jingwei 0.0.1__tar.gz

jingwei-0.0.1/PKG-INFO

@@ -0,0 +1,327 @@
+Metadata-Version: 2.4
+Name: jingwei
+Version: 0.0.1
+Summary: Proteomic data imputation framework with DMF and DCAE methods.
+Author: JINGWEI Contributors
+License: MIT
+Keywords: imputation,proteomics,DMF,DCAE,deep-learning
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+Requires-Dist: torch>=2.0.0
+Requires-Dist: pytorch-lightning>=2.0.0
+Requires-Dist: numpy>=1.24.0
+Requires-Dist: pandas>=2.0.0
+Requires-Dist: tensorboard>=2.13.0
+Requires-Dist: scipy>=1.10.0
+Requires-Dist: scikit-learn>=1.3.0
+Provides-Extra: dev
+Requires-Dist: pytest>=7.4.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.1.0; extra == "dev"
+Requires-Dist: black>=23.0.0; extra == "dev"
+Requires-Dist: flake8>=6.0.0; extra == "dev"
+
+# JINGWEI - Proteomic Data Imputation Framework
+
+JINGWEI is a deep learning framework for missing proteomic data imputation, supporting both **DMF (Deep Matrix Factorization)** and **DCAE (Dilated Convolutional AutoEncoder)** methods.
+
+## Features
+
+- **Multiple Imputation Methods**: Support for DMF and DCAE algorithms
+- **Flexible Architecture**: Configurable network architectures and hyperparameters
+- **GPU Acceleration**: CUDA support with specific GPU selection
+- **Comprehensive Logging**: TensorBoard integration for training monitoring
+- **Early Stopping**: Prevent overfitting with configurable patience
+- **Batch Processing**: Efficient batch training with customizable batch sizes
+
+## Installation
+
+### Requirements
+
+- Python 3.12+
+- CUDA-capable GPU (optional, but recommended)
+It is recommended to use conda to manage the environment.
+```bash
+conda create -n jingwei python=3.12
+conda activate jingwei
+```
+
+### Dependencies
+
+Install the package in editable mode (recommended for development):
+
+```bash
+pip install -e .
+```
+
+If you want runtime-only dependencies without editable install:
+
+```bash
+pip install -r requirements.txt
+```
+
+Optional dev dependencies:
+
+```bash
+pip install -e .[dev]
+```
+
+## Usage
+
+### Quick Start
+
+```bash
+# Basic usage with DMF method
+python -m jingwei.train --data-path data/your_dataset.csv
+
+# Use DCAE method with GPU 1
+python -m jingwei.train --data-path data/Alzheimer.csv --method DCAE --device cuda --gpu-id 1
+
+# Custom parameters with early stopping
+python -m jingwei.train --data-path data/your_dataset.csv \
+    --method DMF \
+    --hidden-dims 512 256 128 \
+    --embedding-dim 128 \
+    --early-stopping \
+    --max-epochs 100
+```
+
+### Python API Example
+
+```python
+import pytorch_lightning as pl
+
+from jingwei import CSVDataset, DMFImputer, DCAEImputer
+
+dataset = CSVDataset("data/Alzheimer.csv")
+
+# Choose one of the two methods
+model = DMFImputer(
+    full_data_tensor=dataset.data_normalized,
+    full_mask_tensor=dataset.mask,
+    embedding_dim=64,
+    hidden_dims=[256, 128],
+    batch_size=1024,
+)
+
+# Or use DCAE
+# model = DCAEImputer(
+#     full_data_tensor=dataset.data_normalized,
+#     full_mask_tensor=dataset.mask,
+#     ae_dim=64,
+#     batch_size=1024,
+# )
+
+trainer = pl.Trainer(max_epochs=5)
+trainer.fit(model)
+
+imputed_normalized = model.get_imputed_data()
+imputed = dataset.inverse_transform(imputed_normalized)
+```
+
+### Available Parameters
+
+#### Required Arguments
+- `--data-path PATH`: Path to input CSV file
+
+#### Method Selection
+- `--method {DMF,DCAE}`: Imputation method (default: DMF)
+
+#### General Network Parameters
+- `--hidden-dims DIMS`: Hidden layer dimensions, space-separated (default: "256 128")
+- `--batch-size SIZE`: Batch size for training (default: 1024)
+- `--learning-rate RATE`: Learning rate (default: 0.001)
+- `--weight-decay DECAY`: Weight decay for optimizer (default: 0.00001)
+- `--gradient-clip VALUE`: Gradient clipping value (default: 1.0)
+
+#### DMF Specific Parameters
+- `--embedding-dim DIM`: Embedding dimension (default: 64)
+
+#### DCAE Specific Parameters
+- `--latent-dim DIM`: Latent dimension (default: 64)
+- `--num-encoder-blocks NUM`: Number of encoder blocks (default: 2)
+- `--num-decoder-blocks NUM`: Number of decoder blocks (default: 2)
+- `--dilation VALUE`: Dilation factor (default: 2)
+
+#### Loss Weights
+- `--mask-weight WEIGHT`: Weight for mask prediction loss (default: 0.5)
+- `--reconstruction-weight WEIGHT`: Weight for reconstruction loss (default: 1.0)
+
+#### Training Control
+- `--max-epochs EPOCHS`: Maximum training epochs (default: 200)
+- `--early-stopping`: Enable early stopping
