diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 0000000..fc34f9a --- /dev/null +++ b/.gitmodules @@ -0,0 +1,3 @@ +[submodule "synthius/TabDiff"] + path = synthius/TabDiff + url = git@github.com:calgo-lab/TabDiff.git diff --git a/README.md b/README.md index 8686857..e1c1313 100644 --- a/README.md +++ b/README.md @@ -34,4 +34,7 @@ Mac users may encounter errors during installation. To resolve these issues, ins ## Acknowledgments -Special thanks to all contributors and the libraries used in this project. \ No newline at end of file +Special thanks to all contributors and the libraries used in this project. + +This package includes TabDiff (Copyright 2024 Minkai Xu) under the MIT License. +For more details, see synthius/TabDiff/LICENSE. \ No newline at end of file diff --git a/examples/data/adult_subset.csv b/examples/data/adult_subset.csv index 94b5b56..1f8e3c8 100644 --- a/examples/data/adult_subset.csv +++ b/examples/data/adult_subset.csv @@ -1,21 +1,21 @@ -,Unnamed: 0,Age,Workclass,Fnlwgt,Education,Education-num,Marital-status,Occupation,Relationship,Race,Sex,Capital-gain,Capital-loss,Hours-per-week,Native-country,Income -0,12,30,Private,149507,HS-grad,9,Married-civ-spouse,Sales,Husband,White,Male,0,0,42,United-States,True -1,142,52,Private,72743,HS-grad,9,Married-spouse-absent,Adm-clerical,Not-in-family,White,Female,0,0,50,United-States,True 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+imbalanced-learn = ">=0.14.0,<0.15" +kaggle = ">=1.7.4.5,<2.0" +transformers = ">=4.50.3,<5.0" +datasets = ">=2.2.1,<3.0" +peft = ">=0.9.0,<1.0" +ml_collections = ">=1.1.0,<2.0" +prdc = ">=0.2,<0.3" +rdt = ">=1.13.2,<2.0" +openpyxl = ">=3.1.5,<4.0" +xgboost = ">=2.1.3,<3.0" +wandb = ">=0.17.3,<1.0" +kaleido = ">=1.2.0,<2.0" [tool.poetry.group.dev.dependencies] jupyter = "^1.0.0" @@ -77,6 +97,9 @@ ignore = [ "FIX002", # allow TODO without author "ERA001", # allow comment code examples ] +"synthius/TabDiff/**" = [ + "ALL", # ignore all rules for everything in TabDiff +] [tool.ruff.lint.pydocstyle] convention = "google" diff --git a/synthius/TabDiff b/synthius/TabDiff new file mode 160000 index 0000000..09b4977 --- /dev/null +++ b/synthius/TabDiff @@ -0,0 +1 @@ +Subproject commit 09b497721a43693affbafc7bb5f4594dc5f99aca diff --git a/synthius/api/generator.py b/synthius/api/generator.py index a7116ba..493a148 100644 --- a/synthius/api/generator.py +++ b/synthius/api/generator.py @@ -14,6 +14,7 @@ SDVTVAESynthesizer, Synthesizer, SynthesizerGaussianMultivariate, + TabDiffSynthesizer, ) @@ -115,6 +116,7 @@ def _generate( # noqa: PLR0913 SDVTVAESynthesizer(), SynthesizerGaussianMultivariate(results_path=synth_dir), ARFSynthesizer(id_column=id_column), + TabDiffSynthesizer(id_column=id_column), ] # Run each model diff --git a/synthius/data/__init__.py b/synthius/data/__init__.py index ee5e5f3..e7faecb 100644 --- a/synthius/data/__init__.py +++ b/synthius/data/__init__.py @@ -1,5 +1,6 @@ from .continuous_transformer import ContinuousDataTransformer from .data_imputer import DataImputationPreprocessor +from .dataset_torch import TorchDataset from .encoder import CategoricalEncoder, NumericalLabelEncoder from .uniform_encoder import UniformDataEncoder @@ -8,5 +9,6 @@ "ContinuousDataTransformer", "DataImputationPreprocessor", "NumericalLabelEncoder", + "TorchDataset", "UniformDataEncoder", ] diff --git a/synthius/data/data_imputer.py b/synthius/data/data_imputer.py index 99910d6..00a128e 100644 --- a/synthius/data/data_imputer.py +++ b/synthius/data/data_imputer.py @@ -78,6 +78,7 @@ def __init__(self: DataImputationPreprocessor, data: pd.DataFrame, id_column: st self.decimal_places: dict[str, int] = {} self.fill_values: dict[str, float] = {} self.id_column_index: int | None = None + self.original_column_order = data.columns.to_list() self.random_generator = np.random.default_rng() @@ -87,6 +88,8 @@ def __init__(self: DataImputationPreprocessor, data: pd.DataFrame, id_column: st self.data = self.data.drop(self.id_column, axis=1) else: logger.warning("The ID column %s does not exist in the dataset.", self.id_column) + self.cat_cols: list = self.data.select_dtypes(include=["object", "bool"]).columns.to_list() + self.num_cols: list = self.data.select_dtypes(include=["int64", "float64"]).columns.to_list() def get_decimal_places(self: DataImputationPreprocessor, series: pd.Series) -> int: """Calculate the number of decimal places in a given series. @@ -135,11 +138,13 @@ def fit_transform(self: DataImputationPreprocessor) -> pd.DataFrame: return processed_data - def inverse_transform(self: DataImputationPreprocessor, processed_data: pd.DataFrame) -> pd.DataFrame: + def inverse_transform(self: DataImputationPreprocessor, processed_data: pd.DataFrame, multiply_categories: bool = True) -> pd.DataFrame: # noqa: FBT001, FBT002 """Reverse the transformation by scaling back and reintroducing missing values. Args: processed_data (pd.DataFrame): The transformed DataFrame to inverse transform. + multiply_categories (bool, optional): Whether to multiply the categorical columns by their cardinality. + (Note: In TabDiff this is implicitly handled, and we want to avoid it here). Returns: pd.DataFrame: The original DataFrame with imputed values and reintroduced missing values. @@ -156,8 +161,9 @@ def inverse_transform(self: DataImputationPreprocessor, processed_data: pd.DataF if col in self.float_cols: original_data[col] = original_data[col].round(self.decimal_places[col]) elif col not in self.bool_cols: - original_data[col] = (original_data[col] * (self.label_encoders[col].classes_.size - 1)).round().astype(int) - original_data[col] = self.label_encoders[col].inverse_transform(original_data[col]) + if multiply_categories: # in TabDiff this is implicitly handled + original_data[col] = (original_data[col] * (self.label_encoders[col].classes_.size - 1)).round() + original_data[col] = self.label_encoders[col].inverse_transform(original_data[col].astype(int)) # Convert boolean columns back to booleans bool_cols = [col for col in self.bool_cols if col in original_data.columns and col != self.id_column] @@ -181,4 +187,4 @@ def inverse_transform(self: DataImputationPreprocessor, processed_data: pd.DataF random_ids = [f"ID-{rng.integers(10000000, 99999999)}" for _ in range(len(original_data))] original_data.insert(self.id_column_index, self.id_column, random_ids) - return original_data + return original_data[self.original_column_order] diff --git a/synthius/data/dataset_torch.py b/synthius/data/dataset_torch.py new file mode 100644 index 0000000..33c5ebb --- /dev/null +++ b/synthius/data/dataset_torch.py @@ -0,0 +1,26 @@ +import numpy as np +import pandas as pd +from torch.utils.data import Dataset + + +class TorchDataset(Dataset): + """A torch Dataset designed for TabDiff.""" + + def __init__(self, data: pd.DataFrame, d_numerical: int, categories: list[int]) -> None: + """Initialize the torch dataset. + + Args: + data (pd.DataFrame): The data as dataframe. + d_numerical (int): The number of numerical features in `data`. + categories(list[int]): A list with the unique number of categories + for every categorical features in `data`. + """ + self.X = data.to_numpy() + self.d_numerical = d_numerical + self.categories = categories + + def __getitem__(self, index: int) -> np.ndarray: # noqa: D105 + return self.X[index] + + def __len__(self) -> int: # noqa: D105 + return self.X.shape[0] diff --git a/synthius/model/__init__.py b/synthius/model/__init__.py index fa72ca3..fd51cc7 100644 --- a/synthius/model/__init__.py +++ b/synthius/model/__init__.py @@ -8,6 +8,7 @@ SDVTVAESynthesizer, ) from .synthesizer import Synthesizer +from .tabdiff import TabDiffSynthesizer from .wgan import WGAN, WGANSynthesizer __all__ = [ @@ -20,9 +21,9 @@ "SDVCTGANSynthesizer", "SDVCopulaGANSynthesizer", "SDVGaussianCopulaSynthesizer", - "SDVSynthesizer", "SDVTVAESynthesizer", "Synthesizer", "SynthesizerGaussianMultivariate", + "TabDiffSynthesizer", "WGANSynthesizer", ] diff --git a/synthius/model/tabdiff.py b/synthius/model/tabdiff.py new file mode 100644 index 0000000..a6bacaf --- /dev/null +++ b/synthius/model/tabdiff.py @@ -0,0 +1,318 @@ +import logging +from dataclasses import asdict, dataclass +from pathlib import Path + +import numpy as np +import pandas as pd +import tomli +import torch +from torch.utils.data import DataLoader + +from synthius.data import DataImputationPreprocessor, TorchDataset +from synthius.model import Synthesizer +from synthius.TabDiff.src import get_categories +from synthius.TabDiff.tabdiff.models.unified_ctime_diffusion import UnifiedCtimeDiffusion +from synthius.TabDiff.tabdiff.modules.main_modules import Model, UniModMLP +from synthius.TabDiff.tabdiff.trainer import Trainer + +logging.basicConfig(level=logging.INFO, format="%(message)s") +logger = logging.getLogger(__name__) + +TABDIFF_BASE_PATH = Path(__file__).parent / "../TabDiff" +CONFIG_PATH = TABDIFF_BASE_PATH / "tabdiff/configs/tabdiff_configs.toml" + + +@dataclass +class DataConfig: # noqa: D101 + dequant_dist: str + int_dequant_factor: int + + +@dataclass +class UniModMLPParams: # noqa: D101 + num_layers: int + d_token: int + n_head: int + factor: int + bias: bool + dim_t: int + use_mlp: bool + d_numerical: int + categories: list[int] + + +@dataclass +class SamplerParams: # noqa: D101 + stochastic_sampler: bool + second_order_correction: bool + + +@dataclass +class EDMParams: # noqa: D101 + precond: bool + sigma_data: float + net_conditioning: str + + +@dataclass +class NoiseDistParams: # noqa: D101 + P_mean: float + P_std: float + + +@dataclass +class NoiseScheduleParams: # noqa: D101 + sigma_min: float + sigma_max: float + rho: float + eps_max: float + eps_min: float + rho_init: float + rho_offset: float + k_init: float + k_offset: float + + +@dataclass +class DiffusionParams: # noqa: D101 + num_timesteps: int + scheduler: str + cat_scheduler: str + noise_dist: str + sampler_params: SamplerParams + edm_params: EDMParams + noise_dist_params: NoiseDistParams + noise_schedule_params: NoiseScheduleParams + + +@dataclass +class TrainMain: # noqa: D101 + steps: int + lr: float + weight_decay: float + ema_decay: float + batch_size: int + check_val_every: int + lr_scheduler: str + factor: float + reduce_lr_patience: int + closs_weight_schedule: str + c_lambda: float + d_lambda: float + num_workers: int + + +@dataclass +class TrainConfig: # noqa: D101 + main: TrainMain + + +@dataclass +class SampleConfig: # noqa: D101 + batch_size: int + + +@dataclass +class TabDiffConfig: # noqa: D101 + data: DataConfig + unimodmlp_params: UniModMLPParams + diffusion_params: DiffusionParams + train: TrainConfig + sample: SampleConfig + model_save_path: str | Path + result_save_path: str | Path + + +def load_config(path: Path) -> TabDiffConfig: + """Loads the config from `path`. + + Parameters: + path: Path + The path to the config. + + Returns: + TabDiffConfig + The config loaded as TabDiffConfig. + """ + with path.open("rb") as f: + logger.warning("!!Loading the model config %s with the provided parameters in it!!", str(path)) + toml_data = tomli.load(f) + # Build the dataclasses from the TOML + data_cfg = DataConfig(**toml_data["data"]) + + unimodmlp_params = UniModMLPParams(**toml_data["unimodmlp_params"], d_numerical=0, categories=[]) + + diffusion_params = DiffusionParams( + num_timesteps=toml_data["diffusion_params"]["num_timesteps"], + scheduler=toml_data["diffusion_params"]["scheduler"], + cat_scheduler=toml_data["diffusion_params"]["cat_scheduler"], + noise_dist=toml_data["diffusion_params"]["noise_dist"], + sampler_params=SamplerParams(**toml_data["diffusion_params"]["sampler_params"]), + edm_params=EDMParams(**toml_data["diffusion_params"]["edm_params"]), + noise_dist_params=NoiseDistParams(**toml_data["diffusion_params"]["noise_dist_params"]), + noise_schedule_params=NoiseScheduleParams(**toml_data["diffusion_params"]["noise_schedule_params"]), + ) + + train_config = TrainConfig(main=TrainMain(**toml_data["train"]["main"])) + sample_config = SampleConfig(**toml_data["sample"]) + + return TabDiffConfig( + data=data_cfg, + unimodmlp_params=unimodmlp_params, + diffusion_params=diffusion_params, + train=train_config, + sample=sample_config, + model_save_path="", + result_save_path="", + ) + + +class TabDiffSynthesizer(Synthesizer): + """Tabular data synthesizer using a TabDiff::UnifiedCtimeDiffusion model.""" + + def __init__(self, id_column: str | None = None, gpu: int = -1) -> None: + """Initialize the TabDiffSynthesizer.""" + self.exp_name = "learnable_schedule" + self.id_column = id_column + if gpu != -1 and torch.cuda.is_available(): + self.device = f"cuda:{gpu}" + else: + self.device = "cpu" + + self.model: Trainer + self.preprocessor: DataImputationPreprocessor + self.name = "TabDiffSynthesizer" + self.raw_config: TabDiffConfig = load_config(CONFIG_PATH) + self.data_cols: list + self.categories: np.ndarray + + def _update_config(self, data: pd.DataFrame) -> None: + """Updates self.raw_config with metadata from `data`. + + Following the template config from TabDiff, we need to update it with metadata derived + from the categorical features from `data`, a well as the number of numerical columns in `data`. + + Parameters: + data : pd.DataFrame + Tabular dataset used for metadata extraction (originally used for the model training). + """ + self.categories = np.array(get_categories(data[self.preprocessor.cat_cols].to_numpy())) + d_numerical = len(self.preprocessor.float_cols) + len(self.preprocessor.int_cols) + self.raw_config.unimodmlp_params.d_numerical = d_numerical + self.raw_config.unimodmlp_params.categories = (self.categories + 1).tolist() + + self.raw_config.model_save_path = TABDIFF_BASE_PATH / "tabdiff" / f"ckpt/{self.exp_name}" + self.raw_config.result_save_path = TABDIFF_BASE_PATH / "tabdiff" / f"result/{self.exp_name}" + + logger.info("TabDiff: Model save path %s", self.raw_config.model_save_path) + logger.info("TabDiff: Result path %s", self.raw_config.result_save_path) + self.raw_config.model_save_path.mkdir(parents=True, exist_ok=True) + self.raw_config.result_save_path.mkdir(parents=True, exist_ok=True) + + def _generate_processor(self, data: pd.DataFrame) -> None: + """Generates DataImputationPreprocessor from `data` and self.id_column. + + Parameters: + data : pd.DataFrame + Tabular dataset used for creating self.preprocessor (originally used for the model training). + """ + self.preprocessor = DataImputationPreprocessor(data, self.id_column) + self.data_cols = self.preprocessor.num_cols + self.preprocessor.cat_cols + self._update_config(data) + + def _generate_torch_dataset(self) -> tuple[TorchDataset, DataLoader]: + """Generates TorchDataset and DataLoader for TabDiff from self.preprocessor. + + Returns: + tuple[TorchDataset, DataLoader]: The dataset and dataloader for training TabDiff::UnifiedCtimeDiffusion. + """ + preprocessed_data = self.preprocessor.fit_transform() + dataset = TorchDataset( + preprocessed_data[self.data_cols], d_numerical=self.raw_config.unimodmlp_params.d_numerical, categories=self.raw_config.unimodmlp_params.categories + ) + train_loader = DataLoader( + dataset, + batch_size=self.raw_config.train.main.batch_size, + shuffle=True, + num_workers=self.raw_config.train.main.num_workers, + ) + return dataset, train_loader + + def _create_model(self, train_loader: DataLoader, train_dataset: TorchDataset) -> Trainer: + """Creates the model for training (TabDiff::Trainer). + + First creates a UniModMLP then the TabDiff diffusion model - UnifiedCtimeDiffusion, + finally, wraps everything in the Trainer wrapper class from TabDiff. + + Parameters: + train_loader: DataLoader + The torch DataLoader for creating TabDiff::UnifiedCtimeDiffusion. + train_dataset: TorchDataset + The dataset TorchDataset for creating TabDiff::UnifiedCtimeDiffusion. + + Returns: + Trainer + The generated Trainer from TabDiff. + """ + backbone = UniModMLP(**asdict(self.raw_config.unimodmlp_params)) + model = Model(backbone, **asdict(self.raw_config.diffusion_params.edm_params)) + model.to(self.device) + + diffusion = UnifiedCtimeDiffusion( + num_classes=self.categories, + num_numerical_features=self.raw_config.unimodmlp_params.d_numerical, + denoise_fn=model, + y_only_model=None, + **asdict(self.raw_config.diffusion_params), + device=self.device, + ) + diffusion.to(self.device) + diffusion.train() + + sample_batch_size = self.raw_config.sample.batch_size + return Trainer( + diffusion=diffusion, + train_iter=train_loader, + dataset=train_dataset, + test_dataset=None, + metrics=None, + logger=None, + **asdict(self.raw_config.train.main), + sample_batch_size=sample_batch_size, + num_samples_to_generate=0, + model_save_path=self.raw_config.model_save_path, + result_save_path=self.raw_config.result_save_path, + device=self.device, + ckpt_path=None, + y_only=False, + id_col=self.id_column, + ) + + def fit(self, train_data: pd.DataFrame) -> None: + """Fit the TabDiff::UnifiedCtimeDiffusion model to training data. + + Parameters: + train_data : pd.DataFrame + Tabular dataset to train the TabDiff::UnifiedCtimeDiffusion model. + """ + self._generate_processor(train_data) + dataset, data_loader = self._generate_torch_dataset() + self.model = self._create_model(train_dataset=dataset, train_loader=data_loader) + self.model.run_loop() + + def generate(self, total_samples: int, conditions: list | None = None) -> pd.DataFrame: # noqa: ARG002 + """Generate synthetic samples from the fitted TabDiff::UnifiedCtimeDiffusion model. + + Parameters: + total_samples : int + Number of synthetic rows to generate. + conditions : list | None, optional + Currently ignored; included for compatibility with the Synthesizer protocol. + + Returns: + pd.DataFrame + Synthetic samples as a DataFrame with preprocessing reversed. + """ + samples = self.model.sample(total_samples) + data = pd.DataFrame(samples, columns=self.data_cols) + return self.preprocessor.inverse_transform(data, multiply_categories=False) # tabdiff does this on its own diff --git a/synthius/model/wgan.py b/synthius/model/wgan.py index 3784311..36e1e3b 100644 --- a/synthius/model/wgan.py +++ b/synthius/model/wgan.py @@ -281,8 +281,9 @@ def gradient_penalty(self: WGAN, real_data: tf.Tensor, fake_data: tf.Tensor) -> class WGANSynthesizer(Synthesizer): """Tabular data synthesizer using a WGAN (Wasserstein GAN) model.""" - def __init__(self) -> None: + def __init__(self, id_column: str | None = None) -> None: """Initialize the WGANSynthesizer.""" + self.id_column = id_column self.model: WGAN self.preprocessor: DataImputationPreprocessor self.processed_data: pd.DataFrame @@ -296,7 +297,7 @@ def fit(self, train_data: pd.DataFrame) -> None: train_data : pd.DataFrame Tabular dataset to train the WGAN model. """ - self.preprocessor = DataImputationPreprocessor(train_data) + self.preprocessor = DataImputationPreprocessor(train_data, self.id_column) self.processed_data = self.preprocessor.fit_transform() n_features = self.processed_data.shape[1]