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Feat - Meta Data Added
Browse files- README.md +49 -23
- configuration_autoencoder.py +25 -3
- modeling_autoencoder.py +359 -21
README.md
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# Autoencoder Implementation for Hugging Face Transformers
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A complete autoencoder implementation that integrates seamlessly with the Hugging Face Transformers ecosystem, providing all the standard functionality you expect from transformer models.
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- **Multiple Loss Functions**: Support for MSE, BCE, L1, Huber, Smooth L1, KL Divergence, Cosine, Focal, Dice, Tversky, SSIM, and Perceptual loss
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- **Multiple Autoencoder Types (7)**: Classic, Variational (VAE), Beta-VAE, Denoising, Sparse, Contractive, and Recurrent autoencoders
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- **Extended Activation Functions**: 18+ activation functions including ReLU, GELU, Swish, Mish, ELU, and more
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- **Learnable Preprocessing**: Neural Scaler
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- **Extensible Design**: Easy to extend for new autoencoder variants and custom loss functions
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- **Production Ready**: Proper serialization, checkpointing, and inference support
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## 📦 Installation
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```bash
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uv sync # or: pip install -e .
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```
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Dependencies (see pyproject.toml):
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- `torch>=2.8.0`
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- `transformers>=4.55.2`
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- `numpy>=2.3.2`
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- `scikit-learn>=1.7.1`
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- `datasets>=4.0.0`
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- `accelerate>=1.10.0`
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## 🏗️ Architecture
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Note: This repository has been trimmed to essentials for easy reuse and distribution. Example scripts and tests were removed by request.
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The implementation consists of three main components:
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### 1. AutoencoderConfig
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autoencoder_type="classic", # Autoencoder type (7 types available)
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# Optional learnable preprocessing
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use_learnable_preprocessing=True,
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preprocessing_type="neural_scaler", # or "normalizing_flow"
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)
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# Create model
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class AutoencoderDataset(Dataset):
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def __init__(self, data):
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self.data = torch.FloatTensor(data)
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def __len__(self):
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return len(self.data)
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def __getitem__(self, idx):
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return {
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"input_values": self.data[idx],
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## 📊 Model Outputs
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### AutoencoderOutput
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```python
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@dataclass
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class AutoencoderOutput(ModelOutput):
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last_hidden_state: torch.FloatTensor = None # Latent representation
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print(f"Preprocessing loss: {outputs.preprocessing_loss}")
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```
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### Variational Autoencoder Extension
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The configuration supports variational autoencoders:
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)
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```
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## 🧪 Testing
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This repository has been trimmed to essential files. Example scripts and test files were removed by request. You can create your own quick checks using the Quick Start snippet above.
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## 📁 Project Structure
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```
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---
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# Metadata for Hugging Face repo card
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library_name: transformers
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pipeline_tag: feature-extraction
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license: apache-2.0
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tags:
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- autoencoder
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- pytorch
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- reconstruction
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- preprocessing
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- normalizing-flow
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- scaler
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---
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# Autoencoder Implementation for Hugging Face Transformers
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A complete autoencoder implementation that integrates seamlessly with the Hugging Face Transformers ecosystem, providing all the standard functionality you expect from transformer models.
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- **Multiple Loss Functions**: Support for MSE, BCE, L1, Huber, Smooth L1, KL Divergence, Cosine, Focal, Dice, Tversky, SSIM, and Perceptual loss
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- **Multiple Autoencoder Types (7)**: Classic, Variational (VAE), Beta-VAE, Denoising, Sparse, Contractive, and Recurrent autoencoders
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- **Extended Activation Functions**: 18+ activation functions including ReLU, GELU, Swish, Mish, ELU, and more
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- **Learnable Preprocessing**: Neural Scaler, Normalizing Flow, MinMax Scaler (learnable), Robust Scaler (learnable), and Yeo-Johnson preprocessors (2D and 3D tensors)
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- **Extensible Design**: Easy to extend for new autoencoder variants and custom loss functions
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- **Production Ready**: Proper serialization, checkpointing, and inference support
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## 🏗️ Architecture
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The implementation consists of three main components:
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### 1. AutoencoderConfig
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autoencoder_type="classic", # Autoencoder type (7 types available)
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# Optional learnable preprocessing
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use_learnable_preprocessing=True,
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preprocessing_type="neural_scaler", # or "normalizing_flow", "minmax_scaler", "robust_scaler", "yeo_johnson"
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)
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# Create model
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class AutoencoderDataset(Dataset):
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def __init__(self, data):
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self.data = torch.FloatTensor(data)
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def __len__(self):
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return len(self.data)
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def __getitem__(self, idx):
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return {
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"input_values": self.data[idx],
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## 📊 Model Outputs
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### AutoencoderOutput
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The base model `AutoencoderModel` returns the following output:
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```
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```python
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@dataclass
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class AutoencoderOutput(ModelOutput):
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last_hidden_state: torch.FloatTensor = None # Latent representation
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print(f"Preprocessing loss: {outputs.preprocessing_loss}")
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```
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```python
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# Learnable MinMax Scaler - scales to [0, 1] with learnable bounds
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config = AutoencoderConfig(
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input_dim=20,
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latent_dim=10,
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use_learnable_preprocessing=True,
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preprocessing_type="minmax_scaler",
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)
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# Learnable Robust Scaler - robust to outliers using median/IQR
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config = AutoencoderConfig(
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input_dim=20,
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latent_dim=10,
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use_learnable_preprocessing=True,
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preprocessing_type="robust_scaler",
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)
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# Learnable Yeo-Johnson - power transform for skewed distributions
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config = AutoencoderConfig(
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input_dim=20,
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latent_dim=10,
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use_learnable_preprocessing=True,
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preprocessing_type="yeo_johnson",
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)
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```
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### Variational Autoencoder Extension
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The configuration supports variational autoencoders:
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)
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```
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## 📁 Project Structure
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```
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configuration_autoencoder.py
CHANGED
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Defaults to 0.5.
