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Application of Ensemble Machine Learning Methods for QSAR Classification of Leukotriene A4 Hydrolase Inhibitors in Drug Discovery Noviandy, Teuku Rizky; Idroes, Ghifari Maulana; Mohd Fauzi, Fazlin; Idroes, Rinaldi
Malacca Pharmaceutics Vol. 2 No. 2 (2024): September 2024
Publisher : Heca Sentra Analitika

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.60084/mp.v2i2.217

Abstract

Inflammatory diseases such as asthma, rheumatoid arthritis, and cardiovascular conditions are driven by overproduction of leukotriene B4 (LTB4), a potent inflammatory mediator. Leukotriene A4 hydrolase (LTA4H) plays a critical role in converting leukotriene A4 into LTB4, making it a prime target for drug discovery. Despite ongoing efforts, developing effective LTA4H inhibitors has been challenging due to the complex binding properties of the enzyme and the structural diversity of potential inhibitors. Traditional drug discovery methods, like high-throughput screening (HTS), are often time-consuming and inefficient, prompting the need for more advanced approaches. Quantitative Structure-Activity Relationship (QSAR) modeling, enhanced by ensemble machine learning techniques, provides a promising solution by enabling accurate prediction of compound bioactivity based on molecular descriptors. In this study, six ensemble machine learning methods—AdaBoost, Extra Trees, Gradient Boosting, LightGBM, Random Forest, and XGBoost—were employed to classify LTA4H inhibitors. The dataset, comprising 636 compounds labeled as active or inactive based on pIC50 values, was processed to extract 450 molecular descriptors after feature engineering. The results show that the LightGBM model achieved the highest classification accuracy (83.59%) and Area Under the Curve (AUC) value (0.901), outperforming other models. XGBoost and Random Forest also demonstrated strong performance, with AUC values of 0.890 and 0.895, respectively. The high sensitivity (95.24%) of the XGBoost model highlights its ability to accurately identify active compounds, though it exhibited slightly lower specificity (61.36%), indicating a higher false-positive rate. These findings suggest that ensemble machine learning models, particularly LightGBM, are highly effective in predicting bioactivity, offering valuable tools for early-stage drug discovery. The results indicate that ensemble methods significantly enhance QSAR model accuracy, making them viable for identifying promising LTA4H inhibitors, potentially accelerating the development of anti-inflammatory therapies.
QSAR Modeling for Predicting Beta-Secretase 1 Inhibitory Activity in Alzheimer's Disease with Support Vector Regression Noviandy, Teuku Rizky; Idroes, Ghifari Maulana; Tallei, Trina Ekawati; Handayani, Dian; Idroes, Rinaldi
Malacca Pharmaceutics Vol. 2 No. 2 (2024): September 2024
Publisher : Heca Sentra Analitika

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.60084/mp.v2i2.226

Abstract

Alzheimer's disease (AD) is a neurodegenerative disorder characterized by cognitive decline, with the accumulation of β-amyloid (Aβ) plaques playing a key role in its progression. Beta-Secretase 1 (BACE1) is a crucial enzyme in Aβ production, making it a prime therapeutic target for AD treatment. However, designing effective BACE1 inhibitors has been challenging due to poor selectivity and limited blood-brain barrier permeability. To address these challenges, we employed a machine learning approach using Support Vector Regression (SVR) in a Quantitative Structure-Activity Relationship (QSAR) model to predict the inhibitory activity of potential BACE1 inhibitors. Our model, trained on a dataset of 7,298 compounds from the ChEMBL database, accurately predicted pIC50 values using molecular descriptors, achieving an R² of 0.690 on the testing set. The model's performance demonstrates its utility in prioritizing drug candidates, potentially accelerating drug discovery. This study highlights the effectiveness of computational approaches in optimizing drug discovery and suggests that further refinement could enhance the model’s predictive power for AD therapeutics.
Bioactive Phytochemicals from Memecylon edule: Targeting Planktonic and Biofilm States of Pseudomonas aeruginosa Suryawati, Suryawati; Idroes, Rinaldi; Hertiani, Triana; Khairan, Khairan
Malacca Pharmaceutics Vol. 3 No. 1 (2025): March 2025
Publisher : Heca Sentra Analitika

