https://www.jstacs.de/index.php?title=First_main_course:_SequenceScores&feed=atom&action=history
First main course: SequenceScores - Revision history
2024-03-29T12:46:16Z
Revision history for this page on the wiki
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https://www.jstacs.de/index.php?title=First_main_course:_SequenceScores&diff=564&oldid=prev
Keilwagen at 07:51, 14 May 2012
2012-05-14T07:51:49Z
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 08:51, 14 May 2012</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l109">Line 109:</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The interface [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/differentiable/DifferentiableSequenceScore.html DifferentiableSequenceScore] extends [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/SequenceScore.html SequenceScore] <del style="font-weight: bold; text-decoration: none;">†and </del>adds all methods that are necessary for a numerical optimization of the parameters</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The interface [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/differentiable/DifferentiableSequenceScore.html DifferentiableSequenceScore] extends [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/SequenceScore.html SequenceScore] <ins style="font-weight: bold; text-decoration: none;">and </ins>adds all methods that are necessary for a numerical optimization of the parameters</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>of a [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/SequenceScore.html SequenceScore]. This especially includes the computation of the gradient w.r.t. the parameters for a given input [http://www.jstacs.de/api-2.0//de/jstacs/data/sequences/Sequence.html Sequence].</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>of a [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/SequenceScore.html SequenceScore]. This especially includes the computation of the gradient w.r.t. the parameters for a given input [http://www.jstacs.de/api-2.0//de/jstacs/data/sequences/Sequence.html Sequence].</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></source></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></source></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>which is tailored to initializing the parameters from a given data set. The parameters have the following meaning: <code>index</code> is the index of the class this [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/differentiable/DifferentiableSequenceScore.html DifferentiableSequenceScore] <del style="font-weight: bold; text-decoration: none;">†represents</del>.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>which is tailored to initializing the parameters from a given data set. The parameters have the following meaning: <code>index</code> is the index of the class this [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/differentiable/DifferentiableSequenceScore.html DifferentiableSequenceScore] <ins style="font-weight: bold; text-decoration: none;">represents</ins>.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>For some parameterizations, we can either optimize (and initialize) only the free parameters of the model, i.e., excluding parameters with values that can be computed from the values of a subset of the remaining parameters, or we can optimize all parameters. For example such parameters could be those of a DNA dice, where the probability of one nucleotide is fixed if we know the probabilities of all other nucleotides.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>For some parameterizations, we can either optimize (and initialize) only the free parameters of the model, i.e., excluding parameters with values that can be computed from the values of a subset of the remaining parameters, or we can optimize all parameters. For example such parameters could be those of a DNA dice, where the probability of one nucleotide is fixed if we know the probabilities of all other nucleotides.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>If <code>freeParams</code> is <code>true</code>, only the free parameters are used.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>If <code>freeParams</code> is <code>true</code>, only the free parameters are used.</div></td></tr>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>where <code>start</code> is the index of the value for the first parameter of this [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/differentiable/DifferentiableSequenceScore.html DifferentiableSequenceScore] <del style="font-weight: bold; text-decoration: none;">†within </del><code>params</code>.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>where <code>start</code> is the index of the value for the first parameter of this [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/differentiable/DifferentiableSequenceScore.html DifferentiableSequenceScore] <ins style="font-weight: bold; text-decoration: none;">within </ins><code>params</code>.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Finally, the method</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Finally, the method</div></td></tr>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The implementation of this method is not always possible. In its default implementation in the abstract implementations of [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/StatisticalModel.html StatisticalModel], this method just throws an Exception and must be explicitly overridden to be functional.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The implementation of this method is not always possible. In its default implementation in the abstract implementations of [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/StatisticalModel.html StatisticalModel], this method just throws an Exception and must be explicitly overridden to be functional.