models.ldamodel:too few updates, training might not converge; consider increasing the number of passes or iterations to improve accuracy\n",
"INFO:gensim.models.ldamodel:-9.032 per-word bound, 523.4 perplexity estimate based on a held-out corpus of 25 documents with 2182 words\n",
"INFO:gensim.models.ldamodel:PROGRESS: pass 0, at document #25/25\n",
"INFO:gensim.models.ldamodel:topic #0 (0.200): 0.025*\"the\" + 0.022*\"to\" + 0.013*\"in\" + 0.011*\"of\" + 0.010*\"and\" + 0.007*\"s\" + 0.007*\"a\" + 0.005*\"said\" + 0.004*\"he\" + 0.004*\"iraqi\"\n",
"INFO:gensim.models.ldamodel:topic #1 (0.200): 0.054*\"the\" + 0.028*\"to\" + 0.023*\"of\" + 0.019*\"and\" + 0.017*\"in\" + 0.016*\"a\" + 0.013*\"s\" + 0.009*\"that\" + 0.008*\"has\" + 0.007*\"on\"\n",
"INFO:gensim.models.ldamodel:topic #2 (0.200): 0.049*\"the\" + 0.027*\"in\" + 0.024*\"to\" + 0.016*\"of\" + 0.012*\"and\" + 0.007*\"a\" + 0.007*\"that\" + 0.006*\"is\" + 0.006*\"for\" + 0.006*\"work\"\n",
"INFO:gensim.models.ldamodel:topic #3 (0.200): 0.041*\"the\" + 0.024*\"of\" + 0.021*\"to\" + 0.016*\"a\" + 0.016*\"and\" + 0.012*\"s\" + 0.010*\"in\" + 0.007*\"as\" + 0.006*\"with\" + 0.006*\"party\"\n",
"INFO:gensim.models.ldamodel:topic #4 (0.200): 0.034*\"the\" + 0.023*\"of\" + 0.016*\"a\" + 0.015*\"and\" + 0.012*\"in\" + 0.011*\"to\" + 0.008*\"as\" + 0.007*\"is\" + 0.007*\"with\" + 0.007*\"that\"\n",
"INFO:gensim.models.ldamodel:topic diff=1.878616, rho=1.000000\n",
"INFO:LdaModel:Epoch 0: Perplexity estimate: 495.948922721\n",
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Please use same logging format as in LdaModel (INFO:gensim.models.ldamodel)

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Done

"INFO:LdaModel:Epoch 0: Perplexity estimate: 609.481073631\n",
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Why perplexity showed twice (and different values)?

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One is for holdout corpus and other for test corpus. Though, updated the log statement now to define metric name from the input parameter title

"INFO:LdaModel:Epoch 0: Coherence estimate: -22.4407925538\n",
"INFO:LdaModel:Epoch 0: Diff estimate: [ 0.44194712 0.96670853 0.8036907 0.72372737 0.63141336]\n",
"INFO:LdaModel:Epoch 0: Convergence estimate: 0.0\n",
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Why always zero ?

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Previous state of model (needed to calculate Convergence) was being saved at wrong place. Corrected it

"INFO:gensim.models.ldamodel:-7.121 per-word bound, 139.2 perplexity estimate based on a held-out corpus of 25 documents with 2182 words\n",
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Perplexity calculates twice, wdyt about it @parulsethi? So, you should disable evaluation flag in a notebook.