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.60084/mp.v3i1.258

Abstract

The rise in antimicrobial resistance has prompted the search for potent antimicrobial agents, with plants from unique environments, such as geothermal areas, offering potential due to their diverse phytochemical profiles. This study evaluated the antiplanktonic and antibiofilm activity of M. edule fractions from the geothermal area, Jaboi, Sabang. Crude extracts of M. edule were sequentially fractionated using hexane, ethyl acetate, and ethanol. The resulting fractions were further analyzed for their phytochemical content and antiplanktonic and antibiofilm activities. The ethyl acetate fraction demonstrated superior antiplanktonic and antibiofilm activities compared to other fractions, inhibiting 50% of Pseudomonas aeruginosa planktonic and biofilm formation at a concentration of 10 mg/mL. The most potent fraction exhibited the phenolic content, 672.84 mg GAE/g extract, surpassing the other fractions. The GC-MS analysis shows the presence of pyrogallol, hexadecanoic acid, cedran-diol, and sitosterol. These findings highlight the potential of the ethyl acetate fraction of M. edule as a source of bioactive compounds with promising antiplanktonic and antibiofilm properties, laying the groundwork for future research into its therapeutic applications against biofilm-associated infections.
Psoriasis severity assessment: Optimizing diagnostic models with deep learning Maulana, Aga; Noviandy, Teuku R.; Suhendra, Rivansyah; Earlia, Nanda; Prakoeswa, Cita RS.; Kairupan, Tara S.; Idroes, Ghifari M.; Subianto, Muhammad; Idroes, Rinaldi
Narra J Vol. 4 No. 3 (2024): December 2024
Publisher : Narra Sains Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.52225/narra.v4i3.1512

Abstract

Psoriasis is a chronic skin condition with challenges in the accurate assessment of its severity due to subtle differences between severity levels. The aim of this study was to evaluate deep learning models for automated classification of psoriasis severity. A dataset containing 1,546 clinical images was subjected to pre-processing techniques, including cropping and applying noise reduction through median filtering. The dataset was categorized into four severity classes: none, mild, moderate, and severe, based on the Psoriasis Area and Severity Index (PASI). It was split into 1,082 images for training (70%) and 463 images for validation and testing (30%). Five modified deep convolutional neural networks (DCNN) were evaluated, including ResNet50, VGGNet19, MobileNetV3, MnasNet, and EfficientNetB0. The data were validated based on accuracy, precision, sensitivity, specificity, and F1-score, which were weighted to reflect class representation; Pairwise McNemar's test, Cochran's Q test, Cohen’s Kappa, and Post-hoc test were performed on the model performance, where overall accuracy and balanced accuracy were determined. Findings revealed that among the five deep learning models, ResNet50 emerged as the optimum model with an accuracy of 92.50% (95%CI: 91.2–93.8%). The precision, sensitivity, specificity, and F1-score of this model were found to be 93.10%, 92.50%, 97.37%, and 92.68%, respectively. In conclusion, ResNet50 has the potential to provide consistent and objective assessments of psoriasis severity, which could aid dermatologists in timely diagnoses and treatment planning. Further clinical validation and model refinement remain required.
Evaluation of Machine Learning Methods for Identifying Carbonic Anhydrase-II Inhibitors as Drug Candidates for Glaucoma Noviandy, Teuku Rizky; Imelda, Eva; Idroes, Ghazi Mauer; Suhendra, Rivansyah; Idroes, Rinaldi
Malacca Pharmaceutics Vol. 3 No. 1 (2025): March 2025
Publisher : Heca Sentra Analitika

