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.

conda create -n jingwei python=3.12
conda activate jingwei

Dependencies

Install the required packages:

pip install -r requirements.txt

Or install manually:

pip install torch pytorch-lightning pandas numpy matplotlib seaborn tensorboard scipy scikit-learn

Usage

Quick Start

# Basic usage with DMF method
./src/JINGWEI.sh --data-path data/your_dataset.csv

# Use DCAE method with GPU 1
./src/JINGWEI.sh --data-path data/Alzheimer.csv --method DCAE --device cuda --gpu-id 1

# Custom parameters with early stopping
./src/JINGWEI.sh --data-path data/your_dataset.csv \
    --method DMF \
    --hidden-dims 512 256 128 \
    --embedding-dim 128 \
    --early-stopping \
    --max-epochs 100

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:

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

./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

./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

./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

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:

./src/JINGWEI.sh --help

File Structure

JINGWEI/
├── README.md
├── requirements.txt
├── src/
│   ├── JINGWEI.sh              # Main training script
│   ├── train.py              # Python training interface
│   ├── datasets.py           # Data loading utilities
│   ├── models.py             # Model architectures
│   └── methods/
│       ├── DMF.py           # DMF implementation
│       └── DCAE.py          # DCAE implementation
└── 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