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/* ----------------------------------------------------------------------- *//**
*
* @file lda.sql_in
*
* @brief SQL functions for Latent Dirichlet Allocation
* @date Dec 2012
*
* @sa For an introduction to Latent Dirichlet Allocation models, see the
module description \ref grp_lda.
*
*//* ------------------------------------------------------------------------*/
m4_include(`SQLCommon.m4')
/**
@addtogroup grp_lda
<div class="toc"><b>Contents</b>
<ul>
<li><a href="#background">Background</a></li>
<li><a href="#train">Training Function</a></li>
<li><a href="#predict">Prediction Function</a></li>
<li><a href="#perplexity">Perplexity</a></li>
<li><a href="#helper">Helper Functions</a></li>
<li><a href="#examples">Examples</a></li>
<li><a href="#literature">Literature</a></li>
<li><a href="#related">Related Topics</a><li>
</ul>
</div>
@brief Generates a Latent Dirichlet Allocation predictive model for a collection of documents.
Latent Dirichlet Allocation (LDA) is a generative probabilistic
model for natural texts. It is used in problems such as automated
topic discovery, collaborative filtering, and document classification.
In addition to an implementation of LDA, this MADlib module also provides a
number of additional helper functions to interpret results of the LDA output.
@note
Topic modeling is often used as part of a larger text processing
pipeline, which may include operations such as term frequency, stemming and
stop word removal. You can use the
function <a href="group__grp__text__utilities.html">Term Frequency</a>
to generate the required vocabulary format from raw documents for the
LDA training function. See
the examples later on this page for more details.
@anchor background
@par Background
The LDA model posits that each document is associated with a mixture of various
topics (e.g., a document is related to Topic 1 with probability 0.7, and Topic 2
with probability 0.3), and that each word in the document is attributable to
one of the document's topics. There is a (symmetric) Dirichlet prior with
parameter \f$ \alpha \f$ on each document's topic mixture. In addition, there
is another (symmetric) Dirichlet prior with parameter \f$ \beta \f$ on the
distribution of words for each topic.
The following generative process then defines a distribution over a corpus of
documents:
- Sample for each topic \f$ i \f$, a per-topic word
distribution \f$ \phi_i \f$ from the Dirichlet (\f$\beta\f$) prior.
- For each document:
- Sample a document length N from a suitable distribution, say, Poisson.
- Sample a topic mixture \f$ \theta \f$ for the document from the
Dirichlet (\f$\alpha\f$) distribution.
- For each of the N words:
- Sample a topic \f$ z_n \f$ from the multinomial topic distribution \f$
\theta \f$.
- Sample a word \f$ w_n \f$ from the multinomial word distribution \f$
\phi_{z_n} \f$ associated with topic \f$ z_n \f$.
In practice, only the words in each document are observable. The topic mixture
of each document and the topic for each word in each document are latent
unobservable variables that need to be inferred from the observables, and this
is referred to as the inference problem for
LDA. Exact inference is intractable, but several approximate inference
algorithms for LDA have been developed. The simple and effective Gibbs sampling
algorithm described in Griffiths and Steyvers [2] appears to be the current
algorithm of choice.
This implementation provides a parallel and scalable in-database solution for
LDA based on Gibbs sampling. It takes advantage of the shared-nothing MPP
architecture and is a different implementation than one would find for
MPI or map/reduce.
@anchor train
@par Training Function
The LDA training function has the following syntax:
<pre class="syntax">
lda_train( data_table,
model_table,
output_data_table,
voc_size,
topic_num,
iter_num,
alpha,
beta,
evaluate_every,
perplexity_tol
)
</pre>
\b Arguments
<dl class="arglist">
<dt>data_table</dt>
<dd>TEXT. Name of the table storing the training dataset. Each row is
in the form <tt>&lt;docid, wordid, count&gt;</tt> where \c docid, \c wordid, and \c count
are non-negative integers.
The \c docid column refers to the document ID, the \c wordid column is the
word ID (the index of a word in the vocabulary), and \c count is the
number of occurrences of the word in the document. Please note:
- \c wordid must be
contiguous integers going from from 0 to \c voc_size &minus; \c 1.
- column names for \c docid, \c wordid, and \c count are currently fixed,
so you must use these exact names in the data_table.
The function <a href="group__grp__text__utilities.html">Term Frequency</a>
can be used to generate vocabulary in the required format from raw documents.
</dd>
<dt>model_table</dt>
<dd>TEXT. This is an output table generated by LDA which contains the learned model.
It has one row with the following columns:
<table class="output">
<tr>
<th>voc_size</th>
<td>INTEGER. Size of the vocabulary. As mentioned above for the input
table, \c wordid consists of contiguous integers going
from 0 to \c voc_size &minus; \c 1.
</td>
</tr>
<tr>
<th>topic_num</th>
<td>INTEGER. Number of topics.</td>
</tr>
<tr>
<th>alpha</th>
<td>DOUBLE PRECISION. Dirichlet prior for the per-document
topic multinomial.</td>
</tr>
<tr>
<th>beta</th>
<td>DOUBLE PRECISION. Dirichlet prior for the per-topic
word multinomial.</td>
</tr>
<tr>
<th>model</th>
<td>BIGINT[]. The encoded model description (not human readable).</td>
</tr>
<tr>
<th>num_iterations</th>
<td>INTEGER. Number of iterations that training ran for, which may
be less than the maximum value specified in the parameter 'iter_num'
if the perplexity tolerance was reached.</td>
</tr>
<tr>
<th>perplexity</th>
<td>DOUBLE PRECISION[]. Array of perplexity values as per the 'evaluate_every' parameter.
For example, if 'evaluate_every=5' this would be an array of perplexity values for
every 5th iteration, plus the last iteration.</td>
</tr>
<tr>
<th>perplexity_iters</th>
<td>INTEGER[]. Array indicating the iterations for which perplexity is calculated, as derived
from the parameters 'iter_num' and 'evaluate_every'. For example, if 'iter_num=5' and 'evaluate_every=2',
then 'perplexity_iters' value would be {2,4,5} indicating that perplexity is computed at
iterations 2, 4 and 5 (at the end), unless of course it terminated earlier due
to 'perplexity_tol'. If 'iter_num=5' and 'evaluate_every=1', then 'perplexity_iters' value
would be {1,2,3,4,5} indicating that perplexity is computed at every iteration,
again assuming it ran the full number of iterations.</td>
</tr>
</table>
</dd>
<dt>output_data_table</dt>
<dd>TEXT. The name of the table generated by LDA that stores
the output data. It has the following columns:
<table class="output">
<tr>
<th>docid</th>
<td>INTEGER. Document id from input 'data_table'.</td>
</tr>
<tr>
<th>wordcount</th>
<td>INTEGER. Count of number of words in the document,
including repeats. For example, if a word appears 3 times
in the document, it is counted 3 times.</td>
</tr>
<tr>
<th>words</th>
<td>INTEGER[]. Array of \c wordid in the document, not
including repeats. For example, if a word appears 3 times
in the document, it appears only once in the \c words array.</td>
</tr>
<tr>
<th>counts</th>
<td>INTEGER[]. Frequency of occurance of a word in the document,
indexed the same as the \c words array above. For example, if the
2nd element of the \c counts array is 4, it means that the word
in the 2nd element of the \c words array occurs 4 times in the
document.</td>
</tr>
<tr>
<th>topic_count</th>
<td>INTEGER[]. Array of the count of words in the document
that correspond to each topic. This array is of
length \c topic_num. Topic ids are continuous integers going
from 0 to \c topic_num &minus; \c 1.</td>
</tr>
<tr>
<th>topic_assignment</th>
<td>INTEGER[]. Array indicating which topic each word in the
document corresponds to. This array is of length \c wordcount.
Words that are repeated \c n times in the document
will show up consecutively \c n times in this array.</td>
</tr>
</table>
</dd>
<dt>voc_size</dt>
<dd>INTEGER. Size of the vocabulary. As mentioned above for the
input 'data_table', \c wordid consists of continuous integers going
from 0 to \c voc_size &minus; \c 1.
