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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.

The libswresample library performs highly optimized audio resampling, rematrixing and sample format conversion operations. Specifically, this library performs the following conversions: Resampling: is the process of changing the audio rate, for example from an high sample rate of 44100Hz to 8000Hz. Audio conversion from high to low sample rate is a lossy process. Several resampling options and algorithms are available. Format conversion: is the process of converting the type of samples, for example from 16-bit signed samples to unsigned 8-bit or float samples. It also handles packing conversion, when passing from packed layout (all samples belonging to distinct channels interleaved in the same buffer), to planar layout (all samples belonging to the same channel stored in a dedicated buffer or "plane"). Rematrixing: is the process of changing the channel layout, for example from stereo to mono. When the input channels cannot be mapped to the output streams, the process is lossy, since it involves different gain factors and mixing. Various other audio conversions (e.g. stretching and padding) are enabled through dedicated options.

The boilerpipe library provides algorithms to detect and remove the surplus "clutter" (boilerplate, templates) around the main textual content of a web page. The library already provides specific strategies for common tasks (for example: news article extraction) and may also be easily extended for individual problem settings. Extracting content is very fast (milliseconds), just needs the input document (no global or site-level information required) and is usually quite accurate. Boilerpipe is a Java library written by Christian Kohlschütter. It is released under the Apache License 2.0. The algorithms used by the library are based on (and extending) some concepts of the paper "Boilerplate Detection using Shallow Text Features" by Christian Kohlschütter et al., presented at WSDM 2010 -- The Third ACM International Conference on Web Search and Data Mining New York City, NY USA.

This package currently contains classes for training multilayer perceptrons with one hidden layer, where the number of hidden units is user specified. MLPClassifier can be used for classification problems and MLPRegressor is the corresponding class for numeric prediction tasks. The former has as many output units as there are classes, the latter only one output unit. Both minimise a penalised squared error with a quadratic penalty on the (non-bias) weights, i.e., they implement "weight decay", where this penalised error is averaged over all training instances. The size of the penalty can be determined by the user by modifying the "ridge" parameter to control overfitting. The sum of squared weights is multiplied by this parameter before added to the squared error. Both classes use BFGS optimisation by default to find parameters that correspond to a local minimum of the error function. but optionally conjugated gradient descent is available, which can be faster for problems with many parameters. Logistic functions are used as the activation functions for all units apart from the output unit in MLPRegressor, which employs the identity function. Input attributes are standardised to zero mean and unit variance. MLPRegressor also rescales the target attribute (i.e., "class") using standardisation. All network parameters are initialised with small normally distributed random values.

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"