/ScaCTM

Scalable inference for Correlated Topic Models

Primary LanguageC++

Scalable inference for Correlated Topic Models (ScaCTM)

Introduction

Correlated Topic Model is a topic model for text or other discrete data that models correlation between the occurrence of different topics in a document (Figure 1).

ScaCTM is software that learn Correlated Topic Model of thousands of topics from millions of documents, with tens of machines.

Figure 1. Correlated Topic Model. (Blue monospace: output file names, Black monospace: input parameter names)

The generative model is described as follows.

Below is the speed of ScaCTM on some corpus. For more details, please refer to our paper.

corpus number of documents number of topics time
NIPS 1.2K 100 8.9 min
20NG 11K 200 9 min
NYTimes 285K 400 0.5 hrs
Wiki 6M 1000 17 hrs

Install

Assume you already have BLAS and LAPACK installed, to build ScaCTM, simply do

    cd third_party
    make                    # Install third-party dependencies, takes 6 minutes on our 12-core server
    cd ..
    cd src
    make -j                 # Build ScaCTM in parallel
    cd ..

See BLAS if you don't have BLAS and LAPACK.

Chinese users: if you have trouble installing, see this.

For offline installation, download everything in https://github.com/cjf00000/ScaCTM/releases, put them in third_party/third_party/src, then do the normal installation sequence above.

Usage

First you need to set some environment variables

    source scripts/setenv_bash      # for bash
    source scripts/setenv_csh       # for csh

Then, copy ScaCTM to every nodes of cluster. We assume you have two nodes, juncluster1 and juncluster2, and ScaCTM is stored at juncluster1:ScaCTM

    scp -r ScaCTM juncluster2:

Note: you need to execute source scripts/setenv_<your shell> in every shell session.

Input data

Download the example data, from Yahoo-LDA

    mkdir work && cd work   # We'll do everything in work/
    wget https://raw.github.com/sudar/Yahoo_LDA/master/test/ydir_1k.txt

Now, take a look at the data. Every document is a single line in the file, every line is

    docid site word_1 word_2 ...

You need to make sure that docid is unique. site is not used by ScaCTM currently, just for compatibility with Yahoo-LDA. Followed by these two fields are all the words in the corpus. You may wish to do some pre-processing, e.g. remove stop words.

Train

First, open a file machinefile, put the following lines

    juncluster1
    juncluster2

Which are the hostnames for your cluster.

Look at help of ctm-train

    ctm-train --help

Now we want to train a model with default parameters

    ctm-train -f machinefile ydir_1k.txt

If you only have one machine, use

    ctm-train ydir_1k.txt

The training is now started, you will see its progress on your console

    Training on juncluster1, juncluster2 (2 nodes).
    Distributing executables...
    Done (7.418916 seconds).
    Starting server...
    Formatting corpus ydir_1k.txt...
    Done (1.675312 seconds).
    Training
    100.000000%
    Done (68.470395 seconds).
    Gathering results...
    Done (13.113103 seconds). Model stored in /home/jianfei/tmp/ScaCTM/work/ydir_1k.txt.model.

When the training is completed, the result in stored in ydir_1k.txt.model/info

  • model.topToWor.txt is learned topics
  • model.dict.json is a list of dictionary / vocabulary
  • model.phi.json is a V * K matrix phi, where V is vocabulary size and K is number of topics. phi[v, k] = p(w=v | z=k, phi) is the probabilty of word v of topic k. Word v is the v-th line in model.dict.json.
  • model.mu.json, model.cov.json are prior mean and covariance. model.corr.json is the correlation matrix.
  • model.top.json is the topic distribution eta for each document. It uses docid provided in data as key and eta as value.

Train and test

We need a training set and testing set

    make_test_data.sh ydir_1k.txt ydir_1k.txt.train ydir_1k.txt.test 0.8

You'll get a training set and a testing set with 8:2 documents.

Train

    ctm-train -f machinefile ydir_1k.txt.train

Test

    ctm-test -m ydir_1k.txt.train.model/ ydir_1k.txt.test

Test result is stored in ydir_1k.txt.test.result/info.

Perplexity evaluation

Sometimes you want to measure the perplexity on a test set. You need to further divide every document in the test set into an observed part and a heldout part. We'll infer eta on the observed part and measure perplexity on the heldout part. See the paper for detail.

    make_test_data.sh ydir_1k.txt ydir_1k.txt.train ydir_1k.txt.test_observed 0.8 ydir_1k.txt.test_heldout

You'll get a training set and a testing set with 8:2 documents, the test set is further divided into an observed part and a heldout part.

Train

    ctm-train -f machinefile ydir_1k.txt.train

Test

    ctm-test -m ydir_1k.txt.train.model/ --heldout ydir_1k.txt.test_heldout ydir_1k.txt.test_observed

Perplexity is shown at the bottom.

Testing on juncluster1, juncluster2 (2 nodes).
Distributing executables...
Done (3.956380 seconds).
Broadcasting model...
Done (2.808829 seconds).
Starting server...
Formatting corpus ydir_1k.txt.test_observed...
Done (0.642709 seconds).
Testing
100.000000%
Done (4.367594 seconds).
Gathering results...
Done (4.367329 seconds). Output stored in ydir_1k.txt.test_observed.result.
Computing held-out perplexity
Perplexity = 1112.114460

BLAS

If you don't have BLAS and LAPACK, you can simply install them by package manager, for example

    sudo apt-get install libblas-dev
    sudo apt-get install liblapack-dev

will install Netlib reference implementation on Ubuntu systems.

If you are working with a lot of short documents and many topics (>=500), you may wish to use a faster BLAS. There are many possible options, for example, to install ATLAS

    sudo apt-get install libatlas3-dev

and rebuild the code

    cd src
    make clean && make -j

make sure ATLAS is used by ScaCTM

    # See which BLAS is ScaCTM using
    $ ldd /bin/learntopics
    <skipped>
    libblas.so.3gf => /usr/lib/libblas.so.3gf (0x00007f7c770e0000)
    <skipped>

    # Find the path of /usr/lib/libblas.so.3gf
    $ ls -l /usr/lib/libblas.so.3gf
    /usr/lib/libblas.so.3gf -> /etc/alternatives/libblas.so.3gf 

    $ ls -l /etc/alternatives/libblas.so.3gf
    /etc/alternatives/libblas.so.3gf -> /usr/lib/atlas-base/atlas/libblas.so.3gf

if you are still using the old BLAS, you can manually link with ATLAS by modifing LDFLAGS in src/Makefile. You can also use other BLAS such as MKL or ACML by modifing INCFLAGS and LDFLAGS in src/Makefile.

NOTE

Be cautious with OpenBLAS, we find ScaCTM works extremely slow with OpenBLAS.

Bugs / New Features

Please create a issue for us if you found any bugs or want any new features. We look forward for your suggestions!

Dependencies

ScaCTM is built upon the Yahoo-LDA, which is a distributed framework for topic modeling.

License

Apache License 2.0

Reference

Please cite our paper if you find ScaCTM is useful!

Jianfei Chen, Jun Zhu, Zi Wang, Xun Zheng, and Bo Zhang. Scalable Inference for Logistic-Normal Topic Models, Advances in Neural Information Processing Systems (NIPS), Lake Tahoe, USA, 2013. (NIPS 2013)

Some demonstration can be found at http://ml.cs.tsinghua.edu.cn/~scalable-ctm/.