Download JAR files tagged by alignment with all dependencies

This module contains the sequence datastructure of the TCS Alignment Toolbox. It defines the possible value sets in the ValueType enum as well as the different KeywordSpecification classes, namely: 1.) StringKeywordSpecification for string type values. 2.) SymbolicKeywordSpecification for values from a discrete alphabet (also refer to the Alphabet class) 3.) VectorialKeywordSpecification for vectors of some length (or for scalars) A NodeSpecification is a vector of such KeywordSpecifications and defines the order of value sets. A node, then, is defined as a vector of values from these value sets (also refer to the Value interface as well as the StringValue, SymbolicValue and VectorialValue classes). Finally a sequence is defined as a list of such nodes.

This module is a custom implementation of the Large Margin Nearest Neighbor classification scheme of Weinberger, Saul, et al. (2009). It contains an implementation of the k-nearest neighbor and LMNN classifier as well as (most importantly) gradient calculation schemes on the LMNN cost function given a sequential data set and a user-choice of alignment algorithm. This enables users to learn parameters of the alignment distance in question using a gradient descent on the LMNN cost function. More information on this approach can be found in the Masters Thesis "Adaptive Affine Sequence Alignment Using Algebraic Dynamic Programming"

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.

This module defines the interfaces for Comparators in the TCS Alignment Toolbox. A Comparator has the purpose of defining the dissimilarity between elements in the input sequences of an Alignment. More specific information on Comparators can be found in the 'Comparator' interface. You can find a lot of helpful standard implementations of Comparators in the comparators-lib module. In the TCS Alignment Toolbox we require the output values of Comparators to lie in the range [0,1]. Many natural dissimilarities on value sets do not meet this criterion, such that additional normalization has to be applied. To that end this package also contains a Normalizer interface for functions that map real values from the range [0, infinity) to the range [0,1]. This package also provides a few convenience implementations of the Comparator interface to make the implementation of custom Comparators simpler, namely: SkipExtendedComparator, ParameterLessSkipExtendedComparator, ComparisonBasedSkipExtendedComparator, and ParameterLessComparisonBasedSkipExtendedComparator. Finally the TCS Alignment Toolbox also provides the means to learn parameters of Comparators. To enable that Comparators must implement the DerivableComparator interface to properly define the parameters that can be learned and the gradient of the dissimilarity with respect to these parameters. Gradients are stored using the Gradient interface as well as some convenience implementations of said interface, namely EmptyGradient, SingletonGradient, ArrayGradient and ListGradient.

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"