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+# Detailed Directory Structure
+
+This document provides a comprehensive breakdown of the ML project template directory structure.
+
+## Root Level Files
+
+| File | Purpose |
+|------|---------|
+| `README.md` | Project documentation, installation guide, usage examples |
+| `TODO.md` | Task tracking with weekly focus and daily tasks |
+| `.gitignore` | Git ignore patterns for Python, Jupyter, IDEs, logs, cache |
+| `pyproject.toml` | Project configuration for build system and dependencies |
+| `uv.lock` | Locked dependency versions for reproducibility |
+
+## run/ - Execution Layer
+
+### pipeline/
+
+Main workflow scripts organized by stage:
+
+| Directory | Purpose |
+|-----------|---------|
+| `training/` | Training execution scripts (training.sh, inference.sh) |
+| `prepare_data/` | Data preparation and preprocessing pipelines |
+| `analysis/` | Evaluation and analysis workflows |
+
+### conf/
+
+Hydra configuration files organized by module:
+
+| Directory | Purpose |
+|-----------|---------|
+| `training/` | Training hyperparameters, model configs, optimizer settings |
+| `dataset/` | Dataset configurations, data paths, preprocessing options |
+| `model/` | Model architecture configurations |
+| `prepare_data/` | Data preparation parameters |
+| `analysis/` | Analysis and evaluation configurations |
+| `dir/` | Directory path configurations |
+| `analysis/` | Analysis-specific settings |
+
+## src/ - Source Code Layer
+
+### data_module/ - Data Processing Module
+
+```
+data_module/
+├── __init__.py              # Module exports
+├── utils.py                 # Data-specific utility functions
+├── dataset/                 # Dataset implementations
+│   ├── __init__.py          # Dataset factory and registry
+│   └── simple_dataset.py    # Simple dataset example
+├── augmentation/            # Data augmentation methods
+│   ├── __init__.py
+│   ├── mixup.py            # Mixup augmentation
+│   ├── random_shift.py     # Random shifting
+│   ├── channel_mask.py     # Channel masking
+│   ├── time_masking.py     # Time masking
+│   └── add_noise.py        # Noise injection
+├── collate_fn/             # Batch collation functions
+│   ├── __init__.py
+│   └── simple_collate_fn.py
+├── compute_metrics/        # Metrics computation
+│   ├── __init__.py
+│   └── simple_compute_metrics.py
+├── prepare_data/           # Data preparation logic
+│   ├── __init__.py
+│   ├── prepare_data.py
+│   └── generate_yaml.py
+└── data_func/              # Data utility functions
+    ├── __init__.py
+    └── simple_data_func.py
+```
+
+### model_module/ - Model Module
+
+```
+model_module/
+├── __init__.py             # Module exports
+└── model/                  # Model implementations
+    └── [model files]
+```
+
+### trainer_module/ - Training Module
+
+Contains training loop logic, validation, and checkpoint management.
+
+### analysis_module/ - Analysis Module
+
+Contains evaluation, visualization, and result analysis code.
+
+### llm/ - LLM Module
+
+LLM-related code and integrations.
+
+### utils/ - Shared Utilities
+
+```
+utils/
+├── __init__.py
+├── helpers.py              # Helper functions (import_modules, etc.)
+├── logging.py              # Logging configuration
+├── get_optimizer.py        # Optimizer factory
+├── get_scheduler.py        # Learning rate scheduler factory
+├── get_callback.py         # Training callbacks
+├── get_activation.py       # Activation functions
+└── get_checkpoint_aggregation.py  # Checkpoint handling
+```
+
+## data/ - Data Layer
+
+Following the Cookiecutter Data Science standard:
+
+| Directory | Purpose |
+|-----------|---------|
+| `raw/` | Original, immutable data dump |
+| `processed/` | Cleaned, transformed data ready for use |
+| `external/` | Data from third-party sources |
+
+## outputs/ - Output Layer
+
+| Directory | Purpose |
+|-----------|---------|
+| `logs/` | Training logs, tensorboard logs |
+| `checkpoints/` | Model checkpoints for resuming training |
+| `tables/` | Result tables, CSV outputs |
+| `figures/` | Plots, visualizations, figures |
+
+## Module Interaction Flow
+
+```
+run/pipeline/    ->  src/trainer_module/  ->  src/model_module/
+                     src/data_module/         src/utils/
+                     src/utils/
+
+run/conf/        ->  Hydra config loader  ->  All modules
+```
+
+## File Naming Conventions
+
+- **Modules**: `simple_dataset.py`, `custom_model.py`
+- **Pipelines**: `training.sh`, `inference.sh`
+- **Configs**: `config.yaml`, dataset-specific names
+- **Utilities**: Descriptive names (`get_optimizer.py`, `helpers.py`)
+
+## Python Package Structure
+
+Each module is a proper Python package:
+- Has `__init__.py` with factory/registry logic
+- Can be imported as `from src.module import Component`
+- Subpackages are automatically discovered via `import_modules()`