marbl
Marginal based learning of Conditional Random Field parameters.
Overview
This implementation roughly corresponds to the algorithm described in the paper:
Getting started
- Make sure that you have a compiler that supports C++11. Recent versions of g++ and clang++ are known to work.
- Install openMPI and/or verify that your compiler supports openMP, if you want parallelism. (Optional; see below)
- Download the code.
- Go to the main code directory, and edit the
make.sh script in two ways.
- Change the
compiler variable to the one for your system.
- Set the
mpi_compiler variable the the one for your system (default will usually be OK).
- Run the
make.sh script. This will compile and install libLBFGS to a local directory, and then build the infer_MRF, infer_CRF, learn_CRF and (if you have MPI installed) learn_CRF_mpi executables.
- Go through a few of the examples to get some idea of what you are doing.
- Read the Frequently Asked Questions.
Note that Marbl has been compiled under Mac OS and Linux, but hasn’t been tested under Windows. If you are able to compile under Windows, please send any information about how you did so.
To uninstall Marbl, just delete the main directory. Nothing is installed anywhere else, and the environment isn’t changed in any way.
Features
- Marbl can handle quite general graphs, with factors of any size, variables taking any number of values, and whatever entropy approximation you desire.
- Marbl can use openMP for parallelism on a single computer with multiple cores.
- Marbl can use openMPI for parallelism, either on a single computer with multiple cores or on a cluster of machines. This is trivial to use on a single machine to get your problem running. (Essentially, you just install openMPI, and then compile using the provided scripts.) Since almost all clusters provide MPI, you can also run Marbl on clusters of computers. We have observed essentially linear speedups using up to several hundred cores.
- Marbl is a command-line tool, with inputs in simple text formats. Thus, you can use whatever (presumably high-level) language to create your problem, by writing a small routine to produce the data and graph specifications in the appropriate format.
Requirements
Strictly speaking, Marbl requires no external libraries. However, learning can be parallelized, using either openMP or openMPI. These are both optional.
openMP
openMP is a platform for shared-memory computing. (i.e. using multiple threads on a single machine). The executable learn_CRF can use openMP if your compiler supports it. Generally, it would be easier to just install a compiler that supports openMP than trying to install openMP separately.
Most recent compilers support openMP out of the box. The major exception is recent versions of xcode/clang on Mac OS. (i.e. the default gcc compiler). Thus, on Mac OS it is recommended to either use MPI for parallelism, or to install a different compiler. (Recent versions of GNU g++ do support it. and can be installed by standard package managers.)
openMPI
Despite the similar name, and despite similar goals of parallel computing, openMPI is completely disjoint from openMP. openMPI is a tool for parallel computing. While openMPI is typically used on clusters, it can manage communication between processes on a single computer. Thus, Marbl’s learn_CRF_mpi uses this single mechanism for parallelism, both on single machines and clusters.
- On linux or Mac OS, openMPI is trivially installed using your favorite package management system. For example, using homebrew on Mac OS, it can be installed with
brew install openmpi.
- On Windows, pre-compiled binaries for Cygwin are available here.
It may be possible to use Marbl with other implementations of MPI, but this hasn’t been tested yet.
Comparison with JGML
Marbl is similar to the JGMT toolbox (implementing essentially the same algorithm), with the following differences:
Language
- JGMT is implemented in a mix of Matlab and C++, and must be used through Matlab.
- Marbl is a command-line tool written in pure C++. Interaction is via the command-line and text files specifying the data and structure of the graph.
- However, one would typically create the inputs to Marbl using a high-level language, and an interface doing this is provided in Matlab.
Limitations
- JGMT can only handle pairwise graphs. Marbl can handle arbitrarily large factors.
- JGMT assumes that all variables have the same possible number of values. Marbl does not assume this.
- JGMT is reasonably efficient. Marbl is still more reasonable.
Parallelism
- Marbl uses openMPI for parallelism. This can be used either on a single machine, or on a cluster of computers.
- JGMT is parallel to some degree, using Matlab’s parfor mechanism. However, this requires the (expensive) parallel computing toolbox to use up to 12 cores, and the (yet more expensive) distributed computing toolbox to use more than that.
Acknowledgements
Marbl includes the code for two other packages:
- Eigen, a template library for linear algebra.
- libLBFG is a C library for the L-BFGS optimization algorithm.
Note that while Marbl and libLBFGS are under the MIT license (under which you are, roughly speaking, allowed to do whatever you want) Eigen is under the Mozilla public license, which places some (very minor) restrictions on how it (and thus Marbl) can be used.