+- `--patience PATIENCE`: Patience for early stopping (default: 20)
+
+#### Device Settings
+- `--device {cpu,cuda,auto}`: Device to use (default: auto)
+- `--gpu-id ID`: Specific GPU ID to use (0, 1, etc.)
+
+#### Output Settings
+- `--results-dir DIR`: Directory for saving results (default: ./results)
+- `--log-interval INTERVAL`: Logging interval in steps (default: 50)
+- `--progress-bar`: Show progress bar during training
+
+## Data Format
+
+The input CSV file should have the following format:
+- First row: Header (will be skipped)
+- First column: Sample IDs/names (will be skipped)
+- Remaining columns: Protein expression data
+- Missing values: Use 0, negative values, or NaN
+
+Example:
+```csv
+Sample_ID,Protein_1,Protein_2,Protein_3,...
+Sample_001,1.23,0.45,NaN,...
+Sample_002,2.34,0,1.67,...
+Sample_003,1.45,1.23,2.89,...
+```
+
+## Output Files
+
+JINGWEI generates the following outputs in the results directory:
+
+```
+results/
+├── checkpoints/           # Model checkpoints
+├── logs/                 # TensorBoard logs
+└── outputs/
+    └── {METHOD}_{DATASET}_{TIMESTAMP}/
+        ├── config.json          # Training configuration
+        ├── imputed_data.csv     # Imputed protein data
+        ├── training_metrics.csv # Training loss history
+        └── model_final.ckpt    # Final trained model
+```
+
+## Examples
+
+### Example 1: DMF with Custom Architecture
+```bash
+./src/JINGWEI.sh --data-path data/Alzheimer.csv \
+    --method DMF \
+    --hidden-dims 512 256 128 64 \
+    --embedding-dim 128 \
+    --mask-weight 0.3 \
+    --learning-rate 0.0005 \
+    --max-epochs 150 \
+    --early-stopping \
+    --progress-bar
+```
+
+### Example 2: DCAE with GPU Acceleration
+```bash
+./src/JINGWEI.sh --data-path data/Alzheimer.csv \
+    --method DCAE \
+    --device cuda \
+    --gpu-id 1 \
+    --latent-dim 128 \
+    --num-encoder-blocks 3 \
+    --num-decoder-blocks 3 \
+    --dilation 4 \
+    --batch-size 512
+```
+
+### Example 3: CPU Training with Custom Output Directory
+```bash
+./src/JINGWEI.sh --data-path data/Alzheimer.csv \
+    --device cpu \
+    --results-dir ./my_results \
+    --max-epochs 50 \
+    --log-interval 10
+```
+
+## Method Descriptions
+
+### DMF (Deep Matrix Factorization)
+- Uses row and column embeddings to capture latent patterns
+- Suitable for collaborative filtering-style missing data
+- Good for datasets with structured missing patterns
+
+### DCAE (Dilated Convolutional AutoEncoder)
+- Uses dilated convolutions to capture long-range dependencies
+- Suitable for sequential or structured protein data
+- Better for complex missing data patterns
+
+## Monitoring Training
+
+### TensorBoard
+```bash
+tensorboard --logdir results/logs
+```
+
+### Training Metrics
+Monitor the following metrics:
+- `train_loss`: Overall training loss
+- `reconstruction_loss`: Data reconstruction quality
+- `mask_loss`: Missing data pattern prediction accuracy
+
+## Troubleshooting
+
+### Common Issues
+
+1. **CUDA Out of Memory**
+   - Reduce `--batch-size`
+   - Use `--device cpu` for CPU training
+
+2. **Shape Mismatch Errors**
+   - Check CSV format (ensure first column is skipped)
+   - Verify data contains only numeric values
+
+3. **Slow Training**
+   - Use GPU acceleration with `--device cuda`
+   - Increase `--batch-size` if memory allows
+
+4. **Poor Performance**
+   - Adjust `--mask-weight` (try 0.1-0.8)
+   - Experiment with different `--hidden-dims`
+   - Enable `--early-stopping`
+
+### Getting Help
+
+For help with parameters:
+```bash
+python -m jingwei.train --help
+```
+
+## File Structure
+
+```
+JINGWEI/
+├── README.md
+├── pyproject.toml
+├── requirements.txt
+├── src/
+│   ├── JINGWEI.sh            # Legacy training script (optional)
+│   ├── train.py              # Thin wrapper for package entry
+│   ├── jingwei/
+│   │   ├── __init__.py
+│   │   ├── train.py           # Package training entry
+│   │   ├── datasets.py        # Data loading utilities
+│   │   ├── models.py          # Model architectures (DMF/DCAE)
+│   │   ├── dmf.py             # DMF trainer
+│   │   └── dcae.py            # DCAE trainer
+│   └── methods/               # Other baselines (not packaged)
+└── data/
+    └── your_datasets.csv
+```
+
+
+## License
+
+This project is licensed under the MIT License 
+
+
+## Changelog
+
+### Version 0.0.1
+- Initial release
+- Support for DMF and DCAE methods
+- GPU acceleration
+- Comprehensive parameter configuration
+- TensorBoard integration