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use_learnable_preprocessing (bool, optional): Whether to use learnable preprocessing. Defaults to False.
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preprocessing_type (str, optional): Type of learnable preprocessing. Options: "none", "neural_scaler",
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"normalizing_flow". Defaults to "none".
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preprocessing_hidden_dim (int, optional): Hidden dimension for preprocessing networks. Defaults to 64.
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preprocessing_num_layers (int, optional): Number of layers in preprocessing networks. Defaults to 2.
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learn_inverse_preprocessing (bool, optional): Whether to learn inverse preprocessing for reconstruction.
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raise ValueError(f"`sequence_length` must be positive when specified, got {sequence_length}.")
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# Preprocessing validation
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valid_preprocessing = [
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if preprocessing_type not in valid_preprocessing:
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raise ValueError(
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f"`preprocessing_type` must be one of {valid_preprocessing}, got {preprocessing_type}."
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def is_normalizing_flow(self) -> bool:
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"""Check if using normalizing flow preprocessing."""
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return self.preprocessing_type == "normalizing_flow"
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-
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def to_dict(self):
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"""
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Serializes this instance to a Python dictionary.
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Defaults to 0.5.
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use_learnable_preprocessing (bool, optional): Whether to use learnable preprocessing. Defaults to False.
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preprocessing_type (str, optional): Type of learnable preprocessing. Options: "none", "neural_scaler",
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"normalizing_flow", "minmax_scaler", "robust_scaler", "yeo_johnson". Defaults to "none".
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preprocessing_hidden_dim (int, optional): Hidden dimension for preprocessing networks. Defaults to 64.
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preprocessing_num_layers (int, optional): Number of layers in preprocessing networks. Defaults to 2.
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learn_inverse_preprocessing (bool, optional): Whether to learn inverse preprocessing for reconstruction.
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raise ValueError(f"`sequence_length` must be positive when specified, got {sequence_length}.")
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# Preprocessing validation
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valid_preprocessing = [
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"none",
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"neural_scaler",
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"normalizing_flow",
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"minmax_scaler",
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"robust_scaler",
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"yeo_johnson",
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]
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if preprocessing_type not in valid_preprocessing:
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raise ValueError(
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f"`preprocessing_type` must be one of {valid_preprocessing}, got {preprocessing_type}."
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def is_normalizing_flow(self) -> bool:
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"""Check if using normalizing flow preprocessing."""
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return self.preprocessing_type == "normalizing_flow"
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@property
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def is_minmax_scaler(self) -> bool:
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"""Check if using learnable MinMax scaler preprocessing."""
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return self.preprocessing_type == "minmax_scaler"
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@property
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def is_robust_scaler(self) -> bool:
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"""Check if using learnable Robust scaler preprocessing."""
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return self.preprocessing_type == "robust_scaler"
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@property
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def is_yeo_johnson(self) -> bool:
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"""Check if using learnable Yeo-Johnson power transform preprocessing."""
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return self.preprocessing_type == "yeo_johnson"
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def to_dict(self):
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"""
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Serializes this instance to a Python dictionary.
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modeling_autoencoder.py
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return x, torch.tensor(0.0, device=x.device)
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class CouplingLayer(nn.Module):
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"""Coupling layer for normalizing flows."""
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self.preprocessor = NeuralScaler(config)
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elif config.is_normalizing_flow:
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self.preprocessor = NormalizingFlowPreprocessor(config)
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else:
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raise ValueError(f"Unknown preprocessing type: {config.preprocessing_type}")
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else:
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# Standard encoder output
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self.fc_out = nn.Linear(input_dim, config.latent_dim)
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-
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def _get_activation(self, activation: str) -> nn.Module:
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"""Get activation function by name."""
