Old config utils

This file is part of the TPOT library.

The current version of TPOT was developed at Cedars-Sinai by: - Pedro Henrique Ribeiro (https://github.com/perib, https://www.linkedin.com/in/pedro-ribeiro/) - Anil Saini (anil.saini@cshs.org) - Jose Hernandez (jgh9094@gmail.com) - Jay Moran (jay.moran@cshs.org) - Nicholas Matsumoto (nicholas.matsumoto@cshs.org) - Hyunjun Choi (hyunjun.choi@cshs.org) - Miguel E. Hernandez (miguel.e.hernandez@cshs.org) - Jason Moore (moorejh28@gmail.com)

The original version of TPOT was primarily developed at the University of Pennsylvania by: - Randal S. Olson (rso@randalolson.com) - Weixuan Fu (weixuanf@upenn.edu) - Daniel Angell (dpa34@drexel.edu) - Jason Moore (moorejh28@gmail.com) - and many more generous open-source contributors

TPOT is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

TPOT is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.

You should have received a copy of the GNU Lesser General Public License along with TPOT. If not, see http://www.gnu.org/licenses/.

convert_config_dict_to_choicepipeline(config_dict)

Takes in a TPOT2 config dictionary and returns a ChoicePipeline search space that represents the config_dict. This space will sample from all included modules in the config_dict.

Parameters:

Name	Type	Description	Default
config_dict	dict	The dictionary representation of the TPOT2 config.	required

Returns:

Type	Description
ChoicePipeline	A ChoicePipeline search space that represents the config_dict.

Source code in tpot2/old_config_utils/old_config_utils.py

def convert_config_dict_to_choicepipeline(config_dict):
    """
    Takes in a TPOT2 config dictionary and returns a ChoicePipeline search space that represents the config_dict.
    This space will sample from all included modules in the config_dict.

    Parameters
    ----------
    config_dict : dict
        The dictionary representation of the TPOT2 config.

    Returns
    -------
    ChoicePipeline
        A ChoicePipeline search space that represents the config_dict.
    """
    search_spaces = []
    for key, value in config_dict.items():
        search_spaces.append(get_node_space(key, value))
    return ChoicePipeline(search_spaces)

convert_config_dict_to_graphpipeline(config_dict)

Takes in a TPOT2 config dictionary and returns a GraphSearchPipeline search space that represents the config_dict. This space will sample from all included modules in the config_dict. It will also identify classifiers/regressors to set the search space for the root node.

Note doesn't convert estimators so they passthrough inputs like in TPOT1

Parameters:

Name	Type	Description	Default
config_dict	dict	The dictionary representation of the TPOT2 config.	required

Returns:

Type	Description
GraphSearchPipeline	A GraphSearchPipeline search space that represents the config_dict.

Source code in tpot2/old_config_utils/old_config_utils.py

def convert_config_dict_to_graphpipeline(config_dict):
    """
    Takes in a TPOT2 config dictionary and returns a GraphSearchPipeline search space that represents the config_dict.
    This space will sample from all included modules in the config_dict. It will also identify classifiers/regressors to set the search space for the root node.

    Note doesn't convert estimators so they passthrough inputs like in TPOT1
    Parameters
    ----------
    config_dict : dict
        The dictionary representation of the TPOT2 config.

    Returns
    -------
    GraphSearchPipeline
        A GraphSearchPipeline search space that represents the config_dict.
    """
    root_search_spaces = []
    inner_search_spaces = []

    for key, value in config_dict.items():
        #if root
        if issubclass(load_get_module_from_string(key), sklearn.base.ClassifierMixin) or issubclass(load_get_module_from_string(key), sklearn.base.RegressorMixin):
            root_search_spaces.append(get_node_space(key, value))
        else:
            inner_search_spaces.append(get_node_space(key, value))

    if len(root_search_spaces) == 0:
        Warning("No classifiers or regressors found, allowing any estimator to be the root node")
        root_search_spaces = inner_search_spaces

    #merge inner and root search spaces

    inner_space = np.concatenate([root_search_spaces,inner_search_spaces])

    root_space = ChoicePipeline(root_search_spaces)
    inner_space = ChoicePipeline(inner_search_spaces)

    final_space = GraphSearchPipeline(root_search_space=root_space, inner_search_space=inner_space)
    return final_space

convert_config_dict_to_linearpipeline(config_dict)

Takes in a TPOT2 config dictionary and returns a GraphSearchPipeline search space that represents the config_dict. This space will sample from all included modules in the config_dict. It will also identify classifiers/regressors to set the search space for the root node.

Note doesn't convert estimators so they passthrough inputs like in TPOT1

Parameters:

Name	Type	Description	Default
config_dict	dict	The dictionary representation of the TPOT2 config.	required

Returns:

Type	Description
GraphSearchPipeline	A GraphSearchPipeline search space that represents the config_dict.

Source code in tpot2/old_config_utils/old_config_utils.py

def convert_config_dict_to_linearpipeline(config_dict):
    """
    Takes in a TPOT2 config dictionary and returns a GraphSearchPipeline search space that represents the config_dict.
    This space will sample from all included modules in the config_dict. It will also identify classifiers/regressors to set the search space for the root node.

    Note doesn't convert estimators so they passthrough inputs like in TPOT1
    Parameters
    ----------
    config_dict : dict
        The dictionary representation of the TPOT2 config.

