RAG-Classic-ML

RAG-Classic-ML is a versatile Python package designed to provide out-of-the-box machine learning pipelines for both basic and advanced tasks. It simplifies the process of building, training, and evaluating models for tasks like classification, regression, autoencoder-based feature extraction, and survival clustering. The package is designed for ease of use, offering pre-built pipelines and customizable parameters for a variety of machine learning algorithms.

Table of Contents

• Features
• Installation
• Usage
  • Basic Machine Learning Pipelines
    • [Classification]
    • [Regression]
  • Advanced Pipelines
    • Autoencoder with Feature Extraction
    • Clustering and Survival Analysis
  • Train Autoencoder Model
  • Survival Clustering Analysis
• Command-Line Arguments
• Dependencies
• License
• Author

Features

• Basic Machine Learning Pipelines: Ready-to-use pipelines for common supervised learning tasks, including classification and regression, with a variety of machine learning models (e.g., Logistic Regression, SVC, Random Forest).
• Advanced Pipelines
  • Autoencoder : Dimensionality reduction and feature extraction using deep learning autoencoders.
  • Survival Clustering Analysis: Performs clustering on patient features and integrates clinical data to generate Kaplan-Meier survival plots and log-rank tests.
• Customizable Models and Parameters: Easily define and customize machine learning models and hyperparameters.
• Prediction and Metrics Generation: Generates and saves predictions, feature importance scores, and various performance metrics for each model and run.
• Aggregation of Results: Aggregates results across runs and models for comprehensive analysis, facilitating comparison and evaluation.
• Visualization Tools: Generates plots including AUC curves, AUC box plots, feature importance charts, radar charts for model performance comparison, and survival analysis plots.

Installation

You can install the package directly from PyPI:

pip install classic-ml

Alternatively, install from source:

git clone https://github.com/yourusername/classic-ml.git
cd benchmark-adv-ml
pip install .

Useage

The classic-ml package provides a command-line interface (CLI) for ease of use. Below are examples of how to use the various components.

Basic Machine Learning Pipelines

Classification

Train and evaluate a classification model using the classic-ml CLI. You can specify different models and hyperparameters.

Example 1: Support Vector Classifier (SVC)

classic-ml classification \
    --data ./Raisin_Dataset.data \
    --target 'label' \
    --output ./results/svc_rbf/ \
    --model SVC \
    --model_params '{"C": 1.0, "kernel": "rbf", "gamma": "scale", "probability": true}' \
    --test_size 0.2 \
    --seed 42

Example 2: Logistic Regression

classic-ml classification \
    --data ./Raisin_Dataset.data \
    --target 'label' \
    --output ./results/logistic_regression/ \
    --model LogisticRegression \
    --model_params '{"C": 0.5, "penalty": "l1", "solver": "saga", "max_iter": 1000, "class_weight": "balanced"}' \
    --test_size 0.2 \
    --seed 42

Example 3: Random Forest Classifier

classic-ml classification \
    --data ./Raisin_Dataset.data \
    --target 'label' \
    --output ./results/random_forest/ \
    --model RandomForestClassifier \
    --model_params '{"n_estimators": 100, "max_depth": 10}' \
    --test_size 0.2 \
    --seed 42

Benchmark Machine Learning Models

Run the benchmark ML pipeline to evaluate model stability across multiple runs.

benchmark-adv-ml benchmark --data ./your_dataset.csv --output ./final_results --prelim_output ./prelim_results --n_runs 10 --seed 42

Train Autoencoder Model

Train and evaluate an autoencoder model for feature extraction.

classic-ml autoencoder \
    --data ./your_dataset.csv \
    --sampleID 'PatientID' \
    --output_dir ./final_results \
    --prelim_output ./prelim_results \
    --latent_dim 10 \
    --epochs 50 \
    --batch_size 32 \
    --validation_split 0.1 \
    --test_size 0.2 \
    --seed 42

Survival Clustering Analysis

classic-ml survival_clustering \
    --data_path ./latent_features.csv \
    --clinical_df_path ./clinical_data.csv \
    --save_dir ./final_results

Command-Line Arguments

Common Arguments

• --data: Path to the existing CSV file containing the dataset.
• --output: Directory to save the final results and plots.
• --prelim_output: Directory to save the preliminary results (predictions).
• --seed: Seed for random state (default is 42).
• --test_size: Fraction of data to use for testing (default: 0.2).

Classification/Regression Command Arguments

• --target: Target column name in the dataset (e.g., 'label' for classification or 'price' for regression).
• --model: Specify the machine learning model to use (e.g., SVC, LogisticRegression, RandomForestClassifier, LinearRegression).
• --model_params: Hyperparameters for the specified model in JSON format (e.g., {"C": 1.0, "kernel": "rbf"}).

Autoencoder Command Arguments

• --sampleID: Column name representing the sample or patient ID (default: 'sampleID').
• --latent_dim: Dimensionality of the latent space (default: input_dim // 8).
• --epochs: Number of training epochs (default: 50).
• --batch_size: Training batch size (default: 32).
• --validation_split: Proportion of training data to use as validation set (default: 0.1).
• --test_size: Proportion of data to use as test set (default: 0.2).
• --early_stopping: Enable early stopping (use flag to activate).
• --patience: Patience for early stopping (default: 5).
• --checkpoint: Enable model checkpointing (use flag to activate).

Benchmark Command Arguments

• --target: Target column name in the dataset (default: 'label').
• --n_runs: Number of runs for model stability evaluation (default: 20).

Survival Clustering Command Arguments

• --data_path: Path to the CSV file containing patient features.
• --clinical_df_path: Path to the CSV file containing clinical data.
• --save_dir: Directory to save the results.

Dependencies

• Python 3.11+
• numpy
• pandas
• scikit-learn
• matplotlib
• seaborn
• tensorflow
• lifelines
• yellowbrick

License

This project is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. See the LICENSE file for details.

Author

Vatsal Patel - VatsalPatel18