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activations = {
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"threshold": nn.Threshold(threshold=0.1, value=0),
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}
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return activations[activation]
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-
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def forward(self, x: torch.Tensor) -> Union[torch.Tensor, Tuple[torch.Tensor, torch.Tensor, torch.Tensor]]:
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"""Forward pass through encoder."""
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# Add noise for denoising autoencoders
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class AutoencoderDecoder(nn.Module):
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"""Decoder part of the autoencoder."""
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-
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def __init__(self, config: AutoencoderConfig):
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super().__init__()
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self.config = config
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-
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# Build decoder layers (reverse of encoder)
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layers = []
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input_dim = config.latent_dim
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decoder_dims = config.decoder_dims + [config.input_dim]
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-
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for i, hidden_dim in enumerate(decoder_dims):
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layers.append(nn.Linear(input_dim, hidden_dim))
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-
|
477 |
# Don't add batch norm, activation, or dropout to the final layer
|
478 |
if i < len(decoder_dims) - 1:
|
479 |
if config.use_batch_norm:
|
480 |
layers.append(nn.BatchNorm1d(hidden_dim))
|
481 |
-
|
482 |
layers.append(self._get_activation(config.activation))
|
483 |
-
|
484 |
if config.dropout_rate > 0:
|
485 |
layers.append(nn.Dropout(config.dropout_rate))
|
486 |
else:
|
487 |
# Final layer - add appropriate activation based on reconstruction loss
|
488 |
if config.reconstruction_loss == "bce":
|
489 |
layers.append(nn.Sigmoid())
|
490 |
-
|
491 |
input_dim = hidden_dim
|
492 |
-
|
493 |
self.decoder = nn.Sequential(*layers)
|
494 |
-
|
495 |
def _get_activation(self, activation: str) -> nn.Module:
|
496 |
"""Get activation function by name."""
|
497 |
activations = {
|
@@ -515,7 +853,7 @@ class AutoencoderDecoder(nn.Module):
|
|
515 |
"threshold": nn.Threshold(threshold=0.1, value=0),
|
516 |
}
|
517 |
return activations[activation]
|
518 |
-
|
519 |
def forward(self, x: torch.Tensor) -> torch.Tensor:
|
520 |
"""Forward pass through decoder."""
|
521 |
return self.decoder(x)
|
@@ -753,19 +1091,19 @@ class RecurrentDecoder(nn.Module):
|
|
753 |
class AutoencoderModel(PreTrainedModel):
|
754 |
"""
|
755 |
The bare Autoencoder Model transformer outputting raw hidden-states without any specific head on top.
|
756 |
-
|
757 |
This model inherits from PreTrainedModel. Check the superclass documentation for the generic methods the
|
758 |
library implements for all its model (such as downloading or saving, resizing the input embeddings, pruning heads
|
759 |
etc.)
|
760 |
-
|
761 |
This model is also a PyTorch torch.nn.Module subclass. Use it as a regular PyTorch Module and refer to the
|
762 |
PyTorch documentation for all matter related to general usage and behavior.
|
763 |
"""
|
764 |
-
|
765 |
config_class = AutoencoderConfig
|
766 |
base_model_prefix = "autoencoder"
|
767 |
supports_gradient_checkpointing = False
|
768 |
-
|
769 |
def __init__(self, config: AutoencoderConfig):
|
770 |
super().__init__(config)
|
771 |
self.config = config
|
@@ -787,23 +1125,23 @@ class AutoencoderModel(PreTrainedModel):
|
|
787 |
# Tie weights if specified
|
788 |
if config.tie_weights:
|
789 |
self._tie_weights()
|
790 |
-
|
791 |
# Initialize weights
|
792 |
self.post_init()
|
793 |
-
|
794 |
def _tie_weights(self):
|
795 |
"""Tie encoder and decoder weights (transpose relationship)."""
|
796 |
# This is a simplified weight tying - in practice, you might want more sophisticated tying
|
797 |
pass
|
798 |
-
|
799 |
def get_input_embeddings(self):
|
800 |
"""Get input embeddings (not applicable for basic autoencoder)."""
|
801 |
return None
|
802 |
-
|
803 |
def set_input_embeddings(self, value):
|
804 |
"""Set input embeddings (not applicable for basic autoencoder)."""
|
805 |
pass
|
806 |
-
|
807 |
def forward(
|
808 |
self,
|
809 |
input_values: torch.Tensor,
|
|
|
143 |
return x, torch.tensor(0.0, device=x.device)
|
144 |
|
145 |
|
146 |
+
|
147 |
+
class LearnableMinMaxScaler(nn.Module):
|
148 |
+
"""Learnable MinMax scaler that adapts bounds during training.
|
149 |
+
|
150 |
+
Scales features to [0, 1] using batch min/range with learnable adjustments and
|
151 |
+
a learnable affine transform. Supports 2D (B, F) and 3D (B, T, F) inputs.
