pyhealth.models.califorest#

Author: Kobe Guo NetID: kobeg2

Paper: CaliForest: Calibrated Random Forests for Healthcare Prediction Link: https://joyceho.github.io/assets/pdf/paper/park-chil20.pdf

Description: Implementation of CaliForest, a calibrated random forest model that applies post-hoc calibration (isotonic or logistic) to improve probability estimates for healthcare prediction tasks.

class pyhealth.models.califorest.RandomForestClassifier(n_estimators=100, *, criterion='gini', max_depth=None, min_samples_split=2, min_samples_leaf=1, min_weight_fraction_leaf=0.0, max_features='sqrt', max_leaf_nodes=None, min_impurity_decrease=0.0, bootstrap=True, oob_score=False, n_jobs=None, random_state=None, verbose=0, warm_start=False, class_weight=None, ccp_alpha=0.0, max_samples=None, monotonic_cst=None)[source]#

Bases: ForestClassifier

A random forest classifier.

A random forest is a meta estimator that fits a number of decision tree classifiers on various sub-samples of the dataset and uses averaging to improve the predictive accuracy and control over-fitting. Trees in the forest use the best split strategy, i.e. equivalent to passing splitter=”best” to the underlying DecisionTreeClassifier. The sub-sample size is controlled with the max_samples parameter if bootstrap=True (default), otherwise the whole dataset is used to build each tree.

For a comparison between tree-based ensemble models see the example sphx_glr_auto_examples_ensemble_plot_forest_hist_grad_boosting_comparison.py.

This estimator has native support for missing values (NaNs). During training, the tree grower learns at each split point whether samples with missing values should go to the left or right child, based on the potential gain. When predicting, samples with missing values are assigned to the left or right child consequently. If no missing values were encountered for a given feature during training, then samples with missing values are mapped to whichever child has the most samples.

See also

sklearn.tree.DecisionTreeClassifier: A decision tree classifier.
sklearn.ensemble.ExtraTreesClassifier: Ensemble of extremely randomized tree classifiers.
sklearn.ensemble.HistGradientBoostingClassifier: A Histogram-based Gradient Boosting Classification Tree, very fast for big datasets (n_samples >= 10_000).

Notes

The default values for the parameters controlling the size of the trees (e.g. max_depth, min_samples_leaf, etc.) lead to fully grown and unpruned trees which can potentially be very large on some data sets. To reduce memory consumption, the complexity and size of the trees should be controlled by setting those parameter values.

The features are always randomly permuted at each split. Therefore, the best found split may vary, even with the same training data, max_features=n_features and bootstrap=False, if the improvement of the criterion is identical for several splits enumerated during the search of the best split. To obtain a deterministic behaviour during fitting, random_state has to be fixed.

References

Examples

>>> from sklearn.ensemble import RandomForestClassifier
>>> from sklearn.datasets import make_classification
>>> X, y = make_classification(n_samples=1000, n_features=4,
...                            n_informative=2, n_redundant=0,
...                            random_state=0, shuffle=False)
>>> clf = RandomForestClassifier(max_depth=2, random_state=0)
>>> clf.fit(X, y)
RandomForestClassifier(...)
>>> print(clf.predict([[0, 0, 0, 0]]))
[1]

apply(X)#

Apply trees in the forest to X, return leaf indices.

Parameters:: X ({array-like, sparse matrix} of shape (n_samples, n_features)) – The input samples. Internally, its dtype will be converted to dtype=np.float32. If a sparse matrix is provided, it will be converted into a sparse csr_matrix.
Returns:: X_leaves – For each datapoint x in X and for each tree in the forest, return the index of the leaf x ends up in.
Return type:: ndarray of shape (n_samples, n_estimators)

decision_path(X)#

Return the decision path in the forest.

New in version 0.18.

Parameters:

X ({array-like, sparse matrix} of shape (n_samples, n_features)) – The input samples. Internally, its dtype will be converted to dtype=np.float32. If a sparse matrix is provided, it will be converted into a sparse csr_matrix.

Returns:

indicator (sparse matrix of shape (n_samples, n_nodes)) – Return a node indicator matrix where non zero elements indicates that the samples goes through the nodes. The matrix is of CSR format.
n_nodes_ptr (ndarray of shape (n_estimators + 1,)) – The columns from indicator[n_nodes_ptr[i]:n_nodes_ptr[i+1]] gives the indicator value for the i-th estimator.

property estimators_samples_#

The subset of drawn samples for each base estimator.

Returns a dynamically generated list of indices identifying the samples used for fitting each member of the ensemble, i.e., the in-bag samples.

Note: the list is re-created at each call to the property in order to reduce the object memory footprint by not storing the sampling data. Thus fetching the property may be slower than expected.

property feature_importances_#

The impurity-based feature importances.

The higher, the more important the feature. The importance of a feature is computed as the (normalized) total reduction of the criterion brought by that feature. It is also known as the Gini importance.

Warning: impurity-based feature importances can be misleading for high cardinality features (many unique values). See sklearn.inspection.permutation_importance() as an alternative.

Returns:: feature_importances_ – The values of this array sum to 1, unless all trees are single node trees consisting of only the root node, in which case it will be an array of zeros.
Return type:: ndarray of shape (n_features,)

fit(X, y, sample_weight=None)#

Build a forest of trees from the training set (X, y).

Parameters:

X ({array-like, sparse matrix} of shape (n_samples, n_features)) – The training input samples. Internally, its dtype will be converted to dtype=np.float32. If a sparse matrix is provided, it will be converted into a sparse csc_matrix.
y (array-like of shape (n_samples,) or (n_samples, n_outputs)) – The target values (class labels in classification, real numbers in regression).
sample_weight (array-like of shape (n_samples,), default=None) – Sample weights. If None, then samples are equally weighted. Splits that would create child nodes with net zero or negative weight are ignored while searching for a split in each node. In the case of classification, splits are also ignored if they would result in any single class carrying a negative weight in either child node.

Returns:

self – Fitted estimator.

Return type:

object

get_metadata_routing()#

Get metadata routing of this object.

Please check User Guide on how the routing mechanism works.

Returns:: routing – A MetadataRequest encapsulating routing information.
Return type:: MetadataRequest

get_params(deep=True)#

Get parameters for this estimator.

Parameters:: deep (bool, default=True) – If True, will return the parameters for this estimator and contained subobjects that are estimators.
Returns:: params – Parameter names mapped to their values.
Return type:: dict

predict(X)#

Predict class for X.

The predicted class of an input sample is a vote by the trees in the forest, weighted by their probability estimates. That is, the predicted class is the one with highest mean probability estimate across the trees.

Parameters:: X ({array-like, sparse matrix} of shape (n_samples, n_features)) – The input samples. Internally, its dtype will be converted to dtype=np.float32. If a sparse matrix is provided, it will be converted into a sparse csr_matrix.
Returns:: y – The predicted classes.
Return type:: ndarray of shape (n_samples,) or (n_samples, n_outputs)

predict_log_proba(X)#

Predict class log-probabilities for X.

The predicted class log-probabilities of an input sample is computed as the log of the mean predicted class probabilities of the trees in the forest.

Parameters:: X ({array-like, sparse matrix} of shape (n_samples, n_features)) – The input samples. Internally, its dtype will be converted to dtype=np.float32. If a sparse matrix is provided, it will be converted into a sparse csr_matrix.
Returns:: p – The class probabilities of the input samples. The order of the classes corresponds to that in the attribute classes_.
Return type:: ndarray of shape (n_samples, n_classes), or a list of such arrays

predict_proba(X)#

Predict class probabilities for X.

The predicted class probabilities of an input sample are computed as the mean predicted class probabilities of the trees in the forest. The class probability of a single tree is the fraction of samples of the same class in a leaf.

Parameters:: X ({array-like, sparse matrix} of shape (n_samples, n_features)) – The input samples. Internally, its dtype will be converted to dtype=np.float32. If a sparse matrix is provided, it will be converted into a sparse csr_matrix.
Returns:: p – The class probabilities of the input samples. The order of the classes corresponds to that in the attribute classes_.
Return type:: ndarray of shape (n_samples, n_classes), or a list of such arrays

score(X, y, sample_weight=None)#

Return accuracy on provided data and labels.

In multi-label classification, this is the subset accuracy which is a harsh metric since you require for each sample that each label set be correctly predicted.

Parameters:

X (array-like of shape (n_samples, n_features)) – Test samples.
y (array-like of shape (n_samples,) or (n_samples, n_outputs)) – True labels for X.
sample_weight (array-like of shape (n_samples,), default=None) – Sample weights.

Returns:

score – Mean accuracy of self.predict(X) w.r.t. y.

Return type:

float

set_fit_request(*, sample_weight: Union[bool, None, str] = '$UNCHANGED$') → RandomForestClassifier#

Configure whether metadata should be requested to be passed to the fit method.

Note that this method is only relevant when this estimator is used as a sub-estimator within a meta-estimator and metadata routing is enabled with enable_metadata_routing=True (see sklearn.set_config()). Please check the User Guide on how the routing mechanism works.

The options for each parameter are:

True: metadata is requested, and passed to fit if provided. The request is ignored if metadata is not provided.
False: metadata is not requested and the meta-estimator will not pass it to fit.
None: metadata is not requested, and the meta-estimator will raise an error if the user provides it.
str: metadata should be passed to the meta-estimator with this given alias instead of the original name.

The default (sklearn.utils.metadata_routing.UNCHANGED) retains the existing request. This allows you to change the request for some parameters and not others.

New in version 1.3.

Parameters:: sample_weight (str, True, False, or None, default=sklearn.utils.metadata_routing.UNCHANGED) – Metadata routing for sample_weight parameter in fit.
Returns:: self – The updated object.
Return type:: object

set_params(**params)#

Set the parameters of this estimator.

The method works on simple estimators as well as on nested objects (such as Pipeline). The latter have parameters of the form <component>__<parameter> so that it’s possible to update each component of a nested object.

Parameters:: **params (dict) – Estimator parameters.
Returns:: self – Estimator instance.
Return type:: estimator instance

set_score_request(*, sample_weight: Union[bool, None, str] = '$UNCHANGED$') → RandomForestClassifier#

Configure whether metadata should be requested to be passed to the score method.

The options for each parameter are:

True: metadata is requested, and passed to score if provided. The request is ignored if metadata is not provided.
False: metadata is not requested and the meta-estimator will not pass it to score.
None: metadata is not requested, and the meta-estimator will raise an error if the user provides it.
str: metadata should be passed to the meta-estimator with this given alias instead of the original name.

The default (sklearn.utils.metadata_routing.UNCHANGED) retains the existing request. This allows you to change the request for some parameters and not others.

New in version 1.3.

Parameters:: sample_weight (str, True, False, or None, default=sklearn.utils.metadata_routing.UNCHANGED) – Metadata routing for sample_weight parameter in score.
Returns:: self – The updated object.
Return type:: object

class pyhealth.models.califorest.IsotonicRegression(*, y_min=None, y_max=None, increasing=True, out_of_bounds='nan')[source]#

Bases: RegressorMixin, TransformerMixin, BaseEstimator

Isotonic regression model.

See also

sklearn.linear_model.LinearRegression: Ordinary least squares Linear Regression.
sklearn.ensemble.HistGradientBoostingRegressor: Gradient boosting that is a non-parametric model accepting monotonicity constraints.
isotonic_regression: Function to solve the isotonic regression model.

Notes

Ties are broken using the secondary method from de Leeuw, 1977.

