Author-topic model #893

olavurmortensen · 2016-09-27T12:20:03Z

I'm implementing the author-topic (AT) model, which is based on "The Author-Topic Model for Authors and Documents" by Rosen-Zvi and co-authors. This project is in connection with my masters thesis at the Technical University of Denmark.

As indicated in the PR title, this is a work in progress.

The original paper presents an algorithm based on collapsed Gibbs sampling. I have derived a variational Bayes algorithm to trained this model instead, and implemented that algorithm. Furthermore, I have made an online algorithm using the method described in "Online Learning For Latent Dirichlet Allocation" by Hoffman and co-authors.

At the moment, the algorithm runs and seems to converge. I intend to run some experiments to see if the resulting topics are good soon. I expect to find that I need to do some improvements, but we will see.

…ent likelihood measure. OnlineAtVb now extends (inherits) LdaModel. Other minor changes.

…o eval_liklihood.

…rparameters. Updated notebook accordingly.

…pts it. Still work to be done in that area.

…thm works. Updated notebook.

…appened to the offline lately.

…moved author_prior_prob from mu update.

…malize. Various other changes.

…nly occasionally. Updated notebook.

… use of log_normalize in offline algo. Update notebook.

…speed up large experiments. Made it possible to initialize the model with LDA topics (lambda).

…s. Also fixed the 'endclass' comment.

…even some mistakes. Cleaned up the code (atmodel.py and tests) w.r.t. PEP8 (disregarding E501, E731, E12 and W503) and removing vertical indent.

tmylk · 2017-01-13T17:49:55Z

gensim/models/atmodel.py

@@ -836,24 +834,28 @@ def bound(self, chunk, chunk_doc_idx=None, subsample_ratio=1.0, author2doc=None,
                if not self.author2doc.get(a):
                    raise ValueError('bound cannot be called with authors not seen during training.')

-            chunk_doc_idx = xrange(len(chunk))
+            if chunk_doc_idx:
+                raise ValueError('Either author dictionaries or chunk_doc_idx must be prodivded, not both. Consult documentation of bound method.')


*typo in provided

tmylk · 2017-01-13T17:59:50Z

docs/notebooks/atmodel_tests.ipynb

@@ -0,0 +1,2097 @@
+{


should this be a part of the codebase? it is a good regression performance test. Could you keep it as a gist elsewhere and keep a link to it in the atmodel.py

I wasn't going to include it at all, it's just easiest for me to keep it there while developing. I have now removed it from the repo.

tmylk · 2017-01-13T18:04:33Z

gensim/models/atmodel.py

+            self.numworkers = 1
+        else:
+            # NOTE: distributed processing is not implemented for the author-topic model.
+            pass


raise a not implemented exception to be explicit

I don't know why I put that there, distributed=False is set explicitly (it is not an input). So now I just do the following:

distributed = False self.dispatcher = None self.numworkers = 1

There is also a comment above that about implementing a distributed version (should be line 209).

tmylk · 2017-01-13T18:11:25Z

gensim/models/atmodel.py

+        if minimum_probability is None:
+            minimum_probability = self.minimum_probability
+
+        # NOTE: this is used in LdaModel:


what does this comment mean? please expand

Well. I was really sceptical about doing that. But now I just decided to do it anyway. So the note is removed and the line is uncommented (so it is doing what LdaModel is doing now).

tmylk · 2017-01-13T18:11:59Z

gensim/test/test_atmodel.py

+# Licensed under the GNU LGPL v2.1 - http://www.gnu.org/licenses/lgpl.html
+
+"""
+Automated tests for checking transformation algorithms (the models package).


please update the docstring

tmylk

Fixmes in ipynb

tmylk · 2017-01-13T18:12:19Z

gensim/test/test_atmodel.py

+# Perhaps test that the bound increases, in general (i.e. in several of the tests below where it makes
+# sense.
+
+# FIXME: remember to remove this, once done using it:


please remove

tmylk · 2017-01-13T18:18:25Z

docs/notebooks/atmodel_tutorial.ipynb

@@ -0,0 +1,1182 @@
+{
+ "cells": [


multiple fixmes in this ipynb need to be resolved before merging

All fixmes removed.

