rsatoolbox.inference.evaluate module¶
evaluate model performance
- rsatoolbox.inference.evaluate.bootstrap_crossval(models, data, method='cosine', fitter=None, k_pattern=None, k_rdm=None, N=1000, n_cv=2, pattern_descriptor='index', rdm_descriptor='index', random=True, boot_type='both', use_correction=True)[source]¶
evaluates a set of models by k-fold crossvalidation within a bootstrap
Crossvalidation creates variance in the results for a single bootstrap sample, because different assginments to the training and test group lead to different results. To correct for this, we apply a formula which estimates the variance we expect if we evaluated all possible crossvalidation assignments from n_cv different assignments per bootstrap sample. In our statistical evaluations we saw that many bootstrap samples and few different crossvalidation assignments are optimal to minimize the variance of the variance estimate. Thus, this function by default applies this correction formula and sets n_cv=2, i.e. performs only two different assignments per fold. This function nonetheless performs full crossvalidation schemes, i.e. in every bootstrap sample all crossvalidation folds are evaluated such that each RDM and each condition is in the test set n_cv times. For the even more optimized version which computes only two randomly chosen test sets see bootstrap_cv_random.
The k_[] parameters control the cross-validation per sample. They give the number of crossvalidation folds to be created along this dimension. If a k is set to 1 no crossvalidation is performed over the corresponding dimension. by default ks are set by rsatoolbox.util.inference_util.default_k_pattern and rsatoolbox.util.inference_util.default_k_rdm based on the number of rdms and patterns provided. the ks are then in the range 2-5.
Using the []_descriptor inputs you may make the crossvalidation and bootstrap aware of groups of rdms or conditions to be handled en block. Conditions with the same entry will be sampled in or out of the bootstrap together and will be assigned to cross-calidation folds together.
Using the boot_type argument you may choose the dimension to bootstrap. By default both conditions and RDMs are resampled. You may alternatively choose to resample only one of them by passing ‘rdm’ or ‘pattern’.
models should be a list of models. data the RDMs object to evaluate against method the method for comparing the predictions and the data. fitter may provide a non-default funcion or list of functions to fit the models.
- Parameters
models (rsatoolbox.model.Model) – models to be evaluated
data (rsatoolbox.rdm.RDMs) – RDM data to use
method (string) – comparison method to use
fitter (function) – fitting method for models
k_pattern (int) – #folds over patterns
k_rdm (int) – #folds over rdms
N (int) – number of bootstrap samples (default: 1000)
n_cv (int) – number of crossvalidation runs per sample (default: 1)
pattern_descriptor (string) – descriptor to group patterns
rdm_descriptor (string) – descriptor to group rdms
random (bool) – randomize group assignments (default: True)
boot_type (String) – which dimension to bootstrap over (default: ‘both’) alternatives: ‘rdm’, ‘pattern’
use_correction (bool) – switch for the correction for the variance caused by crossvalidation (default: True)
- Returns
matrix of evaluations (N x k)
- Return type
numpy.ndarray
- rsatoolbox.inference.evaluate.crossval(models, rdms, train_set, test_set, ceil_set=None, method='cosine', fitter=None, pattern_descriptor='index', calc_noise_ceil=True)[source]¶
evaluates models on cross-validation sets
- Parameters
models (rsatoolbox.model.Model) – models to be evaluated
rdms (rsatoolbox.rdm.RDMs) – full dataset
train_set (list) – a list of the training RDMs with 2-tuple entries: (RDMs, pattern_idx)
test_set (list) – a list of the test RDMs with 2-tuple entries: (RDMs, pattern_idx)
method (string) – comparison method to use
pattern_descriptor (string) – descriptor to group patterns
- Returns
vector of evaluations
- Return type
numpy.ndarray
- rsatoolbox.inference.evaluate.eval_bootstrap(models, data, theta=None, method='cosine', N=1000, pattern_descriptor='index', rdm_descriptor='index', boot_noise_ceil=True)[source]¶
evaluates models on data performs bootstrapping to get a sampling distribution
- Parameters
models (rsatoolbox.model.Model or list) – models to be evaluated
data (rsatoolbox.rdm.RDMs) – data to evaluate on
theta (numpy.ndarray) – parameter vector for the models
method (string) – comparison method to use
N (int) – number of samples
pattern_descriptor (string) – descriptor to group patterns for bootstrap
rdm_descriptor (string) – descriptor to group rdms for bootstrap
- Returns
vector of evaluations
- Return type
numpy.ndarray
- rsatoolbox.inference.evaluate.eval_bootstrap_pattern(models, data, theta=None, method='cosine', N=1000, pattern_descriptor='index', rdm_descriptor='index', boot_noise_ceil=True)[source]¶
evaluates a models on data performs bootstrapping over patterns to get a sampling distribution
- Parameters
models (rsatoolbox.model.Model or list) – models to be evaluated
data (rsatoolbox.rdm.RDMs) – data to evaluate on
theta (numpy.ndarray) – parameter vector for the models
method (string) – comparison method to use
N (int) – number of samples
pattern_descriptor (string) – descriptor to group patterns for bootstrap
rdm_descriptor (string) – descriptor to group patterns for noise ceiling calculation
- Returns
vector of evaluations
- Return type
numpy.ndarray
- rsatoolbox.inference.evaluate.eval_bootstrap_rdm(models, data, theta=None, method='cosine', N=1000, rdm_descriptor='index', boot_noise_ceil=True)[source]¶
evaluates models on data performs bootstrapping to get a sampling distribution
- Parameters
models (rsatoolbox.model.Model or list of these) – models to be evaluated
data (rsatoolbox.rdm.RDMs) – data to evaluate on
theta (numpy.ndarray) – parameter vector for the models
method (string) – comparison method to use
N (int) – number of samples
rdm_descriptor (string) – rdm_descriptor to group rdms for bootstrap
- Returns
vector of evaluations
- Return type
numpy.ndarray
- rsatoolbox.inference.evaluate.eval_dual_bootstrap(models, data, method='cosine', fitter=None, k_pattern=1, k_rdm=1, N=1000, n_cv=2, pattern_descriptor='index', rdm_descriptor='index', use_correction=True)[source]¶
dual bootstrap evaluation of models i.e. models are evaluated in a bootstrap over rdms, one over patterns and a bootstrap over both using the same bootstrap samples for each. The variance estimates from these bootstraps are then combined into a better overall estimate for the variance.