</dd>
<dt>topic_num</dt>
<dd>INTEGER. Desired number of topics.</dd>
<dt>iter_num</dt>
<dd>INTEGER. Maximum number of iterations. If a 'perplexity_tol' is set,
LDA may train for less than the maximum number of iterations if the tolerance is reached.</dd>
<dt>alpha</dt>
<dd>DOUBLE PRECISION. Dirichlet prior for the per-document topic
multinomial (e.g., 50/topic_num is a reasonable value to start with
as per Griffiths and Steyvers [2]).</dd>
<dt>beta</dt>
<dd>DOUBLE PRECISION. Dirichlet prior for the per-topic
word multinomial (e.g., 0.01 is a reasonable value to start with).</dd>
<dt>evaluate_every (optional)</dt>
<dd>INTEGER, default: 0. How often to evaluate perplexity. Set it to 0 or a negative number
to not evaluate perplexity in training at all. Evaluating perplexity can help you check
convergence during the training process, but it will also increase total training time.
For example, evaluating perplexity in every iteration might increase training time
up to two-fold.</dd>
<dt>perplexity_tol (optional)</dt>
<dd>DOUBLE PRECISION, default: 0.1. Perplexity tolerance to stop iteration.
Only used when the parameter 'evaluate_every' is greater than 0.</dd>
</dl>
@anchor predict
@par Prediction Function
Prediction involves labelling test documents using a learned LDA model:
<pre class="syntax">
lda_predict( data_table,
model_table,
output_predict_table
);
</pre>
\b Arguments
<dl class="arglist">
<dt>data_table</dt>
<dd>TEXT. Name of the table storing the test dataset
(new document to be labeled).
</dd>
<dt>model_table</dt>
<dd>TEXT. The model table generated by the training process.
</dd>
<dt>output_predict_table</dt>
<dd>TEXT. The prediction output table.
Each row in the table stores the topic
distribution and the topic assignments for a
document in the dataset. This table has the exact
same columns and interpretation as
the 'output_data_table' from the training function above.
</dd>
</dl>
@anchor perplexity
@par Perplexity
Perplexity describes how well the model fits the data by
computing word likelihoods averaged over the documents.
This function returns a single perplexity value.
<pre class="syntax">
lda_get_perplexity( model_table,
output_data_table
);
</pre>
\b Arguments
<dl class="arglist">
<dt>model_table</dt>
<dd>TEXT. The model table generated by the training process.
</dd>
<dt>output_data_table</dt>
<dd>TEXT. Output table generated by the
training or predict functions, containing the topic assignments
by word.
</dd>
</dl>
@anchor helper
@par Helper Functions
The helper functions can help to interpret the output
from LDA training and LDA prediction.
<b>Topic description by top-k words with highest probability</b>
Applies to LDA training only.
<pre class="syntax">
lda_get_topic_desc( model_table,
vocab_table,
output_table,
top_k
)
</pre>
\b Arguments
<dl class="arglist">
<dt>model_table</dt>
<dd>TEXT. The model table generated by the training process.
</dd>
<dt>vocab_table</dt>
<dd>TEXT. The vocabulary table in the form <wordid, word>.
Reminder that this table can be created using the \c term_frequency
function (\ref grp_text_utilities) with the
parameter \c compute_vocab set to TRUE.
</dd>
<dt>output_table</dt>
<dd>TEXT. The output table with per-topic description
generated by this helper function.
It has the following columns:
<table class="output">
<tr>
<th>topicid</th>
<td>INTEGER. Topic id.</td>
</tr>
<tr>
<th>wordid</th>
<td>INTEGER. Word id.</td>
</tr>
<tr>
<th>prob</th>
<td>DOUBLE PRECISION. Probability that this topic
will generate the word.</td>
</tr>
<tr>
<th>word</th>
<td>TEXT. Word in text form.</td>
</tr>
</table>
</dd>
<dt>top_k</dt>
<dd>TEXT. The desired number of top words to show for each topic.
</dd>
</dl>
<b>Per-word topic counts</b>
Applies to LDA training only.
<pre class="syntax">
lda_get_word_topic_count( model_table,
output_table
)
</pre>
\b Arguments
<dl class="arglist">
<dt>model_table</dt>
<dd>TEXT. The model table generated by the training process.
</dd>
<dt>output_table</dt>
<dd>TEXT. The output table with per-word topic counts
generated by this helper function.
It has the following columns:
<table class="output">
<tr>
<th>wordid</th>
<td>INTEGER. Word id.</td>
</tr>
<tr>
<th>topic_count</th>
<td>INTEGER[]. Count of word association with each topic, i.e.,
shows how many times a given word is
assigned to a topic. Array is of length number of topics.</td>
</tr>
</table>
</dd>
</dl>
<b>Per-topic word counts</b>
Applies to LDA training only.
<pre class="syntax">
lda_get_topic_word_count( model_table,
output_table
)
</pre>
\b Arguments
<dl class="arglist">
<dt>model_table</dt>
<dd>TEXT. The model table generated by the training process.
</dd>
<dt>output_table</dt>
<dd>TEXT. The output table with per-topic word counts
generated by this helper function.
It has the following columns:
<table class="output">
<tr>
<th>topicid</th>
<td>INTEGER. Topic id.</td>
</tr>
<tr>
<th>word_count</th>
<td>INTEGER[]. Array showing which words are associated with the topic
by frequency. Array is of length number of words.</td>
</tr>
</table>
</dd>
</dl>
<b>Per-document word to topic mapping</b>
Applies to both LDA training and LDA prediction.
<pre class="syntax">
lda_get_word_topic_mapping( output_data_table, -- From training or prediction
output_table
)
</pre>
\b Arguments
<dl class="arglist">
<dt>output_data_table</dt>
<dd>TEXT. The output data table generated by either LDA training
or LDA prediction.
</dd>
<dt>output_table</dt>
<dd>TEXT. The output table with word to topic mappings
generated by this helper function.
It has the following columns:
<table class="output">
<tr>
<th>docid</th>
<td>INTEGER. Document id.</td>
</tr>
<tr>
<th>wordid</th>
<td>INTEGER. Word id.</td>
</tr>
<tr>
<th>topicid</th>
<td>INTEGER. Topic id.</td>
</tr>
</table>
</dd>
</dl>
@anchor examples
@examp
-# Prepare a training dataset for LDA. The examples below are small strings extracted from various Wikipedia documents:
<pre class="example">
DROP TABLE IF EXISTS documents;
CREATE TABLE documents(docid INT4, contents TEXT);
INSERT INTO documents VALUES
(0, 'Statistical topic models are a class of Bayesian latent variable models, originally developed for analyzing the semantic content of large document corpora.'),
(1, 'By the late 1960s, the balance between pitching and hitting had swung in favor of the pitchers. In 1968 Carl Yastrzemski won the American League batting title with an average of just .301, the lowest in history.'),
(2, 'Machine learning is closely related to and often overlaps with computational statistics; a discipline that also specializes in prediction-making. It has strong ties to mathematical optimization, which deliver methods, theory and application domains to the field.'),
(3, 'California''s diverse geography ranges from the Sierra Nevada in the east to the Pacific Coast in the west, from the Redwood–Douglas fir forests of the northwest, to the Mojave Desert areas in the southeast. The center of the state is dominated by the Central Valley, a major agricultural area.');
</pre>
You can apply stemming, stop word removal and tokenization
at this point in order to prepare the documents for text
processing. Depending upon your database version, various
tools are available. Databases based on more recent
versions of PostgreSQL may do something like:
<pre class="example">
SELECT tsvector_to_array(to_tsvector('english',contents)) from documents;
</pre>
<pre class="result">
tsvector_to_array
+-----------------------------------------------------------------------
{analyz,bayesian,class,content,corpora,develop,document,larg,...}
{1960s,1968,301,american,averag,balanc,bat,carl,favor,histori,...}
{also,applic,close,comput,deliv,disciplin,domain,field,learn,...}
{agricultur,area,california,center,central,coast,desert,divers,...}
(4 rows)
</pre>
In this example, we assume a database based on an older
version of PostgreSQL and just perform basic punctuation removal
and tokenization. The array of words is added as a new column
to the documents table:
<pre class="example">
ALTER TABLE documents ADD COLUMN words TEXT[];
UPDATE documents SET words =
regexp_split_to_array(lower(
regexp_replace(contents, E'[,.;\']','', 'g')
), E'[\\\\s+]');
SELECT * FROM documents ORDER BY docid;
</pre>
<pre class="result">
-[ RECORD 1 ]---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
docid | 0
contents | Statistical topic models are a class of Bayesian latent variable models, originally developed for analyzing the semantic content of large document corpora.