jingwei-0.0.1/README.md

@@ -0,0 +1,298 @@
+# JINGWEI - Proteomic Data Imputation Framework
+
+JINGWEI is a deep learning framework for missing proteomic data imputation, supporting both **DMF (Deep Matrix Factorization)** and **DCAE (Dilated Convolutional AutoEncoder)** methods.
+
+## Features
+
+- **Multiple Imputation Methods**: Support for DMF and DCAE algorithms
+- **Flexible Architecture**: Configurable network architectures and hyperparameters
+- **GPU Acceleration**: CUDA support with specific GPU selection
+- **Comprehensive Logging**: TensorBoard integration for training monitoring
+- **Early Stopping**: Prevent overfitting with configurable patience
+- **Batch Processing**: Efficient batch training with customizable batch sizes
+
+## Installation
+
+### Requirements
+
+- Python 3.12+
+- CUDA-capable GPU (optional, but recommended)
+It is recommended to use conda to manage the environment.
+```bash
+conda create -n jingwei python=3.12
+conda activate jingwei
+```
+
+### Dependencies
+
+Install the package in editable mode (recommended for development):
+
+```bash
+pip install -e .
+```
+
+If you want runtime-only dependencies without editable install:
+
+```bash
+pip install -r requirements.txt
+```
+
+Optional dev dependencies:
+
+```bash
+pip install -e .[dev]
+```
+
+## Usage
+
+### Quick Start
+
+```bash
+# Basic usage with DMF method
+python -m jingwei.train --data-path data/your_dataset.csv
+
+# Use DCAE method with GPU 1
+python -m jingwei.train --data-path data/Alzheimer.csv --method DCAE --device cuda --gpu-id 1
+
+# Custom parameters with early stopping
+python -m jingwei.train --data-path data/your_dataset.csv \
+    --method DMF \
+    --hidden-dims 512 256 128 \
+    --embedding-dim 128 \
+    --early-stopping \
+    --max-epochs 100
+```
+
+### Python API Example
+
+```python
+import pytorch_lightning as pl
+
+from jingwei import CSVDataset, DMFImputer, DCAEImputer
+
+dataset = CSVDataset("data/Alzheimer.csv")
+
+# Choose one of the two methods
+model = DMFImputer(
+    full_data_tensor=dataset.data_normalized,
+    full_mask_tensor=dataset.mask,
+    embedding_dim=64,
+    hidden_dims=[256, 128],
+    batch_size=1024,
+)
+
+# Or use DCAE
+# model = DCAEImputer(
+#     full_data_tensor=dataset.data_normalized,
+#     full_mask_tensor=dataset.mask,
+#     ae_dim=64,
+#     batch_size=1024,
+# )
+
+trainer = pl.Trainer(max_epochs=5)
+trainer.fit(model)
+
+imputed_normalized = model.get_imputed_data()
+imputed = dataset.inverse_transform(imputed_normalized)
+```
+
+### Available Parameters
+
+#### Required Arguments
+- `--data-path PATH`: Path to input CSV file
+
+#### Method Selection
+- `--method {DMF,DCAE}`: Imputation method (default: DMF)
+
+#### General Network Parameters
+- `--hidden-dims DIMS`: Hidden layer dimensions, space-separated (default: "256 128")
+- `--batch-size SIZE`: Batch size for training (default: 1024)
+- `--learning-rate RATE`: Learning rate (default: 0.001)
+- `--weight-decay DECAY`: Weight decay for optimizer (default: 0.00001)
+- `--gradient-clip VALUE`: Gradient clipping value (default: 1.0)
+
+#### DMF Specific Parameters
+- `--embedding-dim DIM`: Embedding dimension (default: 64)
+
+#### DCAE Specific Parameters
+- `--latent-dim DIM`: Latent dimension (default: 64)
+- `--num-encoder-blocks NUM`: Number of encoder blocks (default: 2)
+- `--num-decoder-blocks NUM`: Number of decoder blocks (default: 2)
+- `--dilation VALUE`: Dilation factor (default: 2)
+
+#### Loss Weights
+- `--mask-weight WEIGHT`: Weight for mask prediction loss (default: 0.5)
+- `--reconstruction-weight WEIGHT`: Weight for reconstruction loss (default: 1.0)
+
+#### Training Control
+- `--max-epochs EPOCHS`: Maximum training epochs (default: 200)
+- `--early-stopping`: Enable early stopping
+- `--patience PATIENCE`: Patience for early stopping (default: 20)
+
+#### Device Settings
+- `--device {cpu,cuda,auto}`: Device to use (default: auto)
+- `--gpu-id ID`: Specific GPU ID to use (0, 1, etc.)
+
+#### Output Settings
+- `--results-dir DIR`: Directory for saving results (default: ./results)
+- `--log-interval INTERVAL`: Logging interval in steps (default: 50)
