muxstep

muxstep is an open-source C++ multiplex HMM library for making inferences on multiple data types.

Building

You will need clang++ to compile the library (on Mac OS X, this compiler is installed by default).

Simply run

$ make

while in the root directory of the repository, and the libraries (both static and dynamic) will be created in the lib/ folder. This command will also compile the documentation files (supplementary data as given in the original publication) in doc/muxstep-suppl.pdf (latexmk and pdflatex are required for compiling the documentation).

Usage example

The folder example/ contains basic_usage.cpp, a file that demonstrates a basic way in which the muxstep library might be used.

If you would like to compile it using the static library, run the following:

$ clang++ -std=c++11 -I../include basic_usage.cpp -L../lib -lmuxstep -o basic

If you would like to use the dynamic library instead, run the following:

$ clang++ -std=c++11 -I../include basic_usage.cpp -L../lib -lmuxstep.dyn -o basic
$ LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/muxstep/lib/
$ export LD_LIBRARY_PATH

where /path/to/muxstep refers to the (absolute) path to the root repository folder.

After doing this, you may run the example using

$ ./basic

(Note, it takes some time for training to complete!)

License

MIT

References

If you make advantage of muxstep or derive it within your research, please cite the following article:

Veličković, P. and Liò, P. (2016) muxstep: an open-source C++ multiplex HMM library for making inferences on multiple data types. Bioinformatics

The models described here were originally investigated in the following manuscript:

Veličković, P. and Liò, P. (2015) Molecular multiplex network inference using Gaussian mixture hidden Markov models. Journal of Complex Networks