This method allows the incorporation of crossvalidation inside the bootstrap to handle fitted models. To activate this set k_rdm and k_pattern as described below.
Crossvalidation creates variance in the results for a single bootstrap sample, because different assginments to the training and test group lead to different results. To correct for this, we apply a formula which estimates the variance we expect if we evaluated all possible crossvalidation assignments from n_cv different assignments per bootstrap sample. In our statistical evaluations we saw that many bootstrap samples and few different crossvalidation assignments are optimal to minimize the variance of the variance estimate. Thus, this function by default applies this correction formula and sets n_cv=2, i.e. performs only two different assignments per fold. This function nonetheless performs full crossvalidation schemes, i.e. in every bootstrap sample all crossvalidation folds are evaluated such that each RDM and each condition is in the test set n_cv times.
The k_[] parameters control the cross-validation per sample. They give the number of crossvalidation folds to be created along this dimension. If a k is set to 1 no crossvalidation is performed over the corresponding dimension. by default ks are set by rsatoolbox.util.inference_util.default_k_pattern and rsatoolbox.util.inference_util.default_k_rdm based on the number of rdms and patterns provided. the ks are then in the range 2-5.
Using the []_descriptor inputs you may make the crossvalidation and bootstrap aware of groups of rdms or conditions to be handled en block. Conditions with the same entry will be sampled in or out of the bootstrap together and will be assigned to cross-calidation folds together.
models should be a list of models. data the RDMs object to evaluate against method the method for comparing the predictions and the data. fitter may provide a non-default funcion or list of functions to fit the models.
- Parameters
models (rsatoolbox.model.Model) – models to be evaluated
data (rsatoolbox.rdm.RDMs) – RDM data to use
method (string) – comparison method to use
fitter (function) – fitting method for models
k_pattern (int) – #folds over patterns
k_rdm (int) – #folds over rdms
N (int) – number of bootstrap samples (default: 1000)
n_cv (int) – number of crossvalidation runs per sample (default: 1)
pattern_descriptor (string) – descriptor to group patterns
rdm_descriptor (string) – descriptor to group rdms
random (bool) – randomize group assignments (default: True)
boot_type (String) – which dimension to bootstrap over (default: ‘both’) alternatives: ‘rdm’, ‘pattern’
use_correction (bool) – switch for the correction for the variance caused by crossvalidation (default: True)
- Returns
matrix of evaluations (N x k)
- Return type
numpy.ndarray
- rsatoolbox.inference.evaluate.eval_dual_bootstrap_random(models, data, method='cosine', fitter=None, n_pattern=None, n_rdm=None, N=1000, n_cv=2, pattern_descriptor='index', rdm_descriptor='index', random=True, boot_type='both', use_correction=True)[source]¶
evaluates a set of models by a evaluating a few random crossvalidation folds per bootstrap.
If a k is set to 1 no crossvalidation is performed over the corresponding dimension.
As especially crossvalidation over patterns/conditions creates variance in the cv result for a single variance the default setting of n_cv=1 inflates the estimated variance. Setting this value higher will decrease this effect at the cost of more computation time.
by default ks are set by rsatoolbox.util.inference_util.default_k_pattern and rsatoolbox.util.inference_util.default_k_rdm based on the number of rdms and patterns provided. the ks are then in the range 2-5.
- Parameters
models (rsatoolbox.model.Model) – models to be evaluated
data (rsatoolbox.rdm.RDMs) – RDM data to use
method (string) – comparison method to use
fitter (function) – fitting method for models
k_pattern (int) – #folds over patterns
k_rdm (int) – #folds over rdms
N (int) – number of bootstrap samples (default: 1000)
n_cv (int) – number of crossvalidation runs per sample (default: 1)
pattern_descriptor (string) – descriptor to group patterns
rdm_descriptor (string) – descriptor to group rdms
random (bool) – randomize group assignments (default: True)
boot_type (String) – which dimension to bootstrap over (default: ‘both’) alternatives: ‘rdm’, ‘pattern’
use_correction (bool) – switch for the correction for the variance caused by crossvalidation (default: True)
- Returns
matrix of evaluations (N x k)
- Return type
numpy.ndarray
- rsatoolbox.inference.evaluate.eval_fixed(models, data, theta=None, method='cosine')[source]¶
evaluates models on data, without any bootstrapping or cross-validation
- Parameters
models (list of rsatoolbox.model.Model or list) – models to be evaluated
data (rsatoolbox.rdm.RDMs) – data to evaluate on
theta (numpy.ndarray) – parameter vector for the models
method (string) – comparison method to use
- Returns
evaluation
- Return type
float