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algorithms
example_data
utils
.gitignore
README.md
config_example.py
example.py
experiments.py
grammar.py
initialization.py
models.py
observations.py
parallel.py
parsing.py
predictive_distributions.py
presentation.py
recursive.py
scoring.py
single_process.py
synthetic_experiments.py

README.md

This software package implements the algorithms described in the paper

Roger B. Grosse, Ruslan Salakhutdinov, William T. Freeman, and Joshua B. Tenenbaum, "Exploiting compositionality to explore a large space of model structures," UAI 2012.

In particular, it takes an input matrix, runs the structure search, and outputs a report summarizing the choices made at each step. There is also a script which runs the synthetic data experiments from the paper.

Caveats

This is a research prototype, and I've made some simplifying assumptions which may or may not match your situation. In particular,

  • Matrices are assumed to be real-valued, and it handles binary matrices by treating the values as real and adding a small amount of noise to prevent degenerate solutions. (As a sanity check, I've also experimented with samplers which handle binary inputs directly, in order to check that the results were consistent with the real-valued version. However, I didn't get the algorithms working robustly enough to include in the experiments or the software package.)
  • It handles missing observations by explicitly sampling the missing values. This seems to work well for matrices with small numbers of missing entries, but might have poor mixing on sparse input matrices.
  • I haven't run the software on matrices larger than 1000 x 1000. There's no conceptual reason the algorithms can't scale beyond this, but there may be implementational reasons.

I am working on a newer version of the software package which shouldn't have these limitations.

Requirements

This code base depends on a number of Python packages, most of which are pretty standard. Most of the packages are available through Enthought Canopy, which all academic users (including professors and postdocs) can use for free under their academic license. We use the following Python packages which are included in Canopy:

Note: I've been told that Anaconda Python is an alternative distribution which includes these same packages, has a comparable academic license, and is easier to get running. I've never tried it myself, though.

There are two additional requirements, which are both easy_installable:

More recent versions than the ones listed above should work fine, though unfortunately the interfaces to some SciPy routines have a tendency to change without warning...

Also, if you want to distribute jobs across multiple cores or machines (highly recommended), you will need to do one of the following:

  • install GNU Parallel (see Configuration section for more details)
  • write a scheduler which better matches your own computing resources (see below)

Configuration

In order to run the structure search, you need to specify some local configuration parameters in config.py. First, in the main project directory, copy the template:

cp config_example.py config.py

In config.py, you need to specify the following paths:

  • CODE_PATH, the directory where you keep the code for this project
  • CACHE_PATH, a directory for storing intermediate results (which can take up a fair amount of disk space and are OK to delete when the experiment is done)
  • RESULTS_PATH, the directory for storing the machine-readable results of the structure search
  • REPORT_PATH, the directory for saving human-readable reports

You also need to specify SCHEDULER to determine how the experiment jobs are to be run. The choices are 'single_process', which runs everything in a single process (not practical except for the smallest matrices), and 'parallel', which uses GNU Parallel to distribute the jobs across different machines, or different processes on the same machine. If you use GNU Parallel, you also need to specify:

  • JOBS_PATH, a directory for saving the status of jobs, if you are using GNU Parallel
  • DEFAULT_NUM_JOBS, the number of jobs to run on each machine

Note that using our GNU Parallel wrapper requires the ability to ssh into the machines without entering a password. We realize this might not correspond to your situation, so see below for how you can write your own job scheduler module geared towards the clusters at your own institution.

Running the example

We provide an example of how to run the structure search in example.py. This runs the structure search on the mammals dataset of Kemp et al. (2006), "Learning systems of concepts with an infinite relational model." This is a 50 x 85 matrix where the rows represent different species of mammal, the columns represent attributes, and each entry is a binary value representing subjects' judgments of whether the animal has that attribute. Our structure search did not result in a clear structure for this dataset, but it serves as an example which can be run quickly (2 CPU minutes for me).

After following the configuration directions above, run the following from the command line:

python example.py
python experiments.py everything example

This will run the structure search, and then output the results to the shell (and also save them to the example subdirectory of config.REPORT_PATH). The results include the following:

  • the best-performing structure at each level of the search, with their improvement in predictive log-likelihood for rows and columns, as well as z-scores for the improvement
  • the total CPU time, also broken down by model
  • the predictive log-liklihood scores for all structures at all levels of the search, sorted from best to worst

Note that the search parameters used in this example are probably insufficient for inference; if you are interested in accurate results for this dataset, change QuickParams to SmallParams in example.py.