|
152 |
+
"""
|
153 |
+
|
154 |
+
def __init__(self, config: AutoencoderConfig):
|
155 |
+
super().__init__()
|
156 |
+
self.config = config
|
157 |
+
input_dim = config.input_dim
|
158 |
+
hidden_dim = config.preprocessing_hidden_dim
|
159 |
+
|
160 |
+
# Networks to learn adjustments to batch min and range
|
161 |
+
self.min_estimator = nn.Sequential(
|
162 |
+
nn.Linear(input_dim, hidden_dim),
|
163 |
+
nn.ReLU(),
|
164 |
+
nn.Linear(hidden_dim, hidden_dim),
|
165 |
+
nn.ReLU(),
|
166 |
+
nn.Linear(hidden_dim, input_dim),
|
167 |
+
)
|
168 |
+
self.range_estimator = nn.Sequential(
|
169 |
+
nn.Linear(input_dim, hidden_dim),
|
170 |
+
nn.ReLU(),
|
171 |
+
nn.Linear(hidden_dim, hidden_dim),
|
172 |
+
nn.ReLU(),
|
173 |
+
nn.Linear(hidden_dim, input_dim),
|
174 |
+
nn.Softplus(), # Ensure positive adjustment to range
|
175 |
+
)
|
176 |
+
|
177 |
+
# Learnable affine transformation parameters
|
178 |
+
self.weight = nn.Parameter(torch.ones(input_dim))
|
179 |
+
self.bias = nn.Parameter(torch.zeros(input_dim))
|
180 |
+
|
181 |
+
# Running statistics for inference
|
182 |
+
self.register_buffer("running_min", torch.zeros(input_dim))
|
183 |
+
self.register_buffer("running_range", torch.ones(input_dim))
|
184 |
+
self.register_buffer("num_batches_tracked", torch.tensor(0, dtype=torch.long))
|
185 |
+
|
186 |
+
self.momentum = 0.1
|
187 |
+
|
188 |
+
def forward(self, x: torch.Tensor, inverse: bool = False) -> Tuple[torch.Tensor, torch.Tensor]:
|
189 |
+
if inverse:
|
190 |
+
return self._inverse_transform(x)
|
191 |
+
|
192 |
+
original_shape = x.shape
|
193 |
+
if x.dim() == 3:
|
194 |
+
x = x.view(-1, x.size(-1))
|
195 |
+
|
196 |
+
eps = 1e-8
|
197 |
+
if self.training:
|
198 |
+
batch_min = x.min(dim=0, keepdim=True).values
|
199 |
+
batch_max = x.max(dim=0, keepdim=True).values
|
200 |
+
batch_range = (batch_max - batch_min).clamp_min(eps)
|
201 |
+
|
202 |
+
# Learn adjustments
|
203 |
+
learned_min_adj = self.min_estimator(batch_min)
|
204 |
+
learned_range_adj = self.range_estimator(batch_range)
|
205 |
+
|
206 |
+
effective_min = batch_min + learned_min_adj
|
207 |
+
effective_range = batch_range + learned_range_adj + eps
|
208 |
+
|
209 |
+
# Update running stats with raw batch min/range for stable inversion
|
210 |
+
with torch.no_grad():
|
211 |
+
self.num_batches_tracked += 1
|
212 |
+
if self.num_batches_tracked == 1:
|
213 |
+
self.running_min.copy_(batch_min.squeeze())
|
214 |
+
self.running_range.copy_(batch_range.squeeze())
|
215 |
+
else:
|
216 |
+
self.running_min.mul_(1 - self.momentum).add_(batch_min.squeeze(), alpha=self.momentum)
|
217 |
+
self.running_range.mul_(1 - self.momentum).add_(batch_range.squeeze(), alpha=self.momentum)
|
218 |
+
else:
|
219 |
+
effective_min = self.running_min.unsqueeze(0)
|
220 |
+
effective_range = self.running_range.unsqueeze(0)
|
221 |
+
|
222 |
+
# Scale to [0, 1]
|
223 |
+
scaled = (x - effective_min) / effective_range
|
224 |
+
|
225 |
+
# Learnable affine transform
|
226 |
+
transformed = scaled * self.weight + self.bias
|
227 |
+
|
228 |
+
if len(original_shape) == 3:
|
229 |
+
transformed = transformed.view(original_shape)
|
230 |
+
|
231 |
+
# Regularization: encourage non-degenerate range and modest affine params
|
232 |
+
reg_loss = 0.01 * (self.weight.var() + self.bias.var())
|
233 |
+
if self.training:
|
234 |
+
reg_loss = reg_loss + 0.001 * (1.0 / effective_range.clamp_min(1e-3)).mean()
|
235 |
+
|
236 |
+
return transformed, reg_loss
|
237 |
+
|
238 |
+
def _inverse_transform(self, x: torch.Tensor) -> Tuple[torch.Tensor, torch.Tensor]:
|
239 |
+
if not self.config.learn_inverse_preprocessing:
|
240 |
+
return x, torch.tensor(0.0, device=x.device)
|
241 |
+
|
242 |
+
original_shape = x.shape
|
243 |
+
if x.dim() == 3:
|
244 |
+
x = x.view(-1, x.size(-1))
|
245 |
+
|
246 |
+
# Reverse affine
|
247 |
+
x = (x - self.bias) / (self.weight + 1e-8)
|
248 |
+
# Reverse MinMax using running stats
|
249 |
+
x = x * self.running_range.unsqueeze(0) + self.running_min.unsqueeze(0)
|
250 |
+
|
251 |
+
if len(original_shape) == 3:
|
252 |
+
x = x.view(original_shape)
|
253 |
+
|
254 |
+
return x, torch.tensor(0.0, device=x.device)
|
255 |
+
|
256 |
+
|
257 |
+
class LearnableRobustScaler(nn.Module):
|
258 |
+
"""Learnable Robust scaler using median and IQR with learnable adjustments.