References

Isotonic Median Regression: A Linear Programming Approach Nilotpal Chakravarti Mathematics of Operations Research Vol. 14, No. 2 (May, 1989), pp. 303-308

Isotone Optimization in R : Pool-Adjacent-Violators Algorithm (PAVA) and Active Set Methods de Leeuw, Hornik, Mair Journal of Statistical Software 2009

Correctness of Kruskal’s algorithms for monotone regression with ties de Leeuw, Psychometrica, 1977

Examples

>>> from sklearn.datasets import make_regression
>>> from sklearn.isotonic import IsotonicRegression
>>> X, y = make_regression(n_samples=10, n_features=1, random_state=41)
>>> iso_reg = IsotonicRegression().fit(X, y)
>>> iso_reg.predict([.1, .2])
array([1.8628, 3.7256])

fit(X, y, sample_weight=None)[source]#

Fit the model using X, y as training data.

Parameters:

X (array-like of shape (n_samples,) or (n_samples, 1)) –
Training data.

Changed in version 0.24: Also accepts 2d array with 1 feature.
y (array-like of shape (n_samples,)) – Training target.
sample_weight (array-like of shape (n_samples,), default=None) – Weights. If set to None, all weights will be set to 1 (equal weights).

Returns:

self – Returns an instance of self.

Return type:

object

Notes

X is stored for future use, as transform() needs X to interpolate new input data.

transform(T)[source]#

Transform new data by linear interpolation.

Parameters:

T (array-like of shape (n_samples,) or (n_samples, 1)) –

Data to transform.

Changed in version 0.24: Also accepts 2d array with 1 feature.

Returns:

y_pred – The transformed data.

Return type:

ndarray of shape (n_samples,)

predict(T)[source]#

Predict new data by linear interpolation.

Parameters:: T (array-like of shape (n_samples,) or (n_samples, 1)) – Data to transform.
Returns:: y_pred – Transformed data.
Return type:: ndarray of shape (n_samples,)

get_feature_names_out(input_features=None)[source]#

Get output feature names for transformation.

Parameters:: input_features (array-like of str or None, default=None) – Ignored.
Returns:: feature_names_out – An ndarray with one string i.e. [“isotonicregression0”].
Return type:: ndarray of str objects

fit_transform(X, y=None, **fit_params)#

Fit to data, then transform it.

Fits transformer to X and y with optional parameters fit_params and returns a transformed version of X.

Parameters:

X (array-like of shape (n_samples, n_features)) – Input samples.
y (array-like of shape (n_samples,) or (n_samples, n_outputs), default=None) – Target values (None for unsupervised transformations).
**fit_params (dict) – Additional fit parameters.

Returns:

X_new – Transformed array.

Return type:

ndarray array of shape (n_samples, n_features_new)

get_metadata_routing()#

Get metadata routing of this object.

Please check User Guide on how the routing mechanism works.

Returns:: routing – A MetadataRequest encapsulating routing information.
Return type:: MetadataRequest

get_params(deep=True)#

Get parameters for this estimator.

Parameters:: deep (bool, default=True) – If True, will return the parameters for this estimator and contained subobjects that are estimators.
Returns:: params – Parameter names mapped to their values.
Return type:: dict

score(X, y, sample_weight=None)#

Return coefficient of determination on test data.

The coefficient of determination, $R^2$, is defined as $(1 - \frac{u}{v})$, where $u$ is the residual sum of squares ((y_true - y_pred)** 2).sum() and $v$ is the total sum of squares ((y_true - y_true.mean()) ** 2).sum(). The best possible score is 1.0 and it can be negative (because the model can be arbitrarily worse). A constant model that always predicts the expected value of y, disregarding the input features, would get a $R^2$ score of 0.0.

Parameters:

X (array-like of shape (n_samples, n_features)) – Test samples. For some estimators this may be a precomputed kernel matrix or a list of generic objects instead with shape (n_samples, n_samples_fitted), where n_samples_fitted is the number of samples used in the fitting for the estimator.
y (array-like of shape (n_samples,) or (n_samples, n_outputs)) – True values for X.
sample_weight (array-like of shape (n_samples,), default=None) – Sample weights.

Returns:

score – $R^2$ of self.predict(X) w.r.t. y.

Return type:

float

Notes

The $R^2$ score used when calling score on a regressor uses multioutput='uniform_average' from version 0.23 to keep consistent with default value of r2_score(). This influences the score method of all the multioutput regressors (except for MultiOutputRegressor).

set_fit_request(*, sample_weight: Union[bool, None, str] = '$UNCHANGED$') → IsotonicRegression#

Configure whether metadata should be requested to be passed to the fit method.

The options for each parameter are:

True: metadata is requested, and passed to fit if provided. The request is ignored if metadata is not provided.
False: metadata is not requested and the meta-estimator will not pass it to fit.
None: metadata is not requested, and the meta-estimator will raise an error if the user provides it.
str: metadata should be passed to the meta-estimator with this given alias instead of the original name.

The default (sklearn.utils.metadata_routing.UNCHANGED) retains the existing request. This allows you to change the request for some parameters and not others.

New in version 1.3.

Parameters:: sample_weight (str, True, False, or None, default=sklearn.utils.metadata_routing.UNCHANGED) – Metadata routing for sample_weight parameter in fit.
Returns:: self – The updated object.
Return type:: object

set_output(*, transform=None)#

Set output container.

See sphx_glr_auto_examples_miscellaneous_plot_set_output.py for an example on how to use the API.

Parameters:

transform ({"default", "pandas", "polars"}, default=None) –

Configure output of transform and fit_transform.

”default”: Default output format of a transformer
”pandas”: DataFrame output
”polars”: Polars output
None: Transform configuration is unchanged

New in version 1.4: “polars” option was added.

Returns:

self – Estimator instance.

Return type:

estimator instance

set_params(**params)#

Set the parameters of this estimator.

Parameters:: **params (dict) – Estimator parameters.
Returns:: self – Estimator instance.
Return type:: estimator instance

set_score_request(*, sample_weight: Union[bool, None, str] = '$UNCHANGED$') → IsotonicRegression#

Configure whether metadata should be requested to be passed to the score method.

The options for each parameter are:

True: metadata is requested, and passed to score if provided. The request is ignored if metadata is not provided.
False: metadata is not requested and the meta-estimator will not pass it to score.
None: metadata is not requested, and the meta-estimator will raise an error if the user provides it.
str: metadata should be passed to the meta-estimator with this given alias instead of the original name.

The default (sklearn.utils.metadata_routing.UNCHANGED) retains the existing request. This allows you to change the request for some parameters and not others.

New in version 1.3.

Parameters:: sample_weight (str, True, False, or None, default=sklearn.utils.metadata_routing.UNCHANGED) – Metadata routing for sample_weight parameter in score.
Returns:: self – The updated object.
Return type:: object

class pyhealth.models.califorest.LogisticRegression(penalty='l2', *, dual=False, tol=0.0001, C=1.0, fit_intercept=True, intercept_scaling=1, class_weight=None, random_state=None, solver='lbfgs', max_iter=100, multi_class='deprecated', verbose=0, warm_start=False, n_jobs=None, l1_ratio=None)[source]#

Bases: LinearClassifierMixin, SparseCoefMixin, BaseEstimator

Logistic Regression (aka logit, MaxEnt) classifier.

This class implements regularized logistic regression using the ‘liblinear’ library, ‘newton-cg’, ‘sag’, ‘saga’ and ‘lbfgs’ solvers. Note that regularization is applied by default. It can handle both dense and sparse input. Use C-ordered arrays or CSR matrices containing 64-bit floats for optimal performance; any other input format will be converted (and copied).

The ‘newton-cg’, ‘sag’, and ‘lbfgs’ solvers support only L2 regularization with primal formulation, or no regularization. The ‘liblinear’ solver supports both L1 and L2 regularization, with a dual formulation only for the L2 penalty. The Elastic-Net regularization is only supported by the ‘saga’ solver.

For multiclass problems, all solvers but ‘liblinear’ optimize the (penalized) multinomial loss. ‘liblinear’ only handle binary classification but can be extended to handle multiclass by using OneVsRestClassifier.

solver	penalty	multinomial multiclass
’lbfgs’	’l2’, None	yes
’liblinear’	’l1’, ‘l2’	no
’newton-cg’	’l2’, None	yes
’newton-cholesky’	’l2’, None	yes
’sag’	’l2’, None	yes
’saga’	’elasticnet’, ‘l1’, ‘l2’, None	yes

See also

Refer to the User Guide for more information regarding LogisticRegression and more specifically the Table summarizing solver/penalty supports.

New in version 0.17: Stochastic Average Gradient (SAG) descent solver. Multinomial support in version 0.18.

New in version 0.19: SAGA solver.

Changed in version 0.22: The default solver changed from ‘liblinear’ to ‘lbfgs’ in 0.22.

New in version 1.2: newton-cholesky solver. Multinomial support in version 1.6.

max_iter (int, default=100) – Maximum number of iterations taken for the solvers to converge.
multi_class ({'auto', 'ovr', 'multinomial'}, default='auto') –
If the option chosen is ‘ovr’, then a binary problem is fit for each label. For ‘multinomial’ the loss minimised is the multinomial loss fit across the entire probability distribution, even when the data is binary. ‘multinomial’ is unavailable when solver=’liblinear’. ‘auto’ selects ‘ovr’ if the data is binary, or if solver=’liblinear’, and otherwise selects ‘multinomial’.

New in version 0.18: Stochastic Average Gradient descent solver for ‘multinomial’ case.

Changed in version 0.22: Default changed from ‘ovr’ to ‘auto’ in 0.22.

Deprecated since version 1.5: multi_class was deprecated in version 1.5 and will be removed in 1.8. From then on, the recommended ‘multinomial’ will always be used for n_classes >= 3. Solvers that do not support ‘multinomial’ will raise an error. Use sklearn.multiclass.OneVsRestClassifier(LogisticRegression()) if you still want to use OvR.
verbose (int, default=0) – For the liblinear and lbfgs solvers set verbose to any positive number for verbosity.
warm_start (bool, default=False) –
When set to True, reuse the solution of the previous call to fit as initialization, otherwise, just erase the previous solution. Useless for liblinear solver. See the Glossary.

New in version 0.17: warm_start to support lbfgs, newton-cg, sag, saga solvers.
n_jobs (int, default=None) – Number of CPU cores used when parallelizing over classes if multi_class=’ovr’”. This parameter is ignored when the solver is set to ‘liblinear’ regardless of whether ‘multi_class’ is specified or not. None means 1 unless in a joblib.parallel_backend context. -1 means using all processors. See Glossary for more details.
l1_ratio (float, default=None) – The Elastic-Net mixing parameter, with 0 <= l1_ratio <= 1. Only used if penalty='elasticnet'. Setting l1_ratio=0 is equivalent to using penalty='l2', while setting l1_ratio=1 is equivalent to using penalty='l1'. For 0 < l1_ratio <1, the penalty is a combination of L1 and L2.

classes_#

A list of class labels known to the classifier.

Type:: ndarray of shape (n_classes, )

coef_#

Coefficient of the features in the decision function.

coef_ is of shape (1, n_features) when the given problem is binary. In particular, when multi_class=’multinomial’, coef_ corresponds to outcome 1 (True) and -coef_ corresponds to outcome 0 (False).

Type:: ndarray of shape (1, n_features) or (n_classes, n_features)

intercept_#

Intercept (a.k.a. bias) added to the decision function.

If fit_intercept is set to False, the intercept is set to zero. intercept_ is of shape (1,) when the given problem is binary. In particular, when multi_class=’multinomial’, intercept_ corresponds to outcome 1 (True) and -intercept_ corresponds to outcome 0 (False).