+- `--progress-bar`: Show progress bar during training
+
+## Data Format
+
+The input CSV file should have the following format:
+- First row: Header (will be skipped)
+- First column: Sample IDs/names (will be skipped)
+- Remaining columns: Protein expression data
+- Missing values: Use 0, negative values, or NaN
+
+Example:
+```csv
+Sample_ID,Protein_1,Protein_2,Protein_3,...
+Sample_001,1.23,0.45,NaN,...
+Sample_002,2.34,0,1.67,...
+Sample_003,1.45,1.23,2.89,...
+```
+
+## Output Files
+
+JINGWEI generates the following outputs in the results directory:
+
+```
+results/
+├── checkpoints/           # Model checkpoints
+├── logs/                 # TensorBoard logs
+└── outputs/
+    └── {METHOD}_{DATASET}_{TIMESTAMP}/
+        ├── config.json          # Training configuration
+        ├── imputed_data.csv     # Imputed protein data
+        ├── training_metrics.csv # Training loss history
+        └── model_final.ckpt    # Final trained model
+```
+
+## Examples
+
+### Example 1: DMF with Custom Architecture
+```bash
+./src/JINGWEI.sh --data-path data/Alzheimer.csv \
+    --method DMF \
+    --hidden-dims 512 256 128 64 \
+    --embedding-dim 128 \
+    --mask-weight 0.3 \
+    --learning-rate 0.0005 \
+    --max-epochs 150 \
+    --early-stopping \
+    --progress-bar
+```
+
+### Example 2: DCAE with GPU Acceleration
+```bash
+./src/JINGWEI.sh --data-path data/Alzheimer.csv \
+    --method DCAE \
+    --device cuda \
+    --gpu-id 1 \
+    --latent-dim 128 \
+    --num-encoder-blocks 3 \
+    --num-decoder-blocks 3 \
+    --dilation 4 \
+    --batch-size 512
+```
+
+### Example 3: CPU Training with Custom Output Directory
+```bash
+./src/JINGWEI.sh --data-path data/Alzheimer.csv \
+    --device cpu \
+    --results-dir ./my_results \
+    --max-epochs 50 \
+    --log-interval 10
+```
+
+## Method Descriptions
+
+### DMF (Deep Matrix Factorization)
+- Uses row and column embeddings to capture latent patterns
+- Suitable for collaborative filtering-style missing data
+- Good for datasets with structured missing patterns
+
+### DCAE (Dilated Convolutional AutoEncoder)
+- Uses dilated convolutions to capture long-range dependencies
+- Suitable for sequential or structured protein data
+- Better for complex missing data patterns
+
+## Monitoring Training
+
+### TensorBoard
+```bash
+tensorboard --logdir results/logs
+```
+
+### Training Metrics
+Monitor the following metrics:
+- `train_loss`: Overall training loss
+- `reconstruction_loss`: Data reconstruction quality
+- `mask_loss`: Missing data pattern prediction accuracy
+
+## Troubleshooting
+
+### Common Issues
+
+1. **CUDA Out of Memory**
+   - Reduce `--batch-size`
+   - Use `--device cpu` for CPU training
+
+2. **Shape Mismatch Errors**
+   - Check CSV format (ensure first column is skipped)
+   - Verify data contains only numeric values
+
+3. **Slow Training**
+   - Use GPU acceleration with `--device cuda`
+   - Increase `--batch-size` if memory allows
+
+4. **Poor Performance**
+   - Adjust `--mask-weight` (try 0.1-0.8)
+   - Experiment with different `--hidden-dims`
+   - Enable `--early-stopping`
+
+### Getting Help
+
+For help with parameters:
+```bash
+python -m jingwei.train --help
+```
+
+## File Structure
+
+```
+JINGWEI/
+├── README.md
+├── pyproject.toml
+├── requirements.txt
+├── src/
+│   ├── JINGWEI.sh            # Legacy training script (optional)
+│   ├── train.py              # Thin wrapper for package entry
+│   ├── jingwei/
+│   │   ├── __init__.py
+│   │   ├── train.py           # Package training entry
+│   │   ├── datasets.py        # Data loading utilities
+│   │   ├── models.py          # Model architectures (DMF/DCAE)
+│   │   ├── dmf.py             # DMF trainer
+│   │   └── dcae.py            # DCAE trainer
+│   └── methods/               # Other baselines (not packaged)
+└── data/
+    └── your_datasets.csv
+```
+
+
+## License
+
+This project is licensed under the MIT License 
+
+
+## Changelog
+
+### Version 0.0.1
+- Initial release
+- Support for DMF and DCAE methods
+- GPU acceleration
+- Comprehensive parameter configuration
+- TensorBoard integration

