Class CBAHSIC, that extends CKernelDependenceMaximization and uses HSIC [1] to compute dependence measures for feature selection using a backward elimination approach as described in [1]. This class serves as a convenience class that initializes the CDependenceMaximization::m_estimator with an instance of CHSIC and allows only shogun::BACKWARD_ELIMINATION algorithm to use which is set internally. Therefore, trying to use other algorithms by set_algorithm() will not work. Plese see the class documentation of CHSIC and [2] for more details on mathematical description of HSIC.
Refrences: [1] Song, Le and Bedo, Justin and Borgwardt, Karsten M. and Gretton, Arthur and Smola, Alex. (2007). Gene Selection via the BAHSIC Family of Algorithms. Journal Bioinformatics. Volume 23 Issue Pages i490-i498. Oxford University Press Oxford, UK [2]: Gretton, A., Fukumizu, K., Teo, C., & Song, L. (2008). A kernel statistical test of independence. Advances in Neural Information Processing Systems, 1-8.
Public 属性 | |
SGIO * | io |
Parallel * | parallel |
Version * | version |
Parameter * | m_parameters |
Parameter * | m_model_selection_parameters |
Parameter * | m_gradient_parameters |
uint32_t | m_hash |
Protected 成员函数 | |
virtual void | precompute () |
virtual CFeatures * | create_transformed_copy (CFeatures *features, index_t idx) |
virtual CFeatures * | apply_backward_elimination (CFeatures *features) |
virtual void | adapt_params (CFeatures *features) |
index_t | get_num_features (CFeatures *features) const |
virtual void | load_serializable_pre () throw (ShogunException) |
virtual void | load_serializable_post () throw (ShogunException) |
virtual void | save_serializable_pre () throw (ShogunException) |
virtual void | save_serializable_post () throw (ShogunException) |
CBAHSIC | ( | ) |
Default constructor
在文件 BAHSIC.cpp 第 36 行定义.
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Destructor
在文件 BAHSIC.cpp 第 48 行定义.
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protectedvirtualinherited |
Tunes the parameters which are required to compute the measure based on current features. Overridden in the subclasses. Here it does nothing.
features | the features based on which parameters are needed to be tuned for computing measures |
Generic interface for applying the feature selection preprocessor. Acts as a wrapper which decides which actual method to call based on the algorithm specified.
features | the input features |
实现了 CPreprocessor.
Applies backward elimination algorithm for performing feature selection. After performing necessary precomputing (defined by subclasses), it iteratively eliminates a number of features based on a measure until target dimension is reached.
features | the input features |
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Builds a dictionary of all parameters in SGObject as well of those of SGObjects that are parameters of this object. Dictionary maps parameters to the objects that own them.
dict | dictionary of parameters to be built. |
在文件 SGObject.cpp 第 597 行定义.
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performs cleanup
实现了 CPreprocessor.
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Creates a clone of the current object. This is done via recursively traversing all parameters, which corresponds to a deep copy. Calling equals on the cloned object always returns true although none of the memory of both objects overlaps.
在文件 SGObject.cpp 第 714 行定义.
Method that computes the measures using test statistic computed by an instance of CIndependenceTest wiht the provided features and the labels
features | the features on which the measure has to be computed |
idx | the index that decides which features should we compute the measure on |
实现了 CFeatureSelection< float64_t >.
在文件 DependenceMaximization.cpp 第 106 行定义.
Helper method which removes the dimension specified via the index. It copies the rest of the features into a separate object via copy_dimension_subset() call.
features | the features |
idx | index of the dimension which is required to be removed |
在文件 DependenceMaximization.cpp 第 78 行定义.
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virtualinherited |
A deep copy. All the instance variables will also be copied.
在文件 SGObject.cpp 第 198 行定义.
Recursively compares the current SGObject to another one. Compares all registered numerical parameters, recursion upon complex (SGObject) parameters. Does not compare pointers!
May be overwritten but please do with care! Should not be necessary in most cases.
other | object to compare with |
accuracy | accuracy to use for comparison (optional) |
tolerant | allows linient check on float equality (within accuracy) |
在文件 SGObject.cpp 第 618 行定义.
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实现了 CPreprocessor.