Type:: ndarray of shape (1,) or (n_classes,)

n_features_in_#

Number of features seen during fit.

New in version 0.24.

Type:: int

feature_names_in_#

Names of features seen during fit. Defined only when X has feature names that are all strings.

New in version 1.0.

Type:: ndarray of shape (n_features_in_,)

n_iter_#

Actual number of iterations for all classes. If binary or multinomial, it returns only 1 element. For liblinear solver, only the maximum number of iteration across all classes is given.

Changed in version 0.20: In SciPy <= 1.0.0 the number of lbfgs iterations may exceed max_iter. n_iter_ will now report at most max_iter.

Type:: ndarray of shape (n_classes,) or (1, )

See also

SGDClassifier: Incrementally trained logistic regression (when given the parameter loss="log_loss").
LogisticRegressionCV: Logistic regression with built-in cross validation.

Notes

The underlying C implementation uses a random number generator to select features when fitting the model. It is thus not uncommon, to have slightly different results for the same input data. If that happens, try with a smaller tol parameter.

Predict output may not match that of standalone liblinear in certain cases. See differences from liblinear in the narrative documentation.

References

L-BFGS-B – Software for Large-scale Bound-constrained Optimization: Ciyou Zhu, Richard Byrd, Jorge Nocedal and Jose Luis Morales. http://users.iems.northwestern.edu/~nocedal/lbfgsb.html
LIBLINEAR – A Library for Large Linear Classification: https://www.csie.ntu.edu.tw/~cjlin/liblinear/
SAG – Mark Schmidt, Nicolas Le Roux, and Francis Bach: Minimizing Finite Sums with the Stochastic Average Gradient https://hal.inria.fr/hal-00860051/document
SAGA – Defazio, A., Bach F. & Lacoste-Julien S. (2014).: :arxiv:`"SAGA: A Fast Incremental Gradient Method With Support for Non-Strongly Convex Composite Objectives" <1407.0202>`
Hsiang-Fu Yu, Fang-Lan Huang, Chih-Jen Lin (2011). Dual coordinate descent: methods for logistic regression and maximum entropy models. Machine Learning 85(1-2):41-75. https://www.csie.ntu.edu.tw/~cjlin/papers/maxent_dual.pdf

Examples

>>> from sklearn.datasets import load_iris
>>> from sklearn.linear_model import LogisticRegression
>>> X, y = load_iris(return_X_y=True)
>>> clf = LogisticRegression(random_state=0).fit(X, y)
>>> clf.predict(X[:2, :])
array([0, 0])
>>> clf.predict_proba(X[:2, :])
array([[9.82e-01, 1.82e-02, 1.44e-08],
       [9.72e-01, 2.82e-02, 3.02e-08]])
>>> clf.score(X, y)
0.97

For a comparison of the LogisticRegression with other classifiers see: sphx_glr_auto_examples_classification_plot_classification_probability.py.

fit(X, y, sample_weight=None)[source]#

Fit the model according to the given training data.

Parameters:

X ({array-like, sparse matrix} of shape (n_samples, n_features)) – Training vector, where n_samples is the number of samples and n_features is the number of features.
y (array-like of shape (n_samples,)) – Target vector relative to X.
sample_weight (array-like of shape (n_samples,) default=None) –
Array of weights that are assigned to individual samples. If not provided, then each sample is given unit weight.

New in version 0.17: sample_weight support to LogisticRegression.

Returns:

Fitted estimator.

Return type:

self

Notes

The SAGA solver supports both float64 and float32 bit arrays.

predict_proba(X)[source]#

Probability estimates.

The returned estimates for all classes are ordered by the label of classes.

For a multi_class problem, if multi_class is set to be “multinomial” the softmax function is used to find the predicted probability of each class. Else use a one-vs-rest approach, i.e. calculate the probability of each class assuming it to be positive using the logistic function and normalize these values across all the classes.

Parameters:: X (array-like of shape (n_samples, n_features)) – Vector to be scored, where n_samples is the number of samples and n_features is the number of features.
Returns:: T – Returns the probability of the sample for each class in the model, where classes are ordered as they are in self.classes_.
Return type:: array-like of shape (n_samples, n_classes)

predict_log_proba(X)[source]#

Predict logarithm of probability estimates.

The returned estimates for all classes are ordered by the label of classes.

Parameters:: X (array-like of shape (n_samples, n_features)) – Vector to be scored, where n_samples is the number of samples and n_features is the number of features.
Returns:: T – Returns the log-probability of the sample for each class in the model, where classes are ordered as they are in self.classes_.
Return type:: array-like of shape (n_samples, n_classes)

decision_function(X)#

Predict confidence scores for samples.

The confidence score for a sample is proportional to the signed distance of that sample to the hyperplane.

Parameters:: X ({array-like, sparse matrix} of shape (n_samples, n_features)) – The data matrix for which we want to get the confidence scores.
Returns:: scores – Confidence scores per (n_samples, n_classes) combination. In the binary case, confidence score for self.classes_[1] where >0 means this class would be predicted.
Return type:: ndarray of shape (n_samples,) or (n_samples, n_classes)

densify()#

Convert coefficient matrix to dense array format.

Converts the coef_ member (back) to a numpy.ndarray. This is the default format of coef_ and is required for fitting, so calling this method is only required on models that have previously been sparsified; otherwise, it is a no-op.

Returns:: Fitted estimator.
Return type:: self

get_metadata_routing()#

Get metadata routing of this object.

Please check User Guide on how the routing mechanism works.

Returns:: routing – A MetadataRequest encapsulating routing information.
Return type:: MetadataRequest

get_params(deep=True)#

Get parameters for this estimator.

Parameters:: deep (bool, default=True) – If True, will return the parameters for this estimator and contained subobjects that are estimators.
Returns:: params – Parameter names mapped to their values.
Return type:: dict

predict(X)#

Predict class labels for samples in X.

Parameters:: X ({array-like, sparse matrix} of shape (n_samples, n_features)) – The data matrix for which we want to get the predictions.
Returns:: y_pred – Vector containing the class labels for each sample.
Return type:: ndarray of shape (n_samples,)

score(X, y, sample_weight=None)#

Return accuracy on provided data and labels.

In multi-label classification, this is the subset accuracy which is a harsh metric since you require for each sample that each label set be correctly predicted.

Parameters:

X (array-like of shape (n_samples, n_features)) – Test samples.
y (array-like of shape (n_samples,) or (n_samples, n_outputs)) – True labels for X.
sample_weight (array-like of shape (n_samples,), default=None) – Sample weights.

Returns:

score – Mean accuracy of self.predict(X) w.r.t. y.

Return type:

float

set_fit_request(*, sample_weight: Union[bool, None, str] = '$UNCHANGED$') → LogisticRegression#

Configure whether metadata should be requested to be passed to the fit method.

The options for each parameter are:

True: metadata is requested, and passed to fit if provided. The request is ignored if metadata is not provided.
False: metadata is not requested and the meta-estimator will not pass it to fit.
None: metadata is not requested, and the meta-estimator will raise an error if the user provides it.
str: metadata should be passed to the meta-estimator with this given alias instead of the original name.

The default (sklearn.utils.metadata_routing.UNCHANGED) retains the existing request. This allows you to change the request for some parameters and not others.

New in version 1.3.

Parameters:: sample_weight (str, True, False, or None, default=sklearn.utils.metadata_routing.UNCHANGED) – Metadata routing for sample_weight parameter in fit.
Returns:: self – The updated object.
Return type:: object

set_params(**params)#

Set the parameters of this estimator.

Parameters:: **params (dict) – Estimator parameters.
Returns:: self – Estimator instance.
Return type:: estimator instance

set_score_request(*, sample_weight: Union[bool, None, str] = '$UNCHANGED$') → LogisticRegression#

Configure whether metadata should be requested to be passed to the score method.

The options for each parameter are:

True: metadata is requested, and passed to score if provided. The request is ignored if metadata is not provided.
False: metadata is not requested and the meta-estimator will not pass it to score.
None: metadata is not requested, and the meta-estimator will raise an error if the user provides it.
str: metadata should be passed to the meta-estimator with this given alias instead of the original name.

The default (sklearn.utils.metadata_routing.UNCHANGED) retains the existing request. This allows you to change the request for some parameters and not others.

New in version 1.3.

Parameters:: sample_weight (str, True, False, or None, default=sklearn.utils.metadata_routing.UNCHANGED) – Metadata routing for sample_weight parameter in score.
Returns:: self – The updated object.
Return type:: object

sparsify()#

Convert coefficient matrix to sparse format.

Converts the coef_ member to a scipy.sparse matrix, which for L1-regularized models can be much more memory- and storage-efficient than the usual numpy.ndarray representation.

The intercept_ member is not converted.

Returns:: Fitted estimator.
Return type:: self

Notes

For non-sparse models, i.e. when there are not many zeros in coef_, this may actually increase memory usage, so use this method with care. A rule of thumb is that the number of zero elements, which can be computed with (coef_ == 0).sum(), must be more than 50% for this to provide significant benefits.

After calling this method, further fitting with the partial_fit method (if any) will not work until you call densify.

class pyhealth.models.califorest.SampleDataset(path, dataset_name=None, task_name=None, **kwargs)[source]#

Bases: StreamingDataset

A streaming dataset that loads sample metadata and processors from disk.

SampleDataset expects the path directory to contain a schema.pkl file created by a SampleBuilder.save(…) call. The schema.pkl must include the fitted input_schema, output_schema, input_processors, output_processors, patient_to_index and record_to_index mappings.

input_schema#: The configuration used to instantiate processors for input features (string aliases or processor specs).

output_schema#: The configuration used to instantiate processors for output features.

input_processors#: A mapping of input feature names to fitted FeatureProcessor instances.

output_processors#: A mapping of output feature names to fitted FeatureProcessor instances.

patient_to_index#: Dictionary mapping patient IDs to the list of sample indices associated with that patient.

record_to_index#: Dictionary mapping record/visit IDs to the list of sample indices associated with that record.

dataset_name#: Optional human friendly dataset name.

task_name#: Optional human friendly task name.

subset(indices)[source]#

Create a StreamingDataset restricted to the provided indices.

Return type:: SampleDataset

close()[source]#

Cleans up any temporary directories used by the dataset.

Return type:: None

get_len(num_workers, batch_size)#

Return type:: int

load_state_dict(state_dict)#

Return type:: None

property on_demand_bytes: bool#

Return type:: bool

reset()#

Return type:: None

reset_state_dict()#

Return type:: None

set_batch_size(batch_size)#

Return type:: None

set_drop_last(drop_last)#

Set the drop_last parameter.

Invalidates the shuffler cache when the parameter changes to ensure subsequent length calculations reflect the new drop_last setting.

Parameters:: drop_last (bool) – Whether to drop the last incomplete batch.
Return type:: None

set_epoch(current_epoch)#

Set the current epoch to the dataset on epoch starts.

When using the StreamingDataLoader, this is done automatically

Return type:: None

set_num_workers(num_workers)#

Return type:: None

set_shuffle(shuffle)#

Set the shuffle parameter.

Invalidates the shuffler cache when the parameter changes to ensure subsequent length calculations reflect the new shuffle setting.

Parameters:: shuffle (bool) – Whether to shuffle the dataset.
Return type:: None

state_dict(num_samples_yielded, num_workers, batch_size)#

Return type:: dict[str, Any]

class pyhealth.models.califorest.BaseModel(dataset)[source]#

Bases: ABC, Module

Abstract class for PyTorch models.

Parameters:: dataset (SampleDataset) – The dataset to train the model. It is used to query certain information such as the set of all tokens.