|
259 |
+
|
260 |
+
Normalizes as (x - median) / IQR with learnable adjustments and an affine head.
|
261 |
+
Supports 2D (B, F) and 3D (B, T, F) inputs.
|
262 |
+
"""
|
263 |
+
|
264 |
+
def __init__(self, config: AutoencoderConfig):
|
265 |
+
super().__init__()
|
266 |
+
self.config = config
|
267 |
+
input_dim = config.input_dim
|
268 |
+
hidden_dim = config.preprocessing_hidden_dim
|
269 |
+
|
270 |
+
self.median_estimator = nn.Sequential(
|
271 |
+
nn.Linear(input_dim, hidden_dim),
|
272 |
+
nn.ReLU(),
|
273 |
+
nn.Linear(hidden_dim, hidden_dim),
|
274 |
+
nn.ReLU(),
|
275 |
+
nn.Linear(hidden_dim, input_dim),
|
276 |
+
)
|
277 |
+
self.iqr_estimator = nn.Sequential(
|
278 |
+
nn.Linear(input_dim, hidden_dim),
|
279 |
+
nn.ReLU(),
|
280 |
+
nn.Linear(hidden_dim, hidden_dim),
|
281 |
+
nn.ReLU(),
|
282 |
+
nn.Linear(hidden_dim, input_dim),
|
283 |
+
nn.Softplus(), # Ensure positive IQR adjustment
|
284 |
+
)
|
285 |
+
|
286 |
+
self.weight = nn.Parameter(torch.ones(input_dim))
|
287 |
+
self.bias = nn.Parameter(torch.zeros(input_dim))
|
288 |
+
|
289 |
+
self.register_buffer("running_median", torch.zeros(input_dim))
|
290 |
+
self.register_buffer("running_iqr", torch.ones(input_dim))
|
291 |
+
self.register_buffer("num_batches_tracked", torch.tensor(0, dtype=torch.long))
|
292 |
+
|
293 |
+
self.momentum = 0.1
|
294 |
+
|
295 |
+
def forward(self, x: torch.Tensor, inverse: bool = False) -> Tuple[torch.Tensor, torch.Tensor]:
|
296 |
+
if inverse:
|
297 |
+
return self._inverse_transform(x)
|
298 |
+
|
299 |
+
original_shape = x.shape
|
300 |
+
if x.dim() == 3:
|
301 |
+
x = x.view(-1, x.size(-1))
|
302 |
+
|
303 |
+
eps = 1e-8
|
304 |
+
if self.training:
|
305 |
+
qs = torch.quantile(x, torch.tensor([0.25, 0.5, 0.75], device=x.device), dim=0)
|
306 |
+
q25, med, q75 = qs[0:1, :], qs[1:2, :], qs[2:3, :]
|
307 |
+
iqr = (q75 - q25).clamp_min(eps)
|
308 |
+
|
309 |
+
learned_med_adj = self.median_estimator(med)
|
310 |
+
learned_iqr_adj = self.iqr_estimator(iqr)
|
311 |
+
|
312 |
+
effective_median = med + learned_med_adj
|
313 |
+
effective_iqr = iqr + learned_iqr_adj + eps
|
314 |
+
|
315 |
+
with torch.no_grad():
|
316 |
+
self.num_batches_tracked += 1
|
317 |
+
if self.num_batches_tracked == 1:
|
318 |
+
self.running_median.copy_(med.squeeze())
|
319 |
+
self.running_iqr.copy_(iqr.squeeze())
|
320 |
+
else:
|
321 |
+
self.running_median.mul_(1 - self.momentum).add_(med.squeeze(), alpha=self.momentum)
|
322 |
+
self.running_iqr.mul_(1 - self.momentum).add_(iqr.squeeze(), alpha=self.momentum)
|
323 |
+
else:
|
324 |
+
effective_median = self.running_median.unsqueeze(0)
|
325 |
+
effective_iqr = self.running_iqr.unsqueeze(0)
|
326 |
+
|
327 |
+
normalized = (x - effective_median) / effective_iqr
|
328 |
+
transformed = normalized * self.weight + self.bias
|
329 |
+
|
330 |
+
if len(original_shape) == 3:
|
331 |
+
transformed = transformed.view(original_shape)
|
332 |
+
|
333 |
+
reg_loss = 0.01 * (self.weight.var() + self.bias.var())
|
334 |
+
if self.training:
|
335 |
+
reg_loss = reg_loss + 0.001 * (1.0 / effective_iqr.clamp_min(1e-3)).mean()
|
336 |
+
|
337 |
+
return transformed, reg_loss
|
338 |
+
|
339 |
+
def _inverse_transform(self, x: torch.Tensor) -> Tuple[torch.Tensor, torch.Tensor]:
|
340 |
+