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Disabled eval_every

"INFO:gensim.models.ldamodel:PROGRESS: pass 1, at document #25/25\n",
"INFO:gensim.models.ldamodel:topic #0 (0.200): 0.024*\"the\" + 0.015*\"to\" + 0.014*\"in\" + 0.008*\"iraqi\" + 0.008*\"of\" + 0.008*\"s\" + 0.007*\"and\" + 0.007*\"said\" + 0.005*\"u\" + 0.005*\"air\"\n",
"INFO:gensim.models.ldamodel:topic #1 (0.200): 0.056*\"the\" + 0.029*\"to\" + 0.025*\"of\" + 0.022*\"and\" + 0.017*\"in\" + 0.015*\"a\" + 0.013*\"s\" + 0.008*\"that\" + 0.008*\"has\" + 0.008*\"on\"\n",
"INFO:gensim.models.ldamodel:topic #2 (0.200): 0.050*\"the\" + 0.027*\"in\" + 0.025*\"to\" + 0.017*\"of\" + 0.010*\"and\" + 0.008*\"is\" + 0.007*\"be\" + 0.007*\"work\" + 0.007*\"a\" + 0.007*\"that\"\n",
"INFO:gensim.models.ldamodel:topic #3 (0.200): 0.031*\"the\" + 0.020*\"of\" + 0.019*\"to\" + 0.018*\"a\" + 0.014*\"and\" + 0.012*\"s\" + 0.009*\"in\" + 0.008*\"as\" + 0.007*\"party\" + 0.007*\"by\"\n",
"INFO:gensim.models.ldamodel:topic #4 (0.200): 0.033*\"the\" + 0.022*\"of\" + 0.014*\"and\" + 0.014*\"a\" + 0.012*\"in\" + 0.010*\"to\" + 0.010*\"iraq\" + 0.008*\"with\" + 0.008*\"that\" + 0.008*\"as\"\n",
"INFO:gensim.models.ldamodel:topic diff=0.570396, rho=0.577350\n",
"INFO:LdaModel:Epoch 1: Perplexity estimate: 439.092043455\n",
"INFO:LdaModel:Epoch 1: Perplexity estimate: 534.74704957\n",
"INFO:LdaModel:Epoch 1: Coherence estimate: -22.4302876151\n",
"INFO:LdaModel:Epoch 1: Diff estimate: [ 0.08300085 0.0312854 0.06168011 0.06740617 0.08645297]\n",
"INFO:LdaModel:Epoch 1: Convergence estimate: 0.0\n",
"INFO:gensim.models.ldamodel:-6.842 per-word bound, 114.7 perplexity estimate based on a held-out corpus of 25 documents with 2182 words\n",
"INFO:gensim.models.ldamodel:PROGRESS: pass 2, at document #25/25\n",
"INFO:gensim.models.ldamodel:topic #0 (0.200): 0.023*\"the\" + 0.014*\"in\" + 0.011*\"to\" + 0.009*\"iraqi\" + 0.008*\"s\" + 0.007*\"said\" + 0.007*\"u\" + 0.007*\"air\" + 0.007*\"coalition\" + 0.007*\"military\"\n",
"INFO:gensim.models.ldamodel:topic #1 (0.200): 0.056*\"the\" + 0.030*\"to\" + 0.026*\"of\" + 0.022*\"and\" + 0.017*\"in\" + 0.014*\"a\" + 0.014*\"s\" + 0.008*\"has\" + 0.008*\"on\" + 0.008*\"that\"\n",
"INFO:gensim.models.ldamodel:topic #2 (0.200): 0.050*\"the\" + 0.026*\"in\" + 0.025*\"to\" + 0.017*\"of\" + 0.008*\"and\" + 0.008*\"is\" + 0.008*\"be\" + 0.008*\"work\" + 0.007*\"a\" + 0.007*\"that\"\n",
"INFO:gensim.models.ldamodel:topic #3 (0.200): 0.027*\"the\" + 0.021*\"a\" + 0.019*\"of\" + 0.019*\"to\" + 0.013*\"s\" + 0.013*\"and\" + 0.009*\"in\" + 0.009*\"as\" + 0.009*\"party\" + 0.008*\"by\"\n",
"INFO:gensim.models.ldamodel:topic #4 (0.200): 0.036*\"the\" + 0.022*\"of\" + 0.015*\"and\" + 0.013*\"a\" + 0.012*\"in\" + 0.011*\"iraq\" + 0.011*\"to\" + 0.010*\"with\" + 0.009*\"that\" + 0.008*\"are\"\n",
"INFO:gensim.models.ldamodel:topic diff=0.363037, rho=0.500000\n",
"INFO:LdaModel:Epoch 2: Perplexity estimate: 413.6047717\n",
"INFO:LdaModel:Epoch 2: Perplexity estimate: 515.596865513\n",
"INFO:LdaModel:Epoch 2: Coherence estimate: -22.4273737487\n",
"INFO:LdaModel:Epoch 2: Diff estimate: [ 0.01187035 0.01098017 0.00861298 0.02232568 0.01953778]\n",
"INFO:LdaModel:Epoch 2: Convergence estimate: 0.0\n"
]
}
],
"source": [
"import logging\n",
"\n",
"logging.basicConfig(level=logging.INFO)\n",
"logger = logging.getLogger(__name__)\n",
"logger.setLevel(logging.DEBUG)\n",
"\n",
"# define perplexity callback for hold_out and test corpus\n",
"pl_holdout = PerplexityMetric(corpus=holdout_corpus, logger=\"shell\")\n",
"pl_test = PerplexityMetric(corpus=test_corpus, logger=\"shell\")\n",
"\n",
"# define other remaining metrics available\n",
"ch_umass = CoherenceMetric(corpus=training_corpus, coherence=\"u_mass\", logger=\"shell\")\n",
"diff_kl = DiffMetric(distance=\"kullback_leibler\", logger=\"shell\")\n",
"convergence_jc = ConvergenceMetric(distance=\"jaccard\", logger=\"shell\")\n",
"\n",
"callbacks = [pl_holdout, pl_test, ch_umass, diff_kl, convergence_jc]\n",
"\n",
"# training LDA model\n",
"model = ldamodel.LdaModel(corpus=training_corpus, id2word=training_dictionary, passes=3, num_topics=5, callbacks=callbacks)"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.4.3"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
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