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实现了 CPreprocessor.
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在文件 KernelDependenceMaximization.cpp 第 131 行定义.
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在文件 KernelDependenceMaximization.cpp 第 137 行定义.
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在文件 SGObject.cpp 第 498 行定义.
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Returns description of a given parameter string, if it exists. SG_ERROR otherwise
param_name | name of the parameter |
在文件 SGObject.cpp 第 522 行定义.
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Returns index of model selection parameter with provided index
param_name | name of model selection parameter |
在文件 SGObject.cpp 第 535 行定义.
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Returns the number of features of the provided feature object. Since the number of features doesn't make sense for all types of features, this helper method checks whether obtaining a num_features is possible and then calls get_num_features() on those features after proper type-cast
features | the feature object |
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Initialize preprocessor from features
features | the features |
实现了 CPreprocessor.
在文件 DependenceMaximization.cpp 第 63 行定义.
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If the SGSerializable is a class template then TRUE will be returned and GENERIC is set to the type of the generic.
generic | set to the type of the generic if returning TRUE |
在文件 SGObject.cpp 第 296 行定义.
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virtualinherited |
Load this object from file. If it will fail (returning FALSE) then this object will contain inconsistent data and should not be used!
file | where to load from |
prefix | prefix for members |
在文件 SGObject.cpp 第 369 行定义.
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protectedvirtualinherited |
Can (optionally) be overridden to post-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::LOAD_SERIALIZABLE_POST is called.
ShogunException | will be thrown if an error occurs. |
被 CKernel, CWeightedDegreePositionStringKernel, CList, CAlphabet, CLinearHMM, CGaussianKernel, CInverseMultiQuadricKernel, CCircularKernel , 以及 CExponentialKernel 重载.
在文件 SGObject.cpp 第 426 行定义.
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protectedvirtualinherited |
Can (optionally) be overridden to pre-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::LOAD_SERIALIZABLE_PRE is called.
ShogunException | will be thrown if an error occurs. |
被 CDynamicArray< T >, CDynamicArray< float64_t >, CDynamicArray< float32_t >, CDynamicArray< int32_t >, CDynamicArray< char >, CDynamicArray< bool > , 以及 CDynamicObjectArray 重载.
在文件 SGObject.cpp 第 421 行定义.
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在文件 SGObject.cpp 第 262 行定义.
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protectedvirtualinherited |
Precomputes the kernel on labels and replaces the m_kernel_labels with an instance of CCustomKernel. Labels features are set via CDependenceMaximization::set_labels call.
重载 CFeatureSelection< float64_t > .
在文件 KernelDependenceMaximization.cpp 第 60 行定义.
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prints all parameter registered for model selection and their type
在文件 SGObject.cpp 第 474 行定义.
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Method which handles the removal of features based on removal policy. see documentation of CFeatureSelection. For dependence maximization approach, the highest scoring features are removed. Therefore, only m_policy can only be shogun::N_LARGEST, shogun::PERCENTILE_LARGEST. See set_policy() method for specifying the exact policy
features | the features object from which specific features has to be removed |
ranks | the ranks of the features based on their measures, 0 being the lowest rank which corresponds to smallest measure. |
实现了 CFeatureSelection< float64_t >.
在文件 DependenceMaximization.cpp 第 130 行定义.
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Save this object to file.
file | where to save the object; will be closed during returning if PREFIX is an empty string. |
prefix | prefix for members |
在文件 SGObject.cpp 第 314 行定义.
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protectedvirtualinherited |
Can (optionally) be overridden to post-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::SAVE_SERIALIZABLE_POST is called.
ShogunException | will be thrown if an error occurs. |
被 CKernel 重载.
在文件 SGObject.cpp 第 436 行定义.
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protectedvirtualinherited |
Can (optionally) be overridden to pre-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::SAVE_SERIALIZABLE_PRE is called.
ShogunException | will be thrown if an error occurs. |
被 CKernel, CDynamicArray< T >, CDynamicArray< float64_t >, CDynamicArray< float32_t >, CDynamicArray< int32_t >, CDynamicArray< char >, CDynamicArray< bool > , 以及 CDynamicObjectArray 重载.
在文件 SGObject.cpp 第 431 行定义.