if not self.config.learn_inverse_preprocessing:
|
341 |
+
return x, torch.tensor(0.0, device=x.device)
|
342 |
+
|
343 |
+
original_shape = x.shape
|
344 |
+
if x.dim() == 3:
|
345 |
+
x = x.view(-1, x.size(-1))
|
346 |
+
|
347 |
+
x = (x - self.bias) / (self.weight + 1e-8)
|
348 |
+
x = x * self.running_iqr.unsqueeze(0) + self.running_median.unsqueeze(0)
|
349 |
+
|
350 |
+
if len(original_shape) == 3:
|
351 |
+
x = x.view(original_shape)
|
352 |
+
|
353 |
+
return x, torch.tensor(0.0, device=x.device)
|
354 |
+
|
355 |
+
|
356 |
+
class LearnableYeoJohnsonPreprocessor(nn.Module):
|
357 |
+
"""Learnable Yeo-Johnson power transform with per-feature λ and affine head.
|
358 |
+
|
359 |
+
Applies Yeo-Johnson transform elementwise with learnable lambda per feature,
|
360 |
+
followed by standardization and a learnable affine transform. Supports 2D and 3D inputs.
|
361 |
+
"""
|
362 |
+
|
363 |
+
def __init__(self, config: AutoencoderConfig):
|
364 |
+
super().__init__()
|
365 |
+
self.config = config
|
366 |
+
input_dim = config.input_dim
|
367 |
+
|
368 |
+
# Learnable lambda per feature (unconstrained). Initialize around 1.0
|
369 |
+
self.lmbda = nn.Parameter(torch.ones(input_dim))
|
370 |
+
|
371 |
+
# Learnable affine parameters after standardization
|
372 |
+
self.weight = nn.Parameter(torch.ones(input_dim))
|
373 |
+
self.bias = nn.Parameter(torch.zeros(input_dim))
|
374 |
+
|
375 |
+
# Running stats for transformed data
|
376 |
+
self.register_buffer("running_mean", torch.zeros(input_dim))
|
377 |
+
self.register_buffer("running_std", torch.ones(input_dim))
|
378 |
+
self.register_buffer("num_batches_tracked", torch.tensor(0, dtype=torch.long))
|
379 |
+
self.momentum = 0.1
|
380 |
+
|
381 |
+
def _yeo_johnson(self, x: torch.Tensor, lmbda: torch.Tensor) -> torch.Tensor:
|
382 |
+
eps = 1e-6
|
383 |
+
lmbda = lmbda.unsqueeze(0) # broadcast over batch
|
384 |
+
pos = x >= 0
|
385 |
+
# For x >= 0
|
386 |
+
if_part = torch.where(
|
387 |
+
torch.abs(lmbda) > eps,
|
388 |
+
((x + 1.0).clamp_min(eps) ** lmbda - 1.0) / lmbda,
|
389 |
+
torch.log((x + 1.0).clamp_min(eps)),
|
390 |
+
)
|
391 |
+
# For x < 0
|
392 |
+
two_minus_lambda = 2.0 - lmbda
|
393 |
+
else_part = torch.where(
|
394 |
+
torch.abs(two_minus_lambda) > eps,
|
395 |
+
-(((1.0 - x).clamp_min(eps)) ** two_minus_lambda - 1.0) / two_minus_lambda,
|
396 |
+
-torch.log((1.0 - x).clamp_min(eps)),
|
397 |
+
)
|
398 |
+
return torch.where(pos, if_part, else_part)
|
399 |
+
|
400 |
+
def _yeo_johnson_inverse(self, y: torch.Tensor, lmbda: torch.Tensor) -> torch.Tensor:
|
401 |
+
eps = 1e-6
|
402 |
+
lmbda = lmbda.unsqueeze(0)
|
403 |
+
pos = y >= 0
|
404 |
+
# Inverse for y >= 0
|
405 |
+
x_pos = torch.where(
|
406 |
+
torch.abs(lmbda) > eps,
|
407 |
+
(y * lmbda + 1.0).clamp_min(eps) ** (1.0 / lmbda) - 1.0,
|
408 |
+
torch.exp(y) - 1.0,
|
409 |
+
)
|
410 |
+
# Inverse for y < 0
|
411 |
+
two_minus_lambda = 2.0 - lmbda
|
412 |
+
x_neg = torch.where(
|
413 |
+
torch.abs(two_minus_lambda) > eps,
|
414 |
+
1.0 - (1.0 - y * two_minus_lambda).clamp_min(eps) ** (1.0 / two_minus_lambda),
|
415 |
+
1.0 - torch.exp(-y),
|
416 |
+
)
|
417 |
+
return torch.where(pos, x_pos, x_neg)
|
418 |
+
|
419 |
+
def forward(self, x: torch.Tensor, inverse: bool = False) -> Tuple[torch.Tensor, torch.Tensor]:
