Source code for api.types

# TODO: type hint the returns

from typing import Dict, List, Optional, Union
import sys

from type_infer.dtype import dtype

if sys.version_info >= (3, 8):
    from typing import TypedDict
    from typing_extensions import TypedDict

from dataclasses import dataclass
from lightwood.helpers.log import log
from dataclasses_json import dataclass_json
from dataclasses_json.core import _asdict, Json
import json

# See: for how this works
# Not very intuitive but very powerful abstraction, might be useful in other places (@TODO)
[docs]class Module(TypedDict): """ Modules are the blocks of code that end up being called from the JSON AI, representing either object instantiations or function calls. :param module: Name of the module (function or class name) :param args: Argument to pass to the function or constructor """ # noqa module: str args: Dict[str, str]
[docs]@dataclass class TimeseriesSettings: """ For time-series specific problems, more specific treatment of the data is necessary. The following attributes \ enable time-series tasks to be carried out properly. :param is_timeseries: Whether the input data should be treated as time series; if true, this flag is checked in \ subsequent internal steps to ensure processing is appropriate for time-series data. :param order_by: Column by which the data should be ordered. :param group_by: Optional list of columns by which the data should be grouped. Each different combination of values\ for these columns will yield a different series. :param window: The temporal horizon (number of rows) that a model intakes to "look back" into when making a\ prediction, after the rows are ordered by the order_by column and split into groups if applicable. :param horizon: The number of points in the future that predictions should be made for, defaults to 1. Once \ trained, the model will be able to predict up to this many points into the future. :param historical_columns: The temporal dynamics of these columns will be used as additional context to train the \ time series predictor. Note that a non-historical column shall still be used to forecast, but without \ considering their change through time. :param target_type: Automatically inferred dtype of the target (e.g. `dtype.integer`, `dtype.float`). :param use_previous_target: Use the previous values of the target column to generate predictions. Defaults to True. :param allow_incomplete_history: whether predictions can be made for rows with incomplete historical context (i.e. less than `window` rows have been observed for the datetime that has to be forecasted). :param eval_incomplete: whether to consider predictions with incomplete history or target information when evaluating mixer accuracy with the validation dataset. :param interval_periods: tuple of tuples with user-provided period lengths for time intervals. Default values will be added for intervals left unspecified. For interval options, check the `timeseries_analyzer.detect_period()` method documentation. e.g.: (('daily', 7),). """ # noqa is_timeseries: bool order_by: str = None window: int = None group_by: List[str] = None use_previous_target: bool = True horizon: int = None historical_columns: List[str] = None target_type: str = ( "" # @TODO: is the current setter (outside of initialization) a sane option? # @TODO: George: No, I don't think it is, we need to pass this some other way ) allow_incomplete_history: bool = True eval_incomplete: bool = False interval_periods: tuple = tuple()
[docs] @staticmethod def from_dict(obj: Dict): """ Creates a TimeseriesSettings object from python dictionary specifications. :param: obj: A python dictionary with the necessary representation for time-series. The only mandatory columns are ``order_by`` and ``window``. :returns: A populated ``TimeseriesSettings`` object. """ # noqa if len(obj) > 0: for mandatory_setting, etype in zip(["order_by", "window"], [str, int]): if mandatory_setting not in obj: err = f"Missing mandatory timeseries setting: {mandatory_setting}" log.error(err) raise Exception(err) if obj[mandatory_setting] and not isinstance(obj[mandatory_setting], etype): err = f"Wrong type for mandatory timeseries setting '{mandatory_setting}': found '{type(obj[mandatory_setting])}', expected '{etype}'" # noqa log.error(err) raise Exception(err) timeseries_settings = TimeseriesSettings( is_timeseries=True, order_by=obj["order_by"], window=obj["window"], use_previous_target=obj.get("use_previous_target", True), historical_columns=[], horizon=obj.get("horizon", 1), allow_incomplete_history=obj.get('allow_incomplete_history', True), eval_incomplete=obj.get('eval_incomplete', False), interval_periods=obj.get('interval_periods', tuple(tuple())) ) for setting in obj: timeseries_settings.__setattr__(setting, obj[setting]) else: timeseries_settings = TimeseriesSettings(is_timeseries=False) return timeseries_settings
[docs] @staticmethod def from_json(data: str): """ Creates a TimeseriesSettings object from JSON specifications via python dictionary. :param: data: JSON-config file with necessary Time-series specifications :returns: A populated ``TimeseriesSettings`` object. """ return TimeseriesSettings.from_dict(json.loads(data))
[docs] def to_dict(self, encode_json=False) -> Dict[str, Json]: """ Creates a dictionary from ``TimeseriesSettings`` object :returns: A python dictionary containing the ``TimeSeriesSettings`` specifications. """ return _asdict(self, encode_json=encode_json)
[docs] def to_json(self) -> Dict[str, Json]: """ Creates JSON config from TimeseriesSettings object :returns: The JSON config syntax containing the ``TimeSeriesSettings`` specifications. """ return json.dumps(self.to_dict())
[docs]@dataclass class ProblemDefinition: """ The ``ProblemDefinition`` object indicates details on how the models that predict the target are prepared. \ The only required specification from a user is the ``target``, which indicates the column within the input \ data that the user is trying to predict. Within the ``ProblemDefinition``, the user can specify aspects \ about how long the feature-engineering preparation may take, and nuances about training the models. :param target: The name of the target column; this is the column that will be used as the goal of the prediction. :param pct_invalid: Number of data points maximally tolerated as invalid/missing/unknown. \ If the data cleaning process exceeds this number, no subsequent steps will be taken. :param unbias_target: all classes are automatically weighted inverse to how often they occur :param seconds_per_mixer: Number of seconds maximum to spend PER mixer trained in the list of possible mixers. :param seconds_per_encoder: Number of seconds maximum to spend when training an encoder that requires data to \ learn a representation. :param expected_additional_time: Time budget for non-encoder/mixer tasks \ (ex: data analysis, pre-processing, model ensembling or model analysis) :param time_aim: Time budget (in seconds) to train all needed components for the predictive tasks, including \ encoders and models. :param target_weights: indicates to the accuracy functions how much to weight every target class. :param positive_domain: For numerical taks, force predictor output to be positive (integer or float). :param timeseries_settings: TimeseriesSettings object for time-series tasks, refer to its documentation for \ available settings. :param anomaly_detection: Whether to conduct unsupervised anomaly detection; currently supported only for time-\ series. :param dtype_dict: Mapping of features to types (see `mindsdb.type_infer` for all possible values). This will \ override the automated type inference results. :param ignore_features: The names of the columns the user wishes to ignore in the ML pipeline. Any column name \ found in this list will be automatically removed from subsequent steps in the ML pipeline. :param use_default_analysis: whether default analysis blocks are enabled. :param fit_on_all: Whether to fit the model on the held-out validation data. Validation data is strictly \ used to evaluate how well a model is doing and is NEVER trained. However, in cases where users anticipate new \ incoming data over time, the user may train the model further using the entire dataset. :param strict_mode: crash if an `unstable` block (mixer, encoder, etc.) fails to run. :param seed_nr: custom seed to use when generating a predictor from this problem definition. """ target: str pct_invalid: float unbias_target: bool seconds_per_mixer: Optional[int] seconds_per_encoder: Optional[int] expected_additional_time: Optional[int] time_aim: Optional[float] target_weights: Optional[List[float]] positive_domain: bool timeseries_settings: TimeseriesSettings anomaly_detection: bool use_default_analysis: bool dtype_dict: Optional[dict] ignore_features: List[str] fit_on_all: bool strict_mode: bool seed_nr: int
[docs] @staticmethod def from_dict(obj: Dict): """ Creates a ProblemDefinition object from a python dictionary with necessary specifications. :param obj: A python dictionary with the necessary features for the ``ProblemDefinition`` class. Only requires ``target`` to be specified. :returns: A populated ``ProblemDefinition`` object. """ target = obj['target'] pct_invalid = obj.get('pct_invalid', 2) unbias_target = obj.get('unbias_target', True) seconds_per_mixer = obj.get('seconds_per_mixer', None) seconds_per_encoder = obj.get('seconds_per_encoder', None) expected_additional_time = obj.get('expected_additional_time', None) time_aim = obj.get('time_aim', None) if time_aim is not None and time_aim < 10: log.warning(f'Your specified time aim of {time_aim} is too short. Setting it to 10 seconds.') target_weights = obj.get('target_weights', None) positive_domain = obj.get('positive_domain', False) dtype_dict = obj.get('dtype_dict', {}) timeseries_settings = TimeseriesSettings.from_dict(obj.get('timeseries_settings', {})) anomaly_detection = obj.get('anomaly_detection', False) ignore_features = obj.get('ignore_features', []) fit_on_all = obj.get('fit_on_all', True) use_default_analysis = obj.get('use_default_analysis', True) strict_mode = obj.get('strict_mode', True) seed_nr = obj.get('seed_nr', 1) problem_definition = ProblemDefinition( target=target, pct_invalid=pct_invalid, unbias_target=unbias_target, seconds_per_mixer=seconds_per_mixer, seconds_per_encoder=seconds_per_encoder, expected_additional_time=expected_additional_time, time_aim=time_aim, target_weights=target_weights, positive_domain=positive_domain, timeseries_settings=timeseries_settings, anomaly_detection=anomaly_detection, dtype_dict=dtype_dict, ignore_features=ignore_features, use_default_analysis=use_default_analysis, fit_on_all=fit_on_all, strict_mode=strict_mode, seed_nr=seed_nr ) return problem_definition
[docs] @staticmethod def from_json(data: str): """ Creates a ProblemDefinition Object from JSON config file. :param data: :returns: A populated ProblemDefinition object. """ return ProblemDefinition.from_dict(json.loads(data))
[docs] def to_dict(self, encode_json=False) -> Dict[str, Json]: """ Creates a python dictionary from the ProblemDefinition object :returns: A python dictionary """ return _asdict(self, encode_json=encode_json)
[docs] def to_json(self) -> Dict[str, Json]: """ Creates a JSON config from the ProblemDefinition object :returns: TODO """ return json.dumps(self.to_dict())
[docs]@dataclass class JsonAI: """ The JsonAI Class allows users to construct flexible JSON config to specify their ML pipeline. JSON-AI follows a \ recipe of how to pre-process data, construct features, and train on the target column. To do so, the following \ specifications are required internally. :param encoders: A dictionary of the form: `column_name -> encoder module` :param dtype_dict: A dictionary of the form: `column_name -> data type` :param dependency_dict: A dictionary of the form: `column_name -> list of columns it depends on` :param model: The ensemble and its submodels :param problem_definition: The ``ProblemDefinition`` criteria. :param identifiers: A dictionary of column names and respective data types that are likely identifiers/IDs within the data. Through the default cleaning process, these are ignored. :param cleaner: The Cleaner object represents the pre-processing step on a dataframe. The user can specify custom subroutines, if they choose, on how to handle preprocessing. Alternatively, "None" suggests the default approach in ``dataprep_ml.cleaners``. :param splitter: The Splitter object is the method in which the input data is split into training/validation/testing data. For more details, refer to the `dataprep_ml` package documentation. :param analyzer: The Analyzer object is used to evaluate how well a model performed on the predictive task. :param explainer: The Explainer object deploys explainability tools of interest on a model to indicate how well a model generalizes its predictions. :param imputers: A list of objects that will impute missing data on each column. They are called inside the cleaner. :param analysis_blocks: The blocks that get used in both analysis and inference inside the analyzer and explainer blocks. :param timeseries_transformer: Procedure used to transform any timeseries task dataframe into the format that lightwood expects for the rest of the pipeline. :param timeseries_analyzer: Procedure that extracts key insights from any timeseries in the data (e.g. measurement frequency, target distribution, etc). :param accuracy_functions: A list of performance metrics used to evaluate the best mixers. """ # noqa encoders: Dict[str, Module] dtype_dict: Dict[str, dtype] dependency_dict: Dict[str, List[str]] model: Dict[str, Module] problem_definition: ProblemDefinition identifiers: Dict[str, str] cleaner: Optional[Module] = None splitter: Optional[Module] = None analyzer: Optional[Module] = None explainer: Optional[Module] = None imputers: Optional[List[Module]] = None analysis_blocks: Optional[List[Module]] = None timeseries_transformer: Optional[Module] = None timeseries_analyzer: Optional[Module] = None accuracy_functions: Optional[List[str]] = None
[docs] @staticmethod def from_dict(obj: Dict): """ Creates a JSON-AI object from dictionary specifications of the JSON-config. """ encoders = obj["encoders"] dtype_dict = obj["dtype_dict"] dependency_dict = obj["dependency_dict"] model = obj["model"] problem_definition = ProblemDefinition.from_dict(obj["problem_definition"]) identifiers = obj["identifiers"] cleaner = obj.get("cleaner", None) splitter = obj.get("splitter", None) analyzer = obj.get("analyzer", None) explainer = obj.get("explainer", None) imputers = obj.get("imputers", None) analysis_blocks = obj.get("analysis_blocks", None) timeseries_transformer = obj.get("timeseries_transformer", None) timeseries_analyzer = obj.get("timeseries_analyzer", None) accuracy_functions = obj.get("accuracy_functions", None) json_ai = JsonAI( encoders=encoders, dtype_dict=dtype_dict, dependency_dict=dependency_dict, model=model, problem_definition=problem_definition, identifiers=identifiers, cleaner=cleaner, splitter=splitter, analyzer=analyzer, explainer=explainer, imputers=imputers, analysis_blocks=analysis_blocks, timeseries_transformer=timeseries_transformer, timeseries_analyzer=timeseries_analyzer, accuracy_functions=accuracy_functions, ) return json_ai
[docs] @staticmethod def from_json(data: str): """ Creates a JSON-AI object from JSON config""" return JsonAI.from_dict(json.loads(data))
[docs] def to_dict(self, encode_json=False) -> Dict[str, Json]: """ Creates a python dictionary with necessary modules within the ML pipeline specified from the JSON-AI object. :returns: A python dictionary that has the necessary components of the ML pipeline for a given dataset. """ as_dict = _asdict(self, encode_json=encode_json) for k in list(as_dict.keys()): if k == "features": feature_dict = {} for name in self.features: feature_dict[name] = self.features[name].to_dict() as_dict[k] = feature_dict if as_dict[k] is None: del as_dict[k] return as_dict
[docs] def to_json(self) -> Dict[str, Json]: """ Creates JSON config to represent the necessary modules within the ML pipeline specified from the JSON-AI object. :returns: A JSON config that has the necessary components of the ML pipeline for a given dataset. """ return json.dumps(self.to_dict(), indent=4)
[docs]@dataclass_json @dataclass class SubmodelData: name: str accuracy: float is_best: bool
[docs]@dataclass_json @dataclass class ModelAnalysis: """ The ``ModelAnalysis`` class stores useful information to describe a model and understand its predictive performance on a validation dataset. For each trained ML algorithm, we store: :param accuracies: Dictionary with obtained values for each accuracy function (specified in JsonAI) :param accuracy_histogram: Dictionary with histograms of reported accuracy by target value. :param accuracy_samples: Dictionary with sampled pairs of observed target values and respective predictions. :param train_sample_size: Size of the training set (data that parameters are updated on) :param test_sample_size: Size of the testing set (explicitly held out) :param column_importances: Dictionary with the importance of each column for the model, as estimated by an approach that closely follows a leave-one-covariate-out strategy. :param confusion_matrix: A confusion matrix for the validation dataset. :param histograms: Histogram for each dataset feature. :param dtypes: Inferred data types for each dataset feature. """ # noqa accuracies: Dict[str, float] accuracy_histogram: Dict[str, list] accuracy_samples: Dict[str, list] train_sample_size: int test_sample_size: int column_importances: Dict[str, float] confusion_matrix: object histograms: object dtypes: object submodel_data: List[SubmodelData]
[docs]@dataclass class PredictionArguments: """ This class contains all possible arguments that can be passed to a Lightwood predictor at inference time. On each predict call, all arguments included in a parameter dictionary will update the respective fields in the `PredictionArguments` instance that the predictor will have. :param predict_proba: triggers (where supported) predictions in raw probability output form. I.e. for classifiers, instead of returning only the predicted class, the output additionally includes the assigned probability for each class. :param all_mixers: forces an ensemble to return predictions emitted by all its internal mixers. :param mixer_weights: a list with coefficients that are normalized into 0-1 bounded scores to mix the output of all mixers available to a compatible ensemble (e.g. [0.5, 0.5] for an ensemble with two mixers would yield the mean prediction). Can be used with WeightedMeanEnsemble, StackedEnsemble or TsStackedEnsemble. :param fixed_confidence: Used in the ICP analyzer module, specifies an `alpha` fixed confidence so that predictions, in average, are correct `alpha` percent of the time. For unsupervised anomaly detection, this also translates into the expected error rate. Bounded between 0.01 and 0.99 (respectively implies wider and tighter bounds, all other parameters being equal). :param anomaly_cooldown: Sets the minimum amount of timesteps between consecutive firings of the the anomaly detector. :param simple_ts_bounds: in forecasting contexts, enabling this parameter disables the usual conformal-based bounds (with Bonferroni correction) and resorts to a simpler way of scaling bounds through the horizon based on the uncertainty estimation for the first value in the forecast (see helpers.ts.add_tn_num_conf_bounds for the implementation). :param anomaly_cooldown: Sets the minimum amount of timesteps between consecutive firings of the the anomaly \ detector. :param time_format: For time series predictors. If set to `infer`, predicted `order_by` timestamps will be formatted back to the original dataset's `order_by` format. Any other string value will be used as a formatting string, unless empty (''), which disables the feature (this is the default behavior). :param force_ts_infer: For time series predictors. If set to `true`, an additional row will be produced per each group in the input DF, corresponding to an out-of-sample forecast w.r.t. to the input timestamps. """ # noqa predict_proba: bool = True all_mixers: bool = False mixer_weights: list = None fixed_confidence: Union[int, float, None] = None anomaly_cooldown: int = 1 forecast_offset: int = 0 simple_ts_bounds: bool = False time_format: str = '' force_ts_infer: bool = False
[docs] @staticmethod def from_dict(obj: Dict): """ Creates a ``PredictionArguments`` object from a python dictionary with necessary specifications. :param obj: A python dictionary with the necessary features for the ``PredictionArguments`` class. :returns: A populated ``PredictionArguments`` object. """ # maybe this should be stateful instead, and save the latest used value for each field? predict_proba = obj.get('predict_proba', PredictionArguments.predict_proba) all_mixers = obj.get('all_mixers', PredictionArguments.all_mixers) mixer_weights = obj.get('mixer_weights', PredictionArguments.mixer_weights) fixed_confidence = obj.get('fixed_confidence', PredictionArguments.fixed_confidence) anomaly_cooldown = obj.get('anomaly_cooldown', PredictionArguments.anomaly_cooldown) forecast_offset = obj.get('forecast_offset', PredictionArguments.forecast_offset) simple_ts_bounds = obj.get('simple_ts_bounds', PredictionArguments.simple_ts_bounds) time_format = obj.get('time_format', PredictionArguments.time_format) force_ts_infer = obj.get('force_ts_infer', PredictionArguments.force_ts_infer) pred_args = PredictionArguments( predict_proba=predict_proba, all_mixers=all_mixers, mixer_weights=mixer_weights, fixed_confidence=fixed_confidence, anomaly_cooldown=anomaly_cooldown, forecast_offset=forecast_offset, simple_ts_bounds=simple_ts_bounds, time_format=time_format, force_ts_infer=force_ts_infer, ) return pred_args
[docs] def to_dict(self, encode_json=False) -> Dict[str, Json]: """ Creates a python dictionary from the ``PredictionArguments`` object :returns: A python dictionary """ return _asdict(self, encode_json=encode_json)