To use a model with interpretability methods, the model must implement a method forward_from_embedding that takes in embeddings as input instead of raw features; for the models that already take in dense features as input, this method can simply call the existing forward method.

For certain gradient-based interpretability methods (e.g., DeepLIFT), the model must also ensure all non-linearity (e.g. ReLU, Sigmoid, Softmax) are using nn.Module versions instead of functional versions (e.g., F.relu, F.sigmoid, F.softmax) so that hooks can be registered properly.

forward(**kwargs)[source]#

Forward pass of the model.

Parameters:: **kwargs (Tensor | tuple[Tensor, ...]) – A variable number of keyword arguments representing input features. Each keyword argument is a tensor or a tuple of tensors of shape (batch_size, …).
Returns:: logit: a tensor of predicted logits. y_prob: a tensor of predicted probabilities. loss [optional]: a scalar tensor representing the final loss, if self.label_keys in kwargs. y_true [optional]: a tensor representing the true labels, if self.label_keys in kwargs.
Return type:: A dictionary with the following keys

property device: device#

Gets the device of the model.

Returns:: The device on which the model is located.
Return type:: torch.device

T_destination#: alias of TypeVar(‘T_destination’, bound=dict[str, Any])

add_module(name, module)#

Add a child module to the current module.

The module can be accessed as an attribute using the given name.

Parameters:

name (str) – name of the child module. The child module can be accessed from this module using the given name
module (Module) – child module to be added to the module.

Return type:

None

apply(fn)#

Apply fn recursively to every submodule (as returned by .children()) as well as self.

Typical use includes initializing the parameters of a model (see also nn-init-doc).

Parameters:: fn (Module -> None) – function to be applied to each submodule
Returns:: self
Return type:: Module

Example:

>>> @torch.no_grad()
>>> def init_weights(m):
>>>     print(m)
>>>     if type(m) == nn.Linear:
>>>         m.weight.fill_(1.0)
>>>         print(m.weight)
>>> net = nn.Sequential(nn.Linear(2, 2), nn.Linear(2, 2))
>>> net.apply(init_weights)
Linear(in_features=2, out_features=2, bias=True)
Parameter containing:
tensor([[1., 1.],
        [1., 1.]], requires_grad=True)
Linear(in_features=2, out_features=2, bias=True)
Parameter containing:
tensor([[1., 1.],
        [1., 1.]], requires_grad=True)
Sequential(
  (0): Linear(in_features=2, out_features=2, bias=True)
  (1): Linear(in_features=2, out_features=2, bias=True)
)

bfloat16()#

Casts all floating point parameters and buffers to bfloat16 datatype.

Note

This method modifies the module in-place.

Returns:: self
Return type:: Module

buffers(recurse=True)#

Return an iterator over module buffers.

Parameters:: recurse (bool) – if True, then yields buffers of this module and all submodules. Otherwise, yields only buffers that are direct members of this module.
Yields:: torch.Tensor – module buffer

Example:

>>> # xdoctest: +SKIP("undefined vars")
>>> for buf in model.buffers():
>>>     print(type(buf), buf.size())
<class 'torch.Tensor'> (20L,)
<class 'torch.Tensor'> (20L, 1L, 5L, 5L)

Return type:: Iterator[Tensor]

call_super_init: bool = False#

children()#

Return an iterator over immediate children modules.

Yields:: Module – a child module
Return type:: Iterator[Module]

compile(*args, **kwargs)#

Compile this Module’s forward using torch.compile().

This Module’s __call__ method is compiled and all arguments are passed as-is to torch.compile().

See torch.compile() for details on the arguments for this function.

cpu()#

Move all model parameters and buffers to the CPU.

Note

This method modifies the module in-place.

Returns:: self
Return type:: Module

cuda(device=None)#

Move all model parameters and buffers to the GPU.

This also makes associated parameters and buffers different objects. So it should be called before constructing the optimizer if the module will live on GPU while being optimized.

Note

This method modifies the module in-place.

Parameters:: device (int, optional) – if specified, all parameters will be copied to that device
Returns:: self
Return type:: Module

double()#

Casts all floating point parameters and buffers to double datatype.

Note

This method modifies the module in-place.

Returns:: self
Return type:: Module

dump_patches: bool = False#

eval()#

Set the module in evaluation mode.

This has an effect only on certain modules. See the documentation of particular modules for details of their behaviors in training/evaluation mode, i.e. whether they are affected, e.g. Dropout, BatchNorm, etc.

This is equivalent with self.train(False).

See locally-disable-grad-doc for a comparison between .eval() and several similar mechanisms that may be confused with it.

Returns:: self
Return type:: Module

extra_repr()#

Return the extra representation of the module.

To print customized extra information, you should re-implement this method in your own modules. Both single-line and multi-line strings are acceptable.

Return type:: str

float()#

Casts all floating point parameters and buffers to float datatype.

Note

This method modifies the module in-place.

Returns:: self
Return type:: Module

get_buffer(target)#

Return the buffer given by target if it exists, otherwise throw an error.

See the docstring for get_submodule for a more detailed explanation of this method’s functionality as well as how to correctly specify target.

Parameters:: target (str) – The fully-qualified string name of the buffer to look for. (See get_submodule for how to specify a fully-qualified string.)
Returns:: The buffer referenced by target
Return type:: torch.Tensor
Raises:: AttributeError – If the target string references an invalid path or resolves to something that is not a buffer

get_extra_state()#

Return any extra state to include in the module’s state_dict.

Implement this and a corresponding set_extra_state() for your module if you need to store extra state. This function is called when building the module’s state_dict().

Note that extra state should be picklable to ensure working serialization of the state_dict. We only provide backwards compatibility guarantees for serializing Tensors; other objects may break backwards compatibility if their serialized pickled form changes.

Returns:: Any extra state to store in the module’s state_dict
Return type:: object

get_output_size()[source]#

Gets the default output size using the label tokenizer and self.mode.

If the mode is “binary”, the output size is 1. If the mode is “multiclass” or “multilabel”, the output size is the number of classes or labels.

Returns:: The output size of the model.
Return type:: int

get_parameter(target)#

Return the parameter given by target if it exists, otherwise throw an error.

See the docstring for get_submodule for a more detailed explanation of this method’s functionality as well as how to correctly specify target.

Parameters:: target (str) – The fully-qualified string name of the Parameter to look for. (See get_submodule for how to specify a fully-qualified string.)
Returns:: The Parameter referenced by target
Return type:: torch.nn.Parameter
Raises:: AttributeError – If the target string references an invalid path or resolves to something that is not an nn.Parameter

get_submodule(target)#

Return the submodule given by target if it exists, otherwise throw an error.

For example, let’s say you have an nn.Module A that looks like this:

A(
    (net_b): Module(
        (net_c): Module(
            (conv): Conv2d(16, 33, kernel_size=(3, 3), stride=(2, 2))
        )
        (linear): Linear(in_features=100, out_features=200, bias=True)
    )
)

(The diagram shows an nn.Module A. A which has a nested submodule net_b, which itself has two submodules net_c and linear. net_c then has a submodule conv.)

To check whether or not we have the linear submodule, we would call get_submodule("net_b.linear"). To check whether we have the conv submodule, we would call get_submodule("net_b.net_c.conv").

The runtime of get_submodule is bounded by the degree of module nesting in target. A query against named_modules achieves the same result, but it is O(N) in the number of transitive modules. So, for a simple check to see if some submodule exists, get_submodule should always be used.

Parameters:: target (str) – The fully-qualified string name of the submodule to look for. (See above example for how to specify a fully-qualified string.)
Returns:: The submodule referenced by target
Return type:: torch.nn.Module
Raises:: AttributeError – If at any point along the path resulting from the target string the (sub)path resolves to a non-existent attribute name or an object that is not an instance of nn.Module.

half()#

Casts all floating point parameters and buffers to half datatype.

Note

This method modifies the module in-place.

Returns:: self
Return type:: Module

ipu(device=None)#

Move all model parameters and buffers to the IPU.

This also makes associated parameters and buffers different objects. So it should be called before constructing the optimizer if the module will live on IPU while being optimized.

Note

This method modifies the module in-place.

Parameters:: device (int, optional) – if specified, all parameters will be copied to that device
Returns:: self
Return type:: Module

load_state_dict(state_dict, strict=True, assign=False)#

Copy parameters and buffers from state_dict into this module and its descendants.

If strict is True, then the keys of state_dict must exactly match the keys returned by this module’s state_dict() function.

Warning

If assign is True the optimizer must be created after the call to load_state_dict unless get_swap_module_params_on_conversion() is True.

Parameters:

state_dict (dict) – a dict containing parameters and persistent buffers.
strict (bool, optional) – whether to strictly enforce that the keys in state_dict match the keys returned by this module’s state_dict() function. Default: True
assign (bool, optional) – When set to False, the properties of the tensors in the current module are preserved whereas setting it to True preserves properties of the Tensors in the state dict. The only exception is the requires_grad field of Default: ``False`

Returns:

missing_keys is a list of str containing any keys that are expected
by this module but missing from the provided state_dict.
unexpected_keys is a list of str containing the keys that are not
expected by this module but present in the provided state_dict.

Return type:

NamedTuple with missing_keys and unexpected_keys fields

Note

If a parameter or buffer is registered as None and its corresponding key exists in state_dict, load_state_dict() will raise a RuntimeError.

modules()#

Return an iterator over all modules in the network.

Yields:: Module – a module in the network

Note

Duplicate modules are returned only once. In the following example, l will be returned only once.

Example:

>>> l = nn.Linear(2, 2)
>>> net = nn.Sequential(l, l)
>>> for idx, m in enumerate(net.modules()):
...     print(idx, '->', m)

0 -> Sequential(
  (0): Linear(in_features=2, out_features=2, bias=True)
  (1): Linear(in_features=2, out_features=2, bias=True)
)
1 -> Linear(in_features=2, out_features=2, bias=True)

Return type:: Iterator[Module]

mtia(device=None)#

Move all model parameters and buffers to the MTIA.

This also makes associated parameters and buffers different objects. So it should be called before constructing the optimizer if the module will live on MTIA while being optimized.

Note

This method modifies the module in-place.

Parameters:: device (int, optional) – if specified, all parameters will be copied to that device
Returns:: self
Return type:: Module

named_buffers(prefix='', recurse=True, remove_duplicate=True)#

Return an iterator over module buffers, yielding both the name of the buffer as well as the buffer itself.

Parameters:

prefix (str) – prefix to prepend to all buffer names.
recurse (bool, optional) – if True, then yields buffers of this module and all submodules. Otherwise, yields only buffers that are direct members of this module. Defaults to True.
remove_duplicate (bool, optional) – whether to remove the duplicated buffers in the result. Defaults to True.

Yields:

(str, torch.Tensor) – Tuple containing the name and buffer

Example:

>>> # xdoctest: +SKIP("undefined vars")
>>> for name, buf in self.named_buffers():
>>>     if name in ['running_var']:
>>>         print(buf.size())

Return type:: Iterator[tuple[str, Tensor]]

named_children()#

Return an iterator over immediate children modules, yielding both the name of the module as well as the module itself.

Yields:: (str, Module) – Tuple containing a name and child module

Example:

>>> # xdoctest: +SKIP("undefined vars")
>>> for name, module in model.named_children():
>>>     if name in ['conv4', 'conv5']:
>>>         print(module)

Return type:: Iterator[tuple[str, Module]]

named_modules(memo=None, prefix='', remove_duplicate=True)#

Return an iterator over all modules in the network, yielding both the name of the module as well as the module itself.