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The last method defined in [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/StatisticalModel.html StatisticalModel] <del style="font-weight: bold; text-decoration: none;">†is</del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The last method defined in [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/StatisticalModel.html StatisticalModel] <ins style="font-weight: bold; text-decoration: none;">is</ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><source lang="java5" enclose="div"></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><source lang="java5" enclose="div"></div></td></tr>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Besides the possibility to implement new statistical models in Jstacs, many of them are already implemented and can readily be used.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Besides the possibility to implement new statistical models in Jstacs, many of them are already implemented and can readily be used.</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>As a central facility for creating [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/trainable/TrainableStatisticalModel.html TrainableStatisticalModel] instances of many standard models, Jstacs provides a [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/trainable/<del style="font-weight: bold; text-decoration: none;">TrainSMFactory</del>.html <del style="font-weight: bold; text-decoration: none;">TrainSMFactory</del>].</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>As a central facility for creating [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/trainable/TrainableStatisticalModel.html TrainableStatisticalModel] instances of many standard models, Jstacs provides a [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/trainable/<ins style="font-weight: bold; text-decoration: none;">TrainableStatisticalModelFactory</ins>.html <ins style="font-weight: bold; text-decoration: none;">TrainableStatisticalModelFactory</ins>].</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Using the [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/trainable/<del style="font-weight: bold; text-decoration: none;">TrainSMFactory</del>.html <del style="font-weight: bold; text-decoration: none;">TrainSMFactory</del>], we can create a new position weight matrix (PWM) model by calling</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Using the [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/trainable/<ins style="font-weight: bold; text-decoration: none;">TrainableStatisticalModelFactory</ins>.html <ins style="font-weight: bold; text-decoration: none;">TrainableStatisticalModelFactory</ins>], we can create a new position weight matrix (PWM) model by calling</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Instead of using the [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/trainable/<del style="font-weight: bold; text-decoration: none;">TrainSMFactory</del>.html <del style="font-weight: bold; text-decoration: none;">TrainSMFactory</del>], we can also create [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/trainable/TrainableStatisticalModel.html TrainableStatisticalModel] s directly using their constructors. For example, we create a homogeneous Markov model of order <math>0</math> by calling</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Instead of using the [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/trainable/<ins style="font-weight: bold; text-decoration: none;">TrainableStatisticalModelFactory</ins>.html <ins style="font-weight: bold; text-decoration: none;">TrainableStatisticalModelFactory</ins>], we can also create [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/trainable/TrainableStatisticalModel.html TrainableStatisticalModel] s directly using their constructors. For example, we create a homogeneous Markov model of order <math>0</math> by calling</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><source lang="java5" enclose="div"></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><source lang="java5" enclose="div"></div></td></tr>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>A special case of a mixture model is the [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/trainable/mixture/StrandTrainSM.html StrandTrainSM], which is a mixture over the two strands of DNA. For both strands, the same component [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/trainable/TrainableStatisticalModel.html TrainableStatisticalModel] is used but it is evaluated once for the original [http://www.jstacs.de/api-2.0//de/jstacs/data/sequences/Sequence.html Sequence] and once for its reverse complement.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>A special case of a mixture model is the [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/trainable/mixture/StrandTrainSM.html StrandTrainSM], which is a mixture over the two strands of DNA. For both strands, the same component [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/trainable/TrainableStatisticalModel.html TrainableStatisticalModel] is used but it is evaluated once for the original [http://www.jstacs.de/api-2.0//de/jstacs/data/sequences/Sequence.html Sequence] and once for its reverse complement.</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>We construct a [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/trainable/mixture/StrandTrainSM.html StrandTrainSM] of the inhomogeneous Markov model created by the [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/trainable/<del style="font-weight: bold; text-decoration: none;">TrainSMFactory</del>.html <del style="font-weight: bold; text-decoration: none;">TrainSMFactory</del>] by calling</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>We construct a [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/trainable/mixture/StrandTrainSM.html StrandTrainSM] of the inhomogeneous Markov model created by the [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/trainable/<ins style="font-weight: bold; text-decoration: none;">TrainableStatisticalModelFactory</ins>.html <ins style="font-weight: bold; text-decoration: none;">TrainableStatisticalModelFactory</ins>] by calling</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><source