The fedbiomed.common.training_plans
module includes training plan classes that are used for federated training
Classes
BaseTrainingPlan
BaseTrainingPlan()
Base class for training plan
All concrete, framework- and/or model-specific training plans should inherit from this class, and implement: * the post_init
method: to process model and training hyper-parameters * the training_routine
method: to train the model for one round * the predict
method: to compute predictions over a given batch * (opt.) the testing_step
method: to override the evaluation behavior and compute a batch-wise (set of) metric(s)
Attributes:
Name | Type | Description |
---|---|---|
dataset_path | Union[str, None] | The path that indicates where dataset has been stored |
pre_processes | Dict[str, PreProcessDict] | Preprocess functions that will be applied to the training data at the beginning of the training routine. |
training_data_loader | Union[DataLoader, NPDataLoader, None] | Data loader used in the training routine. |
testing_data_loader | Union[DataLoader, NPDataLoader, None] | Data loader used in the validation routine. |
Source code in fedbiomed/common/training_plans/_base_training_plan.py
def __init__(self) -> None:
"""Construct the base training plan."""
self._dependencies: List[str] = []
self.dataset_path: Union[str, None] = None
self.pre_processes: Dict[str, PreProcessDict] = OrderedDict()
self.training_data_loader: Union[DataLoader, NPDataLoader, None] = None
self.testing_data_loader: Union[DataLoader, NPDataLoader, None] = None
# Arguments provided by the researcher; they will be populated by post_init
self._model_args: Dict[str, Any] = None
self._aggregator_args: Dict[str, Any] = None
self._optimizer_args: Dict[str, Any] = None
self._loader_args: Dict[str, Any] = None
self._training_args: Dict[str, Any] = None
Attributes
Functions
FedPerceptron
FedPerceptron()
Bases: FedSGDClassifier
Fed-BioMed training plan for scikit-learn Perceptron models.
This class inherits from FedSGDClassifier, and forces the wrapped scikit-learn SGDClassifier model to use a "perceptron" loss, that makes it equivalent to an actual scikit-learn Perceptron model.
Source code in fedbiomed/common/training_plans/_sklearn_models.py
def __init__(self) -> None:
"""Class constructor."""
super().__init__()
Functions
FedSGDClassifier
FedSGDClassifier()
Bases: SKLearnTrainingPlanPartialFit
Fed-BioMed training plan for scikit-learn SGDClassifier models.
Source code in fedbiomed/common/training_plans/_sklearn_models.py
def __init__(self) -> None:
"""Initialize the sklearn SGDClassifier training plan."""
super().__init__()
FedSGDRegressor
FedSGDRegressor()
Bases: SKLearnTrainingPlanPartialFit
Fed-BioMed training plan for scikit-learn SGDRegressor models.
Source code in fedbiomed/common/training_plans/_sklearn_models.py
def __init__(self) -> None:
"""Initialize the sklearn SGDRegressor training plan."""
super().__init__()
SKLearnTrainingPlan
SKLearnTrainingPlan()
Bases: BaseTrainingPlan
Base class for Fed-BioMed wrappers of sklearn classes.
Classes that inherit from this abstract class must: - Specify a _model_cls
class attribute that defines the type of scikit-learn model being wrapped for training. - Implement a set_init_params
method that: - sets and assigns the model's initial trainable weights attributes. - populates the _param_list
attribute with names of these attributes. - Implement a _training_routine
method that performs a training round based on self.train_data_loader
(which is a NPDataLoader
).
Attributes:
Name | Type | Description |
---|---|---|
dataset_path | Optional[str] | The path that indicates where dataset has been stored |
pre_processes | Optional[str] | Preprocess functions that will be applied to the training data at the beginning of the training routine. |
training_data_loader | Optional[str] | Data loader used in the training routine. |
testing_data_loader | Optional[str] | Data loader used in the validation routine. |
Notes
The trained model may be exported via the export_model
method, resulting in a dump file that may be reloded using joblib.load
outside of Fed-BioMed.