Parameters:

memo (Optional[set[Module]]) – a memo to store the set of modules already added to the result
prefix (str) – a prefix that will be added to the name of the module
remove_duplicate (bool) – whether to remove the duplicated module instances in the result or not

Yields:

(str, Module) – Tuple of name and module

Note

Duplicate modules are returned only once. In the following example, l will be returned only once.

Example:

>>> l = nn.Linear(2, 2)
>>> net = nn.Sequential(l, l)
>>> for idx, m in enumerate(net.named_modules()):
...     print(idx, '->', m)

0 -> ('', Sequential(
  (0): Linear(in_features=2, out_features=2, bias=True)
  (1): Linear(in_features=2, out_features=2, bias=True)
))
1 -> ('0', Linear(in_features=2, out_features=2, bias=True))

named_parameters(prefix='', recurse=True, remove_duplicate=True)#

Return an iterator over module parameters, yielding both the name of the parameter as well as the parameter itself.

Parameters:

prefix (str) – prefix to prepend to all parameter names.
recurse (bool) – if True, then yields parameters of this module and all submodules. Otherwise, yields only parameters that are direct members of this module.
remove_duplicate (bool, optional) – whether to remove the duplicated parameters in the result. Defaults to True.

Yields:

(str, Parameter) – Tuple containing the name and parameter

Example:

>>> # xdoctest: +SKIP("undefined vars")
>>> for name, param in self.named_parameters():
>>>     if name in ['bias']:
>>>         print(param.size())

Return type:: Iterator[tuple[str, Parameter]]

parameters(recurse=True)#

Return an iterator over module parameters.

This is typically passed to an optimizer.

Parameters:: recurse (bool) – if True, then yields parameters of this module and all submodules. Otherwise, yields only parameters that are direct members of this module.
Yields:: Parameter – module parameter

Example:

>>> # xdoctest: +SKIP("undefined vars")
>>> for param in model.parameters():
>>>     print(type(param), param.size())
<class 'torch.Tensor'> (20L,)
<class 'torch.Tensor'> (20L, 1L, 5L, 5L)

Return type:: Iterator[Parameter]

register_backward_hook(hook)#

This function is deprecated in favor of register_full_backward_hook() and the behavior of this function will change in future versions.

Returns:: a handle that can be used to remove the added hook by calling handle.remove()
Return type:: torch.utils.hooks.RemovableHandle

register_buffer(name, tensor, persistent=True)#

Add a buffer to the module.

This is typically used to register a buffer that should not to be considered a model parameter. For example, BatchNorm’s running_mean is not a parameter, but is part of the module’s state. Buffers, by default, are persistent and will be saved alongside parameters. This behavior can be changed by setting persistent to False. The only difference between a persistent buffer and a non-persistent buffer is that the latter will not be a part of this module’s state_dict.

Buffers can be accessed as attributes using given names.

Parameters:

name (str) – name of the buffer. The buffer can be accessed from this module using the given name
tensor (Tensor or None) – buffer to be registered. If None, then operations that run on buffers, such as cuda, are ignored. If None, the buffer is not included in the module’s state_dict.
persistent (bool) – whether the buffer is part of this module’s state_dict.

Example:

>>> # xdoctest: +SKIP("undefined vars")
>>> self.register_buffer('running_mean', torch.zeros(num_features))

Return type:: None

register_forward_hook(hook, *, prepend=False, with_kwargs=False, always_call=False)#

The hook will be called every time after forward() has computed an output.

If with_kwargs is False or not specified, the input contains only the positional arguments given to the module. Keyword arguments won’t be passed to the hooks and only to the forward. The hook can modify the output. It can modify the input inplace but it will not have effect on forward since this is called after forward() is called. The hook should have the following signature:

hook(module, args, output) -> None or modified output

If with_kwargs is True, the forward hook will be passed the kwargs given to the forward function and be expected to return the output possibly modified. The hook should have the following signature:

hook(module, args, kwargs, output) -> None or modified output

Parameters:

hook (Callable) – The user defined hook to be registered.
prepend (bool) – If True, the provided hook will be fired before all existing forward hooks on this torch.nn.Module. Otherwise, the provided hook will be fired after all existing forward hooks on this torch.nn.Module. Note that global forward hooks registered with register_module_forward_hook() will fire before all hooks registered by this method. Default: False
with_kwargs (bool) – If True, the hook will be passed the kwargs given to the forward function. Default: False
always_call (bool) – If True the hook will be run regardless of whether an exception is raised while calling the Module. Default: False

Returns:

a handle that can be used to remove the added hook by calling handle.remove()

Return type:

torch.utils.hooks.RemovableHandle

register_forward_pre_hook(hook, *, prepend=False, with_kwargs=False)#

The hook will be called every time before forward() is invoked.

If with_kwargs is false or not specified, the input contains only the positional arguments given to the module. Keyword arguments won’t be passed to the hooks and only to the forward. The hook can modify the input. User can either return a tuple or a single modified value in the hook. We will wrap the value into a tuple if a single value is returned (unless that value is already a tuple). The hook should have the following signature:

hook(module, args) -> None or modified input

If with_kwargs is true, the forward pre-hook will be passed the kwargs given to the forward function. And if the hook modifies the input, both the args and kwargs should be returned. The hook should have the following signature:

hook(module, args, kwargs) -> None or a tuple of modified input and kwargs

Parameters:

hook (Callable) – The user defined hook to be registered.
prepend (bool) – If true, the provided hook will be fired before all existing forward_pre hooks on this torch.nn.Module. Otherwise, the provided hook will be fired after all existing forward_pre hooks on this torch.nn.Module. Note that global forward_pre hooks registered with register_module_forward_pre_hook() will fire before all hooks registered by this method. Default: False
with_kwargs (bool) – If true, the hook will be passed the kwargs given to the forward function. Default: False

Returns:

a handle that can be used to remove the added hook by calling handle.remove()

Return type:

torch.utils.hooks.RemovableHandle

register_full_backward_hook(hook, prepend=False)#

The hook will be called every time the gradients with respect to a module are computed, i.e. the hook will execute if and only if the gradients with respect to module outputs are computed. The hook should have the following signature:

hook(module, grad_input, grad_output) -> tuple(Tensor) or None

The grad_input and grad_output are tuples that contain the gradients with respect to the inputs and outputs respectively. The hook should not modify its arguments, but it can optionally return a new gradient with respect to the input that will be used in place of grad_input in subsequent computations. grad_input will only correspond to the inputs given as positional arguments and all kwarg arguments are ignored. Entries in grad_input and grad_output will be None for all non-Tensor arguments.

For technical reasons, when this hook is applied to a Module, its forward function will receive a view of each Tensor passed to the Module. Similarly the caller will receive a view of each Tensor returned by the Module’s forward function.

Warning

Modifying inputs or outputs inplace is not allowed when using backward hooks and will raise an error.

Parameters:

hook (Callable) – The user-defined hook to be registered.
prepend (bool) – If true, the provided hook will be fired before all existing backward hooks on this torch.nn.Module. Otherwise, the provided hook will be fired after all existing backward hooks on this torch.nn.Module. Note that global backward hooks registered with register_module_full_backward_hook() will fire before all hooks registered by this method.

Returns:

a handle that can be used to remove the added hook by calling handle.remove()

Return type:

torch.utils.hooks.RemovableHandle

register_full_backward_pre_hook(hook, prepend=False)#

The hook will be called every time the gradients for the module are computed. The hook should have the following signature:

hook(module, grad_output) -> tuple[Tensor] or None

The grad_output is a tuple. The hook should not modify its arguments, but it can optionally return a new gradient with respect to the output that will be used in place of grad_output in subsequent computations. Entries in grad_output will be None for all non-Tensor arguments.

Warning

Modifying inputs inplace is not allowed when using backward hooks and will raise an error.

Parameters:

hook (Callable) – The user-defined hook to be registered.
prepend (bool) – If true, the provided hook will be fired before all existing backward_pre hooks on this torch.nn.Module. Otherwise, the provided hook will be fired after all existing backward_pre hooks on this torch.nn.Module. Note that global backward_pre hooks registered with register_module_full_backward_pre_hook() will fire before all hooks registered by this method.

Returns:

a handle that can be used to remove the added hook by calling handle.remove()

Return type:

torch.utils.hooks.RemovableHandle

register_load_state_dict_post_hook(hook)#

It should have the following signature::: hook(module, incompatible_keys) -> None

The module argument is the current module that this hook is registered on, and the incompatible_keys argument is a NamedTuple consisting of attributes missing_keys and unexpected_keys. missing_keys is a list of str containing the missing keys and unexpected_keys is a list of str containing the unexpected keys.

The given incompatible_keys can be modified inplace if needed.

Note that the checks performed when calling load_state_dict() with strict=True are affected by modifications the hook makes to missing_keys or unexpected_keys, as expected. Additions to either set of keys will result in an error being thrown when strict=True, and clearing out both missing and unexpected keys will avoid an error.

Returns:: a handle that can be used to remove the added hook by calling handle.remove()
Return type:: torch.utils.hooks.RemovableHandle

register_load_state_dict_pre_hook(hook)#

It should have the following signature::: hook(module, state_dict, prefix, local_metadata, strict, missing_keys, unexpected_keys, error_msgs) -> None # noqa: B950

Parameters:: hook (Callable) – Callable hook that will be invoked before loading the state dict.

register_module(name, module)#

Alias for add_module().

Return type:: None

register_parameter(name, param)#

Add a parameter to the module.

The parameter can be accessed as an attribute using given name.

Parameters:

name (str) – name of the parameter. The parameter can be accessed from this module using the given name
param (Parameter or None) – parameter to be added to the module. If None, then operations that run on parameters, such as cuda, are ignored. If None, the parameter is not included in the module’s state_dict.

Return type:

None

register_state_dict_post_hook(hook)#

It should have the following signature::: hook(module, state_dict, prefix, local_metadata) -> None

The registered hooks can modify the state_dict inplace.

register_state_dict_pre_hook(hook)#

It should have the following signature::: hook(module, prefix, keep_vars) -> None

The registered hooks can be used to perform pre-processing before the state_dict call is made.

requires_grad_(requires_grad=True)#

Change if autograd should record operations on parameters in this module.

This method sets the parameters’ requires_grad attributes in-place.

This method is helpful for freezing part of the module for finetuning or training parts of a model individually (e.g., GAN training).

See locally-disable-grad-doc for a comparison between .requires_grad_() and several similar mechanisms that may be confused with it.

Parameters:: requires_grad (bool) – whether autograd should record operations on parameters in this module. Default: True.
Returns:: self
Return type:: Module

set_extra_state(state)#

Set extra state contained in the loaded state_dict.

This function is called from load_state_dict() to handle any extra state found within the state_dict. Implement this function and a corresponding get_extra_state() for your module if you need to store extra state within its state_dict.

Parameters:: state (dict) – Extra state from the state_dict
Return type:: None

set_submodule(target, module, strict=False)#

Set the submodule given by target if it exists, otherwise throw an error.

Note

If strict is set to False (default), the method will replace an existing submodule or create a new submodule if the parent module exists. If strict is set to True, the method will only attempt to replace an existing submodule and throw an error if the submodule does not exist.

For example, let’s say you have an nn.Module A that looks like this:

A(
    (net_b): Module(
        (net_c): Module(
            (conv): Conv2d(3, 3, 3)
        )
        (linear): Linear(3, 3)
    )
)

(The diagram shows an nn.Module A. A has a nested submodule net_b, which itself has two submodules net_c and linear. net_c then has a submodule conv.)