words | {statistical,topic,models,are,a,class,of,bayesian,latent,variable,models,originally,developed,for,analyzing,the,semantic,content,of,large,document,corpora}
-[ RECORD 2 ]---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
docid | 1
contents | By the late 1960s, the balance between pitching and hitting had swung in favor of the pitchers. In 1968 Carl Yastrzemski won the American League batting title with an average of just .301, the lowest in history.
words | {by,the,late,1960s,the,balance,between,pitching,and,hitting,had,swung,in,favor,of,the,pitchers,in,1968,carl,yastrzemski,won,the,american,league,batting,title,with,an,average,of,just,301,the,lowest,in,history}
-[ RECORD 3 ]---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
docid | 2
contents | Machine learning is closely related to and often overlaps with computational statistics; a discipline that also specializes in prediction-making. It has strong ties to mathematical optimization, which deliver methods, theory and application domains to the field.
words | {machine,learning,is,closely,related,to,and,often,overlaps,with,computational,statistics,a,discipline,that,also,specializes,in,prediction-making,it,has,strong,ties,to,mathematical,optimization,which,deliver,methods,theory,and,application,domains,to,the,field}
-[ RECORD 4 ]---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
docid | 3
contents | California's diverse geography ranges from the Sierra Nevada in the east to the Pacific Coast in the west, from the Redwood–Douglas fir forests of the northwest, to the Mojave Desert areas in the southeast. The center of the state is dominated by the Central Valley, a major agricultural area.
words | {californias,diverse,geography,ranges,from,the,sierra,nevada,in,the,east,to,the,pacific,coast,in,the,west,from,the,redwood–douglas,fir,forests,of,the,northwest,to,the,mojave,desert,areas,in,the,southeast,the,center,of,the,state,is,dominated,by,the,central,valley,a,major,agricultural,area}
</pre>
-# Build a word count table by extracting the words and building a histogram for
each document using the \c term_frequency function (\ref grp_text_utilities).
<pre class="example">
DROP TABLE IF EXISTS documents_tf, documents_tf_vocabulary;
SELECT madlib.term_frequency('documents', -- input table
'docid', -- document id column
'words', -- vector of words in document
'documents_tf', -- output documents table with term frequency
TRUE); -- TRUE to created vocabulary table
SELECT * FROM documents_tf ORDER BY docid LIMIT 20;
</pre>
<pre class="result">
docid | wordid | count
-------+--------+-------
0 | 71 | 1
0 | 90 | 1
0 | 56 | 1
0 | 68 | 2
0 | 85 | 1
0 | 28 | 1
0 | 35 | 1
0 | 54 | 1
0 | 64 | 2
0 | 8 | 1
0 | 29 | 1
0 | 80 | 1
0 | 24 | 1
0 | 11 | 1
0 | 17 | 1
0 | 32 | 1
0 | 3 | 1
0 | 42 | 1
0 | 97 | 1
0 | 95 | 1
(20 rows)
</pre>
Here is the associated vocabulary table. Note that wordid starts at 0:
<pre class="example">
SELECT * FROM documents_tf_vocabulary ORDER BY wordid LIMIT 20;
</pre>
<pre class="result">
wordid | word
--------+--------------
0 | 1960s
1 | 1968
2 | 301
3 | a
4 | agricultural
5 | also
6 | american
7 | an
8 | analyzing
9 | and
10 | application
11 | are
12 | area
13 | areas
14 | average
15 | balance
16 | batting
17 | bayesian
18 | between
19 | by
(20 rows)
</pre>
The total number of words in the vocabulary across all documents is:
<pre class="example">
SELECT COUNT(*) FROM documents_tf_vocabulary;
</pre>
<pre class="result">
count
+------
103
(1 row)
</pre>
-# Train LDA model. For Dirichlet priors we use initial
rule-of-thumb values of 50/(number of topics) for alpha
and 0.01 for beta.
Reminder that column names for docid, wordid, and count
are currently fixed, so you must use these exact names
in the input table. After a successful run of the LDA
training function two tables are generated, one for
storing the learned model and the other for storing
the output data table.
<pre class="example">
DROP TABLE IF EXISTS lda_model, lda_output_data;
SELECT madlib.lda_train( 'documents_tf', -- documents table in the form of term frequency
'lda_model', -- model table created by LDA training (not human readable)
'lda_output_data', -- readable output data table
103, -- vocabulary size
5, -- number of topics
10, -- number of iterations
5, -- Dirichlet prior for the per-doc topic multinomial (alpha)
0.01 -- Dirichlet prior for the per-topic word multinomial (beta)
);
SELECT * FROM lda_output_data ORDER BY docid;
</pre>
<pre class="result">
-[ RECORD 1 ]----+------------------------------------------------------------------------------------------------------
docid | 0
wordcount | 22
words | {24,17,11,95,90,85,68,54,42,35,28,8,3,97,80,71,64,56,32,29}
counts | {1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,2,1,1,1}
topic_count | {4,2,4,3,9}
topic_assignment | {4,2,4,1,2,1,2,2,0,3,4,4,3,0,0,4,0,4,4,4,3,4}
-[ RECORD 2 ]----+------------------------------------------------------------------------------------------------------
docid | 1
wordcount | 37
words | {1,50,49,46,19,16,14,9,7,0,90,68,57,102,101,100,93,88,75,74,59,55,53,48,39,21,18,15,6,2}
counts | {1,3,1,1,1,1,1,1,1,1,5,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1}
topic_count | {2,5,14,9,7}
topic_assignment | {0,3,3,3,1,4,2,2,2,1,3,1,2,2,2,2,2,2,2,1,4,3,2,0,4,2,4,2,3,4,3,1,3,4,3,2,4}
-[ RECORD 3 ]----+------------------------------------------------------------------------------------------------------
docid | 2
wordcount | 36
words | {10,27,33,40,47,51,58,62,63,69,72,83,100,99,94,92,91,90,89,87,86,79,76,70,60,52,50,36,30,25,9,5,3}
counts | {1,1,1,1,1,1,1,1,1,1,1,1,1,1,3,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1}
topic_count | {15,10,1,7,3}
topic_assignment | {0,3,1,3,0,0,3,3,1,0,1,0,0,0,0,1,1,0,4,2,0,4,1,0,1,0,0,4,3,3,3,0,1,1,1,0}
-[ RECORD 4 ]----+------------------------------------------------------------------------------------------------------
docid | 3
wordcount | 49
words | {77,78,81,82,67,65,51,45,44,43,34,26,13,98,96,94,90,84,73,68,66,61,50,41,38,37,31,23,22,20,19,12,4,3}
counts | {1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,2,11,1,1,2,1,1,3,1,1,1,1,1,1,1,1,1,1,1}
topic_count | {5,5,26,5,8}
topic_assignment | {4,4,4,0,2,0,0,2,4,4,2,2,2,1,2,4,1,0,2,2,2,2,2,2,2,2,2,2,2,1,2,2,2,2,4,3,3,3,2,3,2,3,2,1,4,2,2,1,0}
</pre>
Review summary table:
<pre class="example">
SELECT voc_size, topic_num, alpha, beta, num_iterations, perplexity, perplexity_iters from lda_model;
</pre>
<pre class="result">
-[ RECORD 1 ]----+-----
voc_size | 103
topic_num | 5
alpha | 5
beta | 0.01
num_iterations | 10
perplexity |
perplexity_iters |
</pre>
-# Review learned model using helper functions.