    Returns
    -------
    GraphSearchPipeline
        A GraphSearchPipeline search space that represents the config_dict.
    """
    root_search_spaces = []
    inner_search_spaces = []

    for key, value in config_dict.items():
        #if root
        if issubclass(load_get_module_from_string(key), sklearn.base.ClassifierMixin) or issubclass(load_get_module_from_string(key), sklearn.base.RegressorMixin):
            root_search_spaces.append(get_node_space(key, value))
        else:
            inner_search_spaces.append(get_node_space(key, value))

    if len(root_search_spaces) == 0:
        Warning("No classifiers or regressors found, allowing any estimator to be the root node")
        root_search_spaces = inner_search_spaces

    #merge inner and root search spaces

    inner_space = np.concatenate([root_search_spaces,inner_search_spaces])

    root_space = ChoicePipeline(root_search_spaces)
    inner_space = ChoicePipeline(inner_search_spaces)

    final_space = SequentialPipeline([
        DynamicLinearPipeline(inner_space, 10),
        root_space
    ])
    return final_space

convert_config_dict_to_list(config_dict)

Takes in a TPOT2 config dictionary and returns a list of search spaces (EstimatorNode, WrapperPipeline)

Parameters:

Name	Type	Description	Default
config_dict	dict	The dictionary representation of the TPOT2 config.	required

Returns:

Type	Description
list	A list of search spaces (EstimatorNode, WrapperPipeline) that represent the config_dict.

Source code in tpot2/old_config_utils/old_config_utils.py

def convert_config_dict_to_list(config_dict):
    """
    Takes in a TPOT2 config dictionary and returns a list of search spaces (EstimatorNode, WrapperPipeline)

    Parameters
    ----------
    config_dict : dict
        The dictionary representation of the TPOT2 config.

    Returns
    -------
    list
        A list of search spaces (EstimatorNode, WrapperPipeline) that represent the config_dict.
    """
    search_spaces = []
    for key, value in config_dict.items():
        search_spaces.append(get_node_space(key, value))
    return search_spaces

get_node_space(module_string, params)

Create the search space for a single node in the TPOT2 config.

Parameters:

Name	Type	Description	Default
module_string	str	The string representation of the module and class to load. E.g. 'sklearn.ensemble.RandomForestClassifier'	required
params	dict	The dictionary representation of the hyperparameter search space for the module_string.	required

Returns:

Type	Description
EstimatorNode or WrapperPipeline

Source code in tpot2/old_config_utils/old_config_utils.py

def get_node_space(module_string, params):
    """
    Create the search space for a single node in the TPOT2 config.

    Parameters
    ----------
    module_string : str
        The string representation of the module and class to load. E.g. 'sklearn.ensemble.RandomForestClassifier'
    params : dict
        The dictionary representation of the hyperparameter search space for the module_string.

    Returns
    -------
    EstimatorNode or WrapperPipeline
    """
    method = load_get_module_from_string(module_string)
    config_space = ConfigurationSpace()
    sub_space = None
    sub_space_name = None

    function_params_conversion_dict = {}

    if params is None:
        return EstimatorNode(method=method, space=config_space)

    for param_name, param in params.items():
        if param is None:
            config_space.add(Categorical(param_name, [None]))

        if isinstance(param, range):
            param = list(param)

        if isinstance(param, list) or isinstance(param, np.ndarray):
            if len(param) == 1:
                p = param[0]
                config_space.add(ConfigSpace.hyperparameters.Constant(param_name, p))
            else:
                config_space.add(Categorical(param_name, param))
            # if all(isinstance(i, int) for i in param):
            #     config_space.add_hyperparameter(Integer(param_name, (min(param), max(param))))
            # elif all(isinstance(i, float) for i in param):
            #     config_space.add_hyperparameter(Float(param_name, (min(param), max(param))))
            # else:
            #     config_space.add_hyperparameter(Categorical(param_name, param))
        elif isinstance(param, dict): #TPOT1 config dicts have dictionaries for values of hyperparameters that are either a function or an estimator
            if len(param) > 1:
                    raise ValueError(f"Multiple items in dictionary entry for {param_name}")

            key = list(param.keys())[0]

            innermethod = load_get_module_from_string(key)

            if inspect.isclass(innermethod) and issubclass(innermethod, sklearn.base.BaseEstimator): #is an estimator
                if sub_space is None:
                    sub_space_name = param_name
                    sub_space = get_node_space(key, param[key])   
                else:
                    raise ValueError("Only multiple hyperparameters are estimators. Only one parameter ")

            else: #assume the key is a function and ignore the value
                function_params_conversion_dict[param_name] = innermethod

        else:
            # config_space.add_hyperparameter(Categorical(param_name, param))
            config_space.add(ConfigSpace.hyperparameters.Constant(param_name, param))

    parser=None
    if len(function_params_conversion_dict) > 0:
        parser = partial(hyperparameter_parser, function_params_conversion_dict)


    if sub_space is None:

        if parser is not None:
            return EstimatorNode(method=method, space=config_space, hyperparameter_parser=parser)
        else:
            return EstimatorNode(method=method, space=config_space)


    else:
        if parser is not None:
            return WrapperPipeline(method=method, space=config_space, estimator_search_space=sub_space, wrapped_param_name=sub_space_name, hyperparameter_parser=parser)
        else:
            return WrapperPipeline(method=method, space=config_space, estimator_search_space=sub_space, wrapped_param_name=sub_space_name)

load_get_module_from_string(module_string)

Takes a string in the form of 'module.submodule.class' and returns the class.

Parameters:

Name	Type	Description	Default
module_string	str	The string representation of the module and class to load.	required

Returns:

Type	Description
class	The class that was loaded from the module string.

Source code in tpot2/old_config_utils/old_config_utils.py

def load_get_module_from_string(module_string):
    """
    Takes a string in the form of 'module.submodule.class' and returns the class.

    Parameters
    ----------
    module_string : str
        The string representation of the module and class to load.

    Returns
    -------
    class
        The class that was loaded from the module string.
    """
    module_name, class_name = module_string.rsplit('.', 1)
    module = __import__(module_name, fromlist=[class_name])
    return getattr(module, class_name)