Source code for pypots.imputation.koopa.model

"""
The implementation of Koopa for the partially-observed time-series imputation task.

"""

# Created by Wenjie Du <wenjay.du@gmail.com>
# License: BSD-3-Clause

import math
from typing import Union, Optional

import numpy as np
import torch
from torch.utils.data import DataLoader

from .core import _Koopa
from .data import DatasetForKoopa
from ..base import BaseNNImputer
from ...data.checking import key_in_data_set
from ...data.dataset import BaseDataset
from ...optim.adam import Adam
from ...optim.base import Optimizer


[docs] class Koopa(BaseNNImputer): """The PyTorch implementation of the Koopa model. Koopa is originally proposed by Liu et al. in :cite:`liu2023koopa`. Parameters ---------- n_steps : The number of time steps in the time-series data sample. n_features : The number of features in the time-series data sample. n_seg_steps : Segment length of time series. d_dynamic : Latent dimension of koopman embedding. d_hidden : The dimension of the hidden layers in the model. n_hidden_layers : The number of hidden layers in the model. n_blocks : The number of blocks in the model. multistep : Whether to use the multistep approximation for multistep K in the model. alpha : spectrum filter ratio ORT_weight : The weight for the ORT loss, the same as SAITS. MIT_weight : The weight for the MIT loss, the same as SAITS. batch_size : The batch size for training and evaluating the model. epochs : The number of epochs for training the model. patience : The patience for the early-stopping mechanism. Given a positive integer, the training process will be stopped when the model does not perform better after that number of epochs. Leaving it default as None will disable the early-stopping. optimizer : The optimizer for model training. If not given, will use a default Adam optimizer. num_workers : The number of subprocesses to use for data loading. `0` means data loading will be in the main process, i.e. there won't be subprocesses. device : The device for the model to run on. It can be a string, a :class:`torch.device` object, or a list of them. If not given, will try to use CUDA devices first (will use the default CUDA device if there are multiple), then CPUs, considering CUDA and CPU are so far the main devices for people to train ML models. If given a list of devices, e.g. ['cuda:0', 'cuda:1'], or [torch.device('cuda:0'), torch.device('cuda:1')] , the model will be parallely trained on the multiple devices (so far only support parallel training on CUDA devices). Other devices like Google TPU and Apple Silicon accelerator MPS may be added in the future. saving_path : The path for automatically saving model checkpoints and tensorboard files (i.e. loss values recorded during training into a tensorboard file). Will not save if not given. model_saving_strategy : The strategy to save model checkpoints. It has to be one of [None, "best", "better", "all"]. No model will be saved when it is set as None. The "best" strategy will only automatically save the best model after the training finished. The "better" strategy will automatically save the model during training whenever the model performs better than in previous epochs. The "all" strategy will save every model after each epoch training. """ def __init__( self, n_steps: int, n_features: int, n_seg_steps: int, d_dynamic: int, d_hidden: int, n_hidden_layers: int, n_blocks: int, multistep: bool = False, alpha: int = 0.2, ORT_weight: float = 1, MIT_weight: float = 1, batch_size: int = 32, epochs: int = 100, patience: int = None, optimizer: Optional[Optimizer] = Adam(), num_workers: int = 0, device: Optional[Union[str, torch.device, list]] = None, saving_path: str = None, model_saving_strategy: Optional[str] = "best", ): super().