First, we get topic description by top-k words. These are
the k words with the highest probability for the topic.
Note that if there are ties in probability, more than k
words may actually be reported for each topic. Also note
that topicid starts at 0:
<pre class="example">
DROP TABLE IF EXISTS helper_output_table;
SELECT madlib.lda_get_topic_desc( 'lda_model', -- LDA model generated in training
'documents_tf_vocabulary', -- vocabulary table that maps wordid to word
'helper_output_table', -- output table for per-topic descriptions
5); -- k: number of top words for each topic
SELECT * FROM helper_output_table ORDER BY topicid, prob DESC LIMIT 40;
</pre>
<pre class="result">
topicid | wordid | prob | word
---------+--------+--------------------+-------------------
0 | 3 | 0.111357750647429 | a
0 | 51 | 0.074361820199778 | is
0 | 94 | 0.074361820199778 | to
0 | 70 | 0.0373658897521273 | optimization
0 | 82 | 0.0373658897521273 | southeast
0 | 60 | 0.0373658897521273 | machine
0 | 71 | 0.0373658897521273 | originally
0 | 69 | 0.0373658897521273 | often
0 | 99 | 0.0373658897521273 | which
0 | 83 | 0.0373658897521273 | specializes
0 | 1 | 0.0373658897521273 | 1968
0 | 97 | 0.0373658897521273 | variable
0 | 25 | 0.0373658897521273 | closely
0 | 93 | 0.0373658897521273 | title
0 | 47 | 0.0373658897521273 | has
0 | 65 | 0.0373658897521273 | mojave
0 | 79 | 0.0373658897521273 | related
0 | 89 | 0.0373658897521273 | that
0 | 10 | 0.0373658897521273 | application
0 | 100 | 0.0373658897521273 | with
0 | 92 | 0.0373658897521273 | ties
0 | 54 | 0.0373658897521273 | large
1 | 94 | 0.130699088145897 | to
1 | 9 | 0.130699088145897 | and
1 | 5 | 0.0438558402084238 | also
1 | 57 | 0.0438558402084238 | league
1 | 49 | 0.0438558402084238 | hitting
1 | 13 | 0.0438558402084238 | areas
1 | 39 | 0.0438558402084238 | favor
1 | 85 | 0.0438558402084238 | statistical
1 | 95 | 0.0438558402084238 | topic
1 | 0 | 0.0438558402084238 | 1960s
1 | 76 | 0.0438558402084238 | prediction-making
1 | 86 | 0.0438558402084238 | statistics
1 | 84 | 0.0438558402084238 | state
1 | 72 | 0.0438558402084238 | overlaps
1 | 22 | 0.0438558402084238 | center
1 | 4 | 0.0438558402084238 | agricultural
1 | 63 | 0.0438558402084238 | methods
1 | 33 | 0.0438558402084238 | discipline
(40 rows)
</pre>
Get the per-word topic counts. This mapping shows how
many times a given word is assigned to a topic. E.g.,
wordid 3 is assigned to topicid 0 three times:
<pre class="example">
DROP TABLE IF EXISTS helper_output_table;
SELECT madlib.lda_get_word_topic_count( 'lda_model', -- LDA model generated in training
'helper_output_table'); -- output table for per-word topic counts
SELECT * FROM helper_output_table ORDER BY wordid LIMIT 20;
</pre>
<pre class="result">
wordid | topic_count
--------+-------------
0 | {0,1,0,0,0}
1 | {1,0,0,0,0}
2 | {1,0,0,0,0}
3 | {3,0,0,0,0}
4 | {0,0,0,0,1}
5 | {0,1,0,0,0}
6 | {1,0,0,0,0}
7 | {0,0,0,1,0}
8 | {0,1,0,0,0}
9 | {0,0,0,3,0}
10 | {1,0,0,0,0}
11 | {1,0,0,0,0}
12 | {0,0,1,0,0}
13 | {0,0,0,0,1}
14 | {0,1,0,0,0}
15 | {0,0,0,0,1}
16 | {0,1,0,0,0}
17 | {0,0,1,0,0}
18 | {1,0,0,0,0}
19 | {2,0,0,0,0}
(20 rows)
</pre>
Get the per-topic word counts. This mapping shows
which words are associated with each topic by frequency:
<pre class="example">
DROP TABLE IF EXISTS topic_word_count;
SELECT madlib.lda_get_topic_word_count( 'lda_model',
'topic_word_count');
SELECT * FROM topic_word_count ORDER BY topicid;
</pre>
<pre class="result">
-[ RECORD 1 ]----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
topicid | 1
word_count | {1,1,0,0,0,0,0,1,1,0,1,0,0,0,0,1,0,0,1,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,1,0,0,1,0,1,1,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,0,0,0,1,0,0,0,0,1,0,1,0,1,0,0,1,1,0,0,0,0,0,0,0,1,0}
-[ RECORD 2 ]----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
topicid | 2
word_count | {0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,1,0,0,0,0,1,0,1,0,1,1,2,0,1,1,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,1,0,0,0,0,4,0,0,0,0,1,0,0,1,0,0,1,0,0,0,0,0,0,1,0,0,0,0,0,0,0,5,0,1,0,0,1,0,0,0}
-[ RECORD 3 ]----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
topicid | 3
word_count | {0,0,0,0,0,0,0,0,0,3,0,1,0,1,1,0,0,0,0,2,0,0,0,0,1,0,0,1,0,1,1,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,1,0,0,2,1,0,1,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0}
-[ RECORD 4 ]----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
topicid | 4
word_count | {0,0,1,0,0,1,1,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,1,0,0,1,0,0,1,0,0,0,1,0,0,1,1,1,0,0,0,1,0,0,0,0,0,0,1,0,7,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,1,0,0,0,0,1,0,0,0,0,1,1,1,0,0,0,1,0,0,1,0,0,0,0,0,0,0,0,0,0,1}
-[ RECORD 5 ]----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
topicid | 5
word_count | {0,0,0,3,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,1,1,0,0,1,0,0,1,0,0,0,0,0,0,0,0,18,0,0,0,0,0,0,0,1,0,2,0,0}
</pre>
Get the per-document word to topic mapping:
<pre class="example">
DROP TABLE IF EXISTS helper_output_table;
SELECT madlib.lda_get_word_topic_mapping('lda_output_data', -- Output table from training
'helper_output_table');
SELECT * FROM helper_output_table ORDER BY docid LIMIT 40;
</pre>
<pre class="result">
docid | wordid | topicid
-------+--------+---------
0 | 56 | 1
0 | 54 | 1
0 | 42 | 2
0 | 35 | 1
0 | 32 | 1
0 | 29 | 3
0 | 28 | 4
0 | 24 | 3
0 | 17 | 2
0 | 11 | 0
0 | 8 | 1
0 | 3 | 0
0 | 97 | 0
0 | 95 | 3
0 | 90 | 0
0 | 85 | 0
0 | 80 | 2
0 | 71 | 2
0 | 68 | 0
0 | 64 | 1
1 | 2 | 0
1 | 1 | 0
1 | 0 | 1
1 | 102 | 4
1 | 101 | 2
1 | 100 | 1
1 | 93 | 3
1 | 90 | 2
1 | 90 | 0
1 | 88 | 1
1 | 75 | 1
1 | 74 | 3
1 | 68 | 0
1 | 59 | 2
1 | 57 | 4
1 | 55 | 3
1 | 53 | 3
1 | 50 | 0
1 | 49 | 1
1 | 48 | 0
(40 rows)
</pre>
-# Use a learned LDA model for prediction (that is, to label new documents).
In this example, we use the same input table as we used to train, just for
demonstration purpose. Normally, the test document is a new one that
we want to predict on.