To override the Conv2d with a new submodule Linear, you could call set_submodule("net_b.net_c.conv", nn.Linear(1, 1)) where strict could be True or False

To add a new submodule Conv2d to the existing net_b module, you would call set_submodule("net_b.conv", nn.Conv2d(1, 1, 1)).

In the above if you set strict=True and call set_submodule("net_b.conv", nn.Conv2d(1, 1, 1), strict=True), an AttributeError will be raised because net_b does not have a submodule named conv.

Parameters:

target (str) – The fully-qualified string name of the submodule to look for. (See above example for how to specify a fully-qualified string.)
module (Module) – The module to set the submodule to.
strict (bool) – If False, the method will replace an existing submodule or create a new submodule if the parent module exists. If True, the method will only attempt to replace an existing submodule and throw an error if the submodule doesn’t already exist.

Raises:

ValueError – If the target string is empty or if module is not an instance of nn.Module.
AttributeError – If at any point along the path resulting from the target string the (sub)path resolves to a non-existent attribute name or an object that is not an instance of nn.Module.

Return type:

None

share_memory()#

See torch.Tensor.share_memory_().

Return type:: TypeVar(T, bound= Module)

state_dict(*args, destination=None, prefix='', keep_vars=False)#

Return a dictionary containing references to the whole state of the module.

Both parameters and persistent buffers (e.g. running averages) are included. Keys are corresponding parameter and buffer names. Parameters and buffers set to None are not included.

Note

The returned object is a shallow copy. It contains references to the module’s parameters and buffers.

Warning

Currently state_dict() also accepts positional arguments for destination, prefix and keep_vars in order. However, this is being deprecated and keyword arguments will be enforced in future releases.

Warning

Please avoid the use of argument destination as it is not designed for end-users.

Parameters:

destination (dict, optional) – If provided, the state of module will be updated into the dict and the same object is returned. Otherwise, an OrderedDict will be created and returned. Default: None.
prefix (str, optional) – a prefix added to parameter and buffer names to compose the keys in state_dict. Default: ''.
keep_vars (bool, optional) – by default the Tensor s returned in the state dict are detached from autograd. If it’s set to True, detaching will not be performed. Default: False.

Returns:

a dictionary containing a whole state of the module

Return type:

dict

Example:

>>> # xdoctest: +SKIP("undefined vars")
>>> module.state_dict().keys()
['bias', 'weight']

to(*args, **kwargs)#

Move and/or cast the parameters and buffers.

This can be called as

to(device=None, dtype=None, non_blocking=False)

to(dtype, non_blocking=False)

to(tensor, non_blocking=False)

to(memory_format=torch.channels_last)

Its signature is similar to torch.Tensor.to(), but only accepts floating point or complex dtypes. In addition, this method will only cast the floating point or complex parameters and buffers to dtype (if given). The integral parameters and buffers will be moved device, if that is given, but with dtypes unchanged. When non_blocking is set, it tries to convert/move asynchronously with respect to the host if possible, e.g., moving CPU Tensors with pinned memory to CUDA devices.

See below for examples.

Note

This method modifies the module in-place.

Parameters:

device (torch.device) – the desired device of the parameters and buffers in this module
dtype (torch.dtype) – the desired floating point or complex dtype of the parameters and buffers in this module
tensor (torch.Tensor) – Tensor whose dtype and device are the desired dtype and device for all parameters and buffers in this module
memory_format (torch.memory_format) – the desired memory format for 4D parameters and buffers in this module (keyword only argument)

Returns:

self

Return type:

Module

Examples:

>>> # xdoctest: +IGNORE_WANT("non-deterministic")
>>> linear = nn.Linear(2, 2)
>>> linear.weight
Parameter containing:
tensor([[ 0.1913, -0.3420],
        [-0.5113, -0.2325]])
>>> linear.to(torch.double)
Linear(in_features=2, out_features=2, bias=True)
>>> linear.weight
Parameter containing:
tensor([[ 0.1913, -0.3420],
        [-0.5113, -0.2325]], dtype=torch.float64)
>>> # xdoctest: +REQUIRES(env:TORCH_DOCTEST_CUDA1)
>>> gpu1 = torch.device("cuda:1")
>>> linear.to(gpu1, dtype=torch.half, non_blocking=True)
Linear(in_features=2, out_features=2, bias=True)
>>> linear.weight
Parameter containing:
tensor([[ 0.1914, -0.3420],
        [-0.5112, -0.2324]], dtype=torch.float16, device='cuda:1')
>>> cpu = torch.device("cpu")
>>> linear.to(cpu)
Linear(in_features=2, out_features=2, bias=True)
>>> linear.weight
Parameter containing:
tensor([[ 0.1914, -0.3420],
        [-0.5112, -0.2324]], dtype=torch.float16)

>>> linear = nn.Linear(2, 2, bias=None).to(torch.cdouble)
>>> linear.weight
Parameter containing:
tensor([[ 0.3741+0.j,  0.2382+0.j],
        [ 0.5593+0.j, -0.4443+0.j]], dtype=torch.complex128)
>>> linear(torch.ones(3, 2, dtype=torch.cdouble))
tensor([[0.6122+0.j, 0.1150+0.j],
        [0.6122+0.j, 0.1150+0.j],
        [0.6122+0.j, 0.1150+0.j]], dtype=torch.complex128)

to_empty(*, device, recurse=True)#

Move the parameters and buffers to the specified device without copying storage.

Parameters:

device (torch.device) – The desired device of the parameters and buffers in this module.
recurse (bool) – Whether parameters and buffers of submodules should be recursively moved to the specified device.

Returns:

self

Return type:

Module

train(mode=True)#

Set the module in training mode.

This has an effect only on certain modules. See the documentation of particular modules for details of their behaviors in training/evaluation mode, i.e., whether they are affected, e.g. Dropout, BatchNorm, etc.

Parameters:: mode (bool) – whether to set training mode (True) or evaluation mode (False). Default: True.
Returns:: self
Return type:: Module

type(dst_type)#

Casts all parameters and buffers to dst_type.

Note

This method modifies the module in-place.

Parameters:: dst_type (type or string) – the desired type
Returns:: self
Return type:: Module

xpu(device=None)#

Move all model parameters and buffers to the XPU.

This also makes associated parameters and buffers different objects. So it should be called before constructing optimizer if the module will live on XPU while being optimized.

Note

This method modifies the module in-place.

Parameters:: device (int, optional) – if specified, all parameters will be copied to that device
Returns:: self
Return type:: Module

zero_grad(set_to_none=True)#

Reset gradients of all model parameters.

See similar function under torch.optim.Optimizer for more context.

Parameters:: set_to_none (bool) – instead of setting to zero, set the grads to None. See torch.optim.Optimizer.zero_grad() for details.
Return type:: None

training: bool#

get_loss_function()[source]#

Gets the default loss function using self.mode.

The default loss functions are:

binary: F.binary_cross_entropy_with_logits
multiclass: F.cross_entropy
multilabel: F.binary_cross_entropy_with_logits
regression: F.mse_loss

Returns:: The default loss function.
Return type:: Callable

prepare_y_prob(logits)[source]#

Prepares the predicted probabilities for model evaluation.

This function converts the predicted logits to predicted probabilities depending on the mode. The default formats are:

binary: a tensor of shape (batch_size, 1) with values in [0, 1],
which is obtained with torch.sigmoid()

multiclass: a tensor of shape (batch_size, num_classes) with
values in [0, 1] and sum to 1, which is obtained with torch.softmax()

multilabel: a tensor of shape (batch_size, num_labels) with values
in [0, 1], which is obtained with torch.sigmoid()

regression: a tensor of shape (batch_size, 1) with raw logits

Parameters:: logits (torch.Tensor) – The predicted logit tensor.
Returns:: The predicted probability tensor.
Return type:: torch.Tensor

class pyhealth.models.califorest.CaliForest(dataset, n_estimators=100, max_depth=None, calibration='isotonic', random_state=42, **kwargs)[source]#

Bases: BaseModel

CaliForest model for calibrated probability prediction.

This model wraps a RandomForestClassifier and applies a post-hoc calibration step using out-of-bag (OOB) predictions and prediction variance to improve probability estimates.

Important

CaliForest is fit once on the full training set using fit(train_loader). After fitting, forward() should be used only for inference/evaluation. This implementation currently supports binary classification only.

The overall procedure is:

train a random forest classifier,
compute OOB probabilities for each training sample,
estimate prediction uncertainty using variance across tree outputs,
fit a calibration model using uncertainty-weighted samples.

Parameters:

dataset (SampleDataset) – the dataset used to initialize feature and label schemas.
n_estimators (int) – number of trees in the random forest. Default is 100.
max_depth (Optional[int]) – maximum depth of each tree. Default is None.
calibration (str) – calibration method. Supported values are "isotonic" and "logistic". Default is "isotonic".
random_state (int) – random seed for reproducibility. Default is 42.
**kwargs – additional compatibility arguments.

Example

model = CaliForest(dataset=dataset, n_estimators=10) model.fit(train_loader) ret = model(**batch) print(ret[“y_prob”].shape)

fit(train_loader)[source]#: Fit CaliForest on the full training dataloader

fit_model(**kwargs)[source]#

Fit RF + calibration model.

Return type:: None

predict_proba_numpy(**kwargs)[source]#

Predict calibrated probabilities.

Return type:: ndarray

forward(**kwargs)[source]#

PyHealth forward pass.

Return type:: Dict[str, Tensor]

T_destination#: alias of TypeVar(‘T_destination’, bound=dict[str, Any])

add_module(name, module)#

Add a child module to the current module.

The module can be accessed as an attribute using the given name.

Parameters:

name (str) – name of the child module. The child module can be accessed from this module using the given name
module (Module) – child module to be added to the module.

Return type:

None

apply(fn)#

Apply fn recursively to every submodule (as returned by .children()) as well as self.

Typical use includes initializing the parameters of a model (see also nn-init-doc).

Parameters:: fn (Module -> None) – function to be applied to each submodule
Returns:: self
Return type:: Module

Example:

>>> @torch.no_grad()
>>> def init_weights(m):
>>>     print(m)
>>>     if type(m) == nn.Linear:
>>>         m.weight.fill_(1.0)
>>>         print(m.weight)
>>> net = nn.Sequential(nn.Linear(2, 2), nn.Linear(2, 2))
>>> net.apply(init_weights)
Linear(in_features=2, out_features=2, bias=True)
Parameter containing:
tensor([[1., 1.],
        [1., 1.]], requires_grad=True)
Linear(in_features=2, out_features=2, bias=True)
Parameter containing:
tensor([[1., 1.],
        [1., 1.]], requires_grad=True)
Sequential(
  (0): Linear(in_features=2, out_features=2, bias=True)
  (1): Linear(in_features=2, out_features=2, bias=True)
)

bfloat16()#

Casts all floating point parameters and buffers to bfloat16 datatype.

Note

This method modifies the module in-place.

Returns:: self
Return type:: Module

buffers(recurse=True)#

Return an iterator over module buffers.

Parameters:: recurse (bool) – if True, then yields buffers of this module and all submodules. Otherwise, yields only buffers that are direct members of this module.
Yields:: torch.Tensor – module buffer

Example:

>>> # xdoctest: +SKIP("undefined vars")
>>> for buf in model.buffers():
>>>     print(type(buf), buf.size())
<class 'torch.Tensor'> (20L,)
<class 'torch.Tensor'> (20L, 1L, 5L, 5L)

Return type:: Iterator[Tensor]

call_super_init: bool = False#

children()#

Return an iterator over immediate children modules.

Yields:: Module – a child module
Return type:: Iterator[Module]

compile(*args, **kwargs)#

Compile this Module’s forward using torch.compile().