__init__( batch_size, epochs, patience, num_workers, device, saving_path, model_saving_strategy, ) self.n_steps = n_steps self.n_features = n_features # model hype-parameters self.n_seg_steps = n_seg_steps self.d_dynamic = d_dynamic self.d_hidden = d_hidden self.n_hidden_layers = n_hidden_layers self.n_blocks = n_blocks self.multistep = multistep self.alpha = alpha assert ( math.ceil(n_steps / n_seg_steps) > 1 ), "n_seg_steps should be smaller than n_steps." self.ORT_weight = ORT_weight self.MIT_weight = MIT_weight # set up the model self.model = _Koopa( self.n_steps, self.n_features, self.n_seg_steps, self.d_dynamic, self.d_hidden, self.n_hidden_layers, self.n_blocks, self.multistep, self.alpha, self.ORT_weight, self.MIT_weight, ) self._send_model_to_given_device() self._print_model_size() # set up the optimizer self.optimizer = optimizer self.optimizer.init_optimizer(self.model.parameters()) def _assemble_input_for_training(self, data: list) -> dict: ( indices, X, missing_mask, X_ori, indicating_mask, ) = self._send_data_to_given_device(data) inputs = { "X": X, "missing_mask": missing_mask, "X_ori": X_ori, "indicating_mask": indicating_mask, } return inputs def _assemble_input_for_validating(self, data: list) -> dict: return self._assemble_input_for_training(data) def _assemble_input_for_testing(self, data: list) -> dict: indices, X, missing_mask = self._send_data_to_given_device(data) inputs = { "X": X, "missing_mask": missing_mask, } return inputs
[docs] def fit( self, train_set: Union[dict, str], val_set: Optional[Union[dict, str]] = None, file_type: str = "hdf5", ) -> None: # Step 1: wrap the input data with classes Dataset and DataLoader training_set = DatasetForKoopa( train_set, return_X_ori=False, return_y=False, file_type=file_type ) training_loader = DataLoader( training_set, batch_size=self.batch_size, shuffle=True, num_workers=self.num_workers, ) val_loader = None if val_set is not None: if not key_in_data_set("X_ori", val_set): raise ValueError("val_set must contain 'X_ori' for model validation.") val_set = DatasetForKoopa( val_set, return_X_ori=True, return_y=False, file_type=file_type ) val_loader = DataLoader( val_set, batch_size=self.batch_size, shuffle=False, num_workers=self.num_workers, ) # WDU: init the mask spectrum for the Koopa model self.model.backbone.init_mask_spectrum(training_loader) # Step 2: train the model and freeze it self._train_model(training_loader, val_loader) self.model.load_state_dict(self.best_model_dict) self.model.eval() # set the model as eval status to freeze it. # Step 3: save the model if necessary self._auto_save_model_if_necessary(confirm_saving=True)
[docs] def predict( self, test_set: Union[dict, str], file_type: str = "hdf5", ) -> dict: """Make predictions for the input data with the trained model. Parameters ---------- test_set : dict or str The dataset for model validating, should be a dictionary including keys as 'X', or a path string locating a data file supported by PyPOTS (e.g. h5 file). If it is a dict, X should be array-like of shape [n_samples, sequence length (n_steps), n_features], which is time-series data for validating, can contain missing values, and y should be array-like of shape [n_samples], which is classification labels of X. If it is a path string, the path should point to a data file, e.g. a h5 file, which contains key-value pairs like a dict, and it has to include keys as 'X' and 'y'. file_type : The type of the given file if test_set is a path string. Returns ------- file_type : The dictionary containing the clustering results and latent variables if necessary. """ # Step 1: wrap the input data with classes Dataset and DataLoader self.model.eval() # set the model as eval status to freeze it. test_set = BaseDataset( test_set, return_X_ori=False, return_X_pred=False, return_y=False, file_type=file_type, ) test_loader = DataLoader( test_set, batch_size=self.batch_size, shuffle=False, num_workers=self.num_workers, ) imputation_collector = [] # Step 2: process the data with the model with torch.no_grad(): for idx, data in enumerate(test_loader): inputs = self._assemble_input_for_testing(data) results = self.model.forward(inputs, training=False) imputation_collector.append(results["imputed_data"]) # Step 3: output collection and return imputation = torch.cat(imputation_collector).cpu().detach().numpy() result_dict = { "imputation": imputation, } return result_dict
[docs] def impute( self, test_set: Union[dict, str], file_type: str = "hdf5", ) -> np.ndarray: """Impute missing values in the given data with the trained model. Parameters ---------- test_set : The data samples for testing, should be array-like of shape [n_samples, sequence length (n_steps), n_features], or a path string locating a data file, e.g. h5 file. file_type : The type of the given file if X is a path string. Returns ------- array-like, shape [n_samples, sequence length (n_steps), n_features], Imputed data. """ result_dict = self.predict(test_set, file_type=file_type) return result_dict["imputation"]