<pre class="example">
DROP TABLE IF EXISTS outdata_predict;
SELECT madlib.lda_predict( 'documents_tf', -- Document to predict
'lda_model', -- LDA model from training
'outdata_predict' -- Output table for predict results
);
SELECT * FROM outdata_predict;
</pre>
<pre class="result">
-[ RECORD 1 ]----+------------------------------------------------------------------------------------------------------
docid | 0
wordcount | 22
words | {17,11,28,29,95,3,32,97,85,35,54,80,64,90,8,24,42,71,56,68}
counts | {1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,2}
topic_count | {1,3,16,1,1}
topic_assignment | {2,2,1,0,2,2,2,3,2,2,2,2,2,2,4,2,2,2,2,2,1,1}
-[ RECORD 2 ]----+------------------------------------------------------------------------------------------------------
docid | 1
wordcount | 37
words | {90,101,2,88,6,7,75,46,74,68,39,9,48,49,102,50,59,53,55,57,100,14,15,16,18,19,93,21,0,1}
counts | {5,1,1,1,1,1,1,1,1,2,1,1,1,1,1,3,1,1,1,1,1,1,1,1,1,1,1,1,1,1}
topic_count | {0,1,11,6,19}
topic_assignment | {4,4,4,4,4,4,4,4,4,2,4,2,2,1,3,2,2,4,4,4,3,3,3,4,3,3,2,4,4,2,2,4,2,4,2,4,2}
-[ RECORD 3 ]----+------------------------------------------------------------------------------------------------------
docid | 2
wordcount | 36
words | {90,3,5,9,10,25,27,30,33,36,40,47,50,51,52,58,60,62,63,69,70,72,76,79,83,86,87,89,91,92,94,99,100}
counts | {1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,3,1,1}
topic_count | {26,3,5,1,1}
topic_assignment | {4,0,0,2,2,0,0,0,0,2,0,0,0,3,0,0,0,0,0,0,0,0,0,2,0,2,0,0,0,0,0,1,1,1,0,0}
-[ RECORD 4 ]----+------------------------------------------------------------------------------------------------------
docid | 3
wordcount | 49
words | {41,38,3,77,78,94,37,81,82,19,84,34,96,13,31,98,90,51,26,61,23,22,50,65,66,67,45,44,68,4,12,43,20,73}
counts | {1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,11,1,1,1,1,1,3,1,1,1,1,2,2,1,1,1,1,1}
topic_count | {0,28,0,4,17}
topic_assignment | {1,1,4,1,1,1,1,1,1,4,1,1,1,3,1,1,1,4,4,4,4,4,4,4,4,4,4,4,4,1,1,1,4,3,3,3,1,1,4,4,1,1,1,1,1,1,1,1,1}
</pre>
The test table is expected to be in the same form as the
training table and can be created with the same process.
The LDA prediction results have the same
format as the output table generated by the LDA training function.
-# Review prediction using helper function. (This is the same
per-document word to topic mapping that we used on the learned model.)
<pre class="example">
DROP TABLE IF EXISTS helper_output_table;
SELECT madlib.lda_get_word_topic_mapping('outdata_predict', -- Output table from prediction
'helper_output_table');
SELECT * FROM helper_output_table ORDER BY docid LIMIT 40;
</pre>
<pre class="result">
docid | wordid | topicid
-------+--------+---------
0 | 54 | 4
0 | 42 | 1
0 | 35 | 4
0 | 32 | 4
0 | 29 | 4
0 | 28 | 1
0 | 24 | 4
0 | 17 | 1
0 | 11 | 4
0 | 8 | 4
0 | 3 | 0
0 | 97 | 4
0 | 95 | 1
0 | 90 | 2
0 | 85 | 4
0 | 80 | 0
0 | 71 | 0
0 | 68 | 0
0 | 64 | 4
0 | 64 | 1
0 | 56 | 4
1 | 2 | 4
1 | 1 | 4
1 | 0 | 2
1 | 102 | 4
1 | 101 | 4
1 | 100 | 4
1 | 93 | 4
1 | 90 | 2
1 | 90 | 0
1 | 88 | 2
1 | 75 | 2
1 | 74 | 0
1 | 68 | 0
1 | 59 | 4
1 | 57 | 2
1 | 55 | 2
1 | 53 | 1
1 | 50 | 0
1 | 49 | 2
(40 rows)
</pre>
-# Call the perplexity function to see how well the model fits
the data. Perplexity computes word likelihoods averaged
over the test documents.
<pre class="example">
SELECT madlib.lda_get_perplexity( 'lda_model', -- LDA model from training
'outdata_predict' -- Prediction output
);
</pre>
<pre class="result">
lda_get_perplexity
+--------------------
79.481894411824
(1 row)
</pre>
-# Perplexity by iteration. Now let's look at how perplexity
changes from one iteration to the next:
<pre class="example">
DROP TABLE IF EXISTS lda_model_perp, lda_output_data_perp;
SELECT madlib.lda_train( 'documents_tf', -- documents table in the form of term frequency
'lda_model_perp', -- model table created by LDA training (not human readable)
'lda_output_data_perp', -- readable output data table
103, -- vocabulary size
5, -- number of topics
30, -- number of iterations
5, -- Dirichlet prior for the per-doc topic multinomial (alpha)
0.01, -- Dirichlet prior for the per-topic word multinomial (beta)
2, -- Evaluate perplexity every n iterations
0.3 -- Tolerance to stop iteration
);
SELECT voc_size, topic_num, alpha, beta, num_iterations, perplexity, perplexity_iters from lda_model_perp;
</pre>
<pre class="result">
-[ RECORD 1 ]----+----------------------------------------------------------------------------------------------------
voc_size | 103
topic_num | 5
alpha | 5
beta | 0.01
num_iterations | 14
perplexity | {70.0297335165,65.6497887327,70.2040806534,68.2594871716,70.3816093812,67.9193935299,67.6325562682}
perplexity_iters | {2,4,6,8,10,12,14}
</pre>
Iterating stops at 14 since the tolerance is reached. There are 7
perplexity values because we computed it only every 2nd iteration to save time.
As expected, the perplexity
on the training data is that same as the final iteration value:
<pre class="example">
SELECT madlib.lda_get_perplexity( 'lda_model_perp',
'lda_output_data_perp'
);
</pre>
<pre class="result">
lda_get_perplexity
--------------------+
67.632556268157
</pre>
@anchor literature
@literature
[1] D.M. Blei, A.Y. Ng, M.I. Jordan, <em>Latent Dirichlet Allocation</em>,
Journal of Machine Learning Research, vol. 3, pp. 993-1022, 2003.
[2] T. Griffiths and M. Steyvers, <em>Finding scientific topics</em>, PNAS,
vol. 101, pp. 5228-5235, 2004.
[3] Y. Wang, H. Bai, M. Stanton, W-Y. Chen, and E.Y. Chang, <em>lda: Parallel
Dirichlet Allocation for Large-scale Applications</em>, AAIM, 2009.
[4] http://en.wikipedia.org/wiki/Latent_Dirichlet_allocation
[5] J. Chang, Collapsed Gibbs sampling methods for topic models, R manual,
2010.
@anchor related
@par Related Topics
File lda.sql_in documenting the SQL functions.
*/
-- UDT for summarizing a UDF call
DROP TYPE IF EXISTS MADLIB_SCHEMA.lda_result CASCADE;
CREATE TYPE MADLIB_SCHEMA.lda_result AS
(
output_table TEXT,
description TEXT
);
/**
* @brief This UDF provides an entry for the lda training process.
* @param data_table Table storing the training dataset, each row is in
* the form of <docid, wordid, count> where docid,
* wordid, and count are all non-negative integers.