lang="java5" enclose="div"></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><source lang="java5" enclose="div"></div></td></tr>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>that returns the logarithm of that normalization constant, which only depends on the current parameter values but not on the input sequence. For computing the gradients with respect to the parameters, we also need the partial derivations of the log-normalization constant with respect to the parameters. To this end [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/differentiable/DifferentiableStatisticalModel.html DifferentiableStatisticalModel] <del style="font-weight: bold; text-decoration: none;">†provides </del>a method</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>that returns the logarithm of that normalization constant, which only depends on the current parameter values but not on the input sequence. For computing the gradients with respect to the parameters, we also need the partial derivations of the log-normalization constant with respect to the parameters. To this end [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/differentiable/DifferentiableStatisticalModel.html DifferentiableStatisticalModel] <ins style="font-weight: bold; text-decoration: none;"> provides </ins>a method</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><source lang="java5" enclose="div"></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><source lang="java5" enclose="div"></div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>public double getLogPartialNormalizationConstant(int parameterIndex)</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>public double getLogPartialNormalizationConstant(int parameterIndex) <ins style="font-weight: bold; text-decoration: none;"> </ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></source></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></source></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><source lang="java5" enclose="div"></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><source lang="java5" enclose="div"></div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>public void addGradientOfLogPriorTerm(double[] grad, int start)</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>public void addGradientOfLogPriorTerm(double[] grad, int start) </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></source></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></source></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>where we need to specify the [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/differentiable/DifferentiableStatisticalModel.html DifferentiableStatisticalModel] that shall be learned and the parameters of the numerical optimization (see section <del style="font-weight: bold; text-decoration: none;">[[</del>[[Intermediate course: Optimization<del style="font-weight: bold; text-decoration: none;">]]</del>]] for details). By this means, we can use any [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/differentiable/DifferentiableStatisticalModel.html DifferentiableStatisticalModel] in the world of [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/trainable/TrainableStatisticalModel.html TrainableStatisticalModel] s as well, for instance to build a [http://www.jstacs.de/api-2.0//de/jstacs/classifiers/trainSMBased/TrainSMBasedClassifier.html TrainSMBasedClassifier] (see [[Second main course: Classifiers]]).</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>where we need to specify the [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/differentiable/DifferentiableStatisticalModel.html DifferentiableStatisticalModel] that shall be learned and the parameters of the numerical optimization (see section [[Intermediate course: Optimization]] for details). By this means, we can use any [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/differentiable/DifferentiableStatisticalModel.html DifferentiableStatisticalModel] in the world of [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/trainable/TrainableStatisticalModel.html TrainableStatisticalModel] s as well, for instance to build a [http://www.jstacs.de/api-2.0//de/jstacs/classifiers/trainSMBased/TrainSMBasedClassifier.html TrainSMBasedClassifier] (see [[Second main course: Classifiers]]).</div></td></tr>
</table>
Keilwagen
https://www.jstacs.de/index.php?title=First_main_course:_SequenceScores&diff=539&oldid=prev
Grau at 08:43, 3 February 2012
2012-02-03T08:43:29Z
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 09:43, 3 February 2012</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l6">Line 6:</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Sub-iterfaces of [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/SequenceScore.html SequenceScore] are [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/differentiable/DifferentiableSequenceScore.html DifferentiableSequenceScore], which is tailored to numerical optimization, and [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/StatisticalModel.html StatisticalModel], which represents statistical models </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Sub-iterfaces of [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/SequenceScore.html SequenceScore] are [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/differentiable/DifferentiableSequenceScore.html DifferentiableSequenceScore], which is tailored to numerical optimization, and [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/StatisticalModel.html StatisticalModel], which represents statistical models </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>defining a proper likelihood. [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/StatisticalModel.html StatisticalModel], in turn, has two sub-interfaces [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/trainable/TrainableStatisticalModel.html TrainableStatisticalModel] and [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/differentiable/DifferentiableStatisticalModel.html DifferentiableStatisticalModel], where the latter joins the properties of [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/StatisticalModel.html StatisticalModel] s and [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/differentiable/DifferentiableSequenceScore.html DifferentiableSequenceScore] s. All of these will be explained in the sub-sections of this section.