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.60084/mp.v3i1.271

Abstract

Glaucoma is a leading cause of irreversible blindness, primarily managed by lowering intraocular pressure (IOP). Carbonic Anhydrase-II (CA-II) inhibitors play a crucial role in this treatment by reducing aqueous humor production. However, existing CA-II inhibitors often suffer from poor selectivity, side effects, and limited bioavailability, highlighting the need for more efficient and targeted drug discovery approaches. This study uses machine learning-driven Quantitative Structure-Activity Relationship (QSAR) modeling to predict CA-II inhibition based on molecular descriptors, significantly enhancing screening efficiency over traditional experimental methods. By evaluating multiple machine learning models, including Support Vector Machine, Gradient Boosting, and Random Forest, we identify SVM as the most effective classifier, achieving the highest accuracy (83.70%) and F1-score (89.36%). Class imbalance remains challenging despite high sensitivity, necessitating further improvements through resampling and hyperparameter optimization. Our findings underscore the potential of machine learning-based virtual screening in accelerating CA-II inhibitor identification and advocate for integrating AI-driven approaches with traditional drug discovery techniques. Future directions include deep learning enhancements and hybrid machine learning-docking frameworks to improve prediction accuracy and facilitate the development of more potent and selective glaucoma treatments.
Predicting AXL Tyrosine Kinase Inhibitor Potency Using Machine Learning with Interpretable Insights for Cancer Drug Discovery Noviandy, Teuku Rizky; Idroes, Ghifari Maulana; Harnelly, Essy; Sari, Irma; Fauzi, Fazlin Mohd; Idroes, Rinaldi
Heca Journal of Applied Sciences Vol. 3 No. 1 (2025): March 2025
Publisher : Heca Sentra Analitika

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.60084/hjas.v3i1.270

Abstract

AXL tyrosine kinase plays a critical role in cancer progression, metastasis, and therapy resistance, making it a promising target for therapeutic intervention. However, traditional drug discovery methods for developing AXL inhibitors are resource-intensive, time-consuming, and often fail to provide detailed insights into molecular determinants of potency. To address this gap, we applied machine learning techniques, including Random Forest, Gradient Boosting, Support Vector Regression, and Decision Tree models, to predict the potency (pIC50) of AXL inhibitors using a dataset of 972 compounds with 550 molecular descriptors. Our results demonstrate that the Random Forest model outperformed others with an R² of 0.703, MAE of 0.553, RMSE of 0.720, and PCC of 0.841, showcasing strong predictive accuracy. SHAP analysis identified critical molecular features, such as RNCG and TopoPSA(NO), as key contributors to inhibitor potency, providing interpretable insights into structure-activity relationships. These findings highlight the potential of machine learning to accelerate the identification and optimization of AXL inhibitors, bridging the gap between computational predictions and rational drug design and paving the way for effective cancer therapeutics.
Improving the Environmental Performance of Palm Biodiesel via AgNO₃-Assisted Removal of Polyunsaturated Fatty Acids Helwani, Zuchra; Zahrina, Ida; Amraini, Said Zul; Idroes, Rinaldi; Neonufa, Godlief Frederick; Rahman, Sunarti Abd
Leuser Journal of Environmental Studies Vol. 3 No. 1 (2025): April 2025
Publisher : Heca Sentra Analitika