* @param model_table Table storing the learned models (voc_size, topic_num,
* alpha, beta, per-word topic counts, and
* corpus-level topic counts)
* @param output_data_table Table storing the output data table in the form of
* <docid, wordcount, words, counts, topic_count,
* topic_assignment>
* @param voc_size Size of the vocabulary (Note that the wordid should
* be continous integers starting from 0 to voc_size -
* 1. A data validation rountine will be called to
* validate the dataset.)
* @param topic_num Number of topics (e.g. 100)
* @param iter_num Number of iterations (e.g. 60)
* @param alpha Dirichlet parameter for the per-doc topic multinomial
* (e.g. 50/topic_num)
* @param beta Dirichlet parameter for the per-topic word multinomial
* (e.g. 0.01)
*/
CREATE OR REPLACE FUNCTION
MADLIB_SCHEMA.lda_train
(
data_table TEXT,
model_table TEXT,
output_data_table TEXT,
voc_size INT4,
topic_num INT4,
iter_num INT4,
alpha FLOAT8,
beta FLOAT8
)
RETURNS SETOF MADLIB_SCHEMA.lda_result AS $$
PythonFunctionBodyOnly(`lda', `lda')
from utilities.control import MinWarning
with AOControl(False):
with MinWarning("error"):
lda.lda_train(schema_madlib, data_table, model_table, output_data_table,
voc_size, topic_num, iter_num, alpha, beta, None, None)
return [[model_table, 'model table'],
[output_data_table, 'output data table']]
$$ LANGUAGE plpythonu
m4_ifdef(`__HAS_FUNCTION_PROPERTIES__', `MODIFIES SQL DATA', `');
CREATE OR REPLACE FUNCTION
MADLIB_SCHEMA.lda_train
(
data_table TEXT,
model_table TEXT,
output_data_table TEXT,
voc_size INT4,
topic_num INT4,
iter_num INT4,
alpha FLOAT8,
beta FLOAT8,
evaluate_every INT4,
perplexity_tol FLOAT8
)
RETURNS SETOF MADLIB_SCHEMA.lda_result AS $$
PythonFunctionBodyOnly(`lda', `lda')
with AOControl(False):
lda.lda_train(schema_madlib, data_table, model_table, output_data_table,
voc_size, topic_num, iter_num, alpha, beta,evaluate_every , perplexity_tol)
return [[model_table, 'model table'],
[output_data_table, 'output data table']]
$$ LANGUAGE plpythonu
m4_ifdef(`__HAS_FUNCTION_PROPERTIES__', `MODIFIES SQL DATA', `');
CREATE OR REPLACE FUNCTION
MADLIB_SCHEMA.lda_train
(
data_table TEXT,
model_table TEXT,
output_data_table TEXT,
voc_size INT4,
topic_num INT4,
iter_num INT4,
alpha FLOAT8,
beta FLOAT8,
evaluate_every INT4
)
RETURNS SETOF MADLIB_SCHEMA.lda_result AS $$
PythonFunctionBodyOnly(`lda', `lda')
with AOControl(False):
lda.lda_train(schema_madlib, data_table, model_table, output_data_table,
voc_size, topic_num, iter_num, alpha, beta,evaluate_every , None)
return [[model_table, 'model table'],
[output_data_table, 'output data table']]
$$ LANGUAGE plpythonu
m4_ifdef(`__HAS_FUNCTION_PROPERTIES__', `MODIFIES SQL DATA', `');
/**
* @brief This UDF provides an entry for the lda predicton process.
* @param data_table Table storing the testing dataset, each row is in the
* form of <docid, wordid, count>
* where docid, wordid, and count are all non-negative
* integers.
* @param model_table Table storing the learned models
* @param output_table Table storing per-document topic counts and topic
* assignments
* @note default iter_num = 20
*/
CREATE OR REPLACE FUNCTION
MADLIB_SCHEMA.lda_predict
(
data_table TEXT,
model_table TEXT,
output_table TEXT
)
RETURNS SETOF MADLIB_SCHEMA.lda_result AS $$
PythonFunctionBodyOnly(`lda', `lda')
from utilities.control import MinWarning
with AOControl(False):
with MinWarning("error"):
lda.lda_predict(schema_madlib, data_table, model_table, output_table)
return [[
output_table,
'per-doc topic distribution and per-word topic assignments']]
$$ LANGUAGE plpythonu
m4_ifdef(`__HAS_FUNCTION_PROPERTIES__', `MODIFIES SQL DATA', `');
/**
* @brief A overloaded version which allows users to specify iter_num.
*/
CREATE OR REPLACE FUNCTION
MADLIB_SCHEMA.lda_predict
(
data_table TEXT,
model_table TEXT,
output_table TEXT,
iter_num INT4
)
RETURNS SETOF MADLIB_SCHEMA.lda_result AS $$
PythonFunctionBodyOnly(`lda', `lda')
with AOControl(False):
lda.lda_predict(schema_madlib, data_table, model_table, output_table, iter_num)
return [[
output_table,
'per-doc topic distribution and per-word topic assignments']]
$$ LANGUAGE PLPYTHONU STRICT
m4_ifdef(`__HAS_FUNCTION_PROPERTIES__', `MODIFIES SQL DATA', `');
/**
* @brief This UDF computes the per-topic word counts.
* @param model_table The model table generated by the training process
* @param output_table The output table storing the per-topic word counts
*/
CREATE OR REPLACE FUNCTION
MADLIB_SCHEMA.lda_get_topic_word_count
(
model_table TEXT,
output_table TEXT
)
RETURNS SETOF MADLIB_SCHEMA.lda_result AS $$
PythonFunctionBodyOnly(`lda', `lda')
with AOControl(False):
lda.get_topic_word_count(schema_madlib, model_table, output_table)
return [[output_table, 'per-topic word counts']]
$$ LANGUAGE plpythonu STRICT
m4_ifdef(`__HAS_FUNCTION_PROPERTIES__', `MODIFIES SQL DATA', `');
/**
* @brief This UDF computes the per-word topic counts.
* @param model_table The model table generated by the training process
* @param dist_table The output table storing the per-word topic counts
*/
CREATE OR REPLACE FUNCTION
MADLIB_SCHEMA.lda_get_word_topic_count
(
model_table TEXT,
output_table TEXT
)
RETURNS SETOF MADLIB_SCHEMA.lda_result AS $$
PythonFunctionBodyOnly(`lda', `lda')
from utilities.control import MinWarning
with AOControl(False):
with MinWarning("error"):
lda.get_word_topic_count(schema_madlib, model_table, output_table)
return [[output_table, 'per-word topic counts']]
$$ LANGUAGE plpythonu STRICT
m4_ifdef(`__HAS_FUNCTION_PROPERTIES__', `MODIFIES SQL DATA', `');
/**
* @brief This UDF gets the description for each topic (top-k words)
* @param model_table The model table generated by the training process
* @param vocab_table The vocabulary table (<wordid, word>)
* @param top_k The number of top words for each topic description
* @param desc_table The output table for storing the per-topic description
*/
CREATE OR REPLACE FUNCTION
MADLIB_SCHEMA.lda_get_topic_desc
(
model_table TEXT,
vocab_table TEXT,
desc_table TEXT,
top_k INT4
)
RETURNS SETOF MADLIB_SCHEMA.lda_result AS $$
PythonFunctionBodyOnly(`lda', `lda')
from utilities.control import MinWarning
with AOControl(False):
with MinWarning("error"):
lda.get_topic_desc(schema_madlib, model_table, vocab_table, desc_table, top_k)
return [[
desc_table,
"""topic description, use "ORDER BY topicid, prob DESC" to check the
results"""]]
$$ LANGUAGE plpythonu STRICT
m4_ifdef(`__HAS_FUNCTION_PROPERTIES__', `MODIFIES SQL DATA', `');
/**
* @brief This UDF gets the wordid - topicid mapping from the lda training output table
* @param lda_output_table The output table from lda traning or predicting
* @param mapping_table The result table that saves the mapping info
*/
CREATE OR REPLACE FUNCTION
MADLIB_SCHEMA.lda_get_word_topic_mapping
(
lda_output_table TEXT,
mapping_table TEXT
)
RETURNS SETOF MADLIB_SCHEMA.lda_result AS $$
PythonFunctionBodyOnly(`lda', `lda')
from utilities.control import MinWarning
with AOControl(False):
with MinWarning("error"):
lda.get_word_topic_mapping(schema_madlib, lda_output_table, mapping_table)
return [[mapping_table, 'wordid - topicid mapping']]
$$ LANGUAGE plpythonu STRICT
m4_ifdef(`__HAS_FUNCTION_PROPERTIES__', `MODIFIES SQL DATA', `');
/**
* @brief This UDF assigns topics to words in a document randomly.
