muxstep is an open-source C++ multiplex HMM library for making inferences on multiple data types.
You will need
clang++ to compile the library (on Mac OS X, this compiler is installed by default).
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
pdflatex are required for compiling the documentation).
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
/path/to/muxstep refers to the (absolute) path to the root repository folder.
After doing this, you may run the example using
(Note, it takes some time for training to complete!)
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