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.60084/ljes.v3i1.274

Abstract

Indonesian biodiesel products commonly exhibit low oxidative stability and high cloud points, which limit their performance and widespread use. These drawbacks are primarily due to the high content of polyunsaturated fatty acids (PUFAs) in the fatty acid methyl ester (FAME) mixture that constitutes biodiesel. A more suitable biodiesel composition includes higher proportions of saturated and monounsaturated fatty acids, which offer better combustion properties, higher cetane numbers, and greater resistance to oxidative degradation. In contrast, PUFAs promote oxidation reactions, resulting in fuel instability, increased sludge formation, and higher emissions of unburned hydrocarbons, negatively impacting both engine performance and the environment.This study investigates the use of silver nitrate (AgNO₃) as a selective extraction agent to remove PUFAs from palm oil-derived FAME. The goal is to identify the most effective biodiesel-to-AgNO₃ volume ratio for separating saturated fatty acid fractions from unsaturated ones, in order to produce a more stable and environmentally friendly biodiesel. Experimental results show that a 1:2 volume ratio significantly reduces the iodine number, from 57.22 to 47.38 g I₂/100 g sample, indicating a decrease in unsaturated compounds. Furthermore, oxidative stability improved from 11.18 hours to 11.69 hours after extraction. The removal of PUFAs not only improves the fuel's storage and combustion stability but also enhances its environmental profile. More stable biodiesel burns more completely, reducing emissions of particulate matter and greenhouse gases, and contributing to cleaner air and lower environmental impact. Thus, PUFA extraction using AgNO₃ presents a promising approach for improving the sustainability and performance of palm-based biodiesel fuels.
Characterization of a geothermal system in the shallow structure of Seulawah volcano, Indonesia, using transient electromagnetic methods Marwan, Marwan; Yanis, Muhammad; Abdullah, Faisal; Adhari, Muhammad Ridha; Nugraha, Gartika; Paembonan, Andri Yadi; Idroes, Rinaldi; Yusuf, Muhammad; Dharma, Dian Budi; Muzakir, Muzakir; Saputra, Deni; Ghani, Azman Abdul
International Journal of Renewable Energy Development Vol 14, No 3 (2025): May 2025
Publisher : Center of Biomass & Renewable Energy (CBIORE)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.61435/ijred.2025.60766

Abstract

Seulawah volcano, located in Sumatra, Indonesia, is renowned for its geothermal potential, a crucial source of cleaner energy for Indonesia’s future growth and security. Available studies of Seulawah volcano primarily focus on its general geological, geochemical, and regional characteristics, with limited research on its shallow subsurface conditions. This study aimed to fill this research gap and enhance our understanding of the geothermal system of Seulawah volcano. There are two objectives of this study: (1) to conduct a transient electromagnetic (TEM) survey across the study area and (2) to better visualize and characterize the shallow subsurface conditions of the geothermal system of Seulawah volcano. The TEM method, which employed 60 stations (with distances between stations ranging from 0.5 to 1 km) and intersected several geothermal manifestations as well as local and regional faults, was used to achieve the objectives of this study. The Occam algorithm was applied for 1D inversion of TEM data, which was then validated using magnetotelluric data. The results of this study indicate that the geothermal system of Seulawah volcano has the potential to generate up to 230 Mwe of electrical energy. Moreover, the shallow depth (<200m) of Seulawah volcano is dominated by a resistive zone, which is interpreted to be related to the basaltic rocks of the Lamteuba Formation. The reservoir layer is located at depths of 200–500 m, exhibiting moderate resistivity values of >10 Ωm. At a depth of 500 m, a conductive layer with resistivity values <10 Ωm was observed, interpreted as a clay cap where fluids from the reservoir layer accumulate. Validation with magnetotelluric data shows results consistent with the TEM data, confirming that the findings of this study are reliable. These findings contribute to a deeper understanding of the geothermal system of Seulawah volcano and are expected to support the development of greener, renewable energy sources for Indonesia.
An Explainable Machine Learning Study of Behavioral and Psychological Determinants of Depression in the Academic Environment Noviandy, Teuku Rizky; Idroes, Ghalieb Mutig; Hardi, Irsan; Ringga, Edi Saputra; Idroes, Rinaldi
Journal of Educational Management and Learning Vol. 3 No. 1 (2025): May 2025
Publisher : Heca Sentra Analitika