* @param word_count The number of words in the document
* @param topic_num The number of topics (specified by the user)
* @return The topic counts and topic assignments
*/
CREATE OR REPLACE FUNCTION
MADLIB_SCHEMA.__lda_random_assign
(
word_count INT4,
topic_num INT4
)
RETURNS INT4[]
AS 'MODULE_PATHNAME', 'lda_random_assign'
LANGUAGE C STRICT
m4_ifdef(`__HAS_FUNCTION_PROPERTIES__', `NO SQL', `');
/**
* @brief This UDF learns the topics of words in a document and is the main
* step of a Gibbs sampling iteration. The model parameter (including the
* per-word topic counts and corpus-level topic counts) is passed to this
* function in the first call and then transfered to the rest calls through
* fcinfo->flinfo->fn_extra to allow the immediate update.
* @param words The set of unique words in the document
* @param counts The counts of each unique words in the document
* (sum(counts) = word_count)
* @param doc_topic The current per-doc topic counts and topic
* assignments
* @param model The current model (including the per-word topic counts
* and the corpus-level topic counts)
* @param alpha The Dirichlet parameter for per-document topic multinomial
* @param beta The Dirichlet parameter for per-topic word multinomial
* @param voc_size The size of vocabulary
* @param topic_num The number of topics
* @param iter_num The number of iterations
* @return The learned topic counts and topic assignments
*/
CREATE OR REPLACE FUNCTION
MADLIB_SCHEMA.__lda_gibbs_sample
(
words INT4[],
counts INT4[],
doc_topic INT4[],
model INT8[],
alpha FLOAT8,
beta FLOAT8,
voc_size INT4,
topic_num INT4,
iter_num INT4
)
RETURNS INT4[]
AS 'MODULE_PATHNAME', 'lda_gibbs_sample'
LANGUAGE C
m4_ifdef(`__HAS_FUNCTION_PROPERTIES__', `NO SQL', `');
/**
* @brief This UDF is the sfunc for the aggregator computing the topic counts
* for each word and the topic count in the whole corpus. It scans the topic
* assignments in a document and updates the topic counts.
* @param state The topic counts
* @param words The unique words in the document
* @param counts The counts of each unique words in the document
* (sum(counts) = word_count)
* @param topic_assignment The topic assignments in the document
* @param voc_size The size of vocabulary
* @param topic_num The number of topics
* @return The updated state
*/
CREATE OR REPLACE FUNCTION
MADLIB_SCHEMA.__lda_count_topic_sfunc
(
state INT8[],
words INT4[],
counts INT4[],
topic_assignment INT4[],
voc_size INT4,
topic_num INT4
)
RETURNS INT8[]
AS 'MODULE_PATHNAME', 'lda_count_topic_sfunc'
LANGUAGE C
m4_ifdef(`__HAS_FUNCTION_PROPERTIES__', `NO SQL', `');
/**
* @brief This UDF is the prefunc for the aggregator computing the per-word
* topic counts.
* @param state1 The local word topic counts
* @param state2 The local word topic counts
* @return The element-wise sum of two local states
*/
CREATE OR REPLACE FUNCTION
MADLIB_SCHEMA.__lda_count_topic_prefunc
(
state1 INT8[],
state2 INT8[]
)
RETURNS INT8[]
AS 'MODULE_PATHNAME', 'lda_count_topic_prefunc'
LANGUAGE C IMMUTABLE STRICT
m4_ifdef(`__HAS_FUNCTION_PROPERTIES__', `NO SQL', `');
/**
* @brief This uda computes the word topic counts by scanning and summing
* up topic assignments in each document.
* @param words The unique words in the document
* @param counts The counts of each unique words in the document
* @param topic_assignment The topic assignments in the document
* @param voc_size The size of vocabulary
* @param topic_num The number of topics
* @return The word topic counts (a 1-d array embeding a 2-d array)
*/
DROP AGGREGATE IF EXISTS
MADLIB_SCHEMA.__lda_count_topic_agg
(
INT4[],
INT4[],
INT4[],
INT4,
INT4
);
CREATE AGGREGATE
MADLIB_SCHEMA.__lda_count_topic_agg
(
INT4[],
INT4[],
INT4[],
INT4,
INT4
)
(
stype = INT8[],
sfunc = MADLIB_SCHEMA.__lda_count_topic_sfunc
m4_ifdef(
`__POSTGRESQL__', `',
`, prefunc = MADLIB_SCHEMA.__lda_count_topic_prefunc'
)
);
/**
* @brief This UDF computes the perplexity given the output data table and the
* model table.
* @param model_table The model table generated by lda_train
* @param output_data_table The output data table generated by lda_predict
* @return The perplexity
*/
CREATE OR REPLACE FUNCTION
MADLIB_SCHEMA.lda_get_perplexity
(
model_table TEXT,
output_data_table TEXT
)
RETURNS FLOAT8 AS $$
PythonFunctionBodyOnly(`lda', `lda')
with AOControl(False):
return lda.get_perplexity(schema_madlib, model_table, output_data_table)
$$ LANGUAGE plpythonu STRICT
m4_ifdef(`__HAS_FUNCTION_PROPERTIES__', `READS SQL DATA', `');
/**
* @brief This UDF is the sfunc for the aggregator computing the perpleixty.
* @param state The cached model plus perplexity
* @param words The unique words in the document
* @param counts The counts of each unique words in the document
* @param doc_topic The topic counts in the document
* @param model The learned model
* @param alpha The Dirichlet parameter for per-document topic multinomial
* @param beta The Dirichlet parameter for per-topic word multinomial
* @param voc_size The size of vocabulary
* @param topic_num The number of topics
* @return The updated state
*/
CREATE OR REPLACE FUNCTION
MADLIB_SCHEMA.__lda_perplexity_sfunc
(
state INT8[],
words INT4[],
counts INT4[],
doc_topic INT4[],
model INT8[],
alpha FLOAT8,
beta FLOAT8,
voc_size INT4,
topic_num INT4
)
RETURNS INT8[]
AS 'MODULE_PATHNAME', 'lda_perplexity_sfunc'
LANGUAGE C IMMUTABLE
m4_ifdef(`__HAS_FUNCTION_PROPERTIES__', `NO SQL', `');
/**
* @brief This UDF is the prefunc for the aggregator computing the perplexity.
* @param state1 The local state
* @param state2 The local state
* @return The merged state
*/
CREATE OR REPLACE FUNCTION
MADLIB_SCHEMA.__lda_perplexity_prefunc
(
state1 INT8[],
state2 INT8[]
)
RETURNS INT8[]
AS 'MODULE_PATHNAME', 'lda_perplexity_prefunc'
LANGUAGE C IMMUTABLE STRICT
m4_ifdef(`__HAS_FUNCTION_PROPERTIES__', `NO SQL', `');
/**
* @brief This UDF is the finalfunc for the aggregator computing the perplexity.
* @param state The merged state
* @return The perpleixty
*/
CREATE OR REPLACE FUNCTION
MADLIB_SCHEMA.__lda_perplexity_ffunc
(
state INT8[]
)
RETURNS FLOAT8
AS 'MODULE_PATHNAME', 'lda_perplexity_ffunc'
LANGUAGE C IMMUTABLE STRICT
m4_ifdef(`__HAS_FUNCTION_PROPERTIES__', `NO SQL', `');
/*
* @brief This aggregator computes the perpleixty.