…s well: removed do_mstep method (using LdaModels version directly), using minimum_probability in get_author_topics, removed statement (in log) that said perplexity is evaluated on held-out data.

olavurmortensen · 2017-01-14T15:04:39Z

Tutorial is done. @tmylk please review.

tmylk

Ipynb minor changes

tmylk · 2017-01-15T16:01:48Z

docs/notebooks/atmodel_tutorial.ipynb

+    "* Pre-processing and training LDA: https://github.com/RaRe-Technologies/gensim/blob/develop/docs/notebooks/lda_training_tips.ipynb\n",
+    "\n",
+    "\n",
+    "> **NOTE:**\n",


just give the pip commands

tmylk · 2017-01-15T16:02:25Z

docs/notebooks/atmodel_tutorial.ipynb

+    "\n",
+    "As in the LDA tutorial, we will be performing qualitative analysis of the model, and at times this will require an understanding of the subject matter of the data. If you try running this tutorial on your own, consider applying it on a dataset with subject matter that you are familiar with. For example, try one of the [StackExchange datadump datasets](https://archive.org/details/stackexchange).\n",
+    "\n",
+    "You can download the data from Sam Roweis' website (http://www.cs.nyu.edu/~roweis/data.html).\n",


just add a wget cell please

tmylk · 2017-01-15T16:04:44Z

docs/notebooks/atmodel_tutorial.ipynb

+   "source": [
+    "#### Plotting the authors\n",
+    "\n",
+    "Now we're going to produce the kind of pacific archipelago looking plot below. The goal of this plot is to give you a way to explore the author-topic representation in an intuitive manner.\n",


Please create a blog on wordpress linking to this ipynb with this blue graph as the title image.

tmylk · 2017-01-15T16:05:24Z

docs/notebooks/atmodel_tutorial.ipynb

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what should be the authors if tags are topics?

feel free to link to a GIST with your attempt. it will help people

I meant to write "You can treat the tags on the posts as authors" not "as topics". Fixed.

tmylk · 2017-01-15T16:08:45Z

gensim/models/atmodel.py

+The model is closely related to Latent Dirichlet Allocation. The AuthorTopicModel class
+inherits the LdaModel class, and its usage is thus similar.
+
+Distributed compuation and multiprocessing is not implemented at the moment, but may be


please link to ipynb tutorial on nips from here and to the author-topic paper.

…ks to github.

tmylk · 2017-01-16T17:33:57Z

gensim/models/atmodel.py

+# are included in the code where this is the case, for example in the log_perplexity
+# and do_estep methods.
+
+# FIXME: link to tutorial in docstring above, once the tutorial is available.


remove fixme. it is resolved

Yep, pushed that fix now.

olavurmortensen added 3 commits September 25, 2016 14:44

Initial commit. Very early stages of algorithm development.

2e8f3cb

Fixed some errors.

a21059e

Added online algorithm, removed batch algorithm.

a9bddaa

olavurmortensen changed the title ~~Author topic model [WIP]~~ Author-topic model [WIP] Sep 27, 2016

tmylk changed the title ~~Author-topic model [WIP]~~ [WIP] Author-topic model Sep 27, 2016

tmylk added feature Issue described a new feature difficulty hard Hard issue: required deep gensim understanding & high python/cython skills labels Sep 27, 2016

olavurmortensen added 23 commits September 29, 2016 17:46

Using max change instead of mean change criterion. Computing a differ…

7ea76f2

…ent likelihood measure. OnlineAtVb now extends (inherits) LdaModel. Other minor changes.

Fixed some things with var_mu. Also was passing the wrong arguments t…

839a8b3

…o eval_liklihood.

Added 'offline' algorithm, and notebook for experiments.

bd13c60

Fixed log normalization. Also changed symmetric initilization of hype…

ebc808c

…rparameters. Updated notebook accordingly.