|
420 |
+
if inverse:
|
421 |
+
return self._inverse_transform(x)
|
422 |
+
|
423 |
+
orig_shape = x.shape
|
424 |
+
if x.dim() == 3:
|
425 |
+
x = x.view(-1, x.size(-1))
|
426 |
+
|
427 |
+
# Apply Yeo-Johnson
|
428 |
+
y = self._yeo_johnson(x, self.lmbda)
|
429 |
+
|
430 |
+
# Batch stats and running stats on transformed data
|
431 |
+
if self.training:
|
432 |
+
batch_mean = y.mean(dim=0, keepdim=True)
|
433 |
+
batch_std = y.std(dim=0, keepdim=True).clamp_min(1e-6)
|
434 |
+
with torch.no_grad():
|
435 |
+
self.num_batches_tracked += 1
|
436 |
+
if self.num_batches_tracked == 1:
|
437 |
+
self.running_mean.copy_(batch_mean.squeeze())
|
438 |
+
self.running_std.copy_(batch_std.squeeze())
|
439 |
+
else:
|
440 |
+
self.running_mean.mul_(1 - self.momentum).add_(batch_mean.squeeze(), alpha=self.momentum)
|
441 |
+
self.running_std.mul_(1 - self.momentum).add_(batch_std.squeeze(), alpha=self.momentum)
|
442 |
+
mean = batch_mean
|
443 |
+
std = batch_std
|
444 |
+
else:
|
445 |
+
mean = self.running_mean.unsqueeze(0)
|
446 |
+
std = self.running_std.unsqueeze(0)
|
447 |
+
|
448 |
+
y_norm = (y - mean) / std
|
449 |
+
out = y_norm * self.weight + self.bias
|
450 |
+
|
451 |
+
if len(orig_shape) == 3:
|
452 |
+
out = out.view(orig_shape)
|
453 |
+
|
454 |
+
# Regularize lambda to avoid extreme values; encourage identity around 1
|
455 |
+
reg = 0.001 * (self.lmbda - 1.0).pow(2).mean() + 0.01 * (self.weight.var() + self.bias.var())
|
456 |
+
return out, reg
|
457 |
+
|
458 |
+
def _inverse_transform(self, x: torch.Tensor) -> Tuple[torch.Tensor, torch.Tensor]:
|
459 |
+
if not self.config.learn_inverse_preprocessing:
|
460 |
+
return x, torch.tensor(0.0, device=x.device)
|
461 |
+
|
462 |
+
orig_shape = x.shape
|
463 |
+
if x.dim() == 3:
|
464 |
+
x = x.view(-1, x.size(-1))
|
465 |
+
|
466 |
+
# Reverse affine and normalization with running stats
|
467 |
+
y = (x - self.bias) / (self.weight + 1e-8)
|
468 |
+
y = y * self.running_std.unsqueeze(0) + self.running_mean.unsqueeze(0)
|
469 |
+
|
470 |
+
# Inverse Yeo-Johnson
|
471 |
+
out = self._yeo_johnson_inverse(y, self.lmbda)
|
472 |
+
|
473 |
+
if len(orig_shape) == 3:
|
474 |
+
out = out.view(orig_shape)
|
475 |
+
|
476 |
+
return out, torch.tensor(0.0, device=x.device)
|
477 |
+
|
478 |
class CouplingLayer(nn.Module):
|
479 |
"""Coupling layer for normalizing flows."""
|
480 |
|
|
|
638 |
self.preprocessor = NeuralScaler(config)
|
639 |
elif config.is_normalizing_flow:
|
640 |
self.preprocessor = NormalizingFlowPreprocessor(config)
|
641 |
+
elif getattr(config, "is_minmax_scaler", False):
|
642 |
+
self.preprocessor = LearnableMinMaxScaler(config)
|
643 |
+
elif getattr(config, "is_robust_scaler", False):
|
644 |
+
self.preprocessor = LearnableRobustScaler(config)
|
645 |
+
elif getattr(config, "is_yeo_johnson", False):
|
646 |
+
self.preprocessor = LearnableYeoJohnsonPreprocessor(config)
|
647 |
else:
|
648 |
raise ValueError(f"Unknown preprocessing type: {config.preprocessing_type}")
|
649 |
|
|
|
737 |
else:
|
738 |
# Standard encoder output
|
739 |
self.fc_out = nn.Linear(input_dim, config.latent_dim)
|
740 |
+
|
741 |
def _get_activation(self, activation: str) -> nn.Module:
|
742 |
"""Get activation function by name."""