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.60084/jeml.v3i1.304

Abstract

Depression is a significant and growing concern within academic environments, affecting both students and staff due to factors such as academic pressure, financial stress, and lifestyle challenges. This study explores the use of machine learning, specifically a Random Forest classifier, to predict depression risk among students using behavioral, psychological, and demographic data. A dataset of 27,788 student records was analyzed after thorough preprocessing and exploratory data analysis. The model achieved strong performance, with an accuracy of 83.52% and an AUC of 0.91, indicating reliable classification of depression status. Local Interpretable Model-agnostic Explanations (LIME) were employed to enhance interpretability, revealing key predictive features such as suicidal ideation, academic pressure, sleep duration, and dietary habits. These interpretable insights align with existing psychological research and provide actionable information for mental health professionals. The findings highlight the value of explainable AI in educational settings, offering a scalable and transparent approach to early depression detection and intervention. Future work should focus on longitudinal data integration, multimodal inputs, and real-world implementation to strengthen the model’s utility and impact.
Techniques and Tools in Learning Analytics and Educational Data Mining: A Review Noviandy, Teuku Rizky; Idroes, Ghazi Mauer; Paristiowati, Maria; Idroes, Rinaldi
Journal of Educational Management and Learning Vol. 3 No. 1 (2025): May 2025
Publisher : Heca Sentra Analitika

