Download JAR files tagged by alignmentalgorithm with all dependencies
sets from group de.cit-ec.tcs.alignment (version 3.1.1)
This module provides algorithms to compare sets, that is, order-invariant lists. These
algorithms are implementations of the AlignmentAlgorithm interface defined in the
algorithms module.
In particular, this module contains the StrictSetAlignmentScoreAlgorithm for computing
the cost of the optimal unordered alignment of two sets, the
StrictSetAlignmentFullAlgorithm which provides the Alignment itself as well, and the
GreedySetAlignmentScoreAlgorithm as well as the GreedySetAlignmentFullAlgorithm for
computing a potentially sub-optimal but faster alignment of two sets.
The optimal alignments rely on the HungarianAlgorithm for solving the assignment
problem in bipartite graphs. Here, we rely on the implementation provided by Kevin L. Stern
which is provided within this distribution.
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Artifact sets
Group de.cit-ec.tcs.alignment
Version 3.1.1
Last update 26. October 2018
Organization not specified
URL http://openresearch.cit-ec.de/projects/tcs
License The GNU Affero General Public License, Version 3
Dependencies amount 1
Dependencies algorithms,
There are maybe transitive dependencies!
Group de.cit-ec.tcs.alignment
Version 3.1.1
Last update 26. October 2018
Organization not specified
URL http://openresearch.cit-ec.de/projects/tcs
License The GNU Affero General Public License, Version 3
Dependencies amount 1
Dependencies algorithms,
There are maybe transitive dependencies!
algorithms from group de.cit-ec.tcs.alignment (version 3.1.1)
This module defines the interface for AlignmentAlgorithms as well as some helper classes. An
AlignmentAlgorithm computes an Alignment of two given input sequences, given a Comparator that
works in these sequences.
More details on the AlignmentAlgorithm can be found in the respective interface. More information
on Comparators can be found in the comparators module.
The resulting 'Alignment' may be just a real-valued dissimilarity between the input sequence or
may incorporate additional information, such as a full Alignment, a PathList, a PathMap or a
CooptimalModel. If those results support the calculation of a Gradient, they implement the
DerivableAlignmentDistance interface.
In more detail, the Alignment class represents the result of a backtracing scheme, listing all
Operations that have been applied in one co-optimal Alignment.
A classic AlignmentAlgorithm does not result in a differentiable dissimilarity, because the
minimum function is not differentiable. Therefore, this package also contains utility functions
for a soft approximation of the minimum function, namely Softmin.
For faster (parallel) computation of many different alignments or gradients we also provide the
ParallelProcessingEngine, the SquareParallelProcessingEngine and the ParallelGradientEngine.
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Artifact algorithms
Group de.cit-ec.tcs.alignment
Version 3.1.1
Last update 26. October 2018
Organization not specified
URL http://openresearch.cit-ec.de/projects/tcs
License The GNU Affero General Public License, Version 3
Dependencies amount 3
Dependencies comparators, parallel, lombok,
There are maybe transitive dependencies!
Group de.cit-ec.tcs.alignment
Version 3.1.1
Last update 26. October 2018
Organization not specified
URL http://openresearch.cit-ec.de/projects/tcs
License The GNU Affero General Public License, Version 3
Dependencies amount 3
Dependencies comparators, parallel, lombok,
There are maybe transitive dependencies!
adp from group de.cit-ec.tcs.alignment (version 3.1.1)
This module contains a more general approach to construct
AlignmentAlgorithms by relying on the theoretical concept of Algebraic
Dynamic Programming (ADP) as developed by Giegerich et al.
ADP defines four ingredients for an alignment algorithm:
1.) A signature that defines the permitted alignment operations.
Operations are just function templates with an associated arity, meaning
the number of arguments it takes from the left sequence and from the
right sequence.
In the TCSAlignmentToolbox we have a fixed signature with the following
operations:
REPLACEMENT(1, 1), DELETION(1, 0), INSERTION(0, 1), SKIPDELETION(1, 0)
and SKIPINSERTION(0, 1)
2.) A regular tree grammar that produces alignments, that is: sequences
of operations, in a restricted fashion.
3.) An algebra that can translate such trees to a cost. In the
TCSAlignmentToolbox this is a Comparator.
4.) A choice function, in case of the TCSAlignmentToolbox: the strict
minimum or the soft minimum.
An alignment algorithm in the TCSAlignmentToolbox sense of the word then
is the combination of choice function and grammar. While we provide
hardcoded versions of these combinations in the main package, the adp
package allows you to create your own grammars. You can combine them with
a choice function by instantiating one of the Algorithm classes provided
in this package with a grammar of your choice.
For example:
AlignmentAlgorithm algo = new SoftADPScoreAlgorithm(my_grammar, comparator);
creates an alignment algorithm that implicitly produces all possible
alignments your grammar can construct with the given input, translates them
to a cost using the algebra/comparator you provided and applies the
soft minimum to return the score. This all gets efficient by dynamic
programming.
Note that there is runtime overhead when using this method in comparison
with the hardcoded algorithms. But for complicated grammars this is a much
easier way to go.
For more information on the theory, please refer to my master's thesis:
"Adaptive Affine Sequence Alignment using Algebraic Dynamic Programming"
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Artifact adp
Group de.cit-ec.tcs.alignment
Version 3.1.1
Last update 26. October 2018
Organization not specified
URL http://openresearch.cit-ec.de/projects/tcs
License The GNU Affero General Public License, Version 3
Dependencies amount 1
Dependencies algorithms,
There are maybe transitive dependencies!
Group de.cit-ec.tcs.alignment
Version 3.1.1
Last update 26. October 2018
Organization not specified
URL http://openresearch.cit-ec.de/projects/tcs
License The GNU Affero General Public License, Version 3
Dependencies amount 1
Dependencies algorithms,
There are maybe transitive dependencies!
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