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>defining a proper likelihood. [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/StatisticalModel.html StatisticalModel], in turn, has two sub-interfaces [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/trainable/TrainableStatisticalModel.html TrainableStatisticalModel] and [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/differentiable/DifferentiableStatisticalModel.html DifferentiableStatisticalModel], where the latter joins the properties of [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/StatisticalModel.html StatisticalModel] s and [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/differentiable/DifferentiableSequenceScore.html DifferentiableSequenceScore] s. All of these will be explained in the sub-sections of this section.</div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">__TOC__</ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/SequenceScore.html SequenceScore] extends the standard interface <code>Cloneable</code> and, hence, implementations must provide a <code>clone()</code> method, which returns a deep copy of all fields of an instance:</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/SequenceScore.html SequenceScore] extends the standard interface <code>Cloneable</code> and, hence, implementations must provide a <code>clone()</code> method, which returns a deep copy of all fields of an instance:</div></td></tr>
</table>
Grau
https://www.jstacs.de/index.php?title=First_main_course:_SequenceScores&diff=523&oldid=prev
Grau at 14:25, 2 February 2012
2012-02-02T14:25:50Z
<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 15:25, 2 February 2012</td>
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<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">= First main course: SequenceScores =</del></div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><span id="sequenceScore"> </span></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><span id="sequenceScore"> </span></div></td></tr>
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</table>
Grau
https://www.jstacs.de/index.php?title=First_main_course:_SequenceScores&diff=514&oldid=prev
Grau at 14:19, 2 February 2012
2012-02-02T14:19:30Z
<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 15:19, 2 February 2012</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>= First main course: SequenceScores =</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>= First main course: SequenceScores =</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><span id="sequenceScore"> </span></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><span id="sequenceScore"> </span></div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2" class="diff-side-added"></td></tr>
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<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/SequenceScore.html SequenceScore] s define scoring functions over sequences that can assign a score to each input sequence. Such scores can then be used</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/SequenceScore.html SequenceScore] s define scoring functions over sequences that can assign a score to each input sequence. Such scores can then be used</div></td></tr>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Sub-iterfaces of [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/SequenceScore.html SequenceScore] are [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/differentiable/DifferentiableSequenceScore.html DifferentiableSequenceScore], which is tailored to numerical optimization, and [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/StatisticalModel.html StatisticalModel], which represents statistical models </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Sub-iterfaces of [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/SequenceScore.html SequenceScore] are [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/differentiable/DifferentiableSequenceScore.html DifferentiableSequenceScore], which is tailored to numerical optimization, and [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/StatisticalModel.html StatisticalModel], which represents statistical models </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>defining a proper likelihood. [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/StatisticalModel.html StatisticalModel], in turn, has two sub-interfaces [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/trainable/TrainableStatisticalModel.html TrainableStatisticalModel] and [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/differentiable/DifferentiableStatisticalModel.html DifferentiableStatisticalModel], where the latter joins the properties of [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/StatisticalModel.html StatisticalModel] s and [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/differentiable/DifferentiableSequenceScore.html DifferentiableSequenceScore] s. All of these will be explained in the sub-sections of this section.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>defining a proper likelihood. [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/StatisticalModel.html StatisticalModel], in turn, has two sub-interfaces [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/trainable/TrainableStatisticalModel.html TrainableStatisticalModel] and [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/differentiable/DifferentiableStatisticalModel.html DifferentiableStatisticalModel], where the latter joins the properties of [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/StatisticalModel.html StatisticalModel] s and [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/differentiable/DifferentiableSequenceScore.html DifferentiableSequenceScore] s. All of these will be explained in the sub-sections of this section.</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2" class="diff-side-added"></td></tr>
