Copyright (C) 2013, 2014
Benjamin Paaßen, Charlie Krüger, Georg Zentgraf
AG Theoretical Computer Science
Centre of Excellence Cognitive Interaction Technology (CITEC)
University of Bielefeld
This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
This Java Toolbox provides several algorithms to align two input sequences, where your sequential data is allowed to be multimodal and multidimensional. We also provide additional tools to inspect the alignment results in more detail or even calculate derivatives of the alignment w.r.t. metric parameters such that you can optimize the alignment parameters according to some cost function. It is written in Java 1.7. and is also compatible with Matlab (version 2013b or higher).
To use this software is recommended if
This toolbox is not the right tool for you if you want to do standard computation like DTW on one-dimensional double sequences or simple string edit distance. In that case there are far better and faster tools out there.
The TCSAlignmentToolbox can be directly used in your Matlab/Java-program as a .jar file or via maven. As the project is not yet part of the central maven repository you need to install the toolbox manually via the command
mvn install:install-file -Dfile=TCSAlignmentToolbox-1.3.2.jar -DgroupId=de.unibi.citec.tcs -DartifactId=TCSAlignmentToolbox -Dversion=1.3.2 -Dpackaging=jar
Of course you can also compile and install from the source code.
mvn install
If you do not want to use maven you can use the binary .jar file.
If you want to use the Toolbox as fast as possible it is recommended to use one of the code examples in the "examples" directory and develop your application code from there on.
The idea behind the toolbox is to enable you to not only align DNA/symbol sequences or sequences of vectorial data, but sequences of nodes that each contain multiple values of type 'symbol', 'vector' or 'string'. This allows for much more complex input data. Furthermore we not only provide the alignment score for your specified scoring scheme but also the alignment paths, soft approximations of the generic alignment scheme and means to calculate the derivative of an alignment result.
To understand the toolboxes architecture it is helpful to keep the following concepts in mind:
The architecture is shown in detail in UML diagrams in the "uml" directory.
In order to use the Toolbox, you'll need to execute (some of) the following steps:
Examples are also provided in the "examples" directory.
In our algorithms we currently differentiate between the following types:
You can find further documentation in the "javadoc" and "uml" directory. Examples are also provided in the "examples" directory.
This Toolbox was developed in 2014 in the Theoretical Computer Science for Cognitive Systems Workgroup at the Centre of Excellence 'Cognitive Interaction Technology' (CITEC), Bielefeld University. Development was part of the research project 'Learning Feedback for Intelligent Tutoring Systems' (FIT), which is part of the DFG priority program 'Autonomous Learning'.
The main purpose of this toolbox is metric learning, which is described in more detail in our papers:
For visualization we use the Apache Common Lang library. For the normalized compression distance we use the fast LZ4 implementation by jpountz. Both are used in accordance with the Apache License, Version 2.
Version 3, 19 November 2007
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