This Module’s __call__ method is compiled and all arguments are passed as-is to torch.compile().

See torch.compile() for details on the arguments for this function.

cpu()#

Move all model parameters and buffers to the CPU.

Note

This method modifies the module in-place.

Returns:: self
Return type:: Module

cuda(device=None)#

Move all model parameters and buffers to the GPU.

This also makes associated parameters and buffers different objects. So it should be called before constructing the optimizer if the module will live on GPU while being optimized.

Note

This method modifies the module in-place.

Parameters:: device (int, optional) – if specified, all parameters will be copied to that device
Returns:: self
Return type:: Module

property device: device#

Gets the device of the model.

Returns:: The device on which the model is located.
Return type:: torch.device

double()#

Casts all floating point parameters and buffers to double datatype.

Note

This method modifies the module in-place.

Returns:: self
Return type:: Module

dump_patches: bool = False#

eval()#

Set the module in evaluation mode.

This is equivalent with self.train(False).

See locally-disable-grad-doc for a comparison between .eval() and several similar mechanisms that may be confused with it.

Returns:: self
Return type:: Module

extra_repr()#

Return the extra representation of the module.

To print customized extra information, you should re-implement this method in your own modules. Both single-line and multi-line strings are acceptable.

Return type:: str

float()#

Casts all floating point parameters and buffers to float datatype.

Note

This method modifies the module in-place.

Returns:: self
Return type:: Module

get_buffer(target)#

Return the buffer given by target if it exists, otherwise throw an error.

See the docstring for get_submodule for a more detailed explanation of this method’s functionality as well as how to correctly specify target.

Parameters:: target (str) – The fully-qualified string name of the buffer to look for. (See get_submodule for how to specify a fully-qualified string.)
Returns:: The buffer referenced by target
Return type:: torch.Tensor
Raises:: AttributeError – If the target string references an invalid path or resolves to something that is not a buffer

get_extra_state()#

Return any extra state to include in the module’s state_dict.

Implement this and a corresponding set_extra_state() for your module if you need to store extra state. This function is called when building the module’s state_dict().

Returns:: Any extra state to store in the module’s state_dict
Return type:: object

get_loss_function()#

Gets the default loss function using self.mode.

The default loss functions are:

binary: F.binary_cross_entropy_with_logits
multiclass: F.cross_entropy
multilabel: F.binary_cross_entropy_with_logits
regression: F.mse_loss

Returns:: The default loss function.
Return type:: Callable

get_output_size()#

Gets the default output size using the label tokenizer and self.mode.

If the mode is “binary”, the output size is 1. If the mode is “multiclass” or “multilabel”, the output size is the number of classes or labels.

Returns:: The output size of the model.
Return type:: int

get_parameter(target)#

Return the parameter given by target if it exists, otherwise throw an error.

See the docstring for get_submodule for a more detailed explanation of this method’s functionality as well as how to correctly specify target.

Parameters:: target (str) – The fully-qualified string name of the Parameter to look for. (See get_submodule for how to specify a fully-qualified string.)
Returns:: The Parameter referenced by target
Return type:: torch.nn.Parameter
Raises:: AttributeError – If the target string references an invalid path or resolves to something that is not an nn.Parameter

get_submodule(target)#

Return the submodule given by target if it exists, otherwise throw an error.

For example, let’s say you have an nn.Module A that looks like this:

A(
    (net_b): Module(
        (net_c): Module(
            (conv): Conv2d(16, 33, kernel_size=(3, 3), stride=(2, 2))
        )
        (linear): Linear(in_features=100, out_features=200, bias=True)
    )
)

(The diagram shows an nn.Module A. A which has a nested submodule net_b, which itself has two submodules net_c and linear. net_c then has a submodule conv.)

Parameters:: target (str) – The fully-qualified string name of the submodule to look for. (See above example for how to specify a fully-qualified string.)
Returns:: The submodule referenced by target
Return type:: torch.nn.Module
Raises:: AttributeError – If at any point along the path resulting from the target string the (sub)path resolves to a non-existent attribute name or an object that is not an instance of nn.Module.

half()#

Casts all floating point parameters and buffers to half datatype.

Note

This method modifies the module in-place.

Returns:: self
Return type:: Module

ipu(device=None)#

Move all model parameters and buffers to the IPU.

This also makes associated parameters and buffers different objects. So it should be called before constructing the optimizer if the module will live on IPU while being optimized.

Note

This method modifies the module in-place.

Parameters:: device (int, optional) – if specified, all parameters will be copied to that device
Returns:: self
Return type:: Module

load_state_dict(state_dict, strict=True, assign=False)#

Copy parameters and buffers from state_dict into this module and its descendants.

If strict is True, then the keys of state_dict must exactly match the keys returned by this module’s state_dict() function.

Warning

If assign is True the optimizer must be created after the call to load_state_dict unless get_swap_module_params_on_conversion() is True.

Parameters:

state_dict (dict) – a dict containing parameters and persistent buffers.
strict (bool, optional) – whether to strictly enforce that the keys in state_dict match the keys returned by this module’s state_dict() function. Default: True
assign (bool, optional) – When set to False, the properties of the tensors in the current module are preserved whereas setting it to True preserves properties of the Tensors in the state dict. The only exception is the requires_grad field of Default: ``False`

Returns:

missing_keys is a list of str containing any keys that are expected
by this module but missing from the provided state_dict.
unexpected_keys is a list of str containing the keys that are not
expected by this module but present in the provided state_dict.

Return type:

NamedTuple with missing_keys and unexpected_keys fields

Note

If a parameter or buffer is registered as None and its corresponding key exists in state_dict, load_state_dict() will raise a RuntimeError.

modules()#

Return an iterator over all modules in the network.

Yields:: Module – a module in the network

Note

Duplicate modules are returned only once. In the following example, l will be returned only once.

Example:

>>> l = nn.Linear(2, 2)
>>> net = nn.Sequential(l, l)
>>> for idx, m in enumerate(net.modules()):
...     print(idx, '->', m)

0 -> Sequential(
  (0): Linear(in_features=2, out_features=2, bias=True)
  (1): Linear(in_features=2, out_features=2, bias=True)
)
1 -> Linear(in_features=2, out_features=2, bias=True)

Return type:: Iterator[Module]

mtia(device=None)#

Move all model parameters and buffers to the MTIA.

This also makes associated parameters and buffers different objects. So it should be called before constructing the optimizer if the module will live on MTIA while being optimized.

Note

This method modifies the module in-place.

Parameters:: device (int, optional) – if specified, all parameters will be copied to that device
Returns:: self
Return type:: Module

named_buffers(prefix='', recurse=True, remove_duplicate=True)#

Return an iterator over module buffers, yielding both the name of the buffer as well as the buffer itself.

Parameters:

prefix (str) – prefix to prepend to all buffer names.
recurse (bool, optional) – if True, then yields buffers of this module and all submodules. Otherwise, yields only buffers that are direct members of this module. Defaults to True.
remove_duplicate (bool, optional) – whether to remove the duplicated buffers in the result. Defaults to True.

Yields:

(str, torch.Tensor) – Tuple containing the name and buffer

Example:

>>> # xdoctest: +SKIP("undefined vars")
>>> for name, buf in self.named_buffers():
>>>     if name in ['running_var']:
>>>         print(buf.size())

Return type:: Iterator[tuple[str, Tensor]]

named_children()#

Return an iterator over immediate children modules, yielding both the name of the module as well as the module itself.

Yields:: (str, Module) – Tuple containing a name and child module

Example:

>>> # xdoctest: +SKIP("undefined vars")
>>> for name, module in model.named_children():
>>>     if name in ['conv4', 'conv5']:
>>>         print(module)

Return type:: Iterator[tuple[str, Module]]

named_modules(memo=None, prefix='', remove_duplicate=True)#

Return an iterator over all modules in the network, yielding both the name of the module as well as the module itself.

Parameters:

memo (Optional[set[Module]]) – a memo to store the set of modules already added to the result
prefix (str) – a prefix that will be added to the name of the module
remove_duplicate (bool) – whether to remove the duplicated module instances in the result or not

Yields:

(str, Module) – Tuple of name and module

Note

Duplicate modules are returned only once. In the following example, l will be returned only once.

Example:

>>> l = nn.Linear(2, 2)
>>> net = nn.Sequential(l, l)
>>> for idx, m in enumerate(net.named_modules()):
...     print(idx, '->', m)

0 -> ('', Sequential(
  (0): Linear(in_features=2, out_features=2, bias=True)
  (1): Linear(in_features=2, out_features=2, bias=True)
))
1 -> ('0', Linear(in_features=2, out_features=2, bias=True))

named_parameters(prefix='', recurse=True, remove_duplicate=True)#

Return an iterator over module parameters, yielding both the name of the parameter as well as the parameter itself.

Parameters:

prefix (str) – prefix to prepend to all parameter names.
recurse (bool) – if True, then yields parameters of this module and all submodules. Otherwise, yields only parameters that are direct members of this module.
remove_duplicate (bool, optional) – whether to remove the duplicated parameters in the result. Defaults to True.

Yields:

(str, Parameter) – Tuple containing the name and parameter

Example:

>>> # xdoctest: +SKIP("undefined vars")
>>> for name, param in self.named_parameters():
>>>     if name in ['bias']:
>>>         print(param.size())

Return type:: Iterator[tuple[str, Parameter]]

parameters(recurse=True)#

Return an iterator over module parameters.

This is typically passed to an optimizer.

Parameters:: recurse (bool) – if True, then yields parameters of this module and all submodules. Otherwise, yields only parameters that are direct members of this module.
Yields:: Parameter – module parameter

Example:

>>> # xdoctest: +SKIP("undefined vars")
>>> for param in model.parameters():
>>>     print(type(param), param.size())
<class 'torch.Tensor'> (20L,)
<class 'torch.Tensor'> (20L, 1L, 5L, 5L)

Return type:: Iterator[Parameter]

prepare_y_prob(logits)#

Prepares the predicted probabilities for model evaluation.

This function converts the predicted logits to predicted probabilities depending on the mode. The default formats are:

binary: a tensor of shape (batch_size, 1) with values in [0, 1],
which is obtained with torch.sigmoid()

multiclass: a tensor of shape (batch_size, num_classes) with
values in [0, 1] and sum to 1, which is obtained with torch.softmax()

multilabel: a tensor of shape (batch_size, num_labels) with values
in [0, 1], which is obtained with torch.sigmoid()

regression: a tensor of shape (batch_size, 1) with raw logits

Parameters:: logits (torch.Tensor) – The predicted logit tensor.
Returns:: The predicted probability tensor.
Return type:: torch.Tensor

register_backward_hook(hook)#

This function is deprecated in favor of register_full_backward_hook() and the behavior of this function will change in future versions.

Returns:: a handle that can be used to remove the added hook by calling handle.remove()
Return type:: torch.utils.hooks.RemovableHandle

register_buffer(name, tensor, persistent=True)#

Add a buffer to the module.

Buffers can be accessed as attributes using given names.

Parameters:

name (str) – name of the buffer. The buffer can be accessed from this module using the given name
tensor (Tensor or None) – buffer to be registered. If None, then operations that run on buffers, such as cuda, are ignored. If None, the buffer is not included in the module’s state_dict.
persistent (bool) – whether the buffer is part of this module’s state_dict.