jingwei-0.0.1/pyproject.toml

@@ -0,0 +1,50 @@
+[build-system]
+requires = ["setuptools>=68", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "jingwei"
+version = "0.0.1"
+description = "Proteomic data imputation framework with DMF and DCAE methods."
+readme = "README.md"
+requires-python = ">=3.12"
+license = { text = "MIT" }
+authors = [
+    { name = "JINGWEI Contributors" }
+]
+keywords = ["imputation", "proteomics", "DMF", "DCAE", "deep-learning"]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Scientific/Engineering :: Artificial Intelligence"
+]
+
+dependencies = [
+    "torch>=2.0.0",
+    "pytorch-lightning>=2.0.0",
+    "numpy>=1.24.0",
+    "pandas>=2.0.0",
+    "tensorboard>=2.13.0",
+    "scipy>=1.10.0",
+    "scikit-learn>=1.3.0"
+]
+
+[project.optional-dependencies]
+dev = [
+    "pytest>=7.4.0",
+    "pytest-cov>=4.1.0",
+    "black>=23.0.0",
+    "flake8>=6.0.0"
+]
+
+[tool.setuptools]
+package-dir = {"" = "src"}
+
+[tool.setuptools.packages.find]
+where = ["src"]
+include = ["jingwei*"]
+

jingwei-0.0.1/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

jingwei-0.0.1/src/jingwei/__init__.py

@@ -0,0 +1,21 @@
+"""JINGWEI package for proteomic data imputation."""
+
+__version__ = "0.0.1"
+
+from .datasets import CSVDataset
+from .models import DCAE, DMF
+from .dcae import DCAEImputer
+from .dmf import DMFImputer
+from .train import ImputationTrainer, parse_arguments, main as train_main
+
+__all__ = [
+    "CSVDataset",
+    "DCAE",
+    "DMF",
+    "DCAEImputer",
+    "DMFImputer",
+    "ImputationTrainer",
+    "parse_arguments",
+    "train_main",
+    "__version__",
+]