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Since only shogun::BACKWARD_ELIMINATION algorithm is applicable for BAHSIC, and this is set internally, this method is overridden to prevent this to be set from public API.
algorithm | the feature selection algorithm to use |
实现了 CKernelDependenceMaximization.
在文件 BAHSIC.cpp 第 53 行定义.
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在文件 SGObject.cpp 第 41 行定义.
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在文件 SGObject.cpp 第 46 行定义.
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在文件 SGObject.cpp 第 51 行定义.
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在文件 SGObject.cpp 第 56 行定义.
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在文件 SGObject.cpp 第 61 行定义.
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在文件 SGObject.cpp 第 66 行定义.
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在文件 SGObject.cpp 第 71 行定义.
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在文件 SGObject.cpp 第 76 行定义.
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在文件 SGObject.cpp 第 81 行定义.
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在文件 SGObject.cpp 第 86 行定义.
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在文件 SGObject.cpp 第 91 行定义.
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在文件 SGObject.cpp 第 96 行定义.
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在文件 SGObject.cpp 第 101 行定义.
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在文件 SGObject.cpp 第 106 行定义.
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在文件 SGObject.cpp 第 111 行定义.
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set generic type to T
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kernel | the kernel for features (data) |
在文件 KernelDependenceMaximization.cpp 第 99 行定义.
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kernel | the kernel for labels |
在文件 KernelDependenceMaximization.cpp 第 115 行定义.
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Setter for labels. This method is overridden to internally convert the labels to a dense feature object and set this feature in the independence test estimator. These labels serve as samples \(\mathbf{Y}\sim q\) in the independence test
labels | the labels |
重载 CFeatureSelection< float64_t > .
在文件 DependenceMaximization.cpp 第 187 行定义.
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Use this method to set the number or percentile of features to be removed in each iteration.
num_remove | number or percentage of features to be removed in each iteration |
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policy | feature removal policy |
实现了 CFeatureSelection< float64_t >.
在文件 DependenceMaximization.cpp 第 179 行定义.
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target_dim | the target dimension to achieve |
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A shallow copy. All the SGObject instance variables will be simply assigned and SG_REF-ed.
被 CGaussianKernel 重载.
在文件 SGObject.cpp 第 192 行定义.
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unset generic type
this has to be called in classes specializing a template class
在文件 SGObject.cpp 第 303 行定义.
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Updates the hash of current parameter combination
在文件 SGObject.cpp 第 248 行定义.
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io
在文件 SGObject.h 第 369 行定义.
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Wrapper algorithm for feature selection
在文件 FeatureSelection.h 第 302 行定义.
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The estimator for performing statistical tests for independence which is used for computing measures
在文件 DependenceMaximization.h 第 157 行定义.
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parameters wrt which we can compute gradients
在文件 SGObject.h 第 384 行定义.
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Hash of parameter values
在文件 SGObject.h 第 387 行定义.
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The kernel for data (features) to be used in CKernelIndependenceTest
在文件 KernelDependenceMaximization.h 第 93 行定义.
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The kernel for labels to be used in CKernelIndependenceTest
在文件 KernelDependenceMaximization.h 第 96 行定义.
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The labels for the feature vectors
在文件 FeatureSelection.h 第 316 行定义.
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The feature for the labels
在文件 DependenceMaximization.h 第 160 行定义.
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model selection parameters
在文件 SGObject.h 第 381 行定义.
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Number or percentage of features to be removed. When the policy is set as shogun::N_SMALLEST or shogun::N_LARGEST, this number decides how many features in an iteration. For shogun::PERCENTILE_SMALLEST or shogun::PERCENTILE_LARGEST, this decides the percentage of current number of features to be removed in each iteration
在文件 FeatureSelection.h 第 313 行定义.
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parameters
在文件 SGObject.h 第 378 行定义.
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Feature removal policy
在文件 FeatureSelection.h 第 305 行定义.
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The indices of features that are selected
在文件 FeatureSelection.h 第 319 行定义.
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Target dimension
在文件 FeatureSelection.h 第 299 行定义.
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parallel
在文件 SGObject.h 第 372 行定义.
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version
在文件 SGObject.h 第 375 行定义.