Example:

>>> # xdoctest: +SKIP("undefined vars")
>>> self.register_buffer('running_mean', torch.zeros(num_features))

Return type:: None

register_forward_hook(hook, *, prepend=False, with_kwargs=False, always_call=False)#

The hook will be called every time after forward() has computed an output.

hook(module, args, output) -> None or modified output

hook(module, args, kwargs, output) -> None or modified output

Parameters:

hook (Callable) – The user defined hook to be registered.
prepend (bool) – If True, the provided hook will be fired before all existing forward hooks on this torch.nn.Module. Otherwise, the provided hook will be fired after all existing forward hooks on this torch.nn.Module. Note that global forward hooks registered with register_module_forward_hook() will fire before all hooks registered by this method. Default: False
with_kwargs (bool) – If True, the hook will be passed the kwargs given to the forward function. Default: False
always_call (bool) – If True the hook will be run regardless of whether an exception is raised while calling the Module. Default: False

Returns:

a handle that can be used to remove the added hook by calling handle.remove()

Return type:

torch.utils.hooks.RemovableHandle

register_forward_pre_hook(hook, *, prepend=False, with_kwargs=False)#

The hook will be called every time before forward() is invoked.

hook(module, args) -> None or modified input

hook(module, args, kwargs) -> None or a tuple of modified input and kwargs

Parameters:

hook (Callable) – The user defined hook to be registered.
prepend (bool) – If true, the provided hook will be fired before all existing forward_pre hooks on this torch.nn.Module. Otherwise, the provided hook will be fired after all existing forward_pre hooks on this torch.nn.Module. Note that global forward_pre hooks registered with register_module_forward_pre_hook() will fire before all hooks registered by this method. Default: False
with_kwargs (bool) – If true, the hook will be passed the kwargs given to the forward function. Default: False

Returns:

a handle that can be used to remove the added hook by calling handle.remove()

Return type:

torch.utils.hooks.RemovableHandle

register_full_backward_hook(hook, prepend=False)#

hook(module, grad_input, grad_output) -> tuple(Tensor) or None

Warning

Modifying inputs or outputs inplace is not allowed when using backward hooks and will raise an error.

Parameters:

hook (Callable) – The user-defined hook to be registered.
prepend (bool) – If true, the provided hook will be fired before all existing backward hooks on this torch.nn.Module. Otherwise, the provided hook will be fired after all existing backward hooks on this torch.nn.Module. Note that global backward hooks registered with register_module_full_backward_hook() will fire before all hooks registered by this method.

Returns:

a handle that can be used to remove the added hook by calling handle.remove()

Return type:

torch.utils.hooks.RemovableHandle

register_full_backward_pre_hook(hook, prepend=False)#

The hook will be called every time the gradients for the module are computed. The hook should have the following signature:

hook(module, grad_output) -> tuple[Tensor] or None

Warning

Modifying inputs inplace is not allowed when using backward hooks and will raise an error.

Parameters:

hook (Callable) – The user-defined hook to be registered.
prepend (bool) – If true, the provided hook will be fired before all existing backward_pre hooks on this torch.nn.Module. Otherwise, the provided hook will be fired after all existing backward_pre hooks on this torch.nn.Module. Note that global backward_pre hooks registered with register_module_full_backward_pre_hook() will fire before all hooks registered by this method.

Returns:

a handle that can be used to remove the added hook by calling handle.remove()

Return type:

torch.utils.hooks.RemovableHandle

register_load_state_dict_post_hook(hook)#

It should have the following signature::: hook(module, incompatible_keys) -> None

The given incompatible_keys can be modified inplace if needed.

Returns:: a handle that can be used to remove the added hook by calling handle.remove()
Return type:: torch.utils.hooks.RemovableHandle

register_load_state_dict_pre_hook(hook)#

It should have the following signature::: hook(module, state_dict, prefix, local_metadata, strict, missing_keys, unexpected_keys, error_msgs) -> None # noqa: B950

Parameters:: hook (Callable) – Callable hook that will be invoked before loading the state dict.

register_module(name, module)#

Alias for add_module().

Return type:: None

register_parameter(name, param)#

Add a parameter to the module.

The parameter can be accessed as an attribute using given name.

Parameters:

name (str) – name of the parameter. The parameter can be accessed from this module using the given name
param (Parameter or None) – parameter to be added to the module. If None, then operations that run on parameters, such as cuda, are ignored. If None, the parameter is not included in the module’s state_dict.

Return type:

None

register_state_dict_post_hook(hook)#

It should have the following signature::: hook(module, state_dict, prefix, local_metadata) -> None

The registered hooks can modify the state_dict inplace.

register_state_dict_pre_hook(hook)#

It should have the following signature::: hook(module, prefix, keep_vars) -> None

The registered hooks can be used to perform pre-processing before the state_dict call is made.

requires_grad_(requires_grad=True)#

Change if autograd should record operations on parameters in this module.

This method sets the parameters’ requires_grad attributes in-place.

This method is helpful for freezing part of the module for finetuning or training parts of a model individually (e.g., GAN training).

See locally-disable-grad-doc for a comparison between .requires_grad_() and several similar mechanisms that may be confused with it.

Parameters:: requires_grad (bool) – whether autograd should record operations on parameters in this module. Default: True.
Returns:: self
Return type:: Module

set_extra_state(state)#

Set extra state contained in the loaded state_dict.

Parameters:: state (dict) – Extra state from the state_dict
Return type:: None

set_submodule(target, module, strict=False)#

Set the submodule given by target if it exists, otherwise throw an error.

Note

For example, let’s say you have an nn.Module A that looks like this:

A(
    (net_b): Module(
        (net_c): Module(
            (conv): Conv2d(3, 3, 3)
        )
        (linear): Linear(3, 3)
    )
)

(The diagram shows an nn.Module A. A has a nested submodule net_b, which itself has two submodules net_c and linear. net_c then has a submodule conv.)

To override the Conv2d with a new submodule Linear, you could call set_submodule("net_b.net_c.conv", nn.Linear(1, 1)) where strict could be True or False

To add a new submodule Conv2d to the existing net_b module, you would call set_submodule("net_b.conv", nn.Conv2d(1, 1, 1)).

In the above if you set strict=True and call set_submodule("net_b.conv", nn.Conv2d(1, 1, 1), strict=True), an AttributeError will be raised because net_b does not have a submodule named conv.

Parameters:

target (str) – The fully-qualified string name of the submodule to look for. (See above example for how to specify a fully-qualified string.)
module (Module) – The module to set the submodule to.
strict (bool) – If False, the method will replace an existing submodule or create a new submodule if the parent module exists. If True, the method will only attempt to replace an existing submodule and throw an error if the submodule doesn’t already exist.

Raises:

ValueError – If the target string is empty or if module is not an instance of nn.Module.
AttributeError – If at any point along the path resulting from the target string the (sub)path resolves to a non-existent attribute name or an object that is not an instance of nn.Module.

Return type:

None

share_memory()#

See torch.Tensor.share_memory_().

Return type:: TypeVar(T, bound= Module)

state_dict(*args, destination=None, prefix='', keep_vars=False)#

Return a dictionary containing references to the whole state of the module.

Both parameters and persistent buffers (e.g. running averages) are included. Keys are corresponding parameter and buffer names. Parameters and buffers set to None are not included.

Note

The returned object is a shallow copy. It contains references to the module’s parameters and buffers.

Warning

Please avoid the use of argument destination as it is not designed for end-users.

Parameters:

destination (dict, optional) – If provided, the state of module will be updated into the dict and the same object is returned. Otherwise, an OrderedDict will be created and returned. Default: None.
prefix (str, optional) – a prefix added to parameter and buffer names to compose the keys in state_dict. Default: ''.
keep_vars (bool, optional) – by default the Tensor s returned in the state dict are detached from autograd. If it’s set to True, detaching will not be performed. Default: False.

Returns:

a dictionary containing a whole state of the module

Return type:

dict

Example:

>>> # xdoctest: +SKIP("undefined vars")
>>> module.state_dict().keys()
['bias', 'weight']

to(*args, **kwargs)#

Move and/or cast the parameters and buffers.

This can be called as

to(device=None, dtype=None, non_blocking=False)

to(dtype, non_blocking=False)

to(tensor, non_blocking=False)

to(memory_format=torch.channels_last)

See below for examples.

Note

This method modifies the module in-place.

Parameters:

device (torch.device) – the desired device of the parameters and buffers in this module
dtype (torch.dtype) – the desired floating point or complex dtype of the parameters and buffers in this module
tensor (torch.Tensor) – Tensor whose dtype and device are the desired dtype and device for all parameters and buffers in this module
memory_format (torch.memory_format) – the desired memory format for 4D parameters and buffers in this module (keyword only argument)

Returns:

self

Return type:

Module

Examples:

>>> # xdoctest: +IGNORE_WANT("non-deterministic")
>>> linear = nn.Linear(2, 2)
>>> linear.weight
Parameter containing:
tensor([[ 0.1913, -0.3420],
        [-0.5113, -0.2325]])
>>> linear.to(torch.double)
Linear(in_features=2, out_features=2, bias=True)
>>> linear.weight
Parameter containing:
tensor([[ 0.1913, -0.3420],
        [-0.5113, -0.2325]], dtype=torch.float64)
>>> # xdoctest: +REQUIRES(env:TORCH_DOCTEST_CUDA1)
>>> gpu1 = torch.device("cuda:1")
>>> linear.to(gpu1, dtype=torch.half, non_blocking=True)
Linear(in_features=2, out_features=2, bias=True)
>>> linear.weight
Parameter containing:
tensor([[ 0.1914, -0.3420],
        [-0.5112, -0.2324]], dtype=torch.float16, device='cuda:1')
>>> cpu = torch.device("cpu")
>>> linear.to(cpu)
Linear(in_features=2, out_features=2, bias=True)
>>> linear.weight
Parameter containing:
tensor([[ 0.1914, -0.3420],
        [-0.5112, -0.2324]], dtype=torch.float16)

>>> linear = nn.Linear(2, 2, bias=None).to(torch.cdouble)
>>> linear.weight
Parameter containing:
tensor([[ 0.3741+0.j,  0.2382+0.j],
        [ 0.5593+0.j, -0.4443+0.j]], dtype=torch.complex128)
>>> linear(torch.ones(3, 2, dtype=torch.cdouble))
tensor([[0.6122+0.j, 0.1150+0.j],
        [0.6122+0.j, 0.1150+0.j],
        [0.6122+0.j, 0.1150+0.j]], dtype=torch.complex128)

to_empty(*, device, recurse=True)#

Move the parameters and buffers to the specified device without copying storage.

Parameters:

device (torch.device) – The desired device of the parameters and buffers in this module.
recurse (bool) – Whether parameters and buffers of submodules should be recursively moved to the specified device.

Returns:

self

Return type:

Module

train(mode=True)#

Set the module in training mode.

Parameters:: mode (bool) – whether to set training mode (True) or evaluation mode (False). Default: True.
Returns:: self
Return type:: Module

type(dst_type)#

Casts all parameters and buffers to dst_type.

Note

This method modifies the module in-place.

Parameters:: dst_type (type or string) – the desired type
Returns:: self
Return type:: Module

xpu(device=None)#

Move all model parameters and buffers to the XPU.

This also makes associated parameters and buffers different objects. So it should be called before constructing optimizer if the module will live on XPU while being optimized.

Note

This method modifies the module in-place.

Parameters:: device (int, optional) – if specified, all parameters will be copied to that device
Returns:: self
Return type:: Module

zero_grad(set_to_none=True)#

Reset gradients of all model parameters.

See similar function under torch.optim.Optimizer for more context.

Parameters:: set_to_none (bool) – instead of setting to zero, set the grads to None. See torch.optim.Optimizer.zero_grad() for details.
Return type:: None

training: bool#