* @param words The unique words in the document
* @param counts The counts of each unique words in the document
* @param doc_topic The topic counts in the document
* @param model The learned model
* @param alpha The Dirichlet parameter for per-document topic multinomial
* @param beta The Dirichlet parameter for per-topic word multinomial
* @param voc_size The size of vocabulary
* @param topic_num The number of topics
* @return The updated perplexity
*/
DROP AGGREGATE IF EXISTS
MADLIB_SCHEMA.__lda_perplexity_agg
(
INT4[],
INT4[],
INT4[],
INT8[],
FLOAT8,
FLOAT8,
INT4,
INT4
);
CREATE AGGREGATE
MADLIB_SCHEMA.__lda_perplexity_agg
(
INT4[],
INT4[],
INT4[],
INT8[],
FLOAT8,
FLOAT8,
INT4,
INT4
)
(
stype = INT8[],
sfunc = MADLIB_SCHEMA.__lda_perplexity_sfunc,
finalfunc = MADLIB_SCHEMA.__lda_perplexity_ffunc
m4_ifdef(
`__POSTGRESQL__', `',
`, prefunc = MADLIB_SCHEMA.__lda_perplexity_prefunc'
)
);
CREATE OR REPLACE FUNCTION
MADLIB_SCHEMA.__lda_check_count_ceiling
(
arr INT8[],
r INT4,
c INT4
)
RETURNS INT4[]
AS 'MODULE_PATHNAME', 'lda_check_count_ceiling'
LANGUAGE C IMMUTABLE STRICT
m4_ifdef(`__HAS_FUNCTION_PROPERTIES__', `NO SQL', `');
/**
* @brief Unnest a 2-D array into a set of 1-D arrays
* @param arr The 2-D array to be unnested
* @return The unnested 1-D arrays
*/
CREATE OR REPLACE FUNCTION
MADLIB_SCHEMA.__lda_util_unnest
(
arr INT8[],
r INT4,
c INT4
)
RETURNS SETOF INT4[]
AS 'MODULE_PATHNAME', 'lda_unnest'
LANGUAGE C IMMUTABLE STRICT
m4_ifdef(`__HAS_FUNCTION_PROPERTIES__', `NO SQL', `');
CREATE OR REPLACE FUNCTION
MADLIB_SCHEMA.__lda_util_unnest_transpose
(
arr INT8[],
r INT4,
c INT4
)
RETURNS SETOF INT4[]
AS 'MODULE_PATHNAME', 'lda_unnest_transpose'
LANGUAGE C IMMUTABLE STRICT
m4_ifdef(`__HAS_FUNCTION_PROPERTIES__', `NO SQL', `');
/**
* @brief Transpose a 2-D array
* @param matrix The input 2-D array
* @param The transposed array
*/
CREATE OR REPLACE FUNCTION
MADLIB_SCHEMA.__lda_util_transpose
(
matrix INT8[][]
)
RETURNS INT8[][]
AS 'MODULE_PATHNAME', 'lda_transpose'
LANGUAGE C IMMUTABLE STRICT
m4_ifdef(`__HAS_FUNCTION_PROPERTIES__', `NO SQL', `');
/**
* @brief L1 normalization with smoothing
* @param arr The array to be normalized
* @param smooth The smoothing parameter
* @return The normalized vector
*/
CREATE OR REPLACE FUNCTION
MADLIB_SCHEMA.__lda_util_norm_with_smoothing
(
arr FLOAT8[],
smooth FLOAT8
)
RETURNS FLOAT8[]
AS 'MODULE_PATHNAME', 'l1_norm_with_smoothing'
LANGUAGE C IMMUTABLE STRICT
m4_ifdef(`__HAS_FUNCTION_PROPERTIES__', `NO SQL', `');
/**
* @brief This UDF returns the index of elements in a sorted order
* @param arr The array to be sorted
* @return The index of elements
*/
CREATE OR REPLACE FUNCTION
MADLIB_SCHEMA.__lda_util_index_sort
(
arr FLOAT8[]
)
RETURNS INT4[] AS $$
PythonFunction(`lda', `lda', `index_sort')
$$ LANGUAGE plpythonu STRICT
m4_ifdef(`__HAS_FUNCTION_PROPERTIES__', `NO SQL', `');
/**
* @brief This UDF checks the vocabulary and converts non-continous wordids into
* continuous integers ranging from 0 to voc_size - 1.
* @param vocab_table The vocabulary table in the form of
<wordid::int4, word::text>
* @param output_vocab_table The regularized vocabulary table
*/
CREATE OR REPLACE FUNCTION
MADLIB_SCHEMA.__lda_util_norm_vocab
(
vocab_table TEXT,
output_vocab_table TEXT
)
RETURNS SETOF MADLIB_SCHEMA.lda_result AS $$
PythonFunctionBodyOnly(`lda', `lda')
with AOControl(False):
lda.norm_vocab(vocab_table, output_vocab_table)
return [[output_vocab_table,'normalized vocbulary table']]
$$ LANGUAGE plpythonu STRICT
m4_ifdef(`__HAS_FUNCTION_PROPERTIES__', `MODIFIES SQL DATA', `');
/**
* @brief This UDF converts the data table according to the normalized
* vocabulary, and all rows with non-positive count values will be removed
* @param data_table The data table to be normalized
* @param vocab_table The normalized vocabulary table
* @param output_data_table The normalized data table
*/
CREATE OR REPLACE FUNCTION
MADLIB_SCHEMA.__lda_util_norm_dataset
(
data_table TEXT,
norm_vocab_table TEXT,
output_data_table TEXT
)
RETURNS SETOF MADLIB_SCHEMA.lda_result AS $$
PythonFunctionBodyOnly(`lda', `lda')
with AOControl(False):
lda.norm_dataset(data_table, norm_vocab_table, output_data_table)
return [[output_data_table,'normalized data table']]
$$ LANGUAGE plpythonu STRICT
m4_ifdef(`__HAS_FUNCTION_PROPERTIES__', `MODIFIES SQL DATA', `');
/**
* @brief This UDF extracts the list of wordids from the data table and joins
* it with the vocabulary table to get the list of common wordids, next it will
* normalize the vocabulary based on the common wordids and then normalize the
* data table based on the normalized vocabulary.
* @param data_table The data table to be normalized
* @param vocab_table The vocabulary table to be normalized
* @param output_data_table The normalized data table
* @param output_vocab_table The normalized vocabulary table
*/
CREATE OR REPLACE FUNCTION
MADLIB_SCHEMA.__lda_util_conorm_data
(
data_table TEXT,
vocab_table TEXT,
output_data_table TEXT,
output_vocab_table TEXT
)
RETURNS SETOF MADLIB_SCHEMA.lda_result AS $$
PythonFunctionBodyOnly(`lda', `lda')
with AOControl(False):
lda.conorm_data(data_table, vocab_table, output_data_table, output_vocab_table)
return [[output_data_table,'normalized data table'],
[output_vocab_table,'normalized vocab table']]
$$ LANGUAGE plpythonu STRICT
m4_ifdef(`__HAS_FUNCTION_PROPERTIES__', `MODIFIES SQL DATA', `');
-- UDT contains model matrix (voc_size x topic_num) and total topic counts array
DROP TYPE IF EXISTS MADLIB_SCHEMA._pivotalr_lda_model CASCADE;
CREATE TYPE MADLIB_SCHEMA._pivotalr_lda_model AS
(
model_matrix_part1 integer[],
model_matrix_part2 integer[],
total_topic_counts double precision[]
);
CREATE OR REPLACE FUNCTION
MADLIB_SCHEMA.lda_parse_model
(
lda_model bigint[],
voc_size integer,
topic_num integer
)
RETURNS MADLIB_SCHEMA._pivotalr_lda_model
AS 'MODULE_PATHNAME'
LANGUAGE c STRICT
m4_ifdef(`__HAS_FUNCTION_PROPERTIES__', `NO SQL', `');