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Zuchra Helwani, Zuchra
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Journal : Infolitika Journal of Data Science

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Ensemble Machine Learning Approach for Quantitative Structure Activity Relationship Based Drug Discovery: A Review Noviandy, Teuku Rizky; Maulana, Aga; Idroes, Ghazi Mauer; Emran, Talha Bin; Tallei, Trina Ekawati; Helwani, Zuchra; Idroes, Rinaldi
Infolitika Journal of Data Science Vol. 1 No. 1 (2023): September 2023
Publisher : Heca Sentra Analitika

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.60084/ijds.v1i1.91

Abstract

This comprehensive review explores the pivotal role of ensemble machine learning techniques in Quantitative Structure-Activity Relationship (QSAR) modeling for drug discovery. It emphasizes the significance of accurate QSAR models in streamlining candidate compound selection and highlights how ensemble methods, including AdaBoost, Gradient Boosting, Random Forest, Extra Trees, XGBoost, LightGBM, and CatBoost, effectively address challenges such as overfitting and noisy data. The review presents recent applications of ensemble learning in both classification and regression tasks within QSAR, showcasing the exceptional predictive accuracy of these techniques across diverse datasets and target properties. It also discusses the key challenges and considerations in ensemble QSAR modeling, including data quality, model selection, computational resources, and overfitting. The review outlines future directions in ensemble QSAR modeling, including the integration of multi-modal data, explainability, handling imbalanced data, automation, and personalized medicine applications while emphasizing the need for ethical and regulatory guidelines in this evolving field.
Inductive Biases in Feature Reduction for QSAR: SHAP vs. Autoencoders Noviandy, Teuku Rizky; Idroes, Ghifari Maulana; Lala, Andi; Helwani, Zuchra; Idroes, Rinaldi
Infolitika Journal of Data Science Vol. 3 No. 1 (2025): May 2025
Publisher : Heca Sentra Analitika

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.60084/ijds.v3i1.306

Abstract

Machine learning models in drug discovery often depend on high-dimensional molecular descriptors, many of which may be redundant or irrelevant. Reducing these descriptors is essential for improving model performance, interpretability, and computational efficiency. This study compares two widely used reduction strategies: SHAP-based feature selection and autoencoder-based compression, within the context of Quantitative Structure-Activity Relationship (QSAR) classification. LightGBM is used as a consistent modeling framework to evaluate models trained on all descriptors, the top 50 and 100 SHAP-ranked descriptors, and a 64-dimensional autoencoder embedding. The results show that SHAP-based selection produces interpretable and stable models with minimal performance loss, particularly when using the top 100 descriptors. In contrast, the autoencoder achieves the highest test performance by capturing nonlinear patterns in a compact, low-dimensional representation, although this comes at the cost of interpretability and consistency across data splits. These findings reflect the differing inductive biases of each method. SHAP prioritizes sparsity and attribution, while autoencoders focus on reconstruction and continuity. The analysis emphasizes that descriptor reduction strategies are not interchangeable. SHAP-based selection is suitable for applications where interpretability and reliability are essential, such as in hypothesis-driven or regulatory settings. Autoencoders are more appropriate for performance-driven tasks, including virtual screening. The choice of reduction strategy should be guided not only by performance metrics but also by the specific modeling requirements and assumptions relevant to cheminformatics workflows.
Co-Authors Abd , Ammar Ali Abd Rahman, Sunarti Afriyenti, Mia Agustiyanti, Rini Dwi Agustiyanti, Rini Dwi Ahmad Fadli Ahmad, Khairunnas Akbar, Irfan Sarhadi Amir Awaluddin Amun Amri Anggraini, Diva Putri Anggriani, Rara Dewi Anjani, Putri Anuar, Kaspul Asep Rusyana Aswie, Viqha Bahruddin Bahruddin Bahruddin Boy M. Bachtiar Damayanti, Elok David Andrio Dhani Nur Miftahudin Dizikri, Dizikri Drastinawati Drastinawati Drastinawati Drastinawati, Drastinawati Dwi Septiana Edi Susanto Edy Saputra Eko Suhartono Emran, Talha Bin Febrina Dwi Putri Febrina Dwi Putri, Febrina Dwi Febrina, Wetri Fernando, Rivo Ghazi Mauer Idroes Hafiz, Fadlillahi Hanafi, Muhammad Rifter Hari Rionaldo Hari Rionaldo Hawa, Karfika Ainil Hawa, Karfika Ainil Hutagaol, Martiandes Ida Zahrina Idral Amri Idroes, Ghazi M. Idroes, Ghifari Maulana Jecky Asmura Julhijah, Noni Karfika Ainil Hawa Karina Octaria Putri Kemala, Pati Kesni Savitri Khairan Khairan Komalasari Komalasari Komang, Hendri Kusumo, Fitranto Lala, Andi Lubis, Vanizra F. Lukman Arifin Maulana, Aga Maulydia, Nur B. Miftahudin, Dhani Nur Miftahudin, Dhani Nur Muhammad Mardhiansyah Muhammad Zen, Muhammad Muliadi Ramli Mulya, Dynna Ardilla Putri Muslim Abdurrahman, Muslim Nasution, Muhammad Hatta Nazaris, Nazsha Nayyazsha Neonufa, Godlief Frederick Ningsih, Diana S. Noviandy, Teuku R. Nurfatihayati Nurwijayanti Oktariandi, Vito Oktriyono, Febri Dwi Olsy, Fradilla Othman, Mohd. Roslee Peliciamanuela, Samantha Perdana, Rendy Putra Prasetyo Arva S, Prasetyo Arva Pratama, Teddy Pratama, Yudistira Putra Zelly Nugraha, Putra Zelly Putra, Bayu Eldino Putra, Yogi Lesmana Putri, Karina Octaria Putri, Karina Octaria Qalbi, Tiffani Rafi, M Khaidiz Rahayu, Ricky Puji Rahman, Sunarti Abd Raja Heru Nur Alam Ichsan, Raja Heru Nur Alam Randi Sanjaya Randi Sanjaya, Randi Reno Susanto Reski, M. Rinaldi Idroes Rizki, Juliana Rizky, Muhammad Dian Rozanna Sri Irianty Saparullah, Zulkarnaen Saryono Saryono Setiadi, Fydel Simbolon, Kristin Madelin Siregar, Thasya Nurfadillah Sitorus, Mesakh Fridolin Sugesti, Heni Suhendrayatna Suhendrayatna Sunarno Sunarno Surya, Andry Pratama Susanty, Wenny Susilowati Susilowati Syafi’i, Abdullah Syahputra, Dede SYAIFUL BAHRI Tengku Mukhlis Teuku Rizky Noviandy Topan Herianto Trina E. Tallei, Trina E. TRINA EKAWATI TALLEI Triwahyuni, Vanny Efia Ulfaa, Suci Mas’ama Ulima, Riris Warman Fatra, Warman Wenny Susanty Yelmida Azis Yemita, Sylvia Yudha, Ricky Satria Z Zulfansyah Zahriah, Zahriah Zohera, Zohera Zul Amraini, Said Zulfansyah Zulfansyah Zultiniar, Zultiniar