Formal Concept Analysis (FCA) is an algebraic approach to analyzing data; data which, while it can be more general, here is categorical data given as a relation between objects and attributes. The programs in this repo are utilities for manipulating input to and output from the program colibri-java, which does the FCA computation. To do anything useful, you'll need that program.
The input to colibri-java is in the form of "con" (context) files, and about half
of the programs here either translate to that format, or manipulate those files.
The rest of the programs operate on the output "lattice" in the form of a dot file
(a la graphviz).
colibri-java will generate these when run with the argument --output_format dot.
This output is in the form of a directed graph with the concepts as nodes and
coverings as arcs with no annotation (node positions, colorings, etc.).
The programs here either deal with con files or dot files.
Since this is a refactored set of programs that grew organically,
naming is by some logic lost in the fog of other more interesting things.
I did somehow manage to have executables that end in "con" be those that
manipulate con files, while those ending in "attr" somehow use the attributes of
the concepts of the dot files.
The lattice programs are mostly filters on standard input and produce dot output
for visualization, but some do generate tabular data.
The "dep" programs implement the greedy search used in the conference paper
BJ Keller, F Eichinger, M Kretzler. “Formal concept analysis of disease similarity”, In the Proceedings of the 2012 AMIA Summit on Translational Bioinformatics, 2012, 42–51. [Pubmed: 22779049]
#Building
To build you'll need
then edit the LIBPATH in the src/SConscript file to indicate where TCLAP is
located.
The following shenanagans should get you to a working state
mkdir -p site_scons/site_tools
ln -s /path/to/cxxtest.py site_scons/site_tools/cxxtest.py
mkdir extern_libs
ln -s /path/to/cxxtestdir extern_libs/cxxtest
Alternatively, you can install the cxxtest directory in extern_libs and change
its name.
Otherwise, you may have to adjust test/SConscript.
It should build all of the programs with a simple command line
scons
For testing, use
scons check
should build the tests and run them.
#Limitations
Notes on programs manipulating dot files:
- The code to parse the dot output of colibri-java is naive and does not fully handle the dot grammar. So, I'm not sure what will happen when the dot goes beyond this format. If you give dot input with annotations, at best, the annotations will be ignored and will just not be in the output.
- Because these programs require colibri-java to generate the full lattice output, what may be practical to compute is limited by the ability of that program to write the dot file.
- Some of these programs are just flat out brain dead from an efficiency standpoint: we have to have colibri-java construct the full lattice, and then we read the full lattice, storing a filtered version in memory, and then deciding what is output. Java code built on colibri-java classes are in the project DepChain and do the computation as the lattice is constructed, avoiding building the full thing.