|
743 |
activations = {
|
|
|
761 |
"threshold": nn.Threshold(threshold=0.1, value=0),
|
762 |
}
|
763 |
return activations[activation]
|
764 |
+
|
765 |
def forward(self, x: torch.Tensor) -> Union[torch.Tensor, Tuple[torch.Tensor, torch.Tensor, torch.Tensor]]:
|
766 |
"""Forward pass through encoder."""
|
767 |
# Add noise for denoising autoencoders
|
|
|
799 |
|
800 |
class AutoencoderDecoder(nn.Module):
|
801 |
"""Decoder part of the autoencoder."""
|
802 |
+
|
803 |
def __init__(self, config: AutoencoderConfig):
|
804 |
super().__init__()
|
805 |
self.config = config
|
806 |
+
|
807 |
# Build decoder layers (reverse of encoder)
|
808 |
layers = []
|
809 |
input_dim = config.latent_dim
|
810 |
decoder_dims = config.decoder_dims + [config.input_dim]
|
811 |
+
|
812 |
for i, hidden_dim in enumerate(decoder_dims):
|
813 |
layers.append(nn.Linear(input_dim, hidden_dim))
|
814 |
+
|
815 |
# Don't add batch norm, activation, or dropout to the final layer
|
816 |
if i < len(decoder_dims) - 1:
|
817 |
if config.use_batch_norm:
|
818 |
layers.append(nn.BatchNorm1d(hidden_dim))
|
819 |
+
|
820 |
layers.append(self._get_activation(config.activation))
|
821 |
+
|
822 |
if config.dropout_rate > 0:
|
823 |
layers.append(nn.Dropout(config.dropout_rate))
|
824 |
else:
|
825 |
# Final layer - add appropriate activation based on reconstruction loss
|
826 |
if config.reconstruction_loss == "bce":
|
827 |
layers.append(nn.Sigmoid())
|
828 |
+
|
829 |
input_dim = hidden_dim
|
830 |
+
|
831 |
self.decoder = nn.Sequential(*layers)
|
832 |
+
|
833 |
def _get_activation(self, activation: str) -> nn.Module:
|
834 |
"""Get activation function by name."""
|
835 |
activations = {
|
|
|
853 |
"threshold": nn.Threshold(threshold=0.1, value=0),
|
854 |
}
|
855 |
return activations[activation]
|
856 |
+
|
857 |
def forward(self, x: torch.Tensor) -> torch.Tensor:
|
858 |
"""Forward pass through decoder."""
|
859 |
return self.decoder(x)
|
|
|
1091 |
class AutoencoderModel(PreTrainedModel):
|
1092 |
"""
|
1093 |
The bare Autoencoder Model transformer outputting raw hidden-states without any specific head on top.
|
1094 |
+
|
1095 |
This model inherits from PreTrainedModel. Check the superclass documentation for the generic methods the
|
1096 |
library implements for all its model (such as downloading or saving, resizing the input embeddings, pruning heads
|
1097 |
etc.)
|
1098 |
+
|
1099 |
This model is also a PyTorch torch.nn.Module subclass. Use it as a regular PyTorch Module and refer to the
|
1100 |
PyTorch documentation for all matter related to general usage and behavior.
|
1101 |
"""
|
1102 |
+
|
1103 |
config_class = AutoencoderConfig
|
1104 |
base_model_prefix = "autoencoder"
|
1105 |
supports_gradient_checkpointing = False
|
1106 |
+
|
1107 |
def __init__(self, config: AutoencoderConfig):
|
1108 |
super().__init__(config)
|
1109 |
self.config = config
|
|
|
1125 |
# Tie weights if specified
|
1126 |
if config.tie_weights:
|
1127 |
self._tie_weights()
|
1128 |
+
|
1129 |
# Initialize weights
|
1130 |
self.post_init()
|
1131 |
+
|
1132 |
def _tie_weights(self):
|
1133 |
"""Tie encoder and decoder weights (transpose relationship)."""
|
1134 |
# This is a simplified weight tying - in practice, you might want more sophisticated tying
|
1135 |
pass
|
1136 |
+
|
1137 |
def get_input_embeddings(self):
|
1138 |
"""Get input embeddings (not applicable for basic autoencoder)."""
|
1139 |
return None
|
1140 |
+
|
1141 |
def set_input_embeddings(self, value):
|
1142 |
"""Set input embeddings (not applicable for basic autoencoder)."""
|
1143 |
pass
|
1144 |
+
|
1145 |
def forward(
|
1146 |
self,
|
1147 |
input_values: torch.Tensor,
|