Running the structure search

Suppose you have a real-valued matrix X you're interested in learning the structure of, in the form of a NumPy array. The first step is to create a DataMatrix instance:

from observations import DataMatrix
data_matrix = DataMatrix.from_real_values(X)

This constructor also takes some optional arguments:

  • mask, which is a binary array determining which entries of X are observed. (By default, all entries are assumed to be observed.)
  • row_label and col_label, which are Python lists giving the label of each row or column. These are used for printing the learned clusters and binary components.

The code doesn't do any preprocessing of the data, so it's recommended that you standardize it to have zero mean and unit variance.

Next, you want to initialize an experiment for this matrix. You do this by passing in the DataMatrix instance, along with a parameters object. experiments.SmallParams gives a reasonable set of defaults for small matrices (e.g. 200 x 200), and experiments.LargeParams gives a reasonable set of defaults for larger matrices (e.g. 1000 x 1000). This creates a subdirectories of config.RESULTS_PATH and config.REPORT_PATH where all the computations and results will be stored. For example,

from experiments import init_experiment, LargeParams
init_experiment('experiment_name', data_matrix, LargeParams())

You can also override the default parameters by passing keyword arguments to the parameters constructor. See experiments.DefaultParams for more details. Finally, from the command line, run the whole structure search using the following:

python experiments.py everything experiment_name

You can also specify some optional keyword arguments:

  • --machines, the list of machines to distribute the jobs to if you are using GNU Parallel. This should be a comma-separated list with no spaces. By default, it runs jobs only on the same machine.
  • --njobs, the number of jobs to run on each machine if you are using GNU Parallel. (This overrides the default value in config.DEFAULT_NUM_JOBS.)
  • --email, your e-mail address, if you want it to e-mail you the report when it finishes.

For example,

python experiments.py everything experiment_name --machines machine1,machine2,machine3 --njobs 2 --email me@example.com

If all goes well, a report will be saved to experiment_name/results.txt under config.REPORT_PATH.

Using your own scheduler

As mentioned above, the experiment script assumes you have GNU Parallel installed, and that you're able to SSH into machines without entering a password. This might not match your situation; for instance, your institution might use a queueing system to distribute jobs. I've tried to make it simple to adapt the experiment scripts to your own cluster setup. In particular, you need to do the following:

  1. Write a Python function which takes a list of jobs and distributes them on your cluster. In particular, it should take two arguments:

    • script, the name of the Python file to execute
    • jobs, a list of jobs, where each one is a list of strings, each one corresponding to one command line argument.

    See single_process.run for an example. Note that some of the arguments may contain the single quote character, so you will have to escape them.

  2. Add another case to experiments.run_jobs which calls your scheduler, and change config.SCHEDULER to the appropriate value.

  3. If your scheduler should take any additional command line arguments, you can specify them in experiments.add_scheduler_args.

The above directions assume that all of the machines have access to a common filesystem (e.g. AFS, NFS). If this isn't the case (for instance, if you are running on Amazon EC2), you'll also need to modify the functions in storage.py to read and write from whatever storage system is shared between the machines.

Organization of the code

The main code directly contains the following files which handle the logic of the experiments, and are described above:

  • experiments.py, as mentioned above, which manages the structure search for a single input matrix
  • synthetic_experiments.py, which runs the synthetic data experiments from the paper, i.e. by generating a lot of synthetic matrices and running the structure search on each
  • presentation.py, which formats the results into tables
  • parallel.py and single_process.py, utilities for running jobs

The following files define the main data structures used in the structure search:

  • grammar.py, which defines the conext-free grammar
  • parsing.py, which parses string representations of the models into expression trees
  • observations.py, which defines the DataMatrix and Observations classes used to represent the input matrices
  • recursive.py, which defines the Node classes which store the actual decompositions
  • models.py, which defines model classes which parallel the structure of the Node classes, but define properties of the model itself (such as whether variance parameters for a matrix are associated with rows or columns)

The following handle the posterior inference over decompositions:

  • initialization.py, which does the most interesting algorithmic work, namely initializing the more complex structures using algorithms particular to each production rule.
  • algorithms/dumb_samplers.py, which contains simple MCMC operators which are run after the recursive initialization procedure
  • the algorithms subdirectory contains inference algorithms corresponding to particular production rules: in particular, chains.py, crp.py, ibp.py, low_rank_poisson.py, and sparse_coding.py.

Finally, the following files handle the predictive likelihood scoring:

  • scoring.py, the main procedures for predictive likelihood scoring
  • predictive_distributions.py, which converts the predictive distributions into a sum of terms as in Section 5 of the paper
  • algorithms/variational.py, which implements the variational lower bound of Section 5
  • algorithms/ais_gsm.py, which performs the additional AIS step needed for evaluating the GSM models.