Removed offline algorithm class as it is no longer necessary.

16b26f7

Changed name of online algorithm class and file.

10d2b36

Made some changes to how the likelihood is computed.

c94f516

Changed the name of the online algorithm again.

a1d758f

Brought the offline algorithm back.

46cc8bf

Working on bound computation.

3e53655

Changed the way the data structure is prepared and how the model acce…

09666c4

…pts it. Still work to be done in that area.

Cleaned the code up a bit. Added a simple method to get author topics.

a562fca

Removed some comments, mostly TODOs.

0de43a5

Ran some very successful experiments on 286 documents. Offline algori…

a892564

…thm works. Updated notebook.

Changed the online algorithm according to all the changes that have h…

388a5e9

…appened to the offline lately.

Fixed mistake with mu variable.

2b2a896

Fixed lambda update, multiplication by size of corpus was missing. Re…

3756435

…moved author_prior_prob from mu update.

Added a loop for passing over entire corpus. Discarded use of log_nor…

ed3416d

…malize. Various other changes.

Moved bound computation out of corpus-wide loop.

994f212

Updated notebook.

956fbd5

Computing rho in a different way. Added the possibility to evaluate o…

40bbabf

…nly occasionally. Updated notebook.

Implemented hyperparam MLE for eta and alpha in offline algo. Removed…

ed96b23

… use of log_normalize in offline algo. Update notebook.

Made it possible to sample a subset of documents in lambda update to …

a225399

…speed up large experiments. Made it possible to initialize the model with LDA topics (lambda).

olavurmortensen added 7 commits January 10, 2017 16:04

Removed save and load methods, using LdaModel's methods directly work…

be7bddf

…s. Also fixed the 'endclass' comment.

Removed all temporary files.

ffadaf1

Made changes to model and test in preperation for a merge with upstream.

e218883

Merge remote-tracking branch 'upstream/develop' into author-topic_model

7d2994f

Modified the bound method; it was somewhat confusing, and there were …

616a965

…even some mistakes. Cleaned up the code (atmodel.py and tests) w.r.t. PEP8 (disregarding E501, E731, E12 and W503) and removing vertical indent.

Simplified sum in phi norm computation.

7f98e3a

Fixed some mistakes introduced in bound method in recent commit.

ddfc8f7

tmylk reviewed Jan 13, 2017

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tmylk suggested changes Jan 13, 2017

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olavurmortensen added 4 commits January 14, 2017 12:36

Updated algorithm and tests w.r.t. comments from Lev. Other changes a…

7d03608

…s well: removed do_mstep method (using LdaModels version directly), using minimum_probability in get_author_topics, removed statement (in log) that said perplexity is evaluated on held-out data.

Updated tutorial. Removed test notebook.

661e7e5

Updated notebook.

85123c0

Updated tutorial.

91675a5

Updated tutorial (introduction).

6d961a5

tmylk suggested changes Jan 15, 2017

View reviewed changes

olavurmortensen added 5 commits January 16, 2017 13:15

Changes w.r.t. change requests from @tmylk, plus some other changes.

13fa9ee

Added the URL to view notebook in HTML to tutorial.

018896c

Telling users to view the notebook in nbviewer instead. Docstring lin…

a0a9832

…ks to github.

Removed a fixme about tutorial link.

5d6944a

Fixed a small mistake in bound method.

8e56e9e

tmylk reviewed Jan 16, 2017

View reviewed changes

Added further explanation of tutorial goal in notebook.

aecaecb

tmylk merged commit 739f34e into piskvorky:develop Jan 17, 2017

tmylk changed the title ~~[WIP] Author-topic model~~ Author-topic model Feb 14, 2017

menshikh-iv mentioned this pull request Mar 2, 2018

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Author-topic model #893

Author-topic model #893

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Author-topic model #893

Author-topic model #893

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olavurmortensen commented Sep 27, 2016 • edited Loading

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olavurmortensen commented Jan 14, 2017

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olavurmortensen commented Sep 27, 2016 •

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