Source code in fedbiomed/common/training_plans/_sklearn_training_plan.py
def __init__(self) -> None:
"""Initialize the SKLearnTrainingPlan."""
super().__init__()
self._model: Union[SkLearnModel, None] = None
self._training_args = {} # type: Dict[str, Any]
self.__type = TrainingPlans.SkLearnTrainingPlan
self._batch_maxnum = 0
self.dataset_path: Optional[str] = None
self._optimizer: Optional[BaseOptimizer] = None
self.add_dependency([
"import inspect",
"import numpy as np",
"import pandas as pd",
"from fedbiomed.common.training_plans import SKLearnTrainingPlan",
"from fedbiomed.common.data import DataManager",
])
self.add_dependency(list(self._model_dep))
Attributes
Functions
TorchTrainingPlan
TorchTrainingPlan()
Bases: BaseTrainingPlan
Implements TrainingPlan for torch NN framework
An abstraction over pytorch module to run pytorch models and scripts on node side. Researcher model (resp. params) will be:
- saved on a '.py' (resp. '.mpk') files,
- uploaded on a HTTP server (network layer),
- then Downloaded from the HTTP server on node side,
- finally, read and executed on node side.
Researcher must define/override: - a training_data()
function - a training_step()
function
Researcher may have to add extra dependencies/python imports, by using add_dependencies
method.
Attributes:
Name | Type | Description |
---|---|---|
dataset_path | The path that indicates where dataset has been stored | |
pre_processes | Preprocess functions that will be applied to the training data at the beginning of the training routine. | |
training_data_loader | Data loader used in the training routine. | |
testing_data_loader | Data loader used in the validation routine. | |
correction_state | OrderedDict | an OrderedDict of {'parameter name': torch.Tensor} where the keys correspond to the names of the model parameters contained in self._model.named_parameters(), and the values correspond to the correction to be applied to that parameter. |
Notes
The trained model may be exported via the export_model
method, resulting in a dump file that may be reloded using torch.save
outside of Fed-BioMed.
Source code in fedbiomed/common/training_plans/_torchnn.py
def __init__(self):
""" Construct training plan """
super().__init__()
self.__type = TrainingPlans.TorchTrainingPlan
# Differential privacy support
self._dp_controller: Optional[DPController] = None
self._optimizer: Union[BaseOptimizer, None] = None
self._model: Union[TorchModel, None] = None
self._use_gpu: bool = False
self._share_persistent_buffers = None
self._batch_maxnum: int = 100
self._fedprox_mu: Optional[float] = None
self._log_interval: int = 10
self._epochs: int = 1
self._dry_run = False
self._num_updates: Optional[int] = None
self.correction_state: OrderedDict = OrderedDict()
self.aggregator_name: str = None
# TODO : add random seed init
# self.random_seed_params = None
# self.random_seed_shuffling_data = None
# device to use: cpu/gpu
# - all operations except training only use cpu
# - researcher doesn't request to use gpu by default
self._device_init: str = "cpu"
self._device = self._device_init
# list dependencies of the model
self.add_dependency(["import torch",
"import torch.nn as nn",
"import torch.nn.functional as F",
"from fedbiomed.common.training_plans import TorchTrainingPlan",
"from fedbiomed.common.data import DataManager",
"from fedbiomed.common.constants import ProcessTypes",
"from torch.utils.data import DataLoader",
"from torchvision import datasets, transforms"
])
Attributes
Functions
Accounting class for keeping track of training iterations.
This class has the following responsibilities:
- manage iterators for epochs and batches
- provide up-to-date values for reporting
- handle different semantics in case the researcher asked for num_updates or epochs
We assume that the underlying implementation for the training loop is always made in terms of epochs and batches. So the primary purpose of this class is to provide a way to correctly convert the number of updates into epochs and batches.
For reporting purposes, in the case of num_updates then we think of the training as a single big loop, while in the case of epochs and batches we think of it as two nested loops. This changes the meaning of the values outputted by the reporting functions (see their docstrings for more details).