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<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/SequenceScore.html SequenceScore] extends the standard interface <code>Cloneable</code> and, hence, implementations must provide a <code>clone()</code> method, which returns a deep copy of all fields of an instance:</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/SequenceScore.html SequenceScore] extends the standard interface <code>Cloneable</code> and, hence, implementations must provide a <code>clone()</code> method, which returns a deep copy of all fields of an instance:</div></td></tr>
</table>
Grau
https://www.jstacs.de/index.php?title=First_main_course:_SequenceScores&diff=513&oldid=prev
Grau at 14:19, 2 February 2012
2012-02-02T14:19:06Z
<p></p>
<a href="https://www.jstacs.de/index.php?title=First_main_course:_SequenceScores&diff=513&oldid=491">Show changes</a>
Grau
https://www.jstacs.de/index.php?title=First_main_course:_SequenceScores&diff=491&oldid=prev
Grau at 22:53, 1 February 2012
2012-02-01T22:53:39Z
<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 23:53, 1 February 2012</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Sub-iterfaces of [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/SequenceScore.html SequenceScore] are [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/differentiable/DifferentiableSequenceScore.html DifferentiableSequenceScore], which is tailored to numerical optimization, and [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/StatisticalModel.html StatisticalModel], which represents statistical models </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Sub-iterfaces of [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/SequenceScore.html SequenceScore] are [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/differentiable/DifferentiableSequenceScore.html DifferentiableSequenceScore], which is tailored to numerical optimization, and [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/StatisticalModel.html StatisticalModel], which represents statistical models </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>defining a proper likelihood. [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/StatisticalModel.html StatisticalModel], in turn, has two sub-interfaces [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/trainable/TrainableStatisticalModel.html TrainableStatisticalModel] and [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/differentiable/DifferentiableStatisticalModel.html DifferentiableStatisticalModel], where the latter joins the properties of [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/StatisticalModel.html StatisticalModel] s and [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/differentiable/DifferentiableSequenceScore.html DifferentiableSequenceScore] s. All of these will be explained in the sub-sections of this section.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>defining a proper likelihood. [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/StatisticalModel.html StatisticalModel], in turn, has two sub-interfaces [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/trainable/TrainableStatisticalModel.html TrainableStatisticalModel] and [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/differentiable/DifferentiableStatisticalModel.html DifferentiableStatisticalModel], where the latter joins the properties of [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/statisticalModels/StatisticalModel.html StatisticalModel] s and [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/differentiable/DifferentiableSequenceScore.html DifferentiableSequenceScore] s. All of these will be explained in the sub-sections of this section.</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/SequenceScore.html SequenceScore] extends the standard interface <code>Cloneable</code> and, hence, implementations must provide a <code>clone()</code> method, which returns a deep copy of all fields of an instance:</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/SequenceScore.html SequenceScore] extends the standard interface <code>Cloneable</code> and, hence, implementations must provide a <code>clone()</code> method, which returns a deep copy of all fields of an instance:</div></td></tr>
<tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l107">Line 107:</td>
<td colspan="2" class="diff-lineno">Line 104:</td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== DifferentiableSequenceScores ==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== DifferentiableSequenceScores ==</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The interface [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/differentiable/DifferentiableSequenceScore.html DifferentiableSequenceScore] extends [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/SequenceScore.html SequenceScore] †and adds all methods that are necessary for a numerical optimization of the parameters</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The interface [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/differentiable/DifferentiableSequenceScore.html DifferentiableSequenceScore] extends [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/SequenceScore.html SequenceScore] †and adds all methods that are necessary for a numerical optimization of the parameters</div></td></tr>
</table>
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https://www.jstacs.de/index.php?title=First_main_course:_SequenceScores&diff=490&oldid=prev
Grau: Created page with "<span id="sequenceScore"> </span> [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/SequenceScore.html SequenceScore] s define scoring functions over sequences that can as..."
2012-02-01T22:52:49Z
<p>Created page with "<span id="sequenceScore"> </span> [http://www.jstacs.de/api-2.0//de/jstacs/sequenceScores/SequenceScore.html SequenceScore] s define scoring functions over sequences that can as..."</p>
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