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.60084/jeml.v3i1.308

Abstract

Learning analytics and educational data mining are rapidly evolving fields that leverage data-driven methods to enhance teaching, learning, and institutional decision-making. This review provides a comprehensive overview of the key analytical techniques and tools employed in learning analytics and educational data mining, including classification, clustering, regression, association rule mining, and data visualization. It also highlights the integration of advanced methods such as deep learning and adaptive systems for personalized education. The paper examines various platforms and technologies, including learning management systems, open-source tools, and AI/ML libraries, to evaluate their capabilities, scalability, and practical adoption. Key application areas, such as dropout prediction, engagement analysis, personalized learning, and curriculum design, are examined through selected case studies spanning K–12 and higher education. The review emphasizes the growing importance of ethical considerations, interpretability, and usability in the application of educational analytics. By synthesizing current practices and trends, this work aims to inform educators, researchers, and developers seeking to harness educational data for improved learning outcomes and strategic planning.
Co-Authors - Fakhrurrazi - Mahmud Abas, Abdul Hawil Adi Purnawarman, Adi Afidh, Razief Perucha Fauzie Agus Winarsih Ahmad, Khairunnas Ahmad, Noor Atinah Ahsya, Yahdina Akyuni, Qurrata Amirah, Kelsy Andri Yadi Paembonan Arini, Musfira Asep Rusyana Azhar, Fauzul Azharuddin Azharuddin BAKRI, TEDY KURNIAWAN Binawati Ginting Boy M. Bachtiar Claus Jacob Claus Jacob Claus Jacob, Claus Cundaningsih, Nurvita Deni Saputra Destiana, Khaerunisa Dharma, Aditia Dharma, Dian Budi Diah, Muhammad Dian Handayani Dian Lestari, Nova Diana Setya Ningsih, Diana Earlia, Nanda EKA SAFITRI Eka Safitri Eka Safitri El-Shazly, Mohamed Elisa Purwaendah Emran, Talha Bin Enitan, Seyi Samson Essy Harnelly Estevam, Ethiene Castellucci Ethiene Castellucci Estevam Eti Rohaeti Evi Yufita Ezzat, Abdelrahman O. Faddillah, Vira Faisal Abdullah Faisal, Farassa Rani Faradilla Faradilla FARADILLA, FARADILLA Farnida Farnida Fatimawali . Fauzi, Fazlin M. Fauzi, Fazlin Mohd Fazlin Mohd Fauzi Firaihanil Jannah Ghalieb Mutig Idroes Ghani, Azman Abdul Ghazi Mauer Idroes Haerul Anwar Hakim, Rachmi F. Hanafiah, Olivia A. Harera, Cheariva Firsa Hartono Hartono Hesti Meilina Hizir Sofyan Husdayanti, Noviana Ida Zahrina Idroes, Ghalieb Mutig Idroes, Ghazi M. Idroes, Ghifari M. Idroes, Ghifari Maulana Iin Shabrina Hilal Ilham Maulana Ilham Maulana Imelda, Eva Imran Imran Ira Maya Irma Sari Irsan Hardi Irvanizam, Irvanizam Isa, Illyas Md Ismail Ismail Isnaini, Nadia Isra Firmansyah, Isra Jannah, Firaihanil Jannah, Rizka Auliatul Jasin, Faisal M Kairupan, Tara S. Karl Herbert Schaefer Karl Herbert Schaefer, Karl Herbert Karomah, Alfi Hudatul Kemala, Pati Khairan . Khairan Khairan Khairan Khairan Khairan Khairan Khairan Khairan Khairan Khairan KHAIRI SUHUD Khairi Suhud Khalijah Awang Kurniadinur, Kurniadinur Kusumo, Fitranto Lala, Andi Lelifajri Lelifajri Lelifajri Lelifajri Lubis, Vanizra F. M. Rafi Madya, Muhammad Miftahul Mahmudi Mahmudi Maimun Syukri, Maimun Malahayati Malahayati MARIA BINTANG Maria Paristiowati Marwan Marwan Maulana, Aga Maulydia, Nur B. Maulydia, Nur Balqis Maysarah, Hilda Md Sani, Nor Diyana Mikyal Bulqiah, Mikyal Mirda, Erisna Misbullah, Alim Misrahanum Misrahanum Mohamed Yusof, Nur Intan Saidaah Mohd Fauzi, Fazlin Mohsina Patwekar Mubaraq, Farhil Muhammad Bahi Muhammad Bahi Muhammad Bahi Muhammad Bahi Muhammad Diah Muhammad Ridha Adhari, Muhammad Ridha Muhammad Subianto Muhammad Yanis Muhammad Yusuf Mukhlisuddin Ilyas Muliadi Ramli Munawar, Agus Murniana Murniana Mursal Mursal Mursyida, Waliam Musdalifah, Annisa Muslem Muslem, Muslem Muzakir N. Nazaruddin Nabila, Fiki Farah Nainggolan, Sarah Ika Nanda Earlia Nasrullah Idris Nasrullah Idris NAZARUDDIN NAZARUDDIN Nazaruddin Nazaruddin Neonufa, Godlief Frederick Ningsih, Diana S. Niode, Nurdjannah Jane Nor Diyana Md Sani Novi Reandy Sasmita Noviandy, Teuku R. Nugraha, Gartika Nur Balqis Maulydia Nur, Adrian Rahmat Nurdjannah J. Niode Nurleila, Nurleila Nurul Khaira Oesman, Frida Patwekar, Faheem Patwekar, Mohsina Prakoeswa, Cita RS. Purwaendah, Elisa Putra, Noviandi I. Qurrata Akyuni Rahmadi Rahmadi Rahmadi Rahmadi Rahman, Isra Farliadi Rahman, Sunarti Abd Raihan Raihan Raihan Raihan, Raihan Raudhatul Jannah Razief Perucha Fauzie Afidh Ringga, Edi Saputra Rizka Auliatul Jannah Rizkia, Tatsa Romadhoni, Yenni Rusdi Andid Safhadi, Aulia Al-Jihad Saiful . Saiful Saiful Saiful Saiful Salaswati, Salaswati Salsabila, Indah Sasmita, Novi Reandy Satrio, Justinus Septaningsih, Dewi Anggraini Shafira, Ghina A. Siti Aisyah Solly Aryza Souvia Rahimah Sufriadi, Elly sufriani, sufriani Sugara, Dimas Rendy Suhendra, Rivansyah Suhud, Khairi Supriatno Supriatno Supriatno Suryadi Suryadi Suryawati Suryawati Taopik Ridwan Taufik Ridwan Taufiq Karma Teuku Rizky Noviandy Teuku Zulfikar Thomas Schneider Thomas Schneider, Thomas Triana Hertiani Trina E. Tallei, Trina E. TRINA EKAWATI TALLEI Trina Ekawati Tallei Tuti Fadlilah Yandri, Erkata Zahraty, Ifrah Zahriah, Zahriah Zhilalmuhana, Teuku Zuchra Helwani, Zuchra Zulfiani, Utari Zulkarnain Jalil Zulkarnain Jalil