Attributes:
Name | Type | Description |
---|---|---|
_training_plan | a reference to the training plan executing the training iterations | |
cur_epoch | int | the index of the current epoch during iterations |
cur_batch | int | the index of the current batch during iterations |
epochs | int | the total number of epochs to be performed (we always perform one additional -- possibly empty -- epoch |
num_batches_per_epoch | int | the number of iterations per epoch |
num_batches_in_last_epoch | int | the number of iterations in the last epoch (can be zero) |
num_samples_observed_in_epoch | int | a counter for the number of samples observed in the current epoch, for reporting |
num_samples_observed_in_total | int | a counter for the number of samples observed total, for reporting |
Parameters:
Name | Type | Description | Default |
---|---|---|---|
training_plan | TBaseTrainingPlan | a reference to the training plan that is executing the training iterations | required |
Source code in fedbiomed/common/training_plans/_training_iterations.py
def __init__(self, training_plan: TBaseTrainingPlan):
"""Initialize the class.
Arguments:
training_plan: a reference to the training plan that is executing the training iterations
"""
self._training_plan = training_plan
self.cur_epoch: int = 0
self.cur_batch: int = 0
self.epochs: int = 0
self.num_batches_per_epoch: int = 0
self.num_batches_in_last_epoch: int = 0
self.num_samples_observed_in_epoch: int = 0
self.num_samples_observed_in_total: int = 0
self._n_training_iterations()
Attributes
cur_batch instance-attribute
cur_batch: int = 0
cur_epoch instance-attribute
cur_epoch: int = 0
epochs instance-attribute
epochs: int = 0
num_batches_in_last_epoch instance-attribute
num_batches_in_last_epoch: int = 0
num_batches_per_epoch instance-attribute
num_batches_per_epoch: int = 0
num_samples_observed_in_epoch instance-attribute
num_samples_observed_in_epoch: int = 0
num_samples_observed_in_total instance-attribute
num_samples_observed_in_total: int = 0
Classes
BatchIter
BatchIter(accountant)
Iterator over batches.
Attributes:
Name | Type | Description |
---|---|---|
_accountant | an instance of the class that created this iterator |
Source code in fedbiomed/common/training_plans/_training_iterations.py
def __init__(self, accountant: TTrainingIterationsAccountant):
self._accountant = accountant
EpochsIter
EpochsIter(accountant)
Iterator over epochs.
Attributes:
Name | Type | Description |
---|---|---|
_accountant | an instance of the class that created this iterator |
Source code in fedbiomed/common/training_plans/_training_iterations.py
def __init__(self, accountant: TTrainingIterationsAccountant):
self._accountant = accountant
Functions
increment_sample_counters
increment_sample_counters(n_samples)
Increments internal counter for numbers of observed samples
Source code in fedbiomed/common/training_plans/_training_iterations.py
def increment_sample_counters(self, n_samples: int):
"""Increments internal counter for numbers of observed samples"""
self.num_samples_observed_in_epoch += n_samples
self.num_samples_observed_in_total += n_samples
iterate_batches
iterate_batches()
Returns an instance of a batches iterator.
Source code in fedbiomed/common/training_plans/_training_iterations.py
def iterate_batches(self):
"""Returns an instance of a batches iterator."""
return MiniBatchTrainingIterationsAccountant.BatchIter(self)
iterate_epochs
iterate_epochs()
Returns an instance of an epochs iterator.
Source code in fedbiomed/common/training_plans/_training_iterations.py
def iterate_epochs(self):
"""Returns an instance of an epochs iterator."""
return MiniBatchTrainingIterationsAccountant.EpochsIter(self)
num_batches_in_this_epoch
num_batches_in_this_epoch()
Returns the number of iterations to be performed in the current epoch
Source code in fedbiomed/common/training_plans/_training_iterations.py
def num_batches_in_this_epoch(self) -> int:
"""Returns the number of iterations to be performed in the current epoch"""
if self.cur_epoch == self.epochs:
return self.num_batches_in_last_epoch
else:
return self.num_batches_per_epoch
reporting_on_epoch
reporting_on_epoch()
Returns the optional index of the current epoch, for reporting.
Source code in fedbiomed/common/training_plans/_training_iterations.py
def reporting_on_epoch(self) -> Optional[int]:
"""Returns the optional index of the current epoch, for reporting."""
if self._training_plan.training_args()['num_updates'] is not None:
return None
else:
return self.cur_epoch
reporting_on_num_iter
reporting_on_num_iter()
Outputs useful reporting information about the number of iterations
If the researcher specified num_updates, then the iteration number will be the cumulated total, and similarly the maximum number of iterations will be equal to the requested number of updates. If the researcher specified epochs, then the iteration number will be the batch index in the current epoch, while the maximum number of iterations will be computed specifically for the current epoch.
Returns:
Type | Description |
---|---|
int | the iteration number |
int | the maximum number of iterations to be reported |
Source code in fedbiomed/common/training_plans/_training_iterations.py
def reporting_on_num_iter(self) -> Tuple[int, int]:
"""Outputs useful reporting information about the number of iterations
If the researcher specified num_updates, then the iteration number will be the cumulated total, and
similarly the maximum number of iterations will be equal to the requested number of updates.
If the researcher specified epochs, then the iteration number will be the batch index in the current epoch,
while the maximum number of iterations will be computed specifically for the current epoch.
Returns:
the iteration number
the maximum number of iterations to be reported
"""
if self._training_plan.training_args()['num_updates'] is not None:
num_iter = (self.cur_epoch - 1) * self.num_batches_per_epoch + self.cur_batch
total_batches_to_be_observed = (self.epochs - 1) * self.num_batches_per_epoch + \
self.num_batches_in_last_epoch
num_iter_max = total_batches_to_be_observed
else:
num_iter = self.cur_batch
num_iter_max = self.num_batches_per_epoch
return num_iter, num_iter_max
reporting_on_num_samples
reporting_on_num_samples()
Outputs useful reporting information about the number of observed samples
If the researcher specified num_updates, then the number of observed samples will be the grand total, and similarly the maximum number of samples will be the grand total over all iterations. If the researcher specified epochs, then both values will be specific to the current epoch.
Returns:
Type | Description |
---|---|
int | the number of samples observed until the current iteration |
int | the maximum number of samples to be observed |
Source code in fedbiomed/common/training_plans/_training_iterations.py
def reporting_on_num_samples(self) -> Tuple[int, int]:
"""Outputs useful reporting information about the number of observed samples
If the researcher specified num_updates, then the number of observed samples will be the grand total, and
similarly the maximum number of samples will be the grand total over all iterations.
If the researcher specified epochs, then both values will be specific to the current epoch.
Returns:
the number of samples observed until the current iteration
the maximum number of samples to be observed
"""
# get batch size
if 'batch_size' in self._training_plan.loader_args():
batch_size = self._training_plan.loader_args()['batch_size']
else:
raise FedbiomedUserInputError('Missing required key `batch_size` in `loader_args`.')
# compute number of observed samples
if self._training_plan.training_args()['num_updates'] is not None:
num_samples = self.num_samples_observed_in_total
total_batches_to_be_observed = (self.epochs - 1) * self.num_batches_per_epoch + \
self.num_batches_in_last_epoch
total_n_samples_to_be_observed = batch_size * total_batches_to_be_observed
num_samples_max = total_n_samples_to_be_observed
else:
num_samples = self.num_samples_observed_in_epoch
num_samples_max = batch_size*self.num_batches_in_this_epoch() if \
self.cur_batch < self.num_batches_in_this_epoch() else num_samples
return num_samples, num_samples_max
should_log_this_batch
should_log_this_batch()
Whether the current batch should be logged or not.
A batch shall be logged if at least one of the following conditions is True:
- the cumulative batch index is a multiple of the logging interval
- the dry_run condition was specified by the researcher
- it is the last batch of the epoch
- it is the first batch of the epoch
Source code in fedbiomed/common/training_plans/_training_iterations.py
def should_log_this_batch(self) -> bool:
"""Whether the current batch should be logged or not.
A batch shall be logged if at least one of the following conditions is True:
- the cumulative batch index is a multiple of the logging interval
- the dry_run condition was specified by the researcher
- it is the last batch of the epoch
- it is the first batch of the epoch
"""
current_iter = (self.cur_epoch - 1) * self.num_batches_per_epoch + self.cur_batch
return (current_iter % self._training_plan.training_args()['log_interval'] == 0 or
self._training_plan.training_args()['dry_run'] or
self.cur_batch >= self.num_batches_in_this_epoch() or